Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
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 Community
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DISCUSSION
1
17
[ "B17", "B19", "B20", "B22" ]
18,676,978
NA|pmid-15269332|pmid-17105995|pmid-12955455|pmid-17295027|pmid-14960277|pmid-12080340|pmid-17217467|pmid-16326926
We demonstrate that ZmWHY1 is essential for chloroplast biogenesis, and that it localizes to the chloroplast where it plays multiple roles in gene expression.
[ "17", "19", "20", "22" ]
158
41,619
0
false
We demonstrate that ZmWHY1 is essential for chloroplast biogenesis, and that it localizes to the chloroplast where it plays multiple roles in gene expression.
[]
We demonstrate that ZmWHY1 is essential for chloroplast biogenesis, and that it localizes to the chloroplast where it plays multiple roles in gene expression.
true
true
true
true
true
7,177
0
DISCUSSION
1
17
[ "B17", "B19", "B20", "B22" ]
18,676,978
NA|pmid-15269332|pmid-17105995|pmid-12955455|pmid-17295027|pmid-14960277|pmid-12080340|pmid-17217467|pmid-16326926
We also add RNA binding to WHY1's repertoire of biochemical activities and demonstrate that ZmWHY1 is bound to a subset of chloroplast RNAs in chloroplast extract.
[ "17", "19", "20", "22" ]
163
41,620
0
false
We also add RNA binding to WHY1's repertoire of biochemical activities and demonstrate that ZmWHY1 is bound to a subset of chloroplast RNAs in chloroplast extract.
[]
We also add RNA binding to WHY1's repertoire of biochemical activities and demonstrate that ZmWHY1 is bound to a subset of chloroplast RNAs in chloroplast extract.
true
true
true
true
true
7,177
1
DISCUSSION
0
null
null
18,676,978
pmid-9090875|pmid-11179231|pmid-18065687|pmid-17071648|pmid-12881426|pmid-11565746|pmid-17693527|NA|NA|pmid-17041147|pmid-9090875|pmid-17071648|pmid-12881426|pmid-11565746|pmid-15598799
ZmWHY was identified among proteins that coimmunoprecipitate with CRS1, which is required for the splicing of the group II intron in the chloroplast atpF pre-mRNA.
null
163
41,621
0
false
null
null
ZmWHY was identified among proteins that coimmunoprecipitate with CRS1, which is required for the splicing of the group II intron in the chloroplast atpF pre-mRNA.
true
true
true
true
true
7,178
1
DISCUSSION
0
null
null
18,676,978
pmid-9090875|pmid-11179231|pmid-18065687|pmid-17071648|pmid-12881426|pmid-11565746|pmid-17693527|NA|NA|pmid-17041147|pmid-9090875|pmid-17071648|pmid-12881426|pmid-11565746|pmid-15598799
We showed that ZmWHY1 is associated with atpF intron RNA in vivo and that the coimmunoprecipitation of ZmWHY1 and CRS1 is disrupted by RNAse, indicating that they coimmunoprecipitate due to their association with the same RNA molecule.
null
235
41,622
0
false
null
null
We showed that ZmWHY1 is associated with atpF intron RNA in vivo and that the coimmunoprecipitation of ZmWHY1 and CRS1 is disrupted by RNAse, indicating that they coimmunoprecipitate due to their association with the same RNA molecule.
true
true
true
true
true
7,178
1
DISCUSSION
0
null
null
18,676,978
pmid-9090875|pmid-11179231|pmid-18065687|pmid-17071648|pmid-12881426|pmid-11565746|pmid-17693527|NA|NA|pmid-17041147|pmid-9090875|pmid-17071648|pmid-12881426|pmid-11565746|pmid-15598799
ZmWHY1's association with atpF RNA is functionally significant, as atpF intron splicing is disrupted in ZmWhy1 mutants.
null
119
41,623
0
false
null
null
ZmWHY1's association with atpF RNA is functionally significant, as atpF intron splicing is disrupted in ZmWhy1 mutants.
true
true
true
true
true
7,178
1
DISCUSSION
0
null
null
18,676,978
pmid-9090875|pmid-11179231|pmid-18065687|pmid-17071648|pmid-12881426|pmid-11565746|pmid-17693527|NA|NA|pmid-17041147|pmid-9090875|pmid-17071648|pmid-12881426|pmid-11565746|pmid-15598799
However, the splicing of this intron is more sensitive to a partial loss of CRS1 than to a partial loss of ZmWHY1, suggesting that ZmWHY1 plays an accessory function in atpF splicing but may not be absolutely required.
null
218
41,624
0
false
null
null
However, the splicing of this intron is more sensitive to a partial loss of CRS1 than to a partial loss of ZmWHY1, suggesting that ZmWHY1 plays an accessory function in atpF splicing but may not be absolutely required.
true
true
true
true
true
7,178
2
DISCUSSION
1
11
[ "B11", "B39", "B43 B44 B45 B46" ]
18,676,978
pmid-14960277|pmid-10948264|pmid-14960277|pmid-12080340|pmid-17217467|pmid-15967440|pmid-16326926|pmid-18423020|pmid-11565746|NA|pmid-15891117|pmid-15010617|pmid-15197595|pmid-12678554
The atpF splicing defect in ZmWhy1 mutants cannot account for their loss of plastid ribosomes, as the more severe atpF splicing defect in crs1-1 mutants is not accompanied by a substantial plastid ribosome deficiency (11).
[ "11", "39", "43–46" ]
222
41,625
1
false
The atpF splicing defect in ZmWhy1 mutants cannot account for their loss of plastid ribosomes, as the more severe atpF splicing defect in crs1-1 mutants is not accompanied by a substantial plastid ribosome deficiency.
[ "11" ]
The atpF splicing defect in ZmWhy1 mutants cannot account for their loss of plastid ribosomes, as the more severe atpF splicing defect in crs1-1 mutants is not accompanied by a substantial plastid ribosome deficiency.
true
true
true
true
true
7,179
2
DISCUSSION
1
11
[ "B11", "B39", "B43 B44 B45 B46" ]
18,676,978
pmid-14960277|pmid-10948264|pmid-14960277|pmid-12080340|pmid-17217467|pmid-15967440|pmid-16326926|pmid-18423020|pmid-11565746|NA|pmid-15891117|pmid-15010617|pmid-15197595|pmid-12678554
The specific role of ZmWHY1 in promoting the biogenesis of the plastid translation machinery remains unclear.
[ "11", "39", "43–46" ]
109
41,626
0
false
The specific role of ZmWHY1 in promoting the biogenesis of the plastid translation machinery remains unclear.
[]
The specific role of ZmWHY1 in promoting the biogenesis of the plastid translation machinery remains unclear.
true
true
true
true
true
7,179
2
DISCUSSION
1
11
[ "B11", "B39", "B43 B44 B45 B46" ]
18,676,978
pmid-14960277|pmid-10948264|pmid-14960277|pmid-12080340|pmid-17217467|pmid-15967440|pmid-16326926|pmid-18423020|pmid-11565746|NA|pmid-15891117|pmid-15010617|pmid-15197595|pmid-12678554
Although several RNAs with translation-related functions are among the RNAs that coimmunoprecipitate with ZmWHY1, the abundance and processing of these RNAs are similar in ZmWhy1 mutants and in control mutants that exhibit a ribosome-deficiency of similar severity.
[ "11", "39", "43–46" ]
265
41,627
0
false
Although several RNAs with translation-related functions are among the RNAs that coimmunoprecipitate with ZmWHY1, the abundance and processing of these RNAs are similar in ZmWhy1 mutants and in control mutants that exhibit a ribosome-deficiency of similar severity.
[]
Although several RNAs with translation-related functions are among the RNAs that coimmunoprecipitate with ZmWHY1, the abundance and processing of these RNAs are similar in ZmWhy1 mutants and in control mutants that exhibit a ribosome-deficiency of similar severity.
true
true
true
true
true
7,179
2
DISCUSSION
1
11
[ "B11", "B39", "B43 B44 B45 B46" ]
18,676,978
pmid-14960277|pmid-10948264|pmid-14960277|pmid-12080340|pmid-17217467|pmid-15967440|pmid-16326926|pmid-18423020|pmid-11565746|NA|pmid-15891117|pmid-15010617|pmid-15197595|pmid-12678554
The specific rRNA deficiencies in ZmWhy1 mutants do suggest, however, that ZmWHY1 is most directly involved in the biogenesis of the large ribosomal subunit: the accumulation and processing of the 23S and 4.5S rRNAs are more sensitive to the partial loss of ZmWhy1 function than are those of 16S rRNA, whereas the revers...
[ "11", "39", "43–46" ]
347
41,628
0
false
The specific rRNA deficiencies in ZmWhy1 mutants do suggest, however, that ZmWHY1 is most directly involved in the biogenesis of the large ribosomal subunit: the accumulation and processing of the 23S and 4.5S rRNAs are more sensitive to the partial loss of ZmWhy1 function than are those of 16S rRNA, whereas the revers...
[]
The specific rRNA deficiencies in ZmWhy1 mutants do suggest, however, that ZmWHY1 is most directly involved in the biogenesis of the large ribosomal subunit: the accumulation and processing of the 23S and 4.5S rRNAs are more sensitive to the partial loss of ZmWhy1 function than are those of 16S rRNA, whereas the revers...
true
true
true
true
true
7,179
2
DISCUSSION
1
39
[ "B11", "B39", "B43 B44 B45 B46" ]
18,676,978
pmid-14960277|pmid-10948264|pmid-14960277|pmid-12080340|pmid-17217467|pmid-15967440|pmid-16326926|pmid-18423020|pmid-11565746|NA|pmid-15891117|pmid-15010617|pmid-15197595|pmid-12678554
Furthermore, in ppr5 mutants, whose primary defect is in the maturation of a specific plastid tRNA, the rRNAs from the two ribosomal subunits are impacted to a similar extent (39).
[ "11", "39", "43–46" ]
180
41,629
1
false
Furthermore, in ppr5 mutants, whose primary defect is in the maturation of a specific plastid tRNA, the rRNAs from the two ribosomal subunits are impacted to a similar extent.
[ "39" ]
Furthermore, in ppr5 mutants, whose primary defect is in the maturation of a specific plastid tRNA, the rRNAs from the two ribosomal subunits are impacted to a similar extent.
true
true
true
true
true
7,179
2
DISCUSSION
1
11
[ "B11", "B39", "B43 B44 B45 B46" ]
18,676,978
pmid-14960277|pmid-10948264|pmid-14960277|pmid-12080340|pmid-17217467|pmid-15967440|pmid-16326926|pmid-18423020|pmid-11565746|NA|pmid-15891117|pmid-15010617|pmid-15197595|pmid-12678554
Thus, our results point to the biogenesis of the plastid large ribosomal subunit as one function of ZmWHY1 but definition of its precise role in this process will require additional study.
[ "11", "39", "43–46" ]
188
41,630
0
false
Thus, our results point to the biogenesis of the plastid large ribosomal subunit as one function of ZmWHY1 but definition of its precise role in this process will require additional study.
[]
Thus, our results point to the biogenesis of the plastid large ribosomal subunit as one function of ZmWHY1 but definition of its precise role in this process will require additional study.
true
true
true
true
true
7,179
2
DISCUSSION
1
43–46
[ "B11", "B39", "B43 B44 B45 B46" ]
18,676,978
pmid-14960277|pmid-10948264|pmid-14960277|pmid-12080340|pmid-17217467|pmid-15967440|pmid-16326926|pmid-18423020|pmid-11565746|NA|pmid-15891117|pmid-15010617|pmid-15197595|pmid-12678554
The strong defect in the processing step that separates 23S rRNA from 4.5S rRNA in hypomorphic ZmWhy1 mutants is reminiscent of defects reported for mutations in the DCL, DAL and RNR1 genes in dicots (43–46).
[ "11", "39", "43–46" ]
208
41,631
1
false
The strong defect in the processing step that separates 23S rRNA from 4.5S rRNA in hypomorphic ZmWhy1 mutants is reminiscent of defects reported for mutations in the DCL, DAL and RNR1 genes in dicots.
[ "43–46" ]
The strong defect in the processing step that separates 23S rRNA from 4.5S rRNA in hypomorphic ZmWhy1 mutants is reminiscent of defects reported for mutations in the DCL, DAL and RNR1 genes in dicots.
true
true
true
true
true
7,179
2
DISCUSSION
1
11
[ "B11", "B39", "B43 B44 B45 B46" ]
18,676,978
pmid-14960277|pmid-10948264|pmid-14960277|pmid-12080340|pmid-17217467|pmid-15967440|pmid-16326926|pmid-18423020|pmid-11565746|NA|pmid-15891117|pmid-15010617|pmid-15197595|pmid-12678554
Although it is unclear whether any of these genes function directly in 23S/4.5S rRNA processing, it is possible that WHY1 acts in concert with one or more of these proteins.
[ "11", "39", "43–46" ]
173
41,632
0
false
Although it is unclear whether any of these genes function directly in 23S/4.5S rRNA processing, it is possible that WHY1 acts in concert with one or more of these proteins.
[]
Although it is unclear whether any of these genes function directly in 23S/4.5S rRNA processing, it is possible that WHY1 acts in concert with one or more of these proteins.
true
true
true
true
true
7,179
3
DISCUSSION
1
19
[ "B19", "B20", "B22", "B23" ]
18,676,978
pmid-12080340|pmid-17217467|pmid-16326926|pmid-18423020
We show here that chloroplast DNA coimmunoprecipitates with ZmWHY1 from plastid extract, that a fraction of ZmWHY1 is tethered to the thylakoid membrane in a DNA-dependent fashion, that a fraction of stromal ZmWHY1 is found in DNA-containing particles of ∼400 kDa, and that ZmWHY1 binds ssDNA in vitro.
[ "19", "20", "22", "23" ]
302
41,633
0
false
We show here that chloroplast DNA coimmunoprecipitates with ZmWHY1 from plastid extract, that a fraction of ZmWHY1 is tethered to the thylakoid membrane in a DNA-dependent fashion, that a fraction of stromal ZmWHY1 is found in DNA-containing particles of ∼400 kDa, and that ZmWHY1 binds ssDNA in vitro.
[]
We show here that chloroplast DNA coimmunoprecipitates with ZmWHY1 from plastid extract, that a fraction of ZmWHY1 is tethered to the thylakoid membrane in a DNA-dependent fashion, that a fraction of stromal ZmWHY1 is found in DNA-containing particles of ∼400 kDa, and that ZmWHY1 binds ssDNA in vitro.
true
true
true
true
true
7,180
3
DISCUSSION
1
22
[ "B19", "B20", "B22", "B23" ]
18,676,978
pmid-12080340|pmid-17217467|pmid-16326926|pmid-18423020
These results are consistent with previous reports that dicot WHY1 binds ssDNA (19,20) and that it copurifies with a chloroplast ‘transcriptionally active chromosome’ (22).
[ "19", "20", "22", "23" ]
172
41,634
1
false
These results are consistent with previous reports that dicot WHY1 binds ssDNA and that it copurifies with a chloroplast ‘transcriptionally active chromosome’.
[ "19,20", "22" ]
These results are consistent with previous reports that dicot WHY1 binds ssDNA and that it copurifies with a chloroplast ‘transcriptionally active chromosome’.
true
true
true
true
true
7,180
3
DISCUSSION
1
19
[ "B19", "B20", "B22", "B23" ]
18,676,978
pmid-12080340|pmid-17217467|pmid-16326926|pmid-18423020
Our findings suggest that ZmWHY1 either binds DNA in a sequence non-specific fashion or that it has many binding sites distributed throughout the plastid genome, because DNA sequences from throughout the plastid genome coimmunoprecipitated to a similar extent with ZmWHY1.
[ "19", "20", "22", "23" ]
272
41,635
0
false
Our findings suggest that ZmWHY1 either binds DNA in a sequence non-specific fashion or that it has many binding sites distributed throughout the plastid genome, because DNA sequences from throughout the plastid genome coimmunoprecipitated to a similar extent with ZmWHY1.
[]
Our findings suggest that ZmWHY1 either binds DNA in a sequence non-specific fashion or that it has many binding sites distributed throughout the plastid genome, because DNA sequences from throughout the plastid genome coimmunoprecipitated to a similar extent with ZmWHY1.
true
true
true
true
true
7,180
3
DISCUSSION
1
19
[ "B19", "B20", "B22", "B23" ]
18,676,978
pmid-12080340|pmid-17217467|pmid-16326926|pmid-18423020
It remains possible, however, that ZmWHY1 associates with specific DNA regions in vivo, but that these associations were disrupted during lysate preparation.
[ "19", "20", "22", "23" ]
157
41,636
0
false
It remains possible, however, that ZmWHY1 associates with specific DNA regions in vivo, but that these associations were disrupted during lysate preparation.
[]
It remains possible, however, that ZmWHY1 associates with specific DNA regions in vivo, but that these associations were disrupted during lysate preparation.
true
true
true
true
true
7,180
3
DISCUSSION
1
23
[ "B19", "B20", "B22", "B23" ]
18,676,978
pmid-12080340|pmid-17217467|pmid-16326926|pmid-18423020
A DNA immunoprecipitation experiment was recently reported for AtWHY2, a mitochondrial-localized Whirly protein (23), with analogous results: DNA sequences from a variety of regions throughout the mitochondrial genome coimmunoprecipitated with AtWHY2, when assayed by PCR.
[ "19", "20", "22", "23" ]
272
41,637
1
false
A DNA immunoprecipitation experiment was recently reported for AtWHY2, a mitochondrial-localized Whirly protein, with analogous results: DNA sequences from a variety of regions throughout the mitochondrial genome coimmunoprecipitated with AtWHY2, when assayed by PCR.
[ "23" ]
A DNA immunoprecipitation experiment was recently reported for AtWHY2, a mitochondrial-localized Whirly protein, with analogous results: DNA sequences from a variety of regions throughout the mitochondrial genome coimmunoprecipitated with AtWHY2, when assayed by PCR.
true
true
true
true
true
7,180
4
DISCUSSION
1
42
[ "B42" ]
18,676,978
pmid-16923390
We demonstrate here that ZmWHY1 interacts not only with DNA, as anticipated by previous reports, but that it also binds RNA in vivo and in vitro.
[ "42" ]
145
41,638
0
false
We demonstrate here that ZmWHY1 interacts not only with DNA, as anticipated by previous reports, but that it also binds RNA in vivo and in vitro.
[]
We demonstrate here that ZmWHY1 interacts not only with DNA, as anticipated by previous reports, but that it also binds RNA in vivo and in vitro.
true
true
true
true
true
7,181
4
DISCUSSION
1
42
[ "B42" ]
18,676,978
pmid-16923390
That ZmWHY1 interacts with RNA is, perhaps, not surprising given that a structural homolog of ZmWHY1 has been shown to bind RNAs involved in kinetoplastid RNA editing (42), and that many proteins that bind ssDNA also bind RNA.
[ "42" ]
226
41,639
1
false
That ZmWHY1 interacts with RNA is, perhaps, not surprising given that a structural homolog of ZmWHY1 has been shown to bind RNAs involved in kinetoplastid RNA editing, and that many proteins that bind ssDNA also bind RNA.
[ "42" ]
That ZmWHY1 interacts with RNA is, perhaps, not surprising given that a structural homolog of ZmWHY1 has been shown to bind RNAs involved in kinetoplastid RNA editing, and that many proteins that bind ssDNA also bind RNA.
true
true
true
true
true
7,181
4
DISCUSSION
1
42
[ "B42" ]
18,676,978
pmid-16923390
The atpF intron RNA was the major RNA ligand of ZmWHY1 detected in the RNA coimmunoprecipitation assays.
[ "42" ]
104
41,640
0
false
The atpF intron RNA was the major RNA ligand of ZmWHY1 detected in the RNA coimmunoprecipitation assays.
[]
The atpF intron RNA was the major RNA ligand of ZmWHY1 detected in the RNA coimmunoprecipitation assays.
true
true
true
true
true
7,181
4
DISCUSSION
1
42
[ "B42" ]
18,676,978
pmid-16923390
This RNA is not particularly abundant in vivo so its enrichment in ZmWHY1 immunoprecipitations likely reflects a specific interaction in vivo.
[ "42" ]
142
41,641
0
false
This RNA is not particularly abundant in vivo so its enrichment in ZmWHY1 immunoprecipitations likely reflects a specific interaction in vivo.
[]
This RNA is not particularly abundant in vivo so its enrichment in ZmWHY1 immunoprecipitations likely reflects a specific interaction in vivo.
true
true
true
true
true
7,181
4
DISCUSSION
1
42
[ "B42" ]
18,676,978
pmid-16923390
Although intrinsic specificity for this RNA did not emerge from in vitro binding assays using the entire intron, a high-affinity site within a large RNA such as the atpF intron (∼800 nt) can be masked in vitro due to the overwhelming number of nonspecific sites available for protein binding.
[ "42" ]
292
41,642
0
false
Although intrinsic specificity for this RNA did not emerge from in vitro binding assays using the entire intron, a high-affinity site within a large RNA such as the atpF intron (∼800 nt) can be masked in vitro due to the overwhelming number of nonspecific sites available for protein binding.
[]
Although intrinsic specificity for this RNA did not emerge from in vitro binding assays using the entire intron, a high-affinity site within a large RNA such as the atpF intron (∼800 nt) can be masked in vitro due to the overwhelming number of nonspecific sites available for protein binding.
true
true
true
true
true
7,181
4
DISCUSSION
1
42
[ "B42" ]
18,676,978
pmid-16923390
Therefore, more detailed studies involving smaller RNA ligands will be required to determine whether ZmWHY1 binds RNA with sequence-specificity or whether it is recruited to the atpF intron via protein–protein interactions.
[ "42" ]
223
41,643
0
false
Therefore, more detailed studies involving smaller RNA ligands will be required to determine whether ZmWHY1 binds RNA with sequence-specificity or whether it is recruited to the atpF intron via protein–protein interactions.
[]
Therefore, more detailed studies involving smaller RNA ligands will be required to determine whether ZmWHY1 binds RNA with sequence-specificity or whether it is recruited to the atpF intron via protein–protein interactions.
true
true
true
true
true
7,181
5
DISCUSSION
0
null
null
18,676,978
null
The association of ZmyWHY1 with DNA sequences from throughout the chloroplast genome suggests that it participates in transcription and/or DNA metabolism.
null
154
41,644
0
false
null
null
The association of ZmyWHY1 with DNA sequences from throughout the chloroplast genome suggests that it participates in transcription and/or DNA metabolism.
true
true
true
true
true
7,182
5
DISCUSSION
0
null
null
18,676,978
null
However, our results argue against a general role in transcription, as all plastid mRNAs examined accumulate in hypomorphic Zmwhy1 mutants to levels that are comparable to those in the relevant control mutants.
null
210
41,645
0
false
null
null
However, our results argue against a general role in transcription, as all plastid mRNAs examined accumulate in hypomorphic Zmwhy1 mutants to levels that are comparable to those in the relevant control mutants.
true
true
true
true
true
7,182
5
DISCUSSION
0
null
null
18,676,978
null
The results of chloroplast transcription runon experiments argue that the preferential loss of 23S rRNA in these mutants is due to aberrant ribosome assembly rather than to reduced rRNA transcription rates.
null
206
41,646
0
false
null
null
The results of chloroplast transcription runon experiments argue that the preferential loss of 23S rRNA in these mutants is due to aberrant ribosome assembly rather than to reduced rRNA transcription rates.
true
true
true
true
true
7,182
5
DISCUSSION
0
null
null
18,676,978
null
It remains possible, however, that ZmWHY1 does play a role in chloroplast transcription but that another gene with a partially redundant function serves this purpose in ZmWhy1 mutants.
null
184
41,647
0
false
null
null
It remains possible, however, that ZmWHY1 does play a role in chloroplast transcription but that another gene with a partially redundant function serves this purpose in ZmWhy1 mutants.
true
true
true
true
true
7,182
6
DISCUSSION
1
47
[ "B47" ]
18,676,978
pmid-17189341
It is intriguing that ZmWHY1 binds preferentially to DNA in single stranded form because opportunities to interact with ssDNA in vivo are expected to be limited.
[ "47" ]
161
41,648
0
false
It is intriguing that ZmWHY1 binds preferentially to DNA in single stranded form because opportunities to interact with ssDNA in vivo are expected to be limited.
[]
It is intriguing that ZmWHY1 binds preferentially to DNA in single stranded form because opportunities to interact with ssDNA in vivo are expected to be limited.
true
true
true
true
true
7,183
6
DISCUSSION
1
47
[ "B47" ]
18,676,978
pmid-17189341
DNA replication, recombination and repair involve the transient occurrence of ssDNA, and torsional stress can induce DNA unwinding.
[ "47" ]
131
41,649
0
false
DNA replication, recombination and repair involve the transient occurrence of ssDNA, and torsional stress can induce DNA unwinding.
[]
DNA replication, recombination and repair involve the transient occurrence of ssDNA, and torsional stress can induce DNA unwinding.
true
true
true
true
true
7,183
6
DISCUSSION
1
47
[ "B47" ]
18,676,978
pmid-17189341
The Southern blot data showing that plastid DNA levels are no more than minimally decreased in ZmWhy1 null mutants argue against a central role for ZmWHY1 in DNA replication; however participation of ZmWHY1 in DNA recombination or repair remains possible.
[ "47" ]
255
41,650
0
false
The Southern blot data showing that plastid DNA levels are no more than minimally decreased in ZmWhy1 null mutants argue against a central role for ZmWHY1 in DNA replication; however participation of ZmWHY1 in DNA recombination or repair remains possible.
[]
The Southern blot data showing that plastid DNA levels are no more than minimally decreased in ZmWhy1 null mutants argue against a central role for ZmWHY1 in DNA replication; however participation of ZmWHY1 in DNA recombination or repair remains possible.
true
true
true
true
true
7,183
6
DISCUSSION
1
47
[ "B47" ]
18,676,978
pmid-17189341
In fact, the participation of an unrelated ssDNA-binding protein, OSB1, in plant mitochondrial DNA recombination was reported recently (47).
[ "47" ]
140
41,651
1
false
In fact, the participation of an unrelated ssDNA-binding protein, OSB1, in plant mitochondrial DNA recombination was reported recently.
[ "47" ]
In fact, the participation of an unrelated ssDNA-binding protein, OSB1, in plant mitochondrial DNA recombination was reported recently.
true
true
true
true
true
7,183
7
DISCUSSION
1
48
[ "B48", "B49", "B50", "B50", "B51", "B51 B52 B53", "B54 B55 B56", "B57", "B58", "B23" ]
18,676,978
pmid-12672495|pmid-18096614|pmid-12119376|pmid-12119376|pmid-11286919|pmid-11286919|pmid-11163356|pmid-17371503|pmid-14500788|pmid-16258062|pmid-10027963|pmid-12006568|pmid-11251825|pmid-18423020
There are several parallels between our findings with ZmWHY1 and the activities reported for the bacterial protein HU
[ "48", "49", "50", "50", "51", "51–53", "54–56", "57", "58", "23" ]
117
41,652
0
false
There are several parallels between our findings with ZmWHY1 and the activities reported for the bacterial protein HU
[]
There are several parallels between our findings with ZmWHY1 and the activities reported for the bacterial protein HU
true
true
false
true
false
7,184
7
DISCUSSION
1
48
[ "B48", "B49", "B50", "B50", "B51", "B51 B52 B53", "B54 B55 B56", "B57", "B58", "B23" ]
18,676,978
pmid-12672495|pmid-18096614|pmid-12119376|pmid-12119376|pmid-11286919|pmid-11286919|pmid-11163356|pmid-17371503|pmid-14500788|pmid-16258062|pmid-10027963|pmid-12006568|pmid-11251825|pmid-18423020
HU is associated with the bacterial nucleoid, binds preferentially to DNA with irregular structural features (e.g.
[ "48", "49", "50", "50", "51", "51–53", "54–56", "57", "58", "23" ]
114
41,653
0
false
HU is associated with the bacterial nucleoid, binds preferentially to DNA with irregular structural features (e.g.
[]
HU is associated with the bacterial nucleoid, binds preferentially to DNA with irregular structural features (e.g.
true
true
true
true
true
7,184
7
DISCUSSION
1
48
[ "B48", "B49", "B50", "B50", "B51", "B51 B52 B53", "B54 B55 B56", "B57", "B58", "B23" ]
18,676,978
pmid-12672495|pmid-18096614|pmid-12119376|pmid-12119376|pmid-11286919|pmid-11286919|pmid-11163356|pmid-17371503|pmid-14500788|pmid-16258062|pmid-10027963|pmid-12006568|pmid-11251825|pmid-18423020
single stranded gaps and bulges), and is involved in DNA recombination and repair (48,49).
[ "48", "49", "50", "50", "51", "51–53", "54–56", "57", "58", "23" ]
90
41,654
0
false
single stranded gaps and bulges), and is involved in DNA recombination and repair.
[ "48,49" ]
single stranded gaps and bulges), and is involved in DNA recombination and repair.
false
true
true
true
false
7,184
7
DISCUSSION
1
50
[ "B48", "B49", "B50", "B50", "B51", "B51 B52 B53", "B54 B55 B56", "B57", "B58", "B23" ]
18,676,978
pmid-12672495|pmid-18096614|pmid-12119376|pmid-12119376|pmid-11286919|pmid-11286919|pmid-11163356|pmid-17371503|pmid-14500788|pmid-16258062|pmid-10027963|pmid-12006568|pmid-11251825|pmid-18423020
Despite its high conservation in bacteria and the presence of an HU homolog in a plastid genome in red algae (50), HU homologs are not encoded in the nuclear or plastid genomes of vascular plants (50,51).
[ "48", "49", "50", "50", "51", "51–53", "54–56", "57", "58", "23" ]
204
41,655
1
false
Despite its high conservation in bacteria and the presence of an HU homolog in a plastid genome in red algae, HU homologs are not encoded in the nuclear or plastid genomes of vascular plants.
[ "50", "50,51" ]
Despite its high conservation in bacteria and the presence of an HU homolog in a plastid genome in red algae, HU homologs are not encoded in the nuclear or plastid genomes of vascular plants.
true
true
true
true
true
7,184
7
DISCUSSION
1
48
[ "B48", "B49", "B50", "B50", "B51", "B51 B52 B53", "B54 B55 B56", "B57", "B58", "B23" ]
18,676,978
pmid-12672495|pmid-18096614|pmid-12119376|pmid-12119376|pmid-11286919|pmid-11286919|pmid-11163356|pmid-17371503|pmid-14500788|pmid-16258062|pmid-10027963|pmid-12006568|pmid-11251825|pmid-18423020
Thus, alternative proteins have presumably been recruited in vascular plants to fulfill the functions performed by HU in the chloroplast's cyanobacterial ancestor.
[ "48", "49", "50", "50", "51", "51–53", "54–56", "57", "58", "23" ]
163
41,656
0
false
Thus, alternative proteins have presumably been recruited in vascular plants to fulfill the functions performed by HU in the chloroplast's cyanobacterial ancestor.
[]
Thus, alternative proteins have presumably been recruited in vascular plants to fulfill the functions performed by HU in the chloroplast's cyanobacterial ancestor.
true
true
true
true
true
7,184
7
DISCUSSION
1
51–53
[ "B48", "B49", "B50", "B50", "B51", "B51 B52 B53", "B54 B55 B56", "B57", "B58", "B23" ]
18,676,978
pmid-12672495|pmid-18096614|pmid-12119376|pmid-12119376|pmid-11286919|pmid-11286919|pmid-11163356|pmid-17371503|pmid-14500788|pmid-16258062|pmid-10027963|pmid-12006568|pmid-11251825|pmid-18423020
The nucleoid-associated protein sulfite reductase has been suggested to be one such protein (51–53), and perhaps WHY1 is another.
[ "48", "49", "50", "50", "51", "51–53", "54–56", "57", "58", "23" ]
129
41,657
1
false
The nucleoid-associated protein sulfite reductase has been suggested to be one such protein, and perhaps WHY1 is another.
[ "51–53" ]
The nucleoid-associated protein sulfite reductase has been suggested to be one such protein, and perhaps WHY1 is another.
true
true
true
true
true
7,184
7
DISCUSSION
1
54–56
[ "B48", "B49", "B50", "B50", "B51", "B51 B52 B53", "B54 B55 B56", "B57", "B58", "B23" ]
18,676,978
pmid-12672495|pmid-18096614|pmid-12119376|pmid-12119376|pmid-11286919|pmid-11286919|pmid-11163356|pmid-17371503|pmid-14500788|pmid-16258062|pmid-10027963|pmid-12006568|pmid-11251825|pmid-18423020
HU influences global transcription patterns through its effect on nucleoid architecture, and mediates the formation of DNA loops that repress transcription from specific genes (54–56).
[ "48", "49", "50", "50", "51", "51–53", "54–56", "57", "58", "23" ]
184
41,658
1
false
HU influences global transcription patterns through its effect on nucleoid architecture, and mediates the formation of DNA loops that repress transcription from specific genes.
[ "54–56" ]
HU influences global transcription patterns through its effect on nucleoid architecture, and mediates the formation of DNA loops that repress transcription from specific genes.
true
true
true
true
true
7,184
7
DISCUSSION
1
48
[ "B48", "B49", "B50", "B50", "B51", "B51 B52 B53", "B54 B55 B56", "B57", "B58", "B23" ]
18,676,978
pmid-12672495|pmid-18096614|pmid-12119376|pmid-12119376|pmid-11286919|pmid-11286919|pmid-11163356|pmid-17371503|pmid-14500788|pmid-16258062|pmid-10027963|pmid-12006568|pmid-11251825|pmid-18423020
HU is also an RNA-binding protein, and functions in vivo to repress the translation of the E. coli rpoS mRNA (57,58).
[ "48", "49", "50", "50", "51", "51–53", "54–56", "57", "58", "23" ]
117
41,659
0
false
HU is also an RNA-binding protein, and functions in vivo to repress the translation of the E. coli rpoS mRNA.
[ "57,58" ]
HU is also an RNA-binding protein, and functions in vivo to repress the translation of the E. coli rpoS mRNA.
true
true
true
true
true
7,184
7
DISCUSSION
1
48
[ "B48", "B49", "B50", "B50", "B51", "B51 B52 B53", "B54 B55 B56", "B57", "B58", "B23" ]
18,676,978
pmid-12672495|pmid-18096614|pmid-12119376|pmid-12119376|pmid-11286919|pmid-11286919|pmid-11163356|pmid-17371503|pmid-14500788|pmid-16258062|pmid-10027963|pmid-12006568|pmid-11251825|pmid-18423020
Like HU, ZmWHY1 interacts globally with plastid DNA, but specifically with certain plastid RNAs, and binds preferentially to nucleic acids with single-stranded character.
[ "48", "49", "50", "50", "51", "51–53", "54–56", "57", "58", "23" ]
170
41,660
0
false
Like HU, ZmWHY1 interacts globally with plastid DNA, but specifically with certain plastid RNAs, and binds preferentially to nucleic acids with single-stranded character.
[]
Like HU, ZmWHY1 interacts globally with plastid DNA, but specifically with certain plastid RNAs, and binds preferentially to nucleic acids with single-stranded character.
true
true
true
true
true
7,184
7
DISCUSSION
1
48
[ "B48", "B49", "B50", "B50", "B51", "B51 B52 B53", "B54 B55 B56", "B57", "B58", "B23" ]
18,676,978
pmid-12672495|pmid-18096614|pmid-12119376|pmid-12119376|pmid-11286919|pmid-11286919|pmid-11163356|pmid-17371503|pmid-14500788|pmid-16258062|pmid-10027963|pmid-12006568|pmid-11251825|pmid-18423020
The abundance of several chloroplast mRNAs is increased in ZmWhy1 mutants, consistent with a global repressive role for ZmWHY1 in transcription.
[ "48", "49", "50", "50", "51", "51–53", "54–56", "57", "58", "23" ]
144
41,661
0
false
The abundance of several chloroplast mRNAs is increased in ZmWhy1 mutants, consistent with a global repressive role for ZmWHY1 in transcription.
[]
The abundance of several chloroplast mRNAs is increased in ZmWhy1 mutants, consistent with a global repressive role for ZmWHY1 in transcription.
true
true
true
true
true
7,184
7
DISCUSSION
1
23
[ "B48", "B49", "B50", "B50", "B51", "B51 B52 B53", "B54 B55 B56", "B57", "B58", "B23" ]
18,676,978
pmid-12672495|pmid-18096614|pmid-12119376|pmid-12119376|pmid-11286919|pmid-11286919|pmid-11163356|pmid-17371503|pmid-14500788|pmid-16258062|pmid-10027963|pmid-12006568|pmid-11251825|pmid-18423020
This possibility is in accord with the recent report that over-expression of AtWHY2 in Arabidopsis causes a reduction in the levels of several mitochondrial RNAs (23).
[ "48", "49", "50", "50", "51", "51–53", "54–56", "57", "58", "23" ]
167
41,662
1
false
This possibility is in accord with the recent report that over-expression of AtWHY2 in Arabidopsis causes a reduction in the levels of several mitochondrial RNAs.
[ "23" ]
This possibility is in accord with the recent report that over-expression of AtWHY2 in Arabidopsis causes a reduction in the levels of several mitochondrial RNAs.
true
true
true
true
true
7,184
7
DISCUSSION
1
48
[ "B48", "B49", "B50", "B50", "B51", "B51 B52 B53", "B54 B55 B56", "B57", "B58", "B23" ]
18,676,978
pmid-12672495|pmid-18096614|pmid-12119376|pmid-12119376|pmid-11286919|pmid-11286919|pmid-11163356|pmid-17371503|pmid-14500788|pmid-16258062|pmid-10027963|pmid-12006568|pmid-11251825|pmid-18423020
Although its role in DNA metabolism remains uncertain, our results demonstrate that description of WHY1 as a chloroplast transcription factor is, at best, an over-simplification of the complex roles played by this interesting protein.
[ "48", "49", "50", "50", "51", "51–53", "54–56", "57", "58", "23" ]
234
41,663
0
false
Although its role in DNA metabolism remains uncertain, our results demonstrate that description of WHY1 as a chloroplast transcription factor is, at best, an over-simplification of the complex roles played by this interesting protein.
[]
Although its role in DNA metabolism remains uncertain, our results demonstrate that description of WHY1 as a chloroplast transcription factor is, at best, an over-simplification of the complex roles played by this interesting protein.
true
true
true
true
true
7,184
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4" ]
19,654,939
pmid-16631505|pmid-17684150|pmid-17884367|pmid-11755373
Atherosclerotic plaque progression may lead to coronary artery disease (1), stroke (2), peripheral artery disease (3), and sudden cardiac death (SCD) (4) in humans.
[ "1", "2", "3", "4" ]
164
41,664
1
false
Atherosclerotic plaque progression may lead to coronary artery disease, stroke, peripheral artery disease, and sudden cardiac death (SCD) in humans.
[ "1", "2", "3", "4" ]
Atherosclerotic plaque progression may lead to coronary artery disease, stroke, peripheral artery disease, and sudden cardiac death (SCD) in humans.
true
true
true
true
true
7,185
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4" ]
19,654,939
pmid-16631505|pmid-17684150|pmid-17884367|pmid-11755373
However, the mechanism of plaque growth, destabilization, and rupture has not been fully established.
[ "1", "2", "3", "4" ]
101
41,665
0
false
However, the mechanism of plaque growth, destabilization, and rupture has not been fully established.
[]
However, the mechanism of plaque growth, destabilization, and rupture has not been fully established.
true
true
true
true
true
7,185
1
INTRODUCTION
1
5
[ "B5", "B6", "B7", "B8", "B9", "B10", "B11", "B12", "B13", "B14", "B15", "B16", "B17" ]
19,654,939
pmid-11021830|pmid-11254922|pmid-16801474|pmid-17082488|pmid-17659199|pmid-17729343|pmid-17101043|pmid-17585387|pmid-16814652|pmid-16487837|pmid-16631508|pmid-16781367|pmid-12390948|pmid-15640160
Atherosclerotic plaque assessment has been conducted in the past using histopathology in autopsy specimens (5, 6).
[ "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17" ]
114
41,666
0
false
Atherosclerotic plaque assessment has been conducted in the past using histopathology in autopsy specimens.
[ "5, 6" ]
Atherosclerotic plaque assessment has been conducted in the past using histopathology in autopsy specimens.
true
true
true
true
true
7,186
1
INTRODUCTION
1
9
[ "B5", "B6", "B7", "B8", "B9", "B10", "B11", "B12", "B13", "B14", "B15", "B16", "B17" ]
19,654,939
pmid-11021830|pmid-11254922|pmid-16801474|pmid-17082488|pmid-17659199|pmid-17729343|pmid-17101043|pmid-17585387|pmid-16814652|pmid-16487837|pmid-16631508|pmid-16781367|pmid-12390948|pmid-15640160
Recently, serum biomarker studies (7, 8) and imaging studies such as computerized tomography (9), magnetic resonance imaging (10), intima-media thickness (11), coronary angiography (12), optical coherence tomography (13), intravascular ultrasound (IVUS) (14, 15), and virtual histology IVUS (VH-IVUS) (16, 17) have been ...
[ "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17" ]
343
41,667
1
false
Recently, serum biomarker studies and imaging studies such as computerized tomography, magnetic resonance imaging, intima-media thickness, coronary angiography, optical coherence tomography, intravascular ultrasound (IVUS), and virtual histology IVUS (VH-IVUS) have been used to assess plaques.
[ "7, 8", "9", "10", "11", "12", "13", "14, 15", "16, 17" ]
Recently, serum biomarker studies and imaging studies such as computerized tomography, magnetic resonance imaging, intima-media thickness, coronary angiography, optical coherence tomography, intravascular ultrasound (IVUS), and virtual histology IVUS (VH-IVUS) have been used to assess plaques.
true
true
true
true
true
7,186
1
INTRODUCTION
1
5
[ "B5", "B6", "B7", "B8", "B9", "B10", "B11", "B12", "B13", "B14", "B15", "B16", "B17" ]
19,654,939
pmid-11021830|pmid-11254922|pmid-16801474|pmid-17082488|pmid-17659199|pmid-17729343|pmid-17101043|pmid-17585387|pmid-16814652|pmid-16487837|pmid-16631508|pmid-16781367|pmid-12390948|pmid-15640160
IVUS and VH-IVUS are the most commonly used tools in the evaluation of vulnerable plaques.
[ "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17" ]
90
41,668
0
false
IVUS and VH-IVUS are the most commonly used tools in the evaluation of vulnerable plaques.
[]
IVUS and VH-IVUS are the most commonly used tools in the evaluation of vulnerable plaques.
true
true
true
true
true
7,186
2
INTRODUCTION
1
18
[ "B18" ]
19,654,939
pmid-15640160|pmid-17413036
Nogo-B (reticulon 4 B) has been recently discovered as a member of the reticulon family of proteins.
[ "18" ]
100
41,669
0
false
Nogo-B (reticulon 4 B) has been recently discovered as a member of the reticulon family of proteins.
[]
Nogo-B (reticulon 4 B) has been recently discovered as a member of the reticulon family of proteins.
true
true
true
true
true
7,187
2
INTRODUCTION
1
18
[ "B18" ]
19,654,939
pmid-15640160|pmid-17413036
The biological role of Nogo-B is not well understood.
[ "18" ]
53
41,670
0
false
The biological role of Nogo-B is not well understood.
[]
The biological role of Nogo-B is not well understood.
true
true
true
true
true
7,187
2
INTRODUCTION
1
18
[ "B18" ]
19,654,939
pmid-15640160|pmid-17413036
Some animal data suggest that Nogo-B is associated with the promotion of endothelial migration and the inhibition of vascular smooth muscle cell migration, resulting in homeostasis and remodeling of vascular structures (18).
[ "18" ]
224
41,671
1
false
Some animal data suggest that Nogo-B is associated with the promotion of endothelial migration and the inhibition of vascular smooth muscle cell migration, resulting in homeostasis and remodeling of vascular structures.
[ "18" ]
Some animal data suggest that Nogo-B is associated with the promotion of endothelial migration and the inhibition of vascular smooth muscle cell migration, resulting in homeostasis and remodeling of vascular structures.
true
true
true
true
true
7,187
2
INTRODUCTION
1
18
[ "B18" ]
19,654,939
pmid-15640160|pmid-17413036
However, there is limited human data, and the relationship between Nogo-B and the progression of fibroatheromas (FA) or vulnerable plaques is not well understood.
[ "18" ]
162
41,672
0
false
However, there is limited human data, and the relationship between Nogo-B and the progression of fibroatheromas (FA) or vulnerable plaques is not well understood.
[]
However, there is limited human data, and the relationship between Nogo-B and the progression of fibroatheromas (FA) or vulnerable plaques is not well understood.
true
true
true
true
true
7,187
2
INTRODUCTION
1
18
[ "B18" ]
19,654,939
pmid-15640160|pmid-17413036
Thus, the purpose of this study was to evaluate the relationship between Nogo-B, and FA or plaque progression in human coronary arteries using VH-IVUS.
[ "18" ]
151
41,673
0
false
Thus, the purpose of this study was to evaluate the relationship between Nogo-B, and FA or plaque progression in human coronary arteries using VH-IVUS.
[]
Thus, the purpose of this study was to evaluate the relationship between Nogo-B, and FA or plaque progression in human coronary arteries using VH-IVUS.
true
true
true
true
true
7,187
0
DISCUSSION
0
null
null
19,654,939
pmid-16631505|pmid-17684150|pmid-17884367|pmid-11755373
The present study demonstrated the inverse relation between Nogo-B expression and FA progression in autopsied coronary arteries.
null
128
41,674
0
false
null
null
The present study demonstrated the inverse relation between Nogo-B expression and FA progression in autopsied coronary arteries.
true
true
true
true
true
7,188
0
DISCUSSION
0
null
null
19,654,939
pmid-16631505|pmid-17684150|pmid-17884367|pmid-11755373
This is the first human study assessing the correlation between Nogo-B and plaque composition analyzed by VH-IVUS.
null
114
41,675
0
false
null
null
This is the first human study assessing the correlation between Nogo-B and plaque composition analyzed by VH-IVUS.
true
true
true
true
true
7,188
0
DISCUSSION
0
null
null
19,654,939
pmid-16631505|pmid-17684150|pmid-17884367|pmid-11755373
Our data revealed decreased expression of Nogo-B in advanced FA, including vulnerable TCFA plaques.
null
99
41,676
0
false
null
null
Our data revealed decreased expression of Nogo-B in advanced FA, including vulnerable TCFA plaques.
true
true
true
true
true
7,188
1
DISCUSSION
1
18
[ "B18" ]
19,654,939
pmid-11021830|pmid-11254922|pmid-16801474|pmid-17082488|pmid-17659199|pmid-17729343|pmid-17101043|pmid-17585387|pmid-16814652|pmid-16487837|pmid-16631508|pmid-16781367|pmid-12390948|pmid-15640160
Nogo proteins are composed of three alternative splice forms: 1192-residue Nogo-A, 373-residue Nogo-B, and 199-residue Nogo-C.
[ "18" ]
126
41,677
0
false
Nogo proteins are composed of three alternative splice forms: 1192-residue Nogo-A, 373-residue Nogo-B, and 199-residue Nogo-C.
[]
Nogo proteins are composed of three alternative splice forms: 1192-residue Nogo-A, 373-residue Nogo-B, and 199-residue Nogo-C.
true
true
true
true
true
7,189
1
DISCUSSION
1
18
[ "B18" ]
19,654,939
pmid-11021830|pmid-11254922|pmid-16801474|pmid-17082488|pmid-17659199|pmid-17729343|pmid-17101043|pmid-17585387|pmid-16814652|pmid-16487837|pmid-16631508|pmid-16781367|pmid-12390948|pmid-15640160
Despite their significantly different N-terminal lengths, they share a conserved C-terminal reticulon-homology domain consisting of two transmembrane fragments, a 66-residue extracellular loop (Nogo-66) and a 38-residue C-tail carrying an endoplasmic reticulum retention motif.
[ "18" ]
277
41,678
0
false
Despite their significantly different N-terminal lengths, they share a conserved C-terminal reticulon-homology domain consisting of two transmembrane fragments, a 66-residue extracellular loop (Nogo-66) and a 38-residue C-tail carrying an endoplasmic reticulum retention motif.
[]
Despite their significantly different N-terminal lengths, they share a conserved C-terminal reticulon-homology domain consisting of two transmembrane fragments, a 66-residue extracellular loop (Nogo-66) and a 38-residue C-tail carrying an endoplasmic reticulum retention motif.
true
true
true
true
true
7,189
1
DISCUSSION
1
18
[ "B18" ]
19,654,939
pmid-11021830|pmid-11254922|pmid-16801474|pmid-17082488|pmid-17659199|pmid-17729343|pmid-17101043|pmid-17585387|pmid-16814652|pmid-16487837|pmid-16631508|pmid-16781367|pmid-12390948|pmid-15640160
Nogo-A has the largest N-terminus (1016 residues), while Nogo-B has an N-terminus almost identical to the first 200 residues of Nogo-A (18).
[ "18" ]
140
41,679
1
false
Nogo-A has the largest N-terminus (1016 residues), while Nogo-B has an N-terminus almost identical to the first 200 residues of Nogo-A.
[ "18" ]
Nogo-A has the largest N-terminus, while Nogo-B has an N-terminus almost identical to the first 200 residues of Nogo-A.
true
true
true
true
true
7,189
2
DISCUSSION
1
21
[ "B21" ]
19,654,939
pmid-15640160|pmid-17413036
Rodriguez-Feo et al.
[ "21" ]
20
41,680
0
false
Rodriguez-Feo et al.
[]
Rodriguez-Feo et al.
true
true
true
true
true
7,190
2
DISCUSSION
1
21
[ "B21" ]
19,654,939
pmid-15640160|pmid-17413036
(21) previously reported that Nogo-B levels in carotid plaques are inversely related with the presence of large lipid pools.
[ "21" ]
124
41,681
1
false
previously reported that Nogo-B levels in carotid plaques are inversely related with the presence of large lipid pools.
[ "21" ]
previously reported that Nogo-B levels in carotid plaques are inversely related with the presence of large lipid pools.
false
true
true
true
false
7,190
2
DISCUSSION
1
21
[ "B21" ]
19,654,939
pmid-15640160|pmid-17413036
However, they classified roughly two groups based on a degree of carotid stenosis of 90% and a fat content of 40%.
[ "21" ]
114
41,682
0
false
However, they classified roughly two groups based on a degree of carotid stenosis of 90% and a fat content of 40%.
[]
However, they classified roughly two groups based on a degree of carotid stenosis of 90% and a fat content of 40%.
true
true
true
true
true
7,190
2
DISCUSSION
1
21
[ "B21" ]
19,654,939
pmid-15640160|pmid-17413036
This is insufficient to analyze the relation between Nogo-B and plaque progression over time.
[ "21" ]
93
41,683
0
false
This is insufficient to analyze the relation between Nogo-B and plaque progression over time.
[]
This is insufficient to analyze the relation between Nogo-B and plaque progression over time.
true
true
true
true
true
7,190
3
DISCUSSION
1
19
[ "B19" ]
19,654,939
pmid-16037567
We classified atherosclerotic plaques into 4 groups using VH-IVUS.
[ "19" ]
66
41,684
0
false
We classified atherosclerotic plaques into 4 groups using VH-IVUS.
[]
We classified atherosclerotic plaques into 4 groups using VH-IVUS.
true
true
true
true
true
7,191
3
DISCUSSION
1
19
[ "B19" ]
19,654,939
pmid-16037567
Early FA with NC area <0.1 mm2 and late FA with NC area 0.1-1.0 mm2 were defined in the present study based on a previous investigation by Virmani et al.
[ "19" ]
153
41,685
0
false
Early FA with NC area <0.1 mm2 and late FA with NC area 0.1-1.0 mm2 were defined in the present study based on a previous investigation by Virmani et al.
[]
Early FA with NC area <0.1 mm2 and late FA with NC area 0.1-1.0 mm2 were defined in the present study based on a previous investigation by Virmani et al.
true
true
true
true
true
7,191
3
DISCUSSION
1
19
[ "B19" ]
19,654,939
pmid-16037567
They performed morphometric plaque analysis and suggested four groups based on NC: pathologic intimal thickening without NC, early core FA with NC area 0.06±0.02 mm2, late core FA with NC area 0.84±0.08 mm2, and thin-cap atheroma.
[ "19" ]
230
41,686
0
false
They performed morphometric plaque analysis and suggested four groups based on NC: pathologic intimal thickening without NC, early core FA with NC area 0.06±0.02 mm2, late core FA with NC area 0.84±0.08 mm2, and thin-cap atheroma.
[]
They performed morphometric plaque analysis and suggested four groups based on NC: pathologic intimal thickening without NC, early core FA with NC area 0.06±0.02 mm2, late core FA with NC area 0.84±0.08 mm2, and thin-cap atheroma.
true
true
true
true
true
7,191
4
DISCUSSION
1
22
[ "B22", "B23" ]
19,654,939
pmid-17502324|pmid-17138936
TkCFA and TCFA are widely used VH-IVUS plaque classifications since the pathologic confirmation based on these classifications is very high, as the predictive accuracy is approximately 93.4% for fibrous, 94.6% for fibrofatty tissue, 95.1% for NC, and 96.8% for dense calcium (22).
[ "22", "23" ]
280
41,687
1
false
TkCFA and TCFA are widely used VH-IVUS plaque classifications since the pathologic confirmation based on these classifications is very high, as the predictive accuracy is approximately 93.4% for fibrous, 94.6% for fibrofatty tissue, 95.1% for NC, and 96.8% for dense calcium.
[ "22" ]
TkCFA and TCFA are widely used VH-IVUS plaque classifications since the pathologic confirmation based on these classifications is very high, as the predictive accuracy is approximately 93.4% for fibrous, 94.6% for fibrofatty tissue, 95.1% for NC, and 96.8% for dense calcium.
true
true
true
true
true
7,192
4
DISCUSSION
1
22
[ "B22", "B23" ]
19,654,939
pmid-17502324|pmid-17138936
However, validation of VH-IVUS has a controversy yet.
[ "22", "23" ]
53
41,688
0
false
However, validation of VH-IVUS has a controversy yet.
[]
However, validation of VH-IVUS has a controversy yet.
true
true
true
true
true
7,192
4
DISCUSSION
1
22
[ "B22", "B23" ]
19,654,939
pmid-17502324|pmid-17138936
An animal study by Granada et al.
[ "22", "23" ]
33
41,689
0
false
An animal study by Granada et al.
[]
An animal study by Granada et al.
true
true
true
true
true
7,192
4
DISCUSSION
1
23
[ "B22", "B23" ]
19,654,939
pmid-17502324|pmid-17138936
demonstrated that the sensitivity of IVUS-VH for the detection of fibrous, fibrofatty, and necrotic core tissue was 76.1%, 46%, and 41.1% respectively (23).
[ "22", "23" ]
156
41,690
1
false
demonstrated that the sensitivity of IVUS-VH for the detection of fibrous, fibrofatty, and necrotic core tissue was 76.1%, 46%, and 41.1% respectively.
[ "23" ]
demonstrated that the sensitivity of IVUS-VH for the detection of fibrous, fibrofatty, and necrotic core tissue was 76.1%, 46%, and 41.1% respectively.
false
true
true
true
false
7,192
4
DISCUSSION
1
22
[ "B22", "B23" ]
19,654,939
pmid-17502324|pmid-17138936
In the present study, the correlation of NC and coincidence of FA classification between VH-IVUS and pathology were 71%, and 94% respectively.
[ "22", "23" ]
142
41,691
0
false
In the present study, the correlation of NC and coincidence of FA classification between VH-IVUS and pathology were 71%, and 94% respectively.
[]
In the present study, the correlation of NC and coincidence of FA classification between VH-IVUS and pathology were 71%, and 94% respectively.
true
true
true
true
true
7,192
4
DISCUSSION
1
22
[ "B22", "B23" ]
19,654,939
pmid-17502324|pmid-17138936
The study for validation and accuracy of VH-IVUS will be needed more in future.
[ "22", "23" ]
79
41,692
0
false
The study for validation and accuracy of VH-IVUS will be needed more in future.
[]
The study for validation and accuracy of VH-IVUS will be needed more in future.
true
true
true
true
true
7,192
5
DISCUSSION
1
24
[ "B24", "B1", "B25" ]
19,654,939
pmid-9887164|pmid-16631505|pmid-16387286
Atherosclerotic plaques are caused by abnormal cellular proliferation and migration, lipid deposition, and extracellular matrix accumulation (24).
[ "24", "1", "25" ]
146
41,693
1
false
Atherosclerotic plaques are caused by abnormal cellular proliferation and migration, lipid deposition, and extracellular matrix accumulation.
[ "24" ]
Atherosclerotic plaques are caused by abnormal cellular proliferation and migration, lipid deposition, and extracellular matrix accumulation.
true
true
true
true
true
7,193
5
DISCUSSION
1
24
[ "B24", "B1", "B25" ]
19,654,939
pmid-9887164|pmid-16631505|pmid-16387286
Rupture-prone, vulnerable TCFAs are associated with a high inflammatory component and a large necrotic core accompanied by elevated proteolytic activity (1, 25).
[ "24", "1", "25" ]
161
41,694
0
false
Rupture-prone, vulnerable TCFAs are associated with a high inflammatory component and a large necrotic core accompanied by elevated proteolytic activity.
[ "1, 25" ]
Rupture-prone, vulnerable TCFAs are associated with a high inflammatory component and a large necrotic core accompanied by elevated proteolytic activity.
true
true
true
true
true
7,193
6
DISCUSSION
1
26
[ "B26", "B28", "B18" ]
19,654,939
pmid-12743005|pmid-18929245|pmid-15640160
VH-IVUS revealed that core necrosis and calcification were more significant in advanced FA compared to early FA and late FA.
[ "26", "28", "18" ]
124
41,695
0
false
VH-IVUS revealed that core necrosis and calcification were more significant in advanced FA compared to early FA and late FA.
[]
VH-IVUS revealed that core necrosis and calcification were more significant in advanced FA compared to early FA and late FA.
true
true
true
true
true
7,194
6
DISCUSSION
1
26
[ "B26", "B28", "B18" ]
19,654,939
pmid-12743005|pmid-18929245|pmid-15640160
There have been many studies looking at the positive correlation between coronary artery calcification and atherosclerosis progression or coronary artery disease (26-28).
[ "26", "28", "18" ]
170
41,696
0
false
There have been many studies looking at the positive correlation between coronary artery calcification and atherosclerosis progression or coronary artery disease.
[ "26-28" ]
There have been many studies looking at the positive correlation between coronary artery calcification and atherosclerosis progression or coronary artery disease.
true
true
true
true
true
7,194
6
DISCUSSION
1
18
[ "B26", "B28", "B18" ]
19,654,939
pmid-12743005|pmid-18929245|pmid-15640160
Previous data have shown that the N-terminal regions of both Nogo-A and -B have a putative calcium binding site (18).
[ "26", "28", "18" ]
117
41,697
1
false
Previous data have shown that the N-terminal regions of both Nogo-A and -B have a putative calcium binding site.
[ "18" ]
Previous data have shown that the N-terminal regions of both Nogo-A and -B have a putative calcium binding site.
true
true
true
true
true
7,194
6
DISCUSSION
1
26
[ "B26", "B28", "B18" ]
19,654,939
pmid-12743005|pmid-18929245|pmid-15640160
Therefore, we deduced that decreased expression of Nogo-B proteins could play a role in coronary artery calcification.
[ "26", "28", "18" ]
118
41,698
0
false
Therefore, we deduced that decreased expression of Nogo-B proteins could play a role in coronary artery calcification.
[]
Therefore, we deduced that decreased expression of Nogo-B proteins could play a role in coronary artery calcification.
true
true
true
true
true
7,194
6
DISCUSSION
1
26
[ "B26", "B28", "B18" ]
19,654,939
pmid-12743005|pmid-18929245|pmid-15640160
However, our data showed that only three factors, such as plaque burden, core necrosis, and CD68 activity, were significantly negatively correlated with Nogo-B activity, while calcification, age, and fibrosis were not related with Nogo-B expression.
[ "26", "28", "18" ]
249
41,699
0
false
However, our data showed that only three factors, such as plaque burden, core necrosis, and CD68 activity, were significantly negatively correlated with Nogo-B activity, while calcification, age, and fibrosis were not related with Nogo-B expression.
[]
However, our data showed that only three factors, such as plaque burden, core necrosis, and CD68 activity, were significantly negatively correlated with Nogo-B activity, while calcification, age, and fibrosis were not related with Nogo-B expression.
true
true
true
true
true
7,194
6
DISCUSSION
1
26
[ "B26", "B28", "B18" ]
19,654,939
pmid-12743005|pmid-18929245|pmid-15640160
These findings imply that the principal pathology of plaque progression and instability is increased core necrosis and inflammation, rather than increased calcium deposition.
[ "26", "28", "18" ]
174
41,700
0
false
These findings imply that the principal pathology of plaque progression and instability is increased core necrosis and inflammation, rather than increased calcium deposition.
[]
These findings imply that the principal pathology of plaque progression and instability is increased core necrosis and inflammation, rather than increased calcium deposition.
true
true
true
true
true
7,194
6
DISCUSSION
1
26
[ "B26", "B28", "B18" ]
19,654,939
pmid-12743005|pmid-18929245|pmid-15640160
The role of calcium in atherosclerotic plaque progression is more complicated than we initially thought it to be.
[ "26", "28", "18" ]
113
41,701
0
false
The role of calcium in atherosclerotic plaque progression is more complicated than we initially thought it to be.
[]
The role of calcium in atherosclerotic plaque progression is more complicated than we initially thought it to be.
true
true
true
true
true
7,194
7
DISCUSSION
1
29
[ "B29", "B30" ]
19,654,939
pmid-17599600|pmid-17207665
We also found the expression pattern of Nogo-B to be interesting.
[ "29", "30" ]
65
41,702
0
false
We also found the expression pattern of Nogo-B to be interesting.
[]
We also found the expression pattern of Nogo-B to be interesting.
true
true
true
true
true
7,195
7
DISCUSSION
1
29
[ "B29", "B30" ]
19,654,939
pmid-17599600|pmid-17207665
Diffuse Nogo-B distribution was noted in early FA and in healthy arteries containing non-atherosclerotic plaques, while focal distribution was noted in diseased arteries containing atherosclerotic plaques, such as late FA and advanced FA.
[ "29", "30" ]
238
41,703
0
false
Diffuse Nogo-B distribution was noted in early FA and in healthy arteries containing non-atherosclerotic plaques, while focal distribution was noted in diseased arteries containing atherosclerotic plaques, such as late FA and advanced FA.
[]
Diffuse Nogo-B distribution was noted in early FA and in healthy arteries containing non-atherosclerotic plaques, while focal distribution was noted in diseased arteries containing atherosclerotic plaques, such as late FA and advanced FA.
true
true
true
true
true
7,195
7
DISCUSSION
1
29
[ "B29", "B30" ]
19,654,939
pmid-17599600|pmid-17207665
The mechanism of this differing distribution pattern is unclear, but some mechanisms have been proposed.
[ "29", "30" ]
104
41,704
0
false
The mechanism of this differing distribution pattern is unclear, but some mechanisms have been proposed.
[]
The mechanism of this differing distribution pattern is unclear, but some mechanisms have been proposed.
true
true
true
true
true
7,195
7
DISCUSSION
1
29
[ "B29", "B30" ]
19,654,939
pmid-17599600|pmid-17207665
One is endothelial shear stress (29).
[ "29", "30" ]
37
41,705
1
false
One is endothelial shear stress.
[ "29" ]
One is endothelial shear stress.
true
true
true
true
true
7,195
7
DISCUSSION
1
29
[ "B29", "B30" ]
19,654,939
pmid-17599600|pmid-17207665
Pressure, but not cellular stretch, has been associated with Nogo-B up-regulation in nonvascular cells.
[ "29", "30" ]
103
41,706
0
false
Pressure, but not cellular stretch, has been associated with Nogo-B up-regulation in nonvascular cells.
[]
Pressure, but not cellular stretch, has been associated with Nogo-B up-regulation in nonvascular cells.
true
true
true
true
true
7,195
7
DISCUSSION
1
29
[ "B29", "B30" ]
19,654,939
pmid-17599600|pmid-17207665
Low endothelial shear stress is a powerful local stimulus for atherogenesis, as well as formation and progression of early atherosclerotic plaques and differentiation of high-risk plaques.
[ "29", "30" ]
188
41,707
0
false
Low endothelial shear stress is a powerful local stimulus for atherogenesis, as well as formation and progression of early atherosclerotic plaques and differentiation of high-risk plaques.
[]
Low endothelial shear stress is a powerful local stimulus for atherogenesis, as well as formation and progression of early atherosclerotic plaques and differentiation of high-risk plaques.
true
true
true
true
true
7,195
7
DISCUSSION
1
29
[ "B29", "B30" ]
19,654,939
pmid-17599600|pmid-17207665
Thus, high Nogo-B expression presents in healthy arteries with continuous pulsatile and unidirectional endothelial shear stress.
[ "29", "30" ]
128
41,708
0
false
Thus, high Nogo-B expression presents in healthy arteries with continuous pulsatile and unidirectional endothelial shear stress.
[]
Thus, high Nogo-B expression presents in healthy arteries with continuous pulsatile and unidirectional endothelial shear stress.
true
true
true
true
true
7,195
7
DISCUSSION
1
29
[ "B29", "B30" ]
19,654,939
pmid-17599600|pmid-17207665
Disturbed laminar flow develops, and the pulsatile flow generates low and/or oscillatory endothelial shear stress, which induces low Nogo-B expression.
[ "29", "30" ]
151
41,709
0
false
Disturbed laminar flow develops, and the pulsatile flow generates low and/or oscillatory endothelial shear stress, which induces low Nogo-B expression.
[]
Disturbed laminar flow develops, and the pulsatile flow generates low and/or oscillatory endothelial shear stress, which induces low Nogo-B expression.
true
true
true
true
true
7,195
7
DISCUSSION
1
30
[ "B29", "B30" ]
19,654,939
pmid-17599600|pmid-17207665
Another possible mechanism is a complicated local inflammation, which not fully established yet (30).
[ "29", "30" ]
101
41,710
1
false
Another possible mechanism is a complicated local inflammation, which not fully established yet.
[ "30" ]
Another possible mechanism is a complicated local inflammation, which not fully established yet.
true
true
true
true
true
7,195
7
DISCUSSION
1
29
[ "B29", "B30" ]
19,654,939
pmid-17599600|pmid-17207665
Nogo-B expression was significantly negatively correlated with CD68 activity, but not with MMP-9 activity in the present study.
[ "29", "30" ]
127
41,711
0
false
Nogo-B expression was significantly negatively correlated with CD68 activity, but not with MMP-9 activity in the present study.
[]
Nogo-B expression was significantly negatively correlated with CD68 activity, but not with MMP-9 activity in the present study.
true
true
true
true
true
7,195
7
DISCUSSION
1
29
[ "B29", "B30" ]
19,654,939
pmid-17599600|pmid-17207665
Despite the overall reduced Nogo-B levels in plaques, local accumulation of Nogo-B is noted in macrophage-rich areas.
[ "29", "30" ]
117
41,712
0
false
Despite the overall reduced Nogo-B levels in plaques, local accumulation of Nogo-B is noted in macrophage-rich areas.
[]
Despite the overall reduced Nogo-B levels in plaques, local accumulation of Nogo-B is noted in macrophage-rich areas.
true
true
true
true
true
7,195
7
DISCUSSION
1
29
[ "B29", "B30" ]
19,654,939
pmid-17599600|pmid-17207665
Nogo-B also seems to be concentrated in macrophages or foam cells.
[ "29", "30" ]
66
41,713
0
false
Nogo-B also seems to be concentrated in macrophages or foam cells.
[]
Nogo-B also seems to be concentrated in macrophages or foam cells.
true
true
true
true
true
7,195
7
DISCUSSION
1
29
[ "B29", "B30" ]
19,654,939
pmid-17599600|pmid-17207665
Hence, new materials inhibiting local inflammation and preventing Nogo-B reduction (e.g., through a Nogo-B eluting stent) might be helpful in managing coronary artery disease in the future.
[ "29", "30" ]
189
41,714
0
false
Hence, new materials inhibiting local inflammation and preventing Nogo-B reduction (e.g., through a Nogo-B eluting stent) might be helpful in managing coronary artery disease in the future.
[]
Hence, new materials inhibiting local inflammation and preventing Nogo-B reduction (e.g., through a Nogo-B eluting stent) might be helpful in managing coronary artery disease in the future.
true
true
true
true
true
7,195
8
DISCUSSION
0
null
null
19,654,939
null
There are several limitations to the present study.
null
51
41,715
0
false
null
null
There are several limitations to the present study.
true
true
true
true
true
7,196
8
DISCUSSION
0
null
null
19,654,939
null
We could not investigate circulating levels of Nogo-B.
null
54
41,716
0
false
null
null
We could not investigate circulating levels of Nogo-B.
true
true
true
true
true
7,196
8
DISCUSSION
0
null
null
19,654,939
null
Thus, we could not determine if it serves as a surrogate biomarker of human atherosclerosis.
null
92
41,717
0
false
null
null
Thus, we could not determine if it serves as a surrogate biomarker of human atherosclerosis.
true
true
true
true
true
7,196
8
DISCUSSION
0
null
null
19,654,939
null
Another limitation of our study is the relatively small sample size.
null
68
41,718
0
false
null
null
Another limitation of our study is the relatively small sample size.
true
true
true
true
true
7,196