Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
xet
 Community
1
paragraph_index
int64
sec
string
p_has_citation
int64
cites
string
citeids
list
pmid
int64
cited_id
string
sentences
string
all_sent_cites
list
sent_len
int64
sentence_batch_index
int64
sent_has_citation
float64
qc_fail
bool
cited_sentence
string
cites_in_sentence
list
cln_sentence
string
is_cap
bool
is_alpha
bool
ends_wp
bool
cit_qc
bool
lgtm
bool
__index_level_0__
int64
0
DISCUSSION
1
12
[ "B12" ]
17,329,375
NA|pmid-11839499|pmid-16469698
In wild-type Mfd, the translocation activity is repressed by the action of D7 (red).
[ "12" ]
84
8,700
0
false
In wild-type Mfd, the translocation activity is repressed by the action of D7 (red).
[]
In wild-type Mfd, the translocation activity is repressed by the action of D7 (red).
true
true
true
true
true
1,395
0
DISCUSSION
1
12
[ "B12" ]
17,329,375
NA|pmid-11839499|pmid-16469698
The autoinhibitory effect can be relieved by deletion of D7, and the truncated protein can displace a TFO in the absence of other factors.
[ "12" ]
138
8,701
0
false
The autoinhibitory effect can be relieved by deletion of D7, and the truncated protein can displace a TFO in the absence of other factors.
[]
The autoinhibitory effect can be relieved by deletion of D7, and the truncated protein can displace a TFO in the absence of other factors.
true
true
true
true
true
1,395
0
DISCUSSION
1
12
[ "B12" ]
17,329,375
NA|pmid-11839499|pmid-16469698
The autoinhibitory effect is also relieved by the interaction of wild-type Mfd with RNAP.
[ "12" ]
89
8,702
0
false
The autoinhibitory effect is also relieved by the interaction of wild-type Mfd with RNAP.
[]
The autoinhibitory effect is also relieved by the interaction of wild-type Mfd with RNAP.
true
true
true
true
true
1,395
0
DISCUSSION
1
12
[ "B12" ]
17,329,375
NA|pmid-11839499|pmid-16469698
Mfd binds to RNAP via the RID (magenta), and D7 is repositioned.
[ "12" ]
64
8,703
0
false
Mfd binds to RNAP via the RID (magenta), and D7 is repositioned.
[]
Mfd binds to RNAP via the RID (magenta), and D7 is repositioned.
true
true
true
true
true
1,395
0
DISCUSSION
1
12
[ "B12" ]
17,329,375
NA|pmid-11839499|pmid-16469698
The repositioning of D7 activates the DNA translocation activity of Mfd, and may also reveal a binding site for UvrA (white ellipse: (12)).
[ "12" ]
139
8,704
0
false
The repositioning of D7 activates the DNA translocation activity of Mfd, and may also reveal a binding site for UvrA ).
[ "white ellipse: (12" ]
The repositioning of D7 activates the DNA translocation activity of Mfd, and may also reveal a binding site for UvrA ).
true
true
true
true
true
1,395
0
DISCUSSION
1
12
[ "B12" ]
17,329,375
NA|pmid-11839499|pmid-16469698
TFO displacement may result either from RNAP being pushed through the TFO-binding site (as shown), or by Mfd continuing to translocate DNA after displacing RNAP.
[ "12" ]
161
8,705
0
false
TFO displacement may result either from RNAP being pushed through the TFO-binding site (as shown), or by Mfd continuing to translocate DNA after displacing RNAP.
[]
TFO displacement may result either from RNAP being pushed through the TFO-binding site (as shown), or by Mfd continuing to translocate DNA after displacing RNAP.
true
true
true
true
true
1,395
1
DISCUSSION
1
12
[ "B12" ]
17,329,375
pmid-8465200|pmid-10214918|pmid-15474416|pmid-16464015|pmid-8465200|pmid-2250027|pmid-2554145|pmid-3664636|pmid-9535092|pmid-12787667|pmid-16469698
Model for the control of Mfd activity by autoinhibitory domain D7.
[ "12" ]
66
8,706
0
false
Model for the control of Mfd activity by autoinhibitory domain D7.
[]
Model for the control of Mfd activity by autoinhibitory domain D7.
true
true
true
true
true
1,396
1
DISCUSSION
1
12
[ "B12" ]
17,329,375
pmid-8465200|pmid-10214918|pmid-15474416|pmid-16464015|pmid-8465200|pmid-2250027|pmid-2554145|pmid-3664636|pmid-9535092|pmid-12787667|pmid-16469698
In wild-type Mfd, the translocation activity is repressed by the action of D7 (red).
[ "12" ]
84
8,707
0
false
In wild-type Mfd, the translocation activity is repressed by the action of D7 (red).
[]
In wild-type Mfd, the translocation activity is repressed by the action of D7 (red).
true
true
true
true
true
1,396
1
DISCUSSION
1
12
[ "B12" ]
17,329,375
pmid-8465200|pmid-10214918|pmid-15474416|pmid-16464015|pmid-8465200|pmid-2250027|pmid-2554145|pmid-3664636|pmid-9535092|pmid-12787667|pmid-16469698
The autoinhibitory effect can be relieved by deletion of D7, and the truncated protein can displace a TFO in the absence of other factors.
[ "12" ]
138
8,708
0
false
The autoinhibitory effect can be relieved by deletion of D7, and the truncated protein can displace a TFO in the absence of other factors.
[]
The autoinhibitory effect can be relieved by deletion of D7, and the truncated protein can displace a TFO in the absence of other factors.
true
true
true
true
true
1,396
1
DISCUSSION
1
12
[ "B12" ]
17,329,375
pmid-8465200|pmid-10214918|pmid-15474416|pmid-16464015|pmid-8465200|pmid-2250027|pmid-2554145|pmid-3664636|pmid-9535092|pmid-12787667|pmid-16469698
The autoinhibitory effect is also relieved by the interaction of wild-type Mfd with RNAP.
[ "12" ]
89
8,709
0
false
The autoinhibitory effect is also relieved by the interaction of wild-type Mfd with RNAP.
[]
The autoinhibitory effect is also relieved by the interaction of wild-type Mfd with RNAP.
true
true
true
true
true
1,396
1
DISCUSSION
1
12
[ "B12" ]
17,329,375
pmid-8465200|pmid-10214918|pmid-15474416|pmid-16464015|pmid-8465200|pmid-2250027|pmid-2554145|pmid-3664636|pmid-9535092|pmid-12787667|pmid-16469698
Mfd binds to RNAP via the RID (magenta), and D7 is repositioned.
[ "12" ]
64
8,710
0
false
Mfd binds to RNAP via the RID (magenta), and D7 is repositioned.
[]
Mfd binds to RNAP via the RID (magenta), and D7 is repositioned.
true
true
true
true
true
1,396
1
DISCUSSION
1
12
[ "B12" ]
17,329,375
pmid-8465200|pmid-10214918|pmid-15474416|pmid-16464015|pmid-8465200|pmid-2250027|pmid-2554145|pmid-3664636|pmid-9535092|pmid-12787667|pmid-16469698
The repositioning of D7 activates the DNA translocation activity of Mfd, and may also reveal a binding site for UvrA (white ellipse: (12)).
[ "12" ]
139
8,711
0
false
The repositioning of D7 activates the DNA translocation activity of Mfd, and may also reveal a binding site for UvrA ).
[ "white ellipse: (12" ]
The repositioning of D7 activates the DNA translocation activity of Mfd, and may also reveal a binding site for UvrA ).
true
true
true
true
true
1,396
1
DISCUSSION
1
12
[ "B12" ]
17,329,375
pmid-8465200|pmid-10214918|pmid-15474416|pmid-16464015|pmid-8465200|pmid-2250027|pmid-2554145|pmid-3664636|pmid-9535092|pmid-12787667|pmid-16469698
TFO displacement may result either from RNAP being pushed through the TFO-binding site (as shown), or by Mfd continuing to translocate DNA after displacing RNAP.
[ "12" ]
161
8,712
0
false
TFO displacement may result either from RNAP being pushed through the TFO-binding site (as shown), or by Mfd continuing to translocate DNA after displacing RNAP.
[]
TFO displacement may result either from RNAP being pushed through the TFO-binding site (as shown), or by Mfd continuing to translocate DNA after displacing RNAP.
true
true
true
true
true
1,396
2
DISCUSSION
0
null
null
17,329,375
pmid-8465200|pmid-16469698|pmid-16469698|pmid-16309703|pmid-7876261|pmid-16469698|pmid-12086674|pmid-12554672|pmid-14602898|pmid-16469698|pmid-16469698
How might D7 inhibit DNA translocation activity?
null
48
8,713
0
false
null
null
How might D7 inhibit DNA translocation activity?
true
true
true
true
true
1,397
2
DISCUSSION
0
null
null
17,329,375
pmid-8465200|pmid-16469698|pmid-16469698|pmid-16309703|pmid-7876261|pmid-16469698|pmid-12086674|pmid-12554672|pmid-14602898|pmid-16469698|pmid-16469698
Deletion of D7 increased the ATPase activity of the protein even in the absence of DNA.
null
87
8,714
0
false
null
null
Deletion of D7 increased the ATPase activity of the protein even in the absence of DNA.
true
true
true
true
true
1,397
2
DISCUSSION
0
null
null
17,329,375
pmid-8465200|pmid-16469698|pmid-16469698|pmid-16309703|pmid-7876261|pmid-16469698|pmid-12086674|pmid-12554672|pmid-14602898|pmid-16469698|pmid-16469698
This indicates that the inhibitory effect of the domain occurs at least in part by preventing nucleotide binding, hydrolysis and/or release in a manner that is independent of the interaction of Mfd with its DNA substrate.
null
221
8,715
0
false
null
null
This indicates that the inhibitory effect of the domain occurs at least in part by preventing nucleotide binding, hydrolysis and/or release in a manner that is independent of the interaction of Mfd with its DNA substrate.
true
true
true
true
true
1,397
2
DISCUSSION
0
null
null
17,329,375
pmid-8465200|pmid-16469698|pmid-16469698|pmid-16309703|pmid-7876261|pmid-16469698|pmid-12086674|pmid-12554672|pmid-14602898|pmid-16469698|pmid-16469698
In the crystal structure of Mfd, D7 is not close to the predicted path of DNA across the protein and does not interact directly with domains D5 and D6, which contain the motifs important for ATP hydrolysis and DNA translocation (although it is important to note that the crystal structure was obtained in the absence of ...
null
414
8,716
0
false
null
null
In the crystal structure of Mfd, D7 is not close to the predicted path of DNA across the protein and does not interact directly with domains D5 and D6, which contain the motifs important for ATP hydrolysis and DNA translocation (although it is important to note that the crystal structure was obtained in the absence of ...
true
true
true
true
true
1,397
2
DISCUSSION
0
null
null
17,329,375
pmid-8465200|pmid-16469698|pmid-16469698|pmid-16309703|pmid-7876261|pmid-16469698|pmid-12086674|pmid-12554672|pmid-14602898|pmid-16469698|pmid-16469698
However, D7 is structurally linked to the translocase domains via the hook helices, which lead on from the TRG motif and interact with the relay helix linking the translocase domains to the RID (Figure 1).
null
205
8,717
0
false
null
null
However, D7 is structurally linked to the translocase domains via the hook helices, which lead on from the TRG motif and interact with the relay helix linking the translocase domains to the RID (Figure 1).
true
true
true
true
true
1,397
2
DISCUSSION
0
null
null
17,329,375
pmid-8465200|pmid-16469698|pmid-16469698|pmid-16309703|pmid-7876261|pmid-16469698|pmid-12086674|pmid-12554672|pmid-14602898|pmid-16469698|pmid-16469698
It is therefore feasible that deletion or movement of D7 could affect ATPase and translocation activity via transmission of conformational changes through the structure.
null
169
8,718
0
false
null
null
It is therefore feasible that deletion or movement of D7 could affect ATPase and translocation activity via transmission of conformational changes through the structure.
true
true
true
true
true
1,397
2
DISCUSSION
0
null
null
17,329,375
pmid-8465200|pmid-16469698|pmid-16469698|pmid-16309703|pmid-7876261|pmid-16469698|pmid-12086674|pmid-12554672|pmid-14602898|pmid-16469698|pmid-16469698
In any such allosteric effects of D7 the TRG motif is likely to play an important role.
null
87
8,719
0
false
null
null
In any such allosteric effects of D7 the TRG motif is likely to play an important role.
true
true
true
true
true
1,397
3
DISCUSSION
1
12
[ "B12", "B16", "B12", "B16", "B12" ]
17,329,375
pmid-16469698|pmid-16469698|pmid-12554672|pmid-16469698|pmid-12554672|pmid-16469698
The TRG motif contains a pair of helices that interact with helicase motif VI, providing a link to the ATPase catalytic site (12,16).
[ "12", "16", "12", "16", "12" ]
133
8,720
0
false
The TRG motif contains a pair of helices that interact with helicase motif VI, providing a link to the ATPase catalytic site.
[ "12,16" ]
The TRG motif contains a pair of helices that interact with helicase motif VI, providing a link to the ATPase catalytic site.
true
true
true
true
true
1,398
3
DISCUSSION
1
12
[ "B12", "B16", "B12", "B16", "B12" ]
17,329,375
pmid-16469698|pmid-16469698|pmid-12554672|pmid-16469698|pmid-12554672|pmid-16469698
In the RecG–ADP–DNA structure, these helices form a hairpin with two closely juxtaposed arginine residues at the base, whereas in the Mfd structure, which contains no nucleotide, these helices have moved apart (12,16).
[ "12", "16", "12", "16", "12" ]
218
8,721
0
false
In the RecG–ADP–DNA structure, these helices form a hairpin with two closely juxtaposed arginine residues at the base, whereas in the Mfd structure, which contains no nucleotide, these helices have moved apart.
[ "12,16" ]
In the RecG–ADP–DNA structure, these helices form a hairpin with two closely juxtaposed arginine residues at the base, whereas in the Mfd structure, which contains no nucleotide, these helices have moved apart.
true
true
true
true
true
1,398
3
DISCUSSION
1
12
[ "B12", "B16", "B12", "B16", "B12" ]
17,329,375
pmid-16469698|pmid-16469698|pmid-12554672|pmid-16469698|pmid-12554672|pmid-16469698
It seems that this structure forms a ‘spring-loaded’ switch that changes conformation during the nucleotide hydrolysis cycle: nucleotide binding stabilizes the closed conformation, and charge repulsion between the two arginines favours the open conformation.
[ "12", "16", "12", "16", "12" ]
258
8,722
0
false
It seems that this structure forms a ‘spring-loaded’ switch that changes conformation during the nucleotide hydrolysis cycle: nucleotide binding stabilizes the closed conformation, and charge repulsion between the two arginines favours the open conformation.
[]
It seems that this structure forms a ‘spring-loaded’ switch that changes conformation during the nucleotide hydrolysis cycle: nucleotide binding stabilizes the closed conformation, and charge repulsion between the two arginines favours the open conformation.
true
true
true
true
true
1,398
3
DISCUSSION
1
12
[ "B12", "B16", "B12", "B16", "B12" ]
17,329,375
pmid-16469698|pmid-16469698|pmid-12554672|pmid-16469698|pmid-12554672|pmid-16469698
It has previously been proposed that opening and closing of the TRG helical hairpin may be transmitted to the RID and D7 via the hook helices, and so the state of the TRG motif could control the position of these domains (12).
[ "12", "16", "12", "16", "12" ]
226
8,723
1
false
It has previously been proposed that opening and closing of the TRG helical hairpin may be transmitted to the RID and D7 via the hook helices, and so the state of the TRG motif could control the position of these domains.
[ "12" ]
It has previously been proposed that opening and closing of the TRG helical hairpin may be transmitted to the RID and D7 via the hook helices, and so the state of the TRG motif could control the position of these domains.
true
true
true
true
true
1,398
3
DISCUSSION
1
12
[ "B12", "B16", "B12", "B16", "B12" ]
17,329,375
pmid-16469698|pmid-16469698|pmid-12554672|pmid-16469698|pmid-12554672|pmid-16469698
Our findings suggest the relationship may be reciprocal, and D7 may regulate ATPase and DNA translocation activities by controlling the position of the hook helices and TRG motif.
[ "12", "16", "12", "16", "12" ]
179
8,724
0
false
Our findings suggest the relationship may be reciprocal, and D7 may regulate ATPase and DNA translocation activities by controlling the position of the hook helices and TRG motif.
[]
Our findings suggest the relationship may be reciprocal, and D7 may regulate ATPase and DNA translocation activities by controlling the position of the hook helices and TRG motif.
true
true
true
true
true
1,398
3
DISCUSSION
1
12
[ "B12", "B16", "B12", "B16", "B12" ]
17,329,375
pmid-16469698|pmid-16469698|pmid-12554672|pmid-16469698|pmid-12554672|pmid-16469698
In the isolated full-length protein, D7 may occupy a conformation that constrains the opening and closing of the TRG motif and hence inhibits ATPase activity and DNA translocation; if D7 is deleted this constraint is removed.
[ "12", "16", "12", "16", "12" ]
225
8,725
0
false
In the isolated full-length protein, D7 may occupy a conformation that constrains the opening and closing of the TRG motif and hence inhibits ATPase activity and DNA translocation; if D7 is deleted this constraint is removed.
[]
In the isolated full-length protein, D7 may occupy a conformation that constrains the opening and closing of the TRG motif and hence inhibits ATPase activity and DNA translocation; if D7 is deleted this constraint is removed.
true
true
true
true
true
1,398
3
DISCUSSION
1
12
[ "B12", "B16", "B12", "B16", "B12" ]
17,329,375
pmid-16469698|pmid-16469698|pmid-12554672|pmid-16469698|pmid-12554672|pmid-16469698
However, the TRG motif does not function solely as a relay in the autoinhibitory mechanism as it is clear that the TRG motif is essential for Mfd function even in the absence of D7.
[ "12", "16", "12", "16", "12" ]
181
8,726
0
false
However, the TRG motif does not function solely as a relay in the autoinhibitory mechanism as it is clear that the TRG motif is essential for Mfd function even in the absence of D7.
[]
However, the TRG motif does not function solely as a relay in the autoinhibitory mechanism as it is clear that the TRG motif is essential for Mfd function even in the absence of D7.
true
true
true
true
true
1,398
3
DISCUSSION
1
12
[ "B12", "B16", "B12", "B16", "B12" ]
17,329,375
pmid-16469698|pmid-16469698|pmid-12554672|pmid-16469698|pmid-12554672|pmid-16469698
The RA953 substitution, which removes one of the two key arginines within the TRG motif, abolishes the DNA translocation activity of MfdΔD7.
[ "12", "16", "12", "16", "12" ]
140
8,727
0
false
The RA953 substitution, which removes one of the two key arginines within the TRG motif, abolishes the DNA translocation activity of MfdΔD7.
[]
The RA953 substitution, which removes one of the two key arginines within the TRG motif, abolishes the DNA translocation activity of MfdΔD7.
true
true
true
true
true
1,398
3
DISCUSSION
1
12
[ "B12", "B16", "B12", "B16", "B12" ]
17,329,375
pmid-16469698|pmid-16469698|pmid-12554672|pmid-16469698|pmid-12554672|pmid-16469698
Furthermore, although disruption of the TRG motif has no effect on the ATPase activity of MfdΔD7 in the absence of DNA it reduces the ability of DNA to stimulate the ATPase activity.
[ "12", "16", "12", "16", "12" ]
182
8,728
0
false
Furthermore, although disruption of the TRG motif has no effect on the ATPase activity of MfdΔD7 in the absence of DNA it reduces the ability of DNA to stimulate the ATPase activity.
[]
Furthermore, although disruption of the TRG motif has no effect on the ATPase activity of MfdΔD7 in the absence of DNA it reduces the ability of DNA to stimulate the ATPase activity.
true
true
true
true
true
1,398
4
DISCUSSION
1
14
[ "B14" ]
17,329,375
pmid-12086674|pmid-16551743|pmid-16551743|pmid-12086674|pmid-15695524|pmid-11595187|pmid-11595187|pmid-12086674|pmid-15687384|pmid-7876261
How might interaction with RNAP relieve the inhibitory effect of D7?
[ "14" ]
68
8,729
0
false
How might interaction with RNAP relieve the inhibitory effect of D7?
[]
How might interaction with RNAP relieve the inhibitory effect of D7?
true
true
true
true
true
1,399
4
DISCUSSION
1
14
[ "B14" ]
17,329,375
pmid-12086674|pmid-16551743|pmid-16551743|pmid-12086674|pmid-15695524|pmid-11595187|pmid-11595187|pmid-12086674|pmid-15687384|pmid-7876261
The simplest explanation is that interaction between Mfd and RNAP causes D7 to be repositioned.
[ "14" ]
95
8,730
0
false
The simplest explanation is that interaction between Mfd and RNAP causes D7 to be repositioned.
[]
The simplest explanation is that interaction between Mfd and RNAP causes D7 to be repositioned.
true
true
true
true
true
1,399
4
DISCUSSION
1
14
[ "B14" ]
17,329,375
pmid-12086674|pmid-16551743|pmid-16551743|pmid-12086674|pmid-15695524|pmid-11595187|pmid-11595187|pmid-12086674|pmid-15687384|pmid-7876261
In the Mfd crystal structure, D7 packs between D2 and D4 (the RID).
[ "14" ]
67
8,731
0
false
In the Mfd crystal structure, D7 packs between D2 and D4 (the RID).
[]
In the Mfd crystal structure, D7 packs between D2 and D4 (the RID).
true
true
true
true
true
1,399
4
DISCUSSION
1
14
[ "B14" ]
17,329,375
pmid-12086674|pmid-16551743|pmid-16551743|pmid-12086674|pmid-15695524|pmid-11595187|pmid-11595187|pmid-12086674|pmid-15687384|pmid-7876261
As discussed above the juxtaposition of D4, D7 and the TRG motif is also potentially linked by changes in the interaction between the hook and relay helices.
[ "14" ]
157
8,732
0
false
As discussed above the juxtaposition of D4, D7 and the TRG motif is also potentially linked by changes in the interaction between the hook and relay helices.
[]
As discussed above the juxtaposition of D4, D7 and the TRG motif is also potentially linked by changes in the interaction between the hook and relay helices.
true
true
true
true
true
1,399
4
DISCUSSION
1
14
[ "B14" ]
17,329,375
pmid-12086674|pmid-16551743|pmid-16551743|pmid-12086674|pmid-15695524|pmid-11595187|pmid-11595187|pmid-12086674|pmid-15687384|pmid-7876261
Interaction of RNAP with the RID may therefore directly affect the position of D7.
[ "14" ]
82
8,733
0
false
Interaction of RNAP with the RID may therefore directly affect the position of D7.
[]
Interaction of RNAP with the RID may therefore directly affect the position of D7.
true
true
true
true
true
1,399
4
DISCUSSION
1
14
[ "B14" ]
17,329,375
pmid-12086674|pmid-16551743|pmid-16551743|pmid-12086674|pmid-15695524|pmid-11595187|pmid-11595187|pmid-12086674|pmid-15687384|pmid-7876261
Alternatively, D7 may make a separate interaction with RNAP that results in its repositioning.
[ "14" ]
94
8,734
0
false
Alternatively, D7 may make a separate interaction with RNAP that results in its repositioning.
[]
Alternatively, D7 may make a separate interaction with RNAP that results in its repositioning.
true
true
true
true
true
1,399
4
DISCUSSION
1
14
[ "B14" ]
17,329,375
pmid-12086674|pmid-16551743|pmid-16551743|pmid-12086674|pmid-15695524|pmid-11595187|pmid-11595187|pmid-12086674|pmid-15687384|pmid-7876261
If this is the case this secondary interaction is presumably weaker than the characterized RID–β subunit interaction, as a C-terminal fragment of Mfd containing D7 did not bind to RNAP in pull-down assays that detected the interaction made by fragments that included the RID (14).
[ "14" ]
280
8,735
1
false
If this is the case this secondary interaction is presumably weaker than the characterized RID–β subunit interaction, as a C-terminal fragment of Mfd containing D7 did not bind to RNAP in pull-down assays that detected the interaction made by fragments that included the RID.
[ "14" ]
If this is the case this secondary interaction is presumably weaker than the characterized RID–β subunit interaction, as a C-terminal fragment of Mfd containing D7 did not bind to RNAP in pull-down assays that detected the interaction made by fragments that included the RID.
true
true
true
true
true
1,399
5
DISCUSSION
1
29
[ "B29", "B21", "B18", "B30", "B31", "B19" ]
17,329,375
pmid-8465200|pmid-12581657|pmid-15687384|pmid-16551743|pmid-9182561|pmid-9094712|pmid-15695524
The RID contact site lies within the mobile β1 domain of the RNAP β subunit, movement of which is one of the conformational changes associated with the opening and closing of the main channel of RNAP (29).
[ "29", "21", "18", "30", "31", "19" ]
205
8,736
1
false
The RID contact site lies within the mobile β1 domain of the RNAP β subunit, movement of which is one of the conformational changes associated with the opening and closing of the main channel of RNAP.
[ "29" ]
The RID contact site lies within the mobile β1 domain of the RNAP β subunit, movement of which is one of the conformational changes associated with the opening and closing of the main channel of RNAP.
true
true
true
true
true
1,400
5
DISCUSSION
1
29
[ "B29", "B21", "B18", "B30", "B31", "B19" ]
17,329,375
pmid-8465200|pmid-12581657|pmid-15687384|pmid-16551743|pmid-9182561|pmid-9094712|pmid-15695524
In this work, we found that the interaction between Mfd and the β subunit of RNAP was essential for RNAP displacement by MfdΔD7, despite the fact that the truncated protein was able to rapidly displace a TFO from DNA.
[ "29", "21", "18", "30", "31", "19" ]
217
8,737
0
false
In this work, we found that the interaction between Mfd and the β subunit of RNAP was essential for RNAP displacement by MfdΔD7, despite the fact that the truncated protein was able to rapidly displace a TFO from DNA.
[]
In this work, we found that the interaction between Mfd and the β subunit of RNAP was essential for RNAP displacement by MfdΔD7, despite the fact that the truncated protein was able to rapidly displace a TFO from DNA.
true
true
true
true
true
1,400
5
DISCUSSION
1
29
[ "B29", "B21", "B18", "B30", "B31", "B19" ]
17,329,375
pmid-8465200|pmid-12581657|pmid-15687384|pmid-16551743|pmid-9182561|pmid-9094712|pmid-15695524
This result shows that DNA translocation activity alone is not sufficient to enable MfdΔD7 to displace a stalled transcription complex from DNA: it must also bind to RNAP.
[ "29", "21", "18", "30", "31", "19" ]
171
8,738
0
false
This result shows that DNA translocation activity alone is not sufficient to enable MfdΔD7 to displace a stalled transcription complex from DNA: it must also bind to RNAP.
[]
This result shows that DNA translocation activity alone is not sufficient to enable MfdΔD7 to displace a stalled transcription complex from DNA: it must also bind to RNAP.
true
true
true
true
true
1,400
5
DISCUSSION
1
29
[ "B29", "B21", "B18", "B30", "B31", "B19" ]
17,329,375
pmid-8465200|pmid-12581657|pmid-15687384|pmid-16551743|pmid-9182561|pmid-9094712|pmid-15695524
Why must the MfdΔD7 motor be tethered to RNAP in order to displace it?
[ "29", "21", "18", "30", "31", "19" ]
70
8,739
0
false
Why must the MfdΔD7 motor be tethered to RNAP in order to displace it?
[]
Why must the MfdΔD7 motor be tethered to RNAP in order to displace it?
true
true
true
true
true
1,400
5
DISCUSSION
1
21
[ "B29", "B21", "B18", "B30", "B31", "B19" ]
17,329,375
pmid-8465200|pmid-12581657|pmid-15687384|pmid-16551743|pmid-9182561|pmid-9094712|pmid-15695524
We have suggested previously that translocation by Mfd tethered to β1 might drive a remodelling process that opens the RNAP main channel (21), in addition to rewinding the transcription bubble (18), and this would be consistent with the findings reported here.
[ "29", "21", "18", "30", "31", "19" ]
260
8,740
1
false
We have suggested previously that translocation by Mfd tethered to β1 might drive a remodelling process that opens the RNAP main channel, in addition to rewinding the transcription bubble, and this would be consistent with the findings reported here.
[ "21", "18" ]
We have suggested previously that translocation by Mfd tethered to β1 might drive a remodelling process that opens the RNAP main channel, in addition to rewinding the transcription bubble, and this would be consistent with the findings reported here.
true
true
true
true
true
1,400
5
DISCUSSION
1
29
[ "B29", "B21", "B18", "B30", "B31", "B19" ]
17,329,375
pmid-8465200|pmid-12581657|pmid-15687384|pmid-16551743|pmid-9182561|pmid-9094712|pmid-15695524
An alternative possibility is that the Mfd–RNAP interaction may allow RNAP to act as a ‘processivity factor’ for Mfd, ensuring that Mfd continues to push against the transcription complex until it is displaced.
[ "29", "21", "18", "30", "31", "19" ]
210
8,741
0
false
An alternative possibility is that the Mfd–RNAP interaction may allow RNAP to act as a ‘processivity factor’ for Mfd, ensuring that Mfd continues to push against the transcription complex until it is displaced.
[]
An alternative possibility is that the Mfd–RNAP interaction may allow RNAP to act as a ‘processivity factor’ for Mfd, ensuring that Mfd continues to push against the transcription complex until it is displaced.
true
true
true
true
true
1,400
5
DISCUSSION
1
29
[ "B29", "B21", "B18", "B30", "B31", "B19" ]
17,329,375
pmid-8465200|pmid-12581657|pmid-15687384|pmid-16551743|pmid-9182561|pmid-9094712|pmid-15695524
Stalled transcription complexes are stabilized by multiple interactions between proteins, RNA and DNA, and are likely to present more of an obstacle to a translocating motor protein than a triplex does.
[ "29", "21", "18", "30", "31", "19" ]
202
8,742
0
false
Stalled transcription complexes are stabilized by multiple interactions between proteins, RNA and DNA, and are likely to present more of an obstacle to a translocating motor protein than a triplex does.
[]
Stalled transcription complexes are stabilized by multiple interactions between proteins, RNA and DNA, and are likely to present more of an obstacle to a translocating motor protein than a triplex does.
true
true
true
true
true
1,400
5
DISCUSSION
1
29
[ "B29", "B21", "B18", "B30", "B31", "B19" ]
17,329,375
pmid-8465200|pmid-12581657|pmid-15687384|pmid-16551743|pmid-9182561|pmid-9094712|pmid-15695524
We do not know how many ATPase cycles are required for Mfd to displace a transcription complex, and unlike a TFO the transcription complex is dynamic and may slide backwards to its starting position if Mfd dissociates before displacement is complete (30,31).
[ "29", "21", "18", "30", "31", "19" ]
258
8,743
0
false
We do not know how many ATPase cycles are required for Mfd to displace a transcription complex, and unlike a TFO the transcription complex is dynamic and may slide backwards to its starting position if Mfd dissociates before displacement is complete.
[ "30,31" ]
We do not know how many ATPase cycles are required for Mfd to displace a transcription complex, and unlike a TFO the transcription complex is dynamic and may slide backwards to its starting position if Mfd dissociates before displacement is complete.
true
true
true
true
true
1,400
5
DISCUSSION
1
29
[ "B29", "B21", "B18", "B30", "B31", "B19" ]
17,329,375
pmid-8465200|pmid-12581657|pmid-15687384|pmid-16551743|pmid-9182561|pmid-9094712|pmid-15695524
When associated with a transcription complex Mfd is tethered to the DNA both directly, via its translocase domains, and indirectly, via the contact of the RID with the transcription complex.
[ "29", "21", "18", "30", "31", "19" ]
190
8,744
0
false
When associated with a transcription complex Mfd is tethered to the DNA both directly, via its translocase domains, and indirectly, via the contact of the RID with the transcription complex.
[]
When associated with a transcription complex Mfd is tethered to the DNA both directly, via its translocase domains, and indirectly, via the contact of the RID with the transcription complex.
true
true
true
true
true
1,400
5
DISCUSSION
1
29
[ "B29", "B21", "B18", "B30", "B31", "B19" ]
17,329,375
pmid-8465200|pmid-12581657|pmid-15687384|pmid-16551743|pmid-9182561|pmid-9094712|pmid-15695524
This means that translocation will not necessarily terminate if the translocase domains transiently dissociate from the DNA (in contrast to the situation that would arise with free MfdΔD7).
[ "29", "21", "18", "30", "31", "19" ]
189
8,745
0
false
This means that translocation will not necessarily terminate if the translocase domains transiently dissociate from the DNA (in contrast to the situation that would arise with free MfdΔD7).
[]
This means that translocation will not necessarily terminate if the translocase domains transiently dissociate from the DNA (in contrast to the situation that would arise with free MfdΔD7).
true
true
true
true
true
1,400
5
DISCUSSION
1
19
[ "B29", "B21", "B18", "B30", "B31", "B19" ]
17,329,375
pmid-8465200|pmid-12581657|pmid-15687384|pmid-16551743|pmid-9182561|pmid-9094712|pmid-15695524
In this context, the transcription complex may therefore play a similar role to the wedge domain of RecG, which increases the processivity of that motor by acting as a sliding clamp on the DNA (19).
[ "29", "21", "18", "30", "31", "19" ]
198
8,746
1
false
In this context, the transcription complex may therefore play a similar role to the wedge domain of RecG, which increases the processivity of that motor by acting as a sliding clamp on the DNA.
[ "19" ]
In this context, the transcription complex may therefore play a similar role to the wedge domain of RecG, which increases the processivity of that motor by acting as a sliding clamp on the DNA.
true
true
true
true
true
1,400
6
DISCUSSION
1
32
[ "B32", "B33" ]
17,329,375
pmid-16009938|pmid-16595666
Autoinhibition and context-specific activation may prove to be a widespread strategy for the control of helicase proteins that function within macromolecular assemblies.
[ "32", "33" ]
169
8,747
0
false
Autoinhibition and context-specific activation may prove to be a widespread strategy for the control of helicase proteins that function within macromolecular assemblies.
[]
Autoinhibition and context-specific activation may prove to be a widespread strategy for the control of helicase proteins that function within macromolecular assemblies.
true
true
true
true
true
1,401
6
DISCUSSION
1
32
[ "B32", "B33" ]
17,329,375
pmid-16009938|pmid-16595666
It is important that the activity of such enzymes is strictly regulated, as their activities are costly to the cell in terms of ATP hydrolysis and likely to be deleterious if performed inappropriately.
[ "32", "33" ]
201
8,748
0
false
It is important that the activity of such enzymes is strictly regulated, as their activities are costly to the cell in terms of ATP hydrolysis and likely to be deleterious if performed inappropriately.
[]
It is important that the activity of such enzymes is strictly regulated, as their activities are costly to the cell in terms of ATP hydrolysis and likely to be deleterious if performed inappropriately.
true
true
true
true
true
1,401
6
DISCUSSION
1
32
[ "B32", "B33" ]
17,329,375
pmid-16009938|pmid-16595666
The helicase activity of the E. coli Rep protein (a superfamily 1 helicase that functions in DNA replication), and the ATPase and DNA-binding activities of UvrB (a superfamily 2 helicase that detects DNA damage in complex with UvrA) have both been shown recently to be regulated by autoinhibitory domains (32,33).
[ "32", "33" ]
313
8,749
0
false
The helicase activity of the E. coli Rep protein (a superfamily 1 helicase that functions in DNA replication), and the ATPase and DNA-binding activities of UvrB (a superfamily 2 helicase that detects DNA damage in complex with UvrA) have both been shown recently to be regulated by autoinhibitory domains.
[ "32,33" ]
The helicase activity of the E. coli Rep protein (a superfamily 1 helicase that functions in DNA replication), and the ATPase and DNA-binding activities of UvrB have both been shown recently to be regulated by autoinhibitory domains.
true
true
true
true
true
1,401
6
DISCUSSION
1
32
[ "B32", "B33" ]
17,329,375
pmid-16009938|pmid-16595666
Rep autoinhibition is thought to be relieved by dimerization, and it has been suggested that autoinhibition of UvrB may be relieved by interaction with UvrA.
[ "32", "33" ]
157
8,750
0
false
Rep autoinhibition is thought to be relieved by dimerization, and it has been suggested that autoinhibition of UvrB may be relieved by interaction with UvrA.
[]
Rep autoinhibition is thought to be relieved by dimerization, and it has been suggested that autoinhibition of UvrB may be relieved by interaction with UvrA.
true
true
true
true
true
1,401
6
DISCUSSION
1
32
[ "B32", "B33" ]
17,329,375
pmid-16009938|pmid-16595666
The regulatory mechanism uncovered in our work ensures that DNA translocation by Mfd occurs only in the correct context of an Mfd–RNAP complex.
[ "32", "33" ]
143
8,751
0
false
The regulatory mechanism uncovered in our work ensures that DNA translocation by Mfd occurs only in the correct context of an Mfd–RNAP complex.
[]
The regulatory mechanism uncovered in our work ensures that DNA translocation by Mfd occurs only in the correct context of an Mfd–RNAP complex.
true
true
true
true
true
1,401
6
DISCUSSION
1
32
[ "B32", "B33" ]
17,329,375
pmid-16009938|pmid-16595666
The fact that the control process involves domain D7, which is also implicated in regulating the interaction of Mfd with the repair protein UvrA, suggests that the transcription-coupled repair process as a whole is highly coordinated.
[ "32", "33" ]
234
8,752
0
false
The fact that the control process involves domain D7, which is also implicated in regulating the interaction of Mfd with the repair protein UvrA, suggests that the transcription-coupled repair process as a whole is highly coordinated.
[]
The fact that the control process involves domain D7, which is also implicated in regulating the interaction of Mfd with the repair protein UvrA, suggests that the transcription-coupled repair process as a whole is highly coordinated.
true
true
true
true
true
1,401
0
INTRODUCTION
1
1
[ "b1", "b2" ]
16,935,872
pmid-10357855|pmid-15328417
Homologous recombination (HR) is a high fidelity and template-dependent DNA repair pathway found in all organisms studied.
[ "1", "2" ]
122
8,753
0
false
Homologous recombination (HR) is a high fidelity and template-dependent DNA repair pathway found in all organisms studied.
[]
Homologous recombination (HR) is a high fidelity and template-dependent DNA repair pathway found in all organisms studied.
true
true
true
true
true
1,402
0
INTRODUCTION
1
1
[ "b1", "b2" ]
16,935,872
pmid-10357855|pmid-15328417
HR serves in the non-mutagenic tolerance of DNA damage, in the repair of complex DNA damage, such as single-stranded DNA (ssDNA) gaps, double-stranded DNA breaks (DSBs) and interstrand crosslinks, as well as in the recovery of stalled and collapsed replication forks (1,2).
[ "1", "2" ]
273
8,754
0
false
HR serves in the non-mutagenic tolerance of DNA damage, in the repair of complex DNA damage, such as single-stranded DNA (ssDNA) gaps, double-stranded DNA breaks (DSBs) and interstrand crosslinks, as well as in the recovery of stalled and collapsed replication forks.
[ "1,2" ]
HR serves in the non-mutagenic tolerance of DNA damage, in the repair of complex DNA damage, such as single-stranded DNA (ssDNA) gaps, double-stranded DNA breaks (DSBs) and interstrand crosslinks, as well as in the recovery of stalled and collapsed replication forks.
true
true
true
true
true
1,402
0
INTRODUCTION
1
1
[ "b1", "b2" ]
16,935,872
pmid-10357855|pmid-15328417
Historically prominent is the role of HR during prophase of the first meiotic division, where it contributes to high fidelity segregation of the homologs and to the generation of genetic diversity among the meiotic products.
[ "1", "2" ]
224
8,755
0
false
Historically prominent is the role of HR during prophase of the first meiotic division, where it contributes to high fidelity segregation of the homologs and to the generation of genetic diversity among the meiotic products.
[]
Historically prominent is the role of HR during prophase of the first meiotic division, where it contributes to high fidelity segregation of the homologs and to the generation of genetic diversity among the meiotic products.
true
true
true
true
true
1,402
1
INTRODUCTION
1
3
[ "b3", "b4" ]
16,935,872
NA|pmid-9118215
RAD54 is a core constituent of the RAD52 epistasis group that encodes the proteins that are essential for HR in eukaryotes.
[ "3", "4" ]
123
8,756
0
false
RAD54 is a core constituent of the RAD52 epistasis group that encodes the proteins that are essential for HR in eukaryotes.
[]
RAD54 is a core constituent of the RAD52 epistasis group that encodes the proteins that are essential for HR in eukaryotes.
true
true
true
true
true
1,403
1
INTRODUCTION
1
3
[ "b3", "b4" ]
16,935,872
NA|pmid-9118215
Rad54 protein is a member of the Snf2-family of SF2 helicases that contains many prominent chromatin-remodeling proteins including Snf2, ISWI and others.
[ "3", "4" ]
153
8,757
0
false
Rad54 protein is a member of the Snf2-family of SF2 helicases that contains many prominent chromatin-remodeling proteins including Snf2, ISWI and others.
[]
Rad54 protein is a member of the Snf2-family of SF2 helicases that contains many prominent chromatin-remodeling proteins including Snf2, ISWI and others.
true
true
true
true
true
1,403
1
INTRODUCTION
1
3
[ "b3", "b4" ]
16,935,872
NA|pmid-9118215
This group of proteins shares a common core that includes seven motifs proposed to identify helicases (3).
[ "3", "4" ]
106
8,758
1
false
This group of proteins shares a common core that includes seven motifs proposed to identify helicases.
[ "3" ]
This group of proteins shares a common core that includes seven motifs proposed to identify helicases.
true
true
true
true
true
1,403
1
INTRODUCTION
1
4
[ "b3", "b4" ]
16,935,872
NA|pmid-9118215
However, rather than operating like DNA helicases, which are capable of separating the strands of duplex DNA, the Snf2-related proteins are viewed as motor proteins that translocate on duplex DNA and remodel specific protein–duplex DNA complexes (4).
[ "3", "4" ]
250
8,759
1
false
However, rather than operating like DNA helicases, which are capable of separating the strands of duplex DNA, the Snf2-related proteins are viewed as motor proteins that translocate on duplex DNA and remodel specific protein–duplex DNA complexes.
[ "4" ]
However, rather than operating like DNA helicases, which are capable of separating the strands of duplex DNA, the Snf2-related proteins are viewed as motor proteins that translocate on duplex DNA and remodel specific protein–duplex DNA complexes.
true
true
true
true
true
1,403
1
INTRODUCTION
1
3
[ "b3", "b4" ]
16,935,872
NA|pmid-9118215
The particular functions of these proteins appear to involve specific protein interactions mediated by domains outside the core motor domain.
[ "3", "4" ]
141
8,760
0
false
The particular functions of these proteins appear to involve specific protein interactions mediated by domains outside the core motor domain.
[]
The particular functions of these proteins appear to involve specific protein interactions mediated by domains outside the core motor domain.
true
true
true
true
true
1,403
1
INTRODUCTION
1
3
[ "b3", "b4" ]
16,935,872
NA|pmid-9118215
The budding yeast Saccharomyces cerevisiae genome encodes 17 Snf2-related proteins (Table 1).
[ "3", "4" ]
93
8,761
0
false
The budding yeast Saccharomyces cerevisiae genome encodes 17 Snf2-related proteins (Table 1).
[]
The budding yeast Saccharomyces cerevisiae genome encodes 17 Snf2-related proteins (Table 1).
true
true
true
true
true
1,403
1
INTRODUCTION
1
3
[ "b3", "b4" ]
16,935,872
NA|pmid-9118215
Interestingly, at least seven of them, Rad54, Rdh54/Tid1, Rad5, Rad16, Rad26/CS-B, as well as the Ino80 and Swr1 complex, have specific functions during DNA repair.
[ "3", "4" ]
164
8,762
0
false
Interestingly, at least seven of them, Rad54, Rdh54/Tid1, Rad5, Rad16, Rad26/CS-B, as well as the Ino80 and Swr1 complex, have specific functions during DNA repair.
[]
Interestingly, at least seven of them, Rad54, Rdh54/Tid1, Rad5, Rad16, Rad26/CS-B, as well as the Ino80 and Swr1 complex, have specific functions during DNA repair.
true
true
true
true
true
1,403
2
INTRODUCTION
1
1
[ "b1", "b5", "b8", "b9", "b11", "b12" ]
16,935,872
pmid-10357855|pmid-10915877|pmid-12778123|pmid-10688638|pmid-12672490|pmid-12826279
Previous reviews provide excellent overall outlines of HR and the RAD52 group proteins (1,5–8), as well as detailed discussions of the Snf2-related chromatin remodeling factors (9–11).
[ "1", "5", "8", "9", "11", "12" ]
184
8,763
0
false
Previous reviews provide excellent overall outlines of HR and the RAD52 group proteins, as well as detailed discussions of the Snf2-related chromatin remodeling factors.
[ "1,5–8", "9–11" ]
Previous reviews provide excellent overall outlines of HR and the RAD52 group proteins, as well as detailed discussions of the Snf2-related chromatin remodeling factors.
true
true
true
true
true
1,404
2
INTRODUCTION
1
1
[ "b1", "b5", "b8", "b9", "b11", "b12" ]
16,935,872
pmid-10357855|pmid-10915877|pmid-12778123|pmid-10688638|pmid-12672490|pmid-12826279
In this review, we focus on the Rad54 protein.
[ "1", "5", "8", "9", "11", "12" ]
46
8,764
0
false
In this review, we focus on the Rad54 protein.
[]
In this review, we focus on the Rad54 protein.
true
true
true
true
true
1,404
2
INTRODUCTION
1
1
[ "b1", "b5", "b8", "b9", "b11", "b12" ]
16,935,872
pmid-10357855|pmid-10915877|pmid-12778123|pmid-10688638|pmid-12672490|pmid-12826279
Versatile like the proverbial Swiss Army knife, Rad54 has been postulated to function at multiple stages during HR.
[ "1", "5", "8", "9", "11", "12" ]
115
8,765
0
false
Versatile like the proverbial Swiss Army knife, Rad54 has been postulated to function at multiple stages during HR.
[]
Versatile like the proverbial Swiss Army knife, Rad54 has been postulated to function at multiple stages during HR.
true
true
true
true
true
1,404
2
INTRODUCTION
1
12
[ "b1", "b5", "b8", "b9", "b11", "b12" ]
16,935,872
pmid-10357855|pmid-10915877|pmid-12778123|pmid-10688638|pmid-12672490|pmid-12826279
Biochemical analyses of complex in vitro recombination assays led to a number of mutually non-exclusive models, as reviewed previously (12).
[ "1", "5", "8", "9", "11", "12" ]
140
8,766
1
false
Biochemical analyses of complex in vitro recombination assays led to a number of mutually non-exclusive models, as reviewed previously.
[ "12" ]
Biochemical analyses of complex in vitro recombination assays led to a number of mutually non-exclusive models, as reviewed previously.
true
true
true
true
true
1,404
2
INTRODUCTION
1
1
[ "b1", "b5", "b8", "b9", "b11", "b12" ]
16,935,872
pmid-10357855|pmid-10915877|pmid-12778123|pmid-10688638|pmid-12672490|pmid-12826279
We will discuss results from genetic, biochemical and cytological experiments, as well as insights from the recently accomplished determinations of the Rad54 protein structure to highlight the mechanistic models for the function of Rad54 during HR.
[ "1", "5", "8", "9", "11", "12" ]
248
8,767
0
false
We will discuss results from genetic, biochemical and cytological experiments, as well as insights from the recently accomplished determinations of the Rad54 protein structure to highlight the mechanistic models for the function of Rad54 during HR.
[]
We will discuss results from genetic, biochemical and cytological experiments, as well as insights from the recently accomplished determinations of the Rad54 protein structure to highlight the mechanistic models for the function of Rad54 during HR.
true
true
true
true
true
1,404
0
INTRODUCTION
1
1
[ "B1", "B2 B3 B4", "B5" ]
17,537,820
pmid-12517228|pmid-2021692|pmid-11875246|pmid-85614|NA
Infections with influenza A viruses continue to be a public health problem, causing seasonal epidemics and sporadic but devastating pandemics.
[ "1", "2–4", "5" ]
142
8,768
0
false
Infections with influenza A viruses continue to be a public health problem, causing seasonal epidemics and sporadic but devastating pandemics.
[]
Infections with influenza A viruses continue to be a public health problem, causing seasonal epidemics and sporadic but devastating pandemics.
true
true
true
true
true
1,405
0
INTRODUCTION
1
1
[ "B1", "B2 B3 B4", "B5" ]
17,537,820
pmid-12517228|pmid-2021692|pmid-11875246|pmid-85614|NA
Each year in the US, influenza epidemics cause more than 200 000 hospitalizations and result in over 30 000 influenza-related deaths (1).
[ "1", "2–4", "5" ]
137
8,769
1
false
Each year in the US, influenza epidemics cause more than 200 000 hospitalizations and result in over 30 000 influenza-related deaths.
[ "1" ]
Each year in the US, influenza epidemics cause more than 200 000 hospitalizations and result in over 30 000 influenza-related deaths.
true
true
true
true
true
1,405
0
INTRODUCTION
1
1
[ "B1", "B2 B3 B4", "B5" ]
17,537,820
pmid-12517228|pmid-2021692|pmid-11875246|pmid-85614|NA
Influenza pandemics are infrequent but they can result in high mortality.
[ "1", "2–4", "5" ]
73
8,770
0
false
Influenza pandemics are infrequent but they can result in high mortality.
[]
Influenza pandemics are infrequent but they can result in high mortality.
true
true
true
true
true
1,405
0
INTRODUCTION
1
2–4
[ "B1", "B2 B3 B4", "B5" ]
17,537,820
pmid-12517228|pmid-2021692|pmid-11875246|pmid-85614|NA
It is estimated that ∼20–100 million people were killed worldwide by the 1918–1919 influenza pandemic (2–4).
[ "1", "2–4", "5" ]
108
8,771
1
false
It is estimated that ∼20–100 million people were killed worldwide by the 1918–1919 influenza pandemic.
[ "2–4" ]
It is estimated that ∼20–100 million people were killed worldwide by the 1918–1919 influenza pandemic.
true
true
true
true
true
1,405
0
INTRODUCTION
1
5
[ "B1", "B2 B3 B4", "B5" ]
17,537,820
pmid-12517228|pmid-2021692|pmid-11875246|pmid-85614|NA
The current level of pandemic alert is at the highest level, phase 3, since the most recent pandemic of 1968 (5).
[ "1", "2–4", "5" ]
113
8,772
1
false
The current level of pandemic alert is at the highest level, phase 3, since the most recent pandemic of 1968.
[ "5" ]
The current level of pandemic alert is at the highest level, phase 3, since the most recent pandemic of 1968.
true
true
true
true
true
1,405
1
INTRODUCTION
1
6
[ "B6", "B7", "B6", "B8", "B6", "B9" ]
17,537,820
pmid-1579108|pmid-11779385|pmid-1579108|pmid-15280485|pmid-1579108|pmid-16627734
Influenza viruses belong to the family Orthomyxoviridae and are classified into three types, A, B and C based on the identity of major internal protein antigens (6).
[ "6", "7", "6", "8", "6", "9" ]
165
8,773
1
false
Influenza viruses belong to the family Orthomyxoviridae and are classified into three types, A, B and C based on the identity of major internal protein antigens.
[ "6" ]
Influenza viruses belong to the family Orthomyxoviridae and are classified into three types, A, B and C based on the identity of major internal protein antigens.
true
true
true
true
true
1,406
1
INTRODUCTION
1
7
[ "B6", "B7", "B6", "B8", "B6", "B9" ]
17,537,820
pmid-1579108|pmid-11779385|pmid-1579108|pmid-15280485|pmid-1579108|pmid-16627734
Influenza A and C viruses can infect multiple mammalian species, while influenza B virus is almost exclusively a human pathogen (7).
[ "6", "7", "6", "8", "6", "9" ]
132
8,774
1
false
Influenza A and C viruses can infect multiple mammalian species, while influenza B virus is almost exclusively a human pathogen.
[ "7" ]
Influenza A and C viruses can infect multiple mammalian species, while influenza B virus is almost exclusively a human pathogen.
true
true
true
true
true
1,406
1
INTRODUCTION
1
6
[ "B6", "B7", "B6", "B8", "B6", "B9" ]
17,537,820
pmid-1579108|pmid-11779385|pmid-1579108|pmid-15280485|pmid-1579108|pmid-16627734
Influenza A viruses cause the greatest morbidity and mortality in humans.
[ "6", "7", "6", "8", "6", "9" ]
73
8,775
0
false
Influenza A viruses cause the greatest morbidity and mortality in humans.
[]
Influenza A viruses cause the greatest morbidity and mortality in humans.
true
true
true
true
true
1,406
1
INTRODUCTION
1
6
[ "B6", "B7", "B6", "B8", "B6", "B9" ]
17,537,820
pmid-1579108|pmid-11779385|pmid-1579108|pmid-15280485|pmid-1579108|pmid-16627734
Interestingly, the largest pool of influenza A viruses is maintained by horizontal spread in wild aquatic birds, in which the virus does not normally cause any disease (6,8).
[ "6", "7", "6", "8", "6", "9" ]
174
8,776
0
false
Interestingly, the largest pool of influenza A viruses is maintained by horizontal spread in wild aquatic birds, in which the virus does not normally cause any disease.
[ "6,8" ]
Interestingly, the largest pool of influenza A viruses is maintained by horizontal spread in wild aquatic birds, in which the virus does not normally cause any disease.
true
true
true
true
true
1,406
1
INTRODUCTION
1
6
[ "B6", "B7", "B6", "B8", "B6", "B9" ]
17,537,820
pmid-1579108|pmid-11779385|pmid-1579108|pmid-15280485|pmid-1579108|pmid-16627734
Food and companion animal populations such as poultry, swine, horses and dogs support sustained replication of certain lineages of influenza A, with minimal to lethal disease depending on the virulence of the strain (6).
[ "6", "7", "6", "8", "6", "9" ]
220
8,777
1
false
Food and companion animal populations such as poultry, swine, horses and dogs support sustained replication of certain lineages of influenza A, with minimal to lethal disease depending on the virulence of the strain.
[ "6" ]
Food and companion animal populations such as poultry, swine, horses and dogs support sustained replication of certain lineages of influenza A, with minimal to lethal disease depending on the virulence of the strain.
true
true
true
true
true
1,406
1
INTRODUCTION
1
9
[ "B6", "B7", "B6", "B8", "B6", "B9" ]
17,537,820
pmid-1579108|pmid-11779385|pmid-1579108|pmid-15280485|pmid-1579108|pmid-16627734
Influenza viruses have evolved in association with their various hosts in different continents for extended periods of time (9).
[ "6", "7", "6", "8", "6", "9" ]
128
8,778
1
false
Influenza viruses have evolved in association with their various hosts in different continents for extended periods of time.
[ "9" ]
Influenza viruses have evolved in association with their various hosts in different continents for extended periods of time.
true
true
true
true
true
1,406
1
INTRODUCTION
1
6
[ "B6", "B7", "B6", "B8", "B6", "B9" ]
17,537,820
pmid-1579108|pmid-11779385|pmid-1579108|pmid-15280485|pmid-1579108|pmid-16627734
This co-evolution has resulted in extensive genetic divergence among the extant viruses currently available for analysis.
[ "6", "7", "6", "8", "6", "9" ]
121
8,779
0
false
This co-evolution has resulted in extensive genetic divergence among the extant viruses currently available for analysis.
[]
This co-evolution has resulted in extensive genetic divergence among the extant viruses currently available for analysis.
true
true
true
true
true
1,406
2
INTRODUCTION
1
10
[ "B10", "B11" ]
17,537,820
pmid-15735418|pmid-16690910
Influenza A viruses are classified into subtypes on the basis of antigenic analysis of hemagglutinin (HA) and neuraminidase (NA) glycoproteins.
[ "10", "11" ]
143
8,780
0
false
Influenza A viruses are classified into subtypes on the basis of antigenic analysis of hemagglutinin (HA) and neuraminidase (NA) glycoproteins.
[]
Influenza A viruses are classified into subtypes on the basis of antigenic analysis of hemagglutinin (HA) and neuraminidase (NA) glycoproteins.
true
true
true
true
true
1,407
2
INTRODUCTION
1
10
[ "B10", "B11" ]
17,537,820
pmid-15735418|pmid-16690910
So far, 16 HA subtypes and 9 NA subtypes have been found (10).
[ "10", "11" ]
62
8,781
1
false
So far, 16 HA subtypes and 9 NA subtypes have been found.
[ "10" ]
So far, 16 HA subtypes and 9 NA subtypes have been found.
true
true
true
true
true
1,407
2
INTRODUCTION
1
10
[ "B10", "B11" ]
17,537,820
pmid-15735418|pmid-16690910
In recent years, gene sequences have become available for a large number of viral strains creating a diverse pool of influenza A viruses from historical and current isolates collected in multiple geographic regions.
[ "10", "11" ]
215
8,782
0
false
In recent years, gene sequences have become available for a large number of viral strains creating a diverse pool of influenza A viruses from historical and current isolates collected in multiple geographic regions.
[]
In recent years, gene sequences have become available for a large number of viral strains creating a diverse pool of influenza A viruses from historical and current isolates collected in multiple geographic regions.
true
true
true
true
true
1,407
2
INTRODUCTION
1
10
[ "B10", "B11" ]
17,537,820
pmid-15735418|pmid-16690910
Comparison of the deduced amino acid sequences of the HA and NA revealed an excellent agreement between the results of clustering viruses by the antigenic reactivity and sequence similarity.
[ "10", "11" ]
190
8,783
0
false
Comparison of the deduced amino acid sequences of the HA and NA revealed an excellent agreement between the results of clustering viruses by the antigenic reactivity and sequence similarity.
[]
Comparison of the deduced amino acid sequences of the HA and NA revealed an excellent agreement between the results of clustering viruses by the antigenic reactivity and sequence similarity.
true
true
true
true
true
1,407
2
INTRODUCTION
1
11
[ "B10", "B11" ]
17,537,820
pmid-15735418|pmid-16690910
However, molecular genetic analysis allows a comprehensive analysis of the entire viral genome and is gaining popularity because it is more practical for most laboratories as a method for classification (11).
[ "10", "11" ]
208
8,784
1
false
However, molecular genetic analysis allows a comprehensive analysis of the entire viral genome and is gaining popularity because it is more practical for most laboratories as a method for classification.
[ "11" ]
However, molecular genetic analysis allows a comprehensive analysis of the entire viral genome and is gaining popularity because it is more practical for most laboratories as a method for classification.
true
true
true
true
true
1,407
2
INTRODUCTION
1
10
[ "B10", "B11" ]
17,537,820
pmid-15735418|pmid-16690910
Most importantly, study of the influenza genomic structure, namely genotyping, could reveal mechanisms of virus evolution, spread and disease pathogenesis.
[ "10", "11" ]
155
8,785
0
false
Most importantly, study of the influenza genomic structure, namely genotyping, could reveal mechanisms of virus evolution, spread and disease pathogenesis.
[]
Most importantly, study of the influenza genomic structure, namely genotyping, could reveal mechanisms of virus evolution, spread and disease pathogenesis.
true
true
true
true
true
1,407
3
INTRODUCTION
1
12
[ "B12", "B13", "B14", "B15 B16 B17 B18 B19", "B20", "B21" ]
17,537,820
pmid-6351727|pmid-8387212|pmid-9882316|pmid-2769232|pmid-2939560|pmid-1895397|pmid-2398532|pmid-2800339|pmid-4549487|pmid-277933
The influenza A genome consists of eight negative-stranded RNA segments that encode at least 10 viral proteins (12).
[ "12", "13", "14", "15–19", "20", "21" ]
116
8,786
1
false
The influenza A genome consists of eight negative-stranded RNA segments that encode at least 10 viral proteins.
[ "12" ]
The influenza A genome consists of eight negative-stranded RNA segments that encode at least 10 viral proteins.
true
true
true
true
true
1,408
3
INTRODUCTION
1
13
[ "B12", "B13", "B14", "B15 B16 B17 B18 B19", "B20", "B21" ]
17,537,820
pmid-6351727|pmid-8387212|pmid-9882316|pmid-2769232|pmid-2939560|pmid-1895397|pmid-2398532|pmid-2800339|pmid-4549487|pmid-277933
The viral genome evolves through accumulation of mutation by the viral RNA-dependent RNA polymerase which lacks proofreading ability and through reassortment of entire gene segments(13).
[ "12", "13", "14", "15–19", "20", "21" ]
186
8,787
1
false
The viral genome evolves through accumulation of mutation by the viral RNA-dependent RNA polymerase which lacks proofreading ability and through reassortment of entire gene segments.
[ "13" ]
The viral genome evolves through accumulation of mutation by the viral RNA-dependent RNA polymerase which lacks proofreading ability and through reassortment of entire gene segments.
true
true
true
true
true
1,408
3
INTRODUCTION
1
14
[ "B12", "B13", "B14", "B15 B16 B17 B18 B19", "B20", "B21" ]
17,537,820
pmid-6351727|pmid-8387212|pmid-9882316|pmid-2769232|pmid-2939560|pmid-1895397|pmid-2398532|pmid-2800339|pmid-4549487|pmid-277933
Forces selecting viral variants such as the neutralizing antibody response of vertebrate hosts as well as species-related structural variation can also promote rapid evolution (14).
[ "12", "13", "14", "15–19", "20", "21" ]
181
8,788
1
false
Forces selecting viral variants such as the neutralizing antibody response of vertebrate hosts as well as species-related structural variation can also promote rapid evolution.
[ "14" ]
Forces selecting viral variants such as the neutralizing antibody response of vertebrate hosts as well as species-related structural variation can also promote rapid evolution.
true
true
true
true
true
1,408
3
INTRODUCTION
1
15–19
[ "B12", "B13", "B14", "B15 B16 B17 B18 B19", "B20", "B21" ]
17,537,820
pmid-6351727|pmid-8387212|pmid-9882316|pmid-2769232|pmid-2939560|pmid-1895397|pmid-2398532|pmid-2800339|pmid-4549487|pmid-277933
Each of the segments can evolve at a different rate if they are subject to differential selective pressures and functional constraints (15–19).
[ "12", "13", "14", "15–19", "20", "21" ]
143
8,789
1
false
Each of the segments can evolve at a different rate if they are subject to differential selective pressures and functional constraints.
[ "15–19" ]
Each of the segments can evolve at a different rate if they are subject to differential selective pressures and functional constraints.
true
true
true
true
true
1,408
3
INTRODUCTION
1
12
[ "B12", "B13", "B14", "B15 B16 B17 B18 B19", "B20", "B21" ]
17,537,820
pmid-6351727|pmid-8387212|pmid-9882316|pmid-2769232|pmid-2939560|pmid-1895397|pmid-2398532|pmid-2800339|pmid-4549487|pmid-277933
The segmented nature of the viral genome allows for segment exchange (termed reassortment) when two distinct viruses co-infect a cell and generate progeny with a mixed genome (20,21).
[ "12", "13", "14", "15–19", "20", "21" ]
183
8,790
0
false
The segmented nature of the viral genome allows for segment exchange (termed reassortment) when two distinct viruses co-infect a cell and generate progeny with a mixed genome.
[ "20,21" ]
The segmented nature of the viral genome allows for segment exchange (termed reassortment) when two distinct viruses co-infect a cell and generate progeny with a mixed genome.
true
true
true
true
true
1,408
3
INTRODUCTION
1
12
[ "B12", "B13", "B14", "B15 B16 B17 B18 B19", "B20", "B21" ]
17,537,820
pmid-6351727|pmid-8387212|pmid-9882316|pmid-2769232|pmid-2939560|pmid-1895397|pmid-2398532|pmid-2800339|pmid-4549487|pmid-277933
Reassortment may theoretically yield 254 (28 – 2) different combinations of gene segments from two parent viruses.
[ "12", "13", "14", "15–19", "20", "21" ]
114
8,791
0
false
Reassortment may theoretically yield 254 (28 – 2) different combinations of gene segments from two parent viruses.
[]
Reassortment may theoretically yield 254 different combinations of gene segments from two parent viruses.
true
true
true
true
true
1,408
4
INTRODUCTION
0
null
null
17,537,820
null
A comprehensive influenza genotype database that can be searched using a web tool for the genotyping viruses is not available.
null
126
8,792
0
false
null
null
A comprehensive influenza genotype database that can be searched using a web tool for the genotyping viruses is not available.
true
true
true
true
true
1,409
4
INTRODUCTION
0
null
null
17,537,820
null
Unlike HIV and HCV, the influenza A virus has a segmented genome, so eight separate phylogenies must be analyzed to establish a genotype.
null
137
8,793
0
false
null
null
Unlike HIV and HCV, the influenza A virus has a segmented genome, so eight separate phylogenies must be analyzed to establish a genotype.
true
true
true
true
true
1,409
5
INTRODUCTION
0
null
null
17,537,820
null
We approached the problem of genotyping influenza A viruses by analyzing each gene segment independently, segregating gene segments into subtypes and subsequently into lineages.
null
177
8,794
0
false
null
null
We approached the problem of genotyping influenza A viruses by analyzing each gene segment independently, segregating gene segments into subtypes and subsequently into lineages.
true
true
true
true
true
1,410
5
INTRODUCTION
0
null
null
17,537,820
null
The genotype of an influenza A viral strain is the sequential aggregate of the eight assigned gene segment lineages.
null
116
8,795
0
false
null
null
The genotype of an influenza A viral strain is the sequential aggregate of the eight assigned gene segment lineages.
true
true
true
true
true
1,410
5
INTRODUCTION
0
null
null
17,537,820
null
A nomenclature for influenza A viral genotypes will allow researchers to unequivocally describe influenza A viral genotypes to analyze, compare and communicate the molecular epidemiology of the virus.
null
200
8,796
0
false
null
null
A nomenclature for influenza A viral genotypes will allow researchers to unequivocally describe influenza A viral genotypes to analyze, compare and communicate the molecular epidemiology of the virus.
true
true
true
true
true
1,410
5
INTRODUCTION
0
null
null
17,537,820
null
In this report, we define a nomenclature for influenza A viral genotypes and describe a web tool developed for genotyping influenza A viruses from genome sequences.
null
164
8,797
0
false
null
null
In this report, we define a nomenclature for influenza A viral genotypes and describe a web tool developed for genotyping influenza A viruses from genome sequences.
true
true
true
true
true
1,410
5
INTRODUCTION
0
null
null
17,537,820
null
Our tool facilitates identification of reassortment events between divergent lineages.
null
86
8,798
0
false
null
null
Our tool facilitates identification of reassortment events between divergent lineages.
true
true
true
true
true
1,410
0
INTRODUCTION
1
1
[ "b1", "b12", "b8", "b13", "b14", "b12", "b14", "b1", "b12", "b15", "b1", "b9", "b12", "b15", "b20", "b1", "b9", "b21" ]
16,757,578
pmid-15952899|pmid-15063845|pmid-15948945|pmid-3047111|pmid-15305055|pmid-15063845|pmid-15305055|pmid-15952899|pmid-15063845|pmid-12540921|pmid-15952899|pmid-15519691|pmid-15063845|pmid-12540921|pmid-6397469|pmid-15952899|pmid-15519691|pmid-15659173|pmid-10651244|pmid-8855390|pmid-10385624|pmid-15087487|pmid-8636997|pm...
Two levels of DNA organization in bacterial nucleoid and eukaryotic chromatin have been suggested by earlier physical and chemical studies, these being the supramolecular looped organization and short-range structure (1–12).
[ "1", "12", "8", "13", "14", "12", "14", "1", "12", "15", "1", "9", "12", "15", "20", "1", "9", "21" ]
224
8,799
0
false
Two levels of DNA organization in bacterial nucleoid and eukaryotic chromatin have been suggested by earlier physical and chemical studies, these being the supramolecular looped organization and short-range structure.
[ "1–12" ]
Two levels of DNA organization in bacterial nucleoid and eukaryotic chromatin have been suggested by earlier physical and chemical studies, these being the supramolecular looped organization and short-range structure.
true
true
true
true
true
1,411