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
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cited_id
string
sentences
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all_sent_cites
list
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int64
sentence_batch_index
int64
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float64
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bool
cited_sentence
string
cites_in_sentence
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bool
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ends_wp
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cit_qc
bool
lgtm
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__index_level_0__
int64
1
DISCUSSION
1
25
[ "B25", "B62", "B72", "B25", "B72", "B51 B52 B53", "B62", "B63", "B51", "B11", "B14", "B22", "B51", "B73", "B19", "B20", "B60", "B74", "B24", "B71", "B75 B76 B77 B78 B79 B80 B81", "B21", "B82", "B50", "B51 B52 B53" ]
19,282,450
NA|pmid-9590697|pmid-9774452|pmid-10398342|pmid-9928934|pmid-9590697|pmid-9774452|pmid-10506208|pmid-9171366|pmid-8805304|pmid-9590697|pmid-10506208|pmid-9171366|pmid-11030338|pmid-12887907|pmid-12566442|pmid-11459988|pmid-11292336|pmid-12453424|pmid-8969173|pmid-9321665|pmid-10506208|pmid-12414729|pmid-10209103|pmid-1...
This complex array of behaviors can be understood as different manifestations of the translocation capacity of Rad54.
[ "25", "62", "72", "25", "72", "51–53", "62", "63", "51", "11", "14", "22", "51", "73", "19", "20", "60", "74", "24", "71", "75–81", "21", "82", "50", "51–53" ]
117
36,716
0
false
This complex array of behaviors can be understood as different manifestations of the translocation capacity of Rad54.
[]
This complex array of behaviors can be understood as different manifestations of the translocation capacity of Rad54.
true
true
true
true
true
6,304
1
DISCUSSION
1
51–53
[ "B25", "B62", "B72", "B25", "B72", "B51 B52 B53", "B62", "B63", "B51", "B11", "B14", "B22", "B51", "B73", "B19", "B20", "B60", "B74", "B24", "B71", "B75 B76 B77 B78 B79 B80 B81", "B21", "B82", "B50", "B51 B52 B53" ]
19,282,450
NA|pmid-9590697|pmid-9774452|pmid-10398342|pmid-9928934|pmid-9590697|pmid-9774452|pmid-10506208|pmid-9171366|pmid-8805304|pmid-9590697|pmid-10506208|pmid-9171366|pmid-11030338|pmid-12887907|pmid-12566442|pmid-11459988|pmid-11292336|pmid-12453424|pmid-8969173|pmid-9321665|pmid-10506208|pmid-12414729|pmid-10209103|pmid-1...
Furthermore, we suggested that, in the absence of an interaction with Rad51, the binding of Rad54 to dsDNA is random (50) and, hence, translocation can be in either direction (51–53), resulting in either disruption or elongation of joint molecules.
[ "25", "62", "72", "25", "72", "51–53", "62", "63", "51", "11", "14", "22", "51", "73", "19", "20", "60", "74", "24", "71", "75–81", "21", "82", "50", "51–53" ]
248
36,717
1
false
Furthermore, we suggested that, in the absence of an interaction with Rad51, the binding of Rad54 to dsDNA is random and, hence, translocation can be in either direction, resulting in either disruption or elongation of joint molecules.
[ "50", "51–53" ]
Furthermore, we suggested that, in the absence of an interaction with Rad51, the binding of Rad54 to dsDNA is random and, hence, translocation can be in either direction, resulting in either disruption or elongation of joint molecules.
true
true
true
true
true
6,304
1
DISCUSSION
1
25
[ "B25", "B62", "B72", "B25", "B72", "B51 B52 B53", "B62", "B63", "B51", "B11", "B14", "B22", "B51", "B73", "B19", "B20", "B60", "B74", "B24", "B71", "B75 B76 B77 B78 B79 B80 B81", "B21", "B82", "B50", "B51 B52 B53" ]
19,282,450
NA|pmid-9590697|pmid-9774452|pmid-10398342|pmid-9928934|pmid-9590697|pmid-9774452|pmid-10506208|pmid-9171366|pmid-8805304|pmid-9590697|pmid-10506208|pmid-9171366|pmid-11030338|pmid-12887907|pmid-12566442|pmid-11459988|pmid-11292336|pmid-12453424|pmid-8969173|pmid-9321665|pmid-10506208|pmid-12414729|pmid-10209103|pmid-1...
However, when Rad54 is targeted to the dsDNA by Rad51, the initial direction of translocation may be determined by the interaction with the Rad51 nucleoprotein filament, which has a polarity of pairing defined by the ssDNA.
[ "25", "62", "72", "25", "72", "51–53", "62", "63", "51", "11", "14", "22", "51", "73", "19", "20", "60", "74", "24", "71", "75–81", "21", "82", "50", "51–53" ]
223
36,718
0
false
However, when Rad54 is targeted to the dsDNA by Rad51, the initial direction of translocation may be determined by the interaction with the Rad51 nucleoprotein filament, which has a polarity of pairing defined by the ssDNA.
[]
However, when Rad54 is targeted to the dsDNA by Rad51, the initial direction of translocation may be determined by the interaction with the Rad51 nucleoprotein filament, which has a polarity of pairing defined by the ssDNA.
true
true
true
true
true
6,304
2
DISCUSSION
1
24
[ "B24", "B71", "B75 B76 B77 B78 B79 B80 B81", "B83 B84 B85", "B86", "B87" ]
19,282,450
pmid-270744|pmid-2112744|pmid-9379893|pmid-10413400|pmid-9600949|pmid-12414729|pmid-15806108|pmid-12577053|pmid-12514177|pmid-12887906|pmid-15105430|pmid-15653683|pmid-17544928|pmid-17417655|pmid-10357855|pmid-11551498|pmid-11683384|pmid-11677690|pmid-7809089
Eukaryotic Rad54 protein can also alter the positioning of nucleosomes (24,71,75–81).
[ "24", "71", "75–81", "83–85", "86", "87" ]
85
36,719
0
false
Eukaryotic Rad54 protein can also alter the positioning of nucleosomes.
[ "24,71,75–81" ]
Eukaryotic Rad54 protein can also alter the positioning of nucleosomes.
true
true
true
true
true
6,305
2
DISCUSSION
1
83–85
[ "B24", "B71", "B75 B76 B77 B78 B79 B80 B81", "B83 B84 B85", "B86", "B87" ]
19,282,450
pmid-270744|pmid-2112744|pmid-9379893|pmid-10413400|pmid-9600949|pmid-12414729|pmid-15806108|pmid-12577053|pmid-12514177|pmid-12887906|pmid-15105430|pmid-15653683|pmid-17544928|pmid-17417655|pmid-10357855|pmid-11551498|pmid-11683384|pmid-11677690|pmid-7809089
Such translocation-dependent repositioning likely increases DNA accessibility for basal processes including replication, recombination, and repair (83–85).
[ "24", "71", "75–81", "83–85", "86", "87" ]
155
36,720
1
false
Such translocation-dependent repositioning likely increases DNA accessibility for basal processes including replication, recombination, and repair.
[ "83–85" ]
Such translocation-dependent repositioning likely increases DNA accessibility for basal processes including replication, recombination, and repair.
true
true
true
true
true
6,305
2
DISCUSSION
1
86
[ "B24", "B71", "B75 B76 B77 B78 B79 B80 B81", "B83 B84 B85", "B86", "B87" ]
19,282,450
pmid-270744|pmid-2112744|pmid-9379893|pmid-10413400|pmid-9600949|pmid-12414729|pmid-15806108|pmid-12577053|pmid-12514177|pmid-12887906|pmid-15105430|pmid-15653683|pmid-17544928|pmid-17417655|pmid-10357855|pmid-11551498|pmid-11683384|pmid-11677690|pmid-7809089
There are homologues for eukaryotic chromatin proteins in the archaea (86).
[ "24", "71", "75–81", "83–85", "86", "87" ]
75
36,721
1
false
There are homologues for eukaryotic chromatin proteins in the archaea.
[ "86" ]
There are homologues for eukaryotic chromatin proteins in the archaea.
true
true
true
true
true
6,305
2
DISCUSSION
1
24
[ "B24", "B71", "B75 B76 B77 B78 B79 B80 B81", "B83 B84 B85", "B86", "B87" ]
19,282,450
pmid-270744|pmid-2112744|pmid-9379893|pmid-10413400|pmid-9600949|pmid-12414729|pmid-15806108|pmid-12577053|pmid-12514177|pmid-12887906|pmid-15105430|pmid-15653683|pmid-17544928|pmid-17417655|pmid-10357855|pmid-11551498|pmid-11683384|pmid-11677690|pmid-7809089
Exclusive to euryarchaea, these proteins are generally shorter than their eukaryotic cousins and essentially comprise the histone-core without defined tails.
[ "24", "71", "75–81", "83–85", "86", "87" ]
157
36,722
0
false
Exclusive to euryarchaea, these proteins are generally shorter than their eukaryotic cousins and essentially comprise the histone-core without defined tails.
[]
Exclusive to euryarchaea, these proteins are generally shorter than their eukaryotic cousins and essentially comprise the histone-core without defined tails.
true
true
true
true
true
6,305
2
DISCUSSION
1
24
[ "B24", "B71", "B75 B76 B77 B78 B79 B80 B81", "B83 B84 B85", "B86", "B87" ]
19,282,450
pmid-270744|pmid-2112744|pmid-9379893|pmid-10413400|pmid-9600949|pmid-12414729|pmid-15806108|pmid-12577053|pmid-12514177|pmid-12887906|pmid-15105430|pmid-15653683|pmid-17544928|pmid-17417655|pmid-10357855|pmid-11551498|pmid-11683384|pmid-11677690|pmid-7809089
Archaeal histones can compact DNA and form structures analogous to eukaryotic histones.
[ "24", "71", "75–81", "83–85", "86", "87" ]
87
36,723
0
false
Archaeal histones can compact DNA and form structures analogous to eukaryotic histones.
[]
Archaeal histones can compact DNA and form structures analogous to eukaryotic histones.
true
true
true
true
true
6,305
2
DISCUSSION
1
87
[ "B24", "B71", "B75 B76 B77 B78 B79 B80 B81", "B83 B84 B85", "B86", "B87" ]
19,282,450
pmid-270744|pmid-2112744|pmid-9379893|pmid-10413400|pmid-9600949|pmid-12414729|pmid-15806108|pmid-12577053|pmid-12514177|pmid-12887906|pmid-15105430|pmid-15653683|pmid-17544928|pmid-17417655|pmid-10357855|pmid-11551498|pmid-11683384|pmid-11677690|pmid-7809089
Little is known about the role of archaeal histones in vivo, but changes in chromosome compaction or the distribution of histone subtypes could be used to modulate DNA access (87).
[ "24", "71", "75–81", "83–85", "86", "87" ]
180
36,724
1
false
Little is known about the role of archaeal histones in vivo, but changes in chromosome compaction or the distribution of histone subtypes could be used to modulate DNA access.
[ "87" ]
Little is known about the role of archaeal histones in vivo, but changes in chromosome compaction or the distribution of histone subtypes could be used to modulate DNA access.
true
true
true
true
true
6,305
2
DISCUSSION
1
24
[ "B24", "B71", "B75 B76 B77 B78 B79 B80 B81", "B83 B84 B85", "B86", "B87" ]
19,282,450
pmid-270744|pmid-2112744|pmid-9379893|pmid-10413400|pmid-9600949|pmid-12414729|pmid-15806108|pmid-12577053|pmid-12514177|pmid-12887906|pmid-15105430|pmid-15653683|pmid-17544928|pmid-17417655|pmid-10357855|pmid-11551498|pmid-11683384|pmid-11677690|pmid-7809089
While here we have identified two euryarchaeal sequences with homology to the SsoRad54 protein, whether archaeal Rad54 homologs are involved in archaeal nucleosome remodeling is unknown.
[ "24", "71", "75–81", "83–85", "86", "87" ]
186
36,725
0
false
While here we have identified two euryarchaeal sequences with homology to the SsoRad54 protein, whether archaeal Rad54 homologs are involved in archaeal nucleosome remodeling is unknown.
[]
While here we have identified two euryarchaeal sequences with homology to the SsoRad54 protein, whether archaeal Rad54 homologs are involved in archaeal nucleosome remodeling is unknown.
true
true
true
true
true
6,305
3
DISCUSSION
1
88
[ "B88", "B89 B90 B91", "B92", "B93", "B94", "B95" ]
19,282,450
pmid-11677683|pmid-9757822|pmid-9843941|pmid-11342551|pmid-11160923|pmid-11971263|pmid-14676214|pmid-9003328|pmid-9573041|pmid-10613871|pmid-10903318|pmid-10672022|pmid-11713300|pmid-15537659|pmid-11743724|pmid-11677683|pmid-11029422|pmid-11371344|pmid-9121560|pmid-10545127|pmid-11371344|pmid-12941707|pmid-16030242|pmi...
The SsoRad54 protein we described here is in a member of the crenarchaeal domain, where histones appear to be largely absent (88).
[ "88", "89–91", "92", "93", "94", "95" ]
130
36,726
1
false
The SsoRad54 protein we described here is in a member of the crenarchaeal domain, where histones appear to be largely absent.
[ "88" ]
The SsoRad54 protein we described here is in a member of the crenarchaeal domain, where histones appear to be largely absent.
true
true
true
true
true
6,306
3
DISCUSSION
1
88
[ "B88", "B89 B90 B91", "B92", "B93", "B94", "B95" ]
19,282,450
pmid-11677683|pmid-9757822|pmid-9843941|pmid-11342551|pmid-11160923|pmid-11971263|pmid-14676214|pmid-9003328|pmid-9573041|pmid-10613871|pmid-10903318|pmid-10672022|pmid-11713300|pmid-15537659|pmid-11743724|pmid-11677683|pmid-11029422|pmid-11371344|pmid-9121560|pmid-10545127|pmid-11371344|pmid-12941707|pmid-16030242|pmi...
Instead of classical histones, crenarchaea use highly abundant DNA-binding proteins to compact DNA.
[ "88", "89–91", "92", "93", "94", "95" ]
99
36,727
0
false
Instead of classical histones, crenarchaea use highly abundant DNA-binding proteins to compact DNA.
[]
Instead of classical histones, crenarchaea use highly abundant DNA-binding proteins to compact DNA.
true
true
true
true
true
6,306
3
DISCUSSION
1
89–91
[ "B88", "B89 B90 B91", "B92", "B93", "B94", "B95" ]
19,282,450
pmid-11677683|pmid-9757822|pmid-9843941|pmid-11342551|pmid-11160923|pmid-11971263|pmid-14676214|pmid-9003328|pmid-9573041|pmid-10613871|pmid-10903318|pmid-10672022|pmid-11713300|pmid-15537659|pmid-11743724|pmid-11677683|pmid-11029422|pmid-11371344|pmid-9121560|pmid-10545127|pmid-11371344|pmid-12941707|pmid-16030242|pmi...
The Sul7d protein from the Sulfolobus genus binds DNA non-cooperatively and can compact relaxed or positively supercoiled DNA (89–91).
[ "88", "89–91", "92", "93", "94", "95" ]
134
36,728
1
false
The Sul7d protein from the Sulfolobus genus binds DNA non-cooperatively and can compact relaxed or positively supercoiled DNA.
[ "89–91" ]
The Sul7d protein from the Sulfolobus genus binds DNA non-cooperatively and can compact relaxed or positively supercoiled DNA.
true
true
true
true
true
6,306
3
DISCUSSION
1
92
[ "B88", "B89 B90 B91", "B92", "B93", "B94", "B95" ]
19,282,450
pmid-11677683|pmid-9757822|pmid-9843941|pmid-11342551|pmid-11160923|pmid-11971263|pmid-14676214|pmid-9003328|pmid-9573041|pmid-10613871|pmid-10903318|pmid-10672022|pmid-11713300|pmid-15537659|pmid-11743724|pmid-11677683|pmid-11029422|pmid-11371344|pmid-9121560|pmid-10545127|pmid-11371344|pmid-12941707|pmid-16030242|pmi...
Thermoproteus tenax, Pyrobaculum aerophilum and Aeropyrum pernix use the physically similar CC1 protein that can bind both ssDNA and dsDNA with high cooperativity (92).
[ "88", "89–91", "92", "93", "94", "95" ]
168
36,729
1
false
Thermoproteus tenax, Pyrobaculum aerophilum and Aeropyrum pernix use the physically similar CC1 protein that can bind both ssDNA and dsDNA with high cooperativity.
[ "92" ]
Thermoproteus tenax, Pyrobaculum aerophilum and Aeropyrum pernix use the physically similar CC1 protein that can bind both ssDNA and dsDNA with high cooperativity.
true
true
true
true
true
6,306
3
DISCUSSION
1
88
[ "B88", "B89 B90 B91", "B92", "B93", "B94", "B95" ]
19,282,450
pmid-11677683|pmid-9757822|pmid-9843941|pmid-11342551|pmid-11160923|pmid-11971263|pmid-14676214|pmid-9003328|pmid-9573041|pmid-10613871|pmid-10903318|pmid-10672022|pmid-11713300|pmid-15537659|pmid-11743724|pmid-11677683|pmid-11029422|pmid-11371344|pmid-9121560|pmid-10545127|pmid-11371344|pmid-12941707|pmid-16030242|pmi...
Archaea also have the Alba protein, which binds DNA non-specifically and may be involved in organizing higher-order folding of DNA-histone or DNA-Sul7d nucleoprotein assemblies (93,94).
[ "88", "89–91", "92", "93", "94", "95" ]
185
36,730
0
false
Archaea also have the Alba protein, which binds DNA non-specifically and may be involved in organizing higher-order folding of DNA-histone or DNA-Sul7d nucleoprotein assemblies.
[ "93,94" ]
Archaea also have the Alba protein, which binds DNA non-specifically and may be involved in organizing higher-order folding of DNA-histone or DNA-Sul7d nucleoprotein assemblies.
true
true
true
true
true
6,306
3
DISCUSSION
1
95
[ "B88", "B89 B90 B91", "B92", "B93", "B94", "B95" ]
19,282,450
pmid-11677683|pmid-9757822|pmid-9843941|pmid-11342551|pmid-11160923|pmid-11971263|pmid-14676214|pmid-9003328|pmid-9573041|pmid-10613871|pmid-10903318|pmid-10672022|pmid-11713300|pmid-15537659|pmid-11743724|pmid-11677683|pmid-11029422|pmid-11371344|pmid-9121560|pmid-10545127|pmid-11371344|pmid-12941707|pmid-16030242|pmi...
A second archaeal Alba protein (Alba2) was identified that forms obligate heterodimers with Alba and alters higher-order Alba-mediated DNA packing (95).
[ "88", "89–91", "92", "93", "94", "95" ]
152
36,731
1
false
A second archaeal Alba protein (Alba2) was identified that forms obligate heterodimers with Alba and alters higher-order Alba-mediated DNA packing.
[ "95" ]
A second archaeal Alba protein (Alba2) was identified that forms obligate heterodimers with Alba and alters higher-order Alba-mediated DNA packing.
true
true
true
true
true
6,306
3
DISCUSSION
1
88
[ "B88", "B89 B90 B91", "B92", "B93", "B94", "B95" ]
19,282,450
pmid-11677683|pmid-9757822|pmid-9843941|pmid-11342551|pmid-11160923|pmid-11971263|pmid-14676214|pmid-9003328|pmid-9573041|pmid-10613871|pmid-10903318|pmid-10672022|pmid-11713300|pmid-15537659|pmid-11743724|pmid-11677683|pmid-11029422|pmid-11371344|pmid-9121560|pmid-10545127|pmid-11371344|pmid-12941707|pmid-16030242|pmi...
Differential expression of the Alba proteins could modulate the nucleoid structure in Sulfolobus.
[ "88", "89–91", "92", "93", "94", "95" ]
97
36,732
0
false
Differential expression of the Alba proteins could modulate the nucleoid structure in Sulfolobus.
[]
Differential expression of the Alba proteins could modulate the nucleoid structure in Sulfolobus.
true
true
true
true
true
6,306
3
DISCUSSION
1
88
[ "B88", "B89 B90 B91", "B92", "B93", "B94", "B95" ]
19,282,450
pmid-11677683|pmid-9757822|pmid-9843941|pmid-11342551|pmid-11160923|pmid-11971263|pmid-14676214|pmid-9003328|pmid-9573041|pmid-10613871|pmid-10903318|pmid-10672022|pmid-11713300|pmid-15537659|pmid-11743724|pmid-11677683|pmid-11029422|pmid-11371344|pmid-9121560|pmid-10545127|pmid-11371344|pmid-12941707|pmid-16030242|pmi...
DNA accessibility in these prokaryotes might be tightly controlled through packaging, much as it is in eukaryotes.
[ "88", "89–91", "92", "93", "94", "95" ]
114
36,733
0
false
DNA accessibility in these prokaryotes might be tightly controlled through packaging, much as it is in eukaryotes.
[]
DNA accessibility in these prokaryotes might be tightly controlled through packaging, much as it is in eukaryotes.
true
true
true
true
true
6,306
3
DISCUSSION
1
88
[ "B88", "B89 B90 B91", "B92", "B93", "B94", "B95" ]
19,282,450
pmid-11677683|pmid-9757822|pmid-9843941|pmid-11342551|pmid-11160923|pmid-11971263|pmid-14676214|pmid-9003328|pmid-9573041|pmid-10613871|pmid-10903318|pmid-10672022|pmid-11713300|pmid-15537659|pmid-11743724|pmid-11677683|pmid-11029422|pmid-11371344|pmid-9121560|pmid-10545127|pmid-11371344|pmid-12941707|pmid-16030242|pmi...
SsoRad54 could affect distribution of these crenarchaeal DNA packing proteins, much as eukaryotic Rad54 alters nucleosome positioning.
[ "88", "89–91", "92", "93", "94", "95" ]
134
36,734
0
false
SsoRad54 could affect distribution of these crenarchaeal DNA packing proteins, much as eukaryotic Rad54 alters nucleosome positioning.
[]
SsoRad54 could affect distribution of these crenarchaeal DNA packing proteins, much as eukaryotic Rad54 alters nucleosome positioning.
true
true
true
true
true
6,306
4
DISCUSSION
1
80
[ "B80", "B96", "B15", "B97", "B98", "B99", "B100", "B100", "B67" ]
19,282,450
pmid-11677683|pmid-15882619|pmid-15882619|pmid-17704061|pmid-16818238|pmid-17467735|pmid-17544928|pmid-15465810|pmid-8805304|pmid-9315669|pmid-8834792|pmid-17227544|pmid-16738128|pmid-16738128|pmid-9614128
The N-terminal domain of Rad54 proteins was implicated in direct interactions with Rad51 protein and histone H3 (80,96).
[ "80", "96", "15", "97", "98", "99", "100", "100", "67" ]
120
36,735
0
false
The N-terminal domain of Rad54 proteins was implicated in direct interactions with Rad51 protein and histone H3.
[ "80,96" ]
The N-terminal domain of Rad54 proteins was implicated in direct interactions with Rad51 protein and histone H3.
true
true
true
true
true
6,307
4
DISCUSSION
1
99
[ "B80", "B96", "B15", "B97", "B98", "B99", "B100", "B100", "B67" ]
19,282,450
pmid-11677683|pmid-15882619|pmid-15882619|pmid-17704061|pmid-16818238|pmid-17467735|pmid-17544928|pmid-15465810|pmid-8805304|pmid-9315669|pmid-8834792|pmid-17227544|pmid-16738128|pmid-16738128|pmid-9614128
While a number of eukaryotic Rad54 proteins maintain high homology at the N-terminus (15,97,98), the recently identified Rad54 protein of Arabidopsis thaliana, is highly divergent in this region (99).
[ "80", "96", "15", "97", "98", "99", "100", "100", "67" ]
200
36,736
1
false
While a number of eukaryotic Rad54 proteins maintain high homology at the N-terminus, the recently identified Rad54 protein of Arabidopsis thaliana, is highly divergent in this region.
[ "15,97,98", "99" ]
While a number of eukaryotic Rad54 proteins maintain high homology at the N-terminus, the recently identified Rad54 protein of Arabidopsis thaliana, is highly divergent in this region.
true
true
true
true
true
6,307
4
DISCUSSION
1
80
[ "B80", "B96", "B15", "B97", "B98", "B99", "B100", "B100", "B67" ]
19,282,450
pmid-11677683|pmid-15882619|pmid-15882619|pmid-17704061|pmid-16818238|pmid-17467735|pmid-17544928|pmid-15465810|pmid-8805304|pmid-9315669|pmid-8834792|pmid-17227544|pmid-16738128|pmid-16738128|pmid-9614128
Divergence in this part of the protein may be the result of species-specific interactions with cognate protein partners.
[ "80", "96", "15", "97", "98", "99", "100", "100", "67" ]
120
36,737
0
false
Divergence in this part of the protein may be the result of species-specific interactions with cognate protein partners.
[]
Divergence in this part of the protein may be the result of species-specific interactions with cognate protein partners.
true
true
true
true
true
6,307
4
DISCUSSION
1
80
[ "B80", "B96", "B15", "B97", "B98", "B99", "B100", "B100", "B67" ]
19,282,450
pmid-11677683|pmid-15882619|pmid-15882619|pmid-17704061|pmid-16818238|pmid-17467735|pmid-17544928|pmid-15465810|pmid-8805304|pmid-9315669|pmid-8834792|pmid-17227544|pmid-16738128|pmid-16738128|pmid-9614128
We find no apparent N-terminal homology between SsoRad54 protein and any of the eukaryotic Rad54 proteins identified to date.
[ "80", "96", "15", "97", "98", "99", "100", "100", "67" ]
125
36,738
0
false
We find no apparent N-terminal homology between SsoRad54 protein and any of the eukaryotic Rad54 proteins identified to date.
[]
We find no apparent N-terminal homology between SsoRad54 protein and any of the eukaryotic Rad54 proteins identified to date.
true
true
true
true
true
6,307
4
DISCUSSION
1
80
[ "B80", "B96", "B15", "B97", "B98", "B99", "B100", "B100", "B67" ]
19,282,450
pmid-11677683|pmid-15882619|pmid-15882619|pmid-17704061|pmid-16818238|pmid-17467735|pmid-17544928|pmid-15465810|pmid-8805304|pmid-9315669|pmid-8834792|pmid-17227544|pmid-16738128|pmid-16738128|pmid-9614128
This divergence may be the consequence of the interactions with cellular protein that are necessary and specific to Sulfolobus solfataricus.
[ "80", "96", "15", "97", "98", "99", "100", "100", "67" ]
140
36,739
0
false
This divergence may be the consequence of the interactions with cellular protein that are necessary and specific to Sulfolobus solfataricus.
[]
This divergence may be the consequence of the interactions with cellular protein that are necessary and specific to Sulfolobus solfataricus.
true
true
true
true
true
6,307
4
DISCUSSION
1
80
[ "B80", "B96", "B15", "B97", "B98", "B99", "B100", "B100", "B67" ]
19,282,450
pmid-11677683|pmid-15882619|pmid-15882619|pmid-17704061|pmid-16818238|pmid-17467735|pmid-17544928|pmid-15465810|pmid-8805304|pmid-9315669|pmid-8834792|pmid-17227544|pmid-16738128|pmid-16738128|pmid-9614128
We searched for other prokaryotic Rad54 proteins using the archaeal Rad54 sequence as a query in BLAST analyses.
[ "80", "96", "15", "97", "98", "99", "100", "100", "67" ]
112
36,740
0
false
We searched for other prokaryotic Rad54 proteins using the archaeal Rad54 sequence as a query in BLAST analyses.
[]
We searched for other prokaryotic Rad54 proteins using the archaeal Rad54 sequence as a query in BLAST analyses.
true
true
true
true
true
6,307
4
DISCUSSION
1
80
[ "B80", "B96", "B15", "B97", "B98", "B99", "B100", "B100", "B67" ]
19,282,450
pmid-11677683|pmid-15882619|pmid-15882619|pmid-17704061|pmid-16818238|pmid-17467735|pmid-17544928|pmid-15465810|pmid-8805304|pmid-9315669|pmid-8834792|pmid-17227544|pmid-16738128|pmid-16738128|pmid-9614128
Homologous sequences are apparent in archaeal methanogens, as well as in bacterial systems including cyanobacterium, B. subtilis, and Mycoplasma gallisepticum.
[ "80", "96", "15", "97", "98", "99", "100", "100", "67" ]
159
36,741
0
false
Homologous sequences are apparent in archaeal methanogens, as well as in bacterial systems including cyanobacterium, B. subtilis, and Mycoplasma gallisepticum.
[]
Homologous sequences are apparent in archaeal methanogens, as well as in bacterial systems including cyanobacterium, B. subtilis, and Mycoplasma gallisepticum.
true
true
true
true
true
6,307
4
DISCUSSION
1
100
[ "B80", "B96", "B15", "B97", "B98", "B99", "B100", "B100", "B67" ]
19,282,450
pmid-11677683|pmid-15882619|pmid-15882619|pmid-17704061|pmid-16818238|pmid-17467735|pmid-17544928|pmid-15465810|pmid-8805304|pmid-9315669|pmid-8834792|pmid-17227544|pmid-16738128|pmid-16738128|pmid-9614128
Relatively recently, there was an effort to categorize the Snf2 family of proteins (100).
[ "80", "96", "15", "97", "98", "99", "100", "100", "67" ]
89
36,742
1
false
Relatively recently, there was an effort to categorize the Snf2 family of proteins.
[ "100" ]
Relatively recently, there was an effort to categorize the Snf2 family of proteins.
true
true
true
true
true
6,307
4
DISCUSSION
1
80
[ "B80", "B96", "B15", "B97", "B98", "B99", "B100", "B100", "B67" ]
19,282,450
pmid-11677683|pmid-15882619|pmid-15882619|pmid-17704061|pmid-16818238|pmid-17467735|pmid-17544928|pmid-15465810|pmid-8805304|pmid-9315669|pmid-8834792|pmid-17227544|pmid-16738128|pmid-16738128|pmid-9614128
Snf2-related sequences are found in over two thirds of complete microbial genomes and can be divided into two groups: the SSO1653 subfamily, which is anchored by the Sulfolobus solfataricus SsoRad54 sequence, and the RapA/HepA group.
[ "80", "96", "15", "97", "98", "99", "100", "100", "67" ]
233
36,743
0
false
Snf2-related sequences are found in over two thirds of complete microbial genomes and can be divided into two groups: the SSO1653 subfamily, which is anchored by the Sulfolobus solfataricus SsoRad54 sequence, and the RapA/HepA group.
[]
Snf2-related sequences are found in over two thirds of complete microbial genomes and can be divided into two groups: the SSO1653 subfamily, which is anchored by the Sulfolobus solfataricus SsoRad54 sequence, and the RapA/HepA group.
true
true
true
true
true
6,307
4
DISCUSSION
1
80
[ "B80", "B96", "B15", "B97", "B98", "B99", "B100", "B100", "B67" ]
19,282,450
pmid-11677683|pmid-15882619|pmid-15882619|pmid-17704061|pmid-16818238|pmid-17467735|pmid-17544928|pmid-15465810|pmid-8805304|pmid-9315669|pmid-8834792|pmid-17227544|pmid-16738128|pmid-16738128|pmid-9614128
The broad distribution of Snf2 sequences in microbial organisms suggests that these proteins perform non-essential functions that are sufficiently advantageous to maintain their prevalence.
[ "80", "96", "15", "97", "98", "99", "100", "100", "67" ]
189
36,744
0
false
The broad distribution of Snf2 sequences in microbial organisms suggests that these proteins perform non-essential functions that are sufficiently advantageous to maintain their prevalence.
[]
The broad distribution of Snf2 sequences in microbial organisms suggests that these proteins perform non-essential functions that are sufficiently advantageous to maintain their prevalence.
true
true
true
true
true
6,307
4
DISCUSSION
1
80
[ "B80", "B96", "B15", "B97", "B98", "B99", "B100", "B100", "B67" ]
19,282,450
pmid-11677683|pmid-15882619|pmid-15882619|pmid-17704061|pmid-16818238|pmid-17467735|pmid-17544928|pmid-15465810|pmid-8805304|pmid-9315669|pmid-8834792|pmid-17227544|pmid-16738128|pmid-16738128|pmid-9614128
The sequences that we find through BLAST searches can be categorized within the SSO1653 subfamily of Snf2 proteins.
[ "80", "96", "15", "97", "98", "99", "100", "100", "67" ]
115
36,745
0
false
The sequences that we find through BLAST searches can be categorized within the SSO1653 subfamily of Snf2 proteins.
[]
The sequences that we find through BLAST searches can be categorized within the SSO1653 subfamily of Snf2 proteins.
true
true
true
true
true
6,307
4
DISCUSSION
1
100
[ "B80", "B96", "B15", "B97", "B98", "B99", "B100", "B100", "B67" ]
19,282,450
pmid-11677683|pmid-15882619|pmid-15882619|pmid-17704061|pmid-16818238|pmid-17467735|pmid-17544928|pmid-15465810|pmid-8805304|pmid-9315669|pmid-8834792|pmid-17227544|pmid-16738128|pmid-16738128|pmid-9614128
Proteins identified within the RapA/HepA group are, by strict definition, outside the Snf2 family of proteins because they lack several features of Snf2 family proteins (100).
[ "80", "96", "15", "97", "98", "99", "100", "100", "67" ]
175
36,746
1
false
Proteins identified within the RapA/HepA group are, by strict definition, outside the Snf2 family of proteins because they lack several features of Snf2 family proteins.
[ "100" ]
Proteins identified within the RapA/HepA group are, by strict definition, outside the Snf2 family of proteins because they lack several features of Snf2 family proteins.
true
true
true
true
true
6,307
4
DISCUSSION
1
80
[ "B80", "B96", "B15", "B97", "B98", "B99", "B100", "B100", "B67" ]
19,282,450
pmid-11677683|pmid-15882619|pmid-15882619|pmid-17704061|pmid-16818238|pmid-17467735|pmid-17544928|pmid-15465810|pmid-8805304|pmid-9315669|pmid-8834792|pmid-17227544|pmid-16738128|pmid-16738128|pmid-9614128
Our BLAST analyses found homology between the SsoRad54 protein sequence and bacterial sequences annotated as HepA.
[ "80", "96", "15", "97", "98", "99", "100", "100", "67" ]
114
36,747
0
false
Our BLAST analyses found homology between the SsoRad54 protein sequence and bacterial sequences annotated as HepA.
[]
Our BLAST analyses found homology between the SsoRad54 protein sequence and bacterial sequences annotated as HepA.
true
true
true
true
true
6,307
4
DISCUSSION
1
67
[ "B80", "B96", "B15", "B97", "B98", "B99", "B100", "B100", "B67" ]
19,282,450
pmid-11677683|pmid-15882619|pmid-15882619|pmid-17704061|pmid-16818238|pmid-17467735|pmid-17544928|pmid-15465810|pmid-8805304|pmid-9315669|pmid-8834792|pmid-17227544|pmid-16738128|pmid-16738128|pmid-9614128
The bacterial HepA sequence is of particular interest since disruption of this gene in E. coli results in a clear DNA-damage sensitivity phenotype (67).
[ "80", "96", "15", "97", "98", "99", "100", "100", "67" ]
152
36,748
1
false
The bacterial HepA sequence is of particular interest since disruption of this gene in E. coli results in a clear DNA-damage sensitivity phenotype.
[ "67" ]
The bacterial HepA sequence is of particular interest since disruption of this gene in E. coli results in a clear DNA-damage sensitivity phenotype.
true
true
true
true
true
6,307
4
DISCUSSION
1
80
[ "B80", "B96", "B15", "B97", "B98", "B99", "B100", "B100", "B67" ]
19,282,450
pmid-11677683|pmid-15882619|pmid-15882619|pmid-17704061|pmid-16818238|pmid-17467735|pmid-17544928|pmid-15465810|pmid-8805304|pmid-9315669|pmid-8834792|pmid-17227544|pmid-16738128|pmid-16738128|pmid-9614128
Biochemical analyses of bacterial HepA protein have not, however, further addressed the potential involvement of the protein in recombination or repair processes.
[ "80", "96", "15", "97", "98", "99", "100", "100", "67" ]
162
36,749
0
false
Biochemical analyses of bacterial HepA protein have not, however, further addressed the potential involvement of the protein in recombination or repair processes.
[]
Biochemical analyses of bacterial HepA protein have not, however, further addressed the potential involvement of the protein in recombination or repair processes.
true
true
true
true
true
6,307
4
DISCUSSION
1
80
[ "B80", "B96", "B15", "B97", "B98", "B99", "B100", "B100", "B67" ]
19,282,450
pmid-11677683|pmid-15882619|pmid-15882619|pmid-17704061|pmid-16818238|pmid-17467735|pmid-17544928|pmid-15465810|pmid-8805304|pmid-9315669|pmid-8834792|pmid-17227544|pmid-16738128|pmid-16738128|pmid-9614128
Characterization of the SsoRad54 protein will aid in identification of proteins with similar function in other prokaryotes.
[ "80", "96", "15", "97", "98", "99", "100", "100", "67" ]
123
36,750
0
false
Characterization of the SsoRad54 protein will aid in identification of proteins with similar function in other prokaryotes.
[]
Characterization of the SsoRad54 protein will aid in identification of proteins with similar function in other prokaryotes.
true
true
true
true
true
6,307
4
DISCUSSION
1
80
[ "B80", "B96", "B15", "B97", "B98", "B99", "B100", "B100", "B67" ]
19,282,450
pmid-11677683|pmid-15882619|pmid-15882619|pmid-17704061|pmid-16818238|pmid-17467735|pmid-17544928|pmid-15465810|pmid-8805304|pmid-9315669|pmid-8834792|pmid-17227544|pmid-16738128|pmid-16738128|pmid-9614128
The SsoRad54 protein is a significant phylogenetic link in the evolution of recombination mechanisms and its further characterization will serve to define the steps of this important process in prokaryotic organisms.
[ "80", "96", "15", "97", "98", "99", "100", "100", "67" ]
216
36,751
0
false
The SsoRad54 protein is a significant phylogenetic link in the evolution of recombination mechanisms and its further characterization will serve to define the steps of this important process in prokaryotic organisms.
[]
The SsoRad54 protein is a significant phylogenetic link in the evolution of recombination mechanisms and its further characterization will serve to define the steps of this important process in prokaryotic organisms.
true
true
true
true
true
6,307
0
DISCUSSION
1
(4
[ "B4", "B32", "B33", "B32" ]
20,026,682
NA|NA|NA|NA
Upon breaching the luminal endometrial epithelium, the implanting blastocyst becomes rapidly encapsulated by decidualizing endometrial stromal cells.
[ "(4", ", 32)", "(33)", "(32)" ]
149
36,752
0
false
Upon breaching the luminal endometrial epithelium, the implanting blastocyst becomes rapidly encapsulated by decidualizing endometrial stromal cells.
[]
Upon breaching the luminal endometrial epithelium, the implanting blastocyst becomes rapidly encapsulated by decidualizing endometrial stromal cells.
true
true
true
true
true
6,308
0
DISCUSSION
1
(4
[ "B4", "B32", "B33", "B32" ]
20,026,682
NA|NA|NA|NA
From a functional perspective, the decidual process, which denotes the remodeling of the endometrial stromal compartment in response to pregnancy, establishes maternal immunological tolerance to fetal antigens, ensures tissue integrity and hemostasis during the process of trophoblast invasion and placenta formation, an...
[ "(4", ", 32)", "(33)", "(32)" ]
394
36,753
0
false
From a functional perspective, the decidual process, which denotes the remodeling of the endometrial stromal compartment in response to pregnancy, establishes maternal immunological tolerance to fetal antigens, ensures tissue integrity and hemostasis during the process of trophoblast invasion and placenta formation, an...
[]
From a functional perspective, the decidual process, which denotes the remodeling of the endometrial stromal compartment in response to pregnancy, establishes maternal immunological tolerance to fetal antigens, ensures tissue integrity and hemostasis during the process of trophoblast invasion and placenta formation, an...
true
true
true
true
true
6,308
0
DISCUSSION
1
(4
[ "B4", "B32", "B33", "B32" ]
20,026,682
NA|NA|NA|NA
The last few weeks of the first trimester of pregnancy are particularly perilous for the conceptus, as the onset of placental perfusion causes a dramatic increase in local oxygen tension interface, which in turn poses a considerable oxidative challenge (33).
[ "(4", ", 32)", "(33)", "(32)" ]
258
36,754
0
false
The last few weeks of the first trimester of pregnancy are particularly perilous for the conceptus, as the onset of placental perfusion causes a dramatic increase in local oxygen tension interface, which in turn poses a considerable oxidative challenge (33).
[]
The last few weeks of the first trimester of pregnancy are particularly perilous for the conceptus, as the onset of placental perfusion causes a dramatic increase in local oxygen tension interface, which in turn poses a considerable oxidative challenge (33).
true
true
true
true
true
6,308
0
DISCUSSION
1
(4
[ "B4", "B32", "B33", "B32" ]
20,026,682
NA|NA|NA|NA
Once placental perfusion is established between 9 and 11 wk gestation, the likelihood of pregnancy failure drops significantly, although oxidative injury of the decidua-placental interface at this time of pregnancy leads to subsequent obstetrical complications, such as placental abruption, fetal growth restriction, and...
[ "(4", ", 32)", "(33)", "(32)" ]
339
36,755
0
false
Once placental perfusion is established between 9 and 11 wk gestation, the likelihood of pregnancy failure drops significantly, although oxidative injury of the decidua-placental interface at this time of pregnancy leads to subsequent obstetrical complications, such as placental abruption, fetal growth restriction, and...
[]
Once placental perfusion is established between 9 and 11 wk gestation, the likelihood of pregnancy failure drops significantly, although oxidative injury of the decidua-placental interface at this time of pregnancy leads to subsequent obstetrical complications, such as placental abruption, fetal growth restriction, and...
true
true
true
true
true
6,308
1
DISCUSSION
1
(34)
[ "B34", "B35", "B18", "B36", "B37", "B11", "B12", "B38" ]
20,026,682
NA|NA|NA|NA|NA|NA|NA|NA
Although differentiation of HESCs requires elevated cAMP levels and sustained activation of the protein kinase A pathway, maintenance of the decidual phenotype depends on continuous progesterone signaling, mediated by PR-A (34).
[ "(34)", "(35)", "(18)", "(36", ", 37)", "(11", ", 12)", "(38)" ]
228
36,756
0
false
Although differentiation of HESCs requires elevated cAMP levels and sustained activation of the protein kinase A pathway, maintenance of the decidual phenotype depends on continuous progesterone signaling, mediated by PR-A (34).
[]
Although differentiation of HESCs requires elevated cAMP levels and sustained activation of the protein kinase A pathway, maintenance of the decidual phenotype depends on continuous progesterone signaling, mediated by PR-A.
true
true
true
true
true
6,309
1
DISCUSSION
1
(34)
[ "B34", "B35", "B18", "B36", "B37", "B11", "B12", "B38" ]
20,026,682
NA|NA|NA|NA|NA|NA|NA|NA
Withdrawal of progesterone after initiation of the decidual process invariably causes a degree of cell death in vitro and, clinically, antiprogestins such as RU486 are widely used for termination of unwanted pregnancies (35).
[ "(34)", "(35)", "(18)", "(36", ", 37)", "(11", ", 12)", "(38)" ]
225
36,757
0
false
Withdrawal of progesterone after initiation of the decidual process invariably causes a degree of cell death in vitro and, clinically, antiprogestins such as RU486 are widely used for termination of unwanted pregnancies (35).
[]
Withdrawal of progesterone after initiation of the decidual process invariably causes a degree of cell death in vitro and, clinically, antiprogestins such as RU486 are widely used for termination of unwanted pregnancies.
true
true
true
true
true
6,309
1
DISCUSSION
1
(34)
[ "B34", "B35", "B18", "B36", "B37", "B11", "B12", "B38" ]
20,026,682
NA|NA|NA|NA|NA|NA|NA|NA
Thus, the integrity of the fetomaternal interface is not only dependent on resistance to oxidative cell death but also on the ability to maintain progesterone responses and cellular homeostasis under adverse environmental conditions.
[ "(34)", "(35)", "(18)", "(36", ", 37)", "(11", ", 12)", "(38)" ]
233
36,758
0
false
Thus, the integrity of the fetomaternal interface is not only dependent on resistance to oxidative cell death but also on the ability to maintain progesterone responses and cellular homeostasis under adverse environmental conditions.
[]
Thus, the integrity of the fetomaternal interface is not only dependent on resistance to oxidative cell death but also on the ability to maintain progesterone responses and cellular homeostasis under adverse environmental conditions.
true
true
true
true
true
6,309
1
DISCUSSION
1
(34)
[ "B34", "B35", "B18", "B36", "B37", "B11", "B12", "B38" ]
20,026,682
NA|NA|NA|NA|NA|NA|NA|NA
Sumoylation has emerged as a central regulatory post-translational modification, responsive to a variety of environmental stresses (18), which controls the function of numerous proteins and, ultimately, cell fate (36, 37).
[ "(34)", "(35)", "(18)", "(36", ", 37)", "(11", ", 12)", "(38)" ]
222
36,759
0
false
Sumoylation has emerged as a central regulatory post-translational modification, responsive to a variety of environmental stresses (18), which controls the function of numerous proteins and, ultimately, cell fate (36, 37).
[]
Sumoylation has emerged as a central regulatory post-translational modification, responsive to a variety of environmental stresses (18), which controls the function of numerous proteins and, ultimately, cell fate.
true
true
true
true
true
6,309
1
DISCUSSION
1
(34)
[ "B34", "B35", "B18", "B36", "B37", "B11", "B12", "B38" ]
20,026,682
NA|NA|NA|NA|NA|NA|NA|NA
Several mechanisms have been implicated in redox regulation of the SUMO pathway, including reversible oxidative inhibition of E1-E2 ligases and inactivation of SENPs by intramolecular disulfide linkage (11, 12).
[ "(34)", "(35)", "(18)", "(36", ", 37)", "(11", ", 12)", "(38)" ]
211
36,760
0
false
Several mechanisms have been implicated in redox regulation of the SUMO pathway, including reversible oxidative inhibition of E1-E2 ligases and inactivation of SENPs by intramolecular disulfide linkage (11, 12).
[]
Several mechanisms have been implicated in redox regulation of the SUMO pathway, including reversible oxidative inhibition of E1-E2 ligases and inactivation of SENPs by intramolecular disulfide linkage (11, 12).
true
true
true
true
true
6,309
1
DISCUSSION
1
(34)
[ "B34", "B35", "B18", "B36", "B37", "B11", "B12", "B38" ]
20,026,682
NA|NA|NA|NA|NA|NA|NA|NA
Both mechanisms are operational in undifferentiated and decidual cells but only at relatively high H2O2 concentrations, which may be achieved during the respiratory burst in activated macrophages but unlikely to be relevant to pregnancy.
[ "(34)", "(35)", "(18)", "(36", ", 37)", "(11", ", 12)", "(38)" ]
237
36,761
0
false
Both mechanisms are operational in undifferentiated and decidual cells but only at relatively high H2O2 concentrations, which may be achieved during the respiratory burst in activated macrophages but unlikely to be relevant to pregnancy.
[]
Both mechanisms are operational in undifferentiated and decidual cells but only at relatively high H2O2 concentrations, which may be achieved during the respiratory burst in activated macrophages but unlikely to be relevant to pregnancy.
true
true
true
true
true
6,309
1
DISCUSSION
1
(34)
[ "B34", "B35", "B18", "B36", "B37", "B11", "B12", "B38" ]
20,026,682
NA|NA|NA|NA|NA|NA|NA|NA
At lower concentrations, however, H2O2 induced a global hypersumoylation response in undifferentiated but not decidualized cells, which was not only sustained but also sufficient to modify PR-A and to limit its trans-activation potential.
[ "(34)", "(35)", "(18)", "(36", ", 37)", "(11", ", 12)", "(38)" ]
238
36,762
0
false
At lower concentrations, however, H2O2 induced a global hypersumoylation response in undifferentiated but not decidualized cells, which was not only sustained but also sufficient to modify PR-A and to limit its trans-activation potential.
[]
At lower concentrations, however, H2O2 induced a global hypersumoylation response in undifferentiated but not decidualized cells, which was not only sustained but also sufficient to modify PR-A and to limit its trans-activation potential.
true
true
true
true
true
6,309
1
DISCUSSION
1
(34)
[ "B34", "B35", "B18", "B36", "B37", "B11", "B12", "B38" ]
20,026,682
NA|NA|NA|NA|NA|NA|NA|NA
Several lines of evidence implicated JNK activation in this hypersumoylation response, including the observations that pretreatment of undifferentiated HESCs with an inhibitor against JNK (JNKVIII) attenuated ROS-induced hypersumoylation and that induction of JNK activity in the absence of primary stress, using the 4-O...
[ "(34)", "(35)", "(18)", "(36", ", 37)", "(11", ", 12)", "(38)" ]
488
36,763
0
false
Several lines of evidence implicated JNK activation in this hypersumoylation response, including the observations that pretreatment of undifferentiated HESCs with an inhibitor against JNK (JNKVIII) attenuated ROS-induced hypersumoylation and that induction of JNK activity in the absence of primary stress, using the 4-O...
[]
Several lines of evidence implicated JNK activation in this hypersumoylation response, including the observations that pretreatment of undifferentiated HESCs with an inhibitor against JNK (JNKVIII) attenuated ROS-induced hypersumoylation and that induction of JNK activity in the absence of primary stress, using the 4-O...
true
true
true
true
true
6,309
1
DISCUSSION
1
(34)
[ "B34", "B35", "B18", "B36", "B37", "B11", "B12", "B38" ]
20,026,682
NA|NA|NA|NA|NA|NA|NA|NA
3D and data not shown).
[ "(34)", "(35)", "(18)", "(36", ", 37)", "(11", ", 12)", "(38)" ]
23
36,764
0
false
3D and data not shown).
[]
3D and data not shown).
false
false
true
true
false
6,309
1
DISCUSSION
1
(34)
[ "B34", "B35", "B18", "B36", "B37", "B11", "B12", "B38" ]
20,026,682
NA|NA|NA|NA|NA|NA|NA|NA
Further, the ability of low levels of H2O2 to perturb PR activity or the sumoylation-desumoylation equilibrium was either markedly reduced or absent on decidualization of HESCs with 8-br-cAMP and MPA in concert with attenuated JNK activation.
[ "(34)", "(35)", "(18)", "(36", ", 37)", "(11", ", 12)", "(38)" ]
242
36,765
0
false
Further, the ability of low levels of H2O2 to perturb PR activity or the sumoylation-desumoylation equilibrium was either markedly reduced or absent on decidualization of HESCs with 8-br-cAMP and MPA in concert with attenuated JNK activation.
[]
Further, the ability of low levels of H2O2 to perturb PR activity or the sumoylation-desumoylation equilibrium was either markedly reduced or absent on decidualization of HESCs with 8-br-cAMP and MPA in concert with attenuated JNK activation.
true
true
true
true
true
6,309
1
DISCUSSION
1
(34)
[ "B34", "B35", "B18", "B36", "B37", "B11", "B12", "B38" ]
20,026,682
NA|NA|NA|NA|NA|NA|NA|NA
Interestingly, a recent study reported that comparable levels of H2O2 stabilize the SUMO-2/3-specific protease SENP3, limiting the overall abundance of SUMO-2/3 modified proteins (38).
[ "(34)", "(35)", "(18)", "(36", ", 37)", "(11", ", 12)", "(38)" ]
184
36,766
0
false
Interestingly, a recent study reported that comparable levels of H2O2 stabilize the SUMO-2/3-specific protease SENP3, limiting the overall abundance of SUMO-2/3 modified proteins (38).
[]
Interestingly, a recent study reported that comparable levels of H2O2 stabilize the SUMO-2/3-specific protease SENP3, limiting the overall abundance of SUMO-2/3 modified proteins.
true
true
true
true
true
6,309
1
DISCUSSION
1
(34)
[ "B34", "B35", "B18", "B36", "B37", "B11", "B12", "B38" ]
20,026,682
NA|NA|NA|NA|NA|NA|NA|NA
Whether or not the increase in SUMO-1 modification is reciprocated by changes in SUMO-2/3 conjugation in H2O2-treated HESCs remains to be determined.
[ "(34)", "(35)", "(18)", "(36", ", 37)", "(11", ", 12)", "(38)" ]
149
36,767
0
false
Whether or not the increase in SUMO-1 modification is reciprocated by changes in SUMO-2/3 conjugation in H2O2-treated HESCs remains to be determined.
[]
Whether or not the increase in SUMO-1 modification is reciprocated by changes in SUMO-2/3 conjugation in H2O2-treated HESCs remains to be determined.
true
true
true
true
true
6,309
2
DISCUSSION
1
(39)
[ "B39", "B40", "B41", "B42", "B43", "B44", "B45", "B46" ]
20,026,682
NA|NA|NA|NA|NA|NA|NA|NA
In view of the increased scavenging potential, altered ROS signaling and its uncoupling of the SUMO-1 conjugation pathway, it was anticipated that the cellular response to an oxidative challenge would profoundly change on decidualization of HESCs.
[ "(39)", "(40)", "(41", "42", "43", "44", "45)", "(46)" ]
247
36,768
0
false
In view of the increased scavenging potential, altered ROS signaling and its uncoupling of the SUMO-1 conjugation pathway, it was anticipated that the cellular response to an oxidative challenge would profoundly change on decidualization of HESCs.
[]
In view of the increased scavenging potential, altered ROS signaling and its uncoupling of the SUMO-1 conjugation pathway, it was anticipated that the cellular response to an oxidative challenge would profoundly change on decidualization of HESCs.
true
true
true
true
true
6,310
2
DISCUSSION
1
(39)
[ "B39", "B40", "B41", "B42", "B43", "B44", "B45", "B46" ]
20,026,682
NA|NA|NA|NA|NA|NA|NA|NA
Our microarray analysis confirmed this supposition, demonstrating that only a minor subset of genes (21%) is responsive to H2O2 in both undifferentiated and decidualizing cells.
[ "(39)", "(40)", "(41", "42", "43", "44", "45)", "(46)" ]
177
36,769
0
false
Our microarray analysis confirmed this supposition, demonstrating that only a minor subset of genes (21%) is responsive to H2O2 in both undifferentiated and decidualizing cells.
[]
Our microarray analysis confirmed this supposition, demonstrating that only a minor subset of genes (21%) is responsive to H2O2 in both undifferentiated and decidualizing cells.
true
true
true
true
true
6,310
2
DISCUSSION
1
(39)
[ "B39", "B40", "B41", "B42", "B43", "B44", "B45", "B46" ]
20,026,682
NA|NA|NA|NA|NA|NA|NA|NA
Extrapolating to the in vivo situation, this suggests that the oxidative challenge at the end of the first trimester of pregnancy may in fact play a physiological role in reprogramming the decidual response, which perhaps facilitates further trophoblast invasion and placenta formation.
[ "(39)", "(40)", "(41", "42", "43", "44", "45)", "(46)" ]
286
36,770
0
false
Extrapolating to the in vivo situation, this suggests that the oxidative challenge at the end of the first trimester of pregnancy may in fact play a physiological role in reprogramming the decidual response, which perhaps facilitates further trophoblast invasion and placenta formation.
[]
Extrapolating to the in vivo situation, this suggests that the oxidative challenge at the end of the first trimester of pregnancy may in fact play a physiological role in reprogramming the decidual response, which perhaps facilitates further trophoblast invasion and placenta formation.
true
true
true
true
true
6,310
2
DISCUSSION
1
(39)
[ "B39", "B40", "B41", "B42", "B43", "B44", "B45", "B46" ]
20,026,682
NA|NA|NA|NA|NA|NA|NA|NA
Although speculative, this notion is supported by clinical studies demonstrating that dietary antioxidative supplements can adversely affect pregnancy outcome (39).
[ "(39)", "(40)", "(41", "42", "43", "44", "45)", "(46)" ]
164
36,771
0
false
Although speculative, this notion is supported by clinical studies demonstrating that dietary antioxidative supplements can adversely affect pregnancy outcome (39).
[]
Although speculative, this notion is supported by clinical studies demonstrating that dietary antioxidative supplements can adversely affect pregnancy outcome.
true
true
true
true
true
6,310
2
DISCUSSION
1
(39)
[ "B39", "B40", "B41", "B42", "B43", "B44", "B45", "B46" ]
20,026,682
NA|NA|NA|NA|NA|NA|NA|NA
The array also demonstrated that highly sensitive PR-induced genes (e.g., PRL, IGFBP1, CNR1, FKBP5, DKK1, etc.)
[ "(39)", "(40)", "(41", "42", "43", "44", "45)", "(46)" ]
111
36,772
0
false
The array also demonstrated that highly sensitive PR-induced genes (e.g., PRL, IGFBP1, CNR1, FKBP5, DKK1, etc.)
[]
The array also demonstrated that highly sensitive PR-induced genes (e.g., PRL, IGFBP1, CNR1, FKBP5, DKK1, etc.)
true
true
false
true
false
6,310
2
DISCUSSION
1
(39)
[ "B39", "B40", "B41", "B42", "B43", "B44", "B45", "B46" ]
20,026,682
NA|NA|NA|NA|NA|NA|NA|NA
are not affected on H2O2 treatment of decidual cells, indicating that PR signaling will be maintained at the fetomaternal interface under oxidative stress conditions as long as the endometrium is adequately decidualized.
[ "(39)", "(40)", "(41", "42", "43", "44", "45)", "(46)" ]
220
36,773
0
false
are not affected on H2O2 treatment of decidual cells, indicating that PR signaling will be maintained at the fetomaternal interface under oxidative stress conditions as long as the endometrium is adequately decidualized.
[]
are not affected on H2O2 treatment of decidual cells, indicating that PR signaling will be maintained at the fetomaternal interface under oxidative stress conditions as long as the endometrium is adequately decidualized.
false
true
true
true
false
6,310
2
DISCUSSION
1
(39)
[ "B39", "B40", "B41", "B42", "B43", "B44", "B45", "B46" ]
20,026,682
NA|NA|NA|NA|NA|NA|NA|NA
Targeted pathway analysis also yielded important insights into the mechanism of JNK inhibition on decidualization of HESCs.
[ "(39)", "(40)", "(41", "42", "43", "44", "45)", "(46)" ]
123
36,774
0
false
Targeted pathway analysis also yielded important insights into the mechanism of JNK inhibition on decidualization of HESCs.
[]
Targeted pathway analysis also yielded important insights into the mechanism of JNK inhibition on decidualization of HESCs.
true
true
true
true
true
6,310
2
DISCUSSION
1
(39)
[ "B39", "B40", "B41", "B42", "B43", "B44", "B45", "B46" ]
20,026,682
NA|NA|NA|NA|NA|NA|NA|NA
Of particular relevance is the reduced expression of the GAB1 mRNA, which encodes a docking protein involved in selective JNK but not ERK or p38 activation upon H2O2 (40).
[ "(39)", "(40)", "(41", "42", "43", "44", "45)", "(46)" ]
171
36,775
0
false
Of particular relevance is the reduced expression of the GAB1 mRNA, which encodes a docking protein involved in selective JNK but not ERK or p38 activation upon H2O2 (40).
[]
Of particular relevance is the reduced expression of the GAB1 mRNA, which encodes a docking protein involved in selective JNK but not ERK or p38 activation upon H2O2 (40).
true
true
true
true
true
6,310
2
DISCUSSION
1
(39)
[ "B39", "B40", "B41", "B42", "B43", "B44", "B45", "B46" ]
20,026,682
NA|NA|NA|NA|NA|NA|NA|NA
This is further accompanied by inhibition of genes encoding for MEKK1, MAP4K5, and ZAK, kinases whose activities converge on MKK4/7, which, in turn, is responsible for JNK phosphorylation (4142434445).
[ "(39)", "(40)", "(41", "42", "43", "44", "45)", "(46)" ]
201
36,776
0
false
This is further accompanied by inhibition of genes encoding for MEKK1, MAP4K5, and ZAK, kinases whose activities converge on MKK4/7, which, in turn, is responsible for JNK phosphorylation.
[ "4142434445" ]
This is further accompanied by inhibition of genes encoding for MEKK1, MAP4K5, and ZAK, kinases whose activities converge on MKK4/7, which, in turn, is responsible for JNK phosphorylation.
true
true
true
true
true
6,310
2
DISCUSSION
1
(39)
[ "B39", "B40", "B41", "B42", "B43", "B44", "B45", "B46" ]
20,026,682
NA|NA|NA|NA|NA|NA|NA|NA
Therefore, it appears that decidualization leads to widespread dampening of the signaling circuitry upstream of JNK, raising the possibility that activation of this pathway by stimuli other than H2O2 will also be diminished.
[ "(39)", "(40)", "(41", "42", "43", "44", "45)", "(46)" ]
224
36,777
0
false
Therefore, it appears that decidualization leads to widespread dampening of the signaling circuitry upstream of JNK, raising the possibility that activation of this pathway by stimuli other than H2O2 will also be diminished.
[]
Therefore, it appears that decidualization leads to widespread dampening of the signaling circuitry upstream of JNK, raising the possibility that activation of this pathway by stimuli other than H2O2 will also be diminished.
true
true
true
true
true
6,310
2
DISCUSSION
1
(39)
[ "B39", "B40", "B41", "B42", "B43", "B44", "B45", "B46" ]
20,026,682
NA|NA|NA|NA|NA|NA|NA|NA
Another interesting observation is the concomitant reduction in JNK1 and increase in JNK3 transcripts on decidualization.
[ "(39)", "(40)", "(41", "42", "43", "44", "45)", "(46)" ]
121
36,778
0
false
Another interesting observation is the concomitant reduction in JNK1 and increase in JNK3 transcripts on decidualization.
[]
Another interesting observation is the concomitant reduction in JNK1 and increase in JNK3 transcripts on decidualization.
true
true
true
true
true
6,310
2
DISCUSSION
1
(39)
[ "B39", "B40", "B41", "B42", "B43", "B44", "B45", "B46" ]
20,026,682
NA|NA|NA|NA|NA|NA|NA|NA
Although JNK isoforms can target common substrates, isoform-selective substrates also exist (46), and this would provide a further point of divergence for the differential transcriptional response to stress on differentiation of HESCs.
[ "(39)", "(40)", "(41", "42", "43", "44", "45)", "(46)" ]
235
36,779
0
false
Although JNK isoforms can target common substrates, isoform-selective substrates also exist (46), and this would provide a further point of divergence for the differential transcriptional response to stress on differentiation of HESCs.
[]
Although JNK isoforms can target common substrates, isoform-selective substrates also exist (46), and this would provide a further point of divergence for the differential transcriptional response to stress on differentiation of HESCs.
true
true
true
true
true
6,310
3
DISCUSSION
1
(47
[ "B47", "B48", "B48", "B49", "B31", "B50", "B51", "B52", "B19", "B53" ]
20,026,682
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
For functional analysis, we focused on MKP1, the founding member of the family of dual-specificity protein phosphatases and capable of dephosphorylating/deactivating JNK and p38 MAP kinases activated by stress (47, 48).
[ "(47", ", 48)", "(48", ", 49)", "(31", ", 50", "51", "52)", "(19)", "(53)" ]
219
36,780
0
false
For functional analysis, we focused on MKP1, the founding member of the family of dual-specificity protein phosphatases and capable of dephosphorylating/deactivating JNK and p38 MAP kinases activated by stress (47, 48).
[]
For functional analysis, we focused on MKP1, the founding member of the family of dual-specificity protein phosphatases and capable of dephosphorylating/deactivating JNK and p38 MAP kinases activated by stress.
true
true
true
true
true
6,311
3
DISCUSSION
1
(47
[ "B47", "B48", "B48", "B49", "B31", "B50", "B51", "B52", "B19", "B53" ]
20,026,682
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
Although the abundance of MKP1 transcripts increased on decidualization of HESCs in vitro, and even more so on secretory transformation of the endometrium in vivo, induction at protein level was far greater.
[ "(47", ", 48)", "(48", ", 49)", "(31", ", 50", "51", "52)", "(19)", "(53)" ]
207
36,781
0
false
Although the abundance of MKP1 transcripts increased on decidualization of HESCs in vitro, and even more so on secretory transformation of the endometrium in vivo, induction at protein level was far greater.
[]
Although the abundance of MKP1 transcripts increased on decidualization of HESCs in vitro, and even more so on secretory transformation of the endometrium in vivo, induction at protein level was far greater.
true
true
true
true
true
6,311
3
DISCUSSION
1
(47
[ "B47", "B48", "B48", "B49", "B31", "B50", "B51", "B52", "B19", "B53" ]
20,026,682
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
In agreement, MKP1 expression is known to be subject to posttranscriptional regulation, including enhanced translation on binding of RNA-binding proteins, such as HuR, to the 3β€²-untranslated region of MKP1 transcripts (48, 49).
[ "(47", ", 48)", "(48", ", 49)", "(31", ", 50", "51", "52)", "(19)", "(53)" ]
227
36,782
0
false
In agreement, MKP1 expression is known to be subject to posttranscriptional regulation, including enhanced translation on binding of RNA-binding proteins, such as HuR, to the 3β€²-untranslated region of MKP1 transcripts (48, 49).
[]
In agreement, MKP1 expression is known to be subject to posttranscriptional regulation, including enhanced translation on binding of RNA-binding proteins, such as HuR, to the 3β€²-untranslated region of MKP1 transcripts.
true
true
true
true
true
6,311
3
DISCUSSION
1
(47
[ "B47", "B48", "B48", "B49", "B31", "B50", "B51", "B52", "B19", "B53" ]
20,026,682
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
Several studies have shown that MKP1 confers protection against apoptosis induced by a wide range of noxious stimuli, including cisplatin, ethanol, ischemia/reperfusion injury, and H2O2, by attenuating the magnitude and duration of JNK signal (31, 505152).
[ "(47", ", 48)", "(48", ", 49)", "(31", ", 50", "51", "52)", "(19)", "(53)" ]
256
36,783
0
false
Several studies have shown that MKP1 confers protection against apoptosis induced by a wide range of noxious stimuli, including cisplatin, ethanol, ischemia/reperfusion injury, and H2O2, by attenuating the magnitude and duration of JNK signal.
[ "31, 505152" ]
Several studies have shown that MKP1 confers protection against apoptosis induced by a wide range of noxious stimuli, including cisplatin, ethanol, ischemia/reperfusion injury, and H2O2, by attenuating the magnitude and duration of JNK signal.
true
true
true
true
true
6,311
3
DISCUSSION
1
(47
[ "B47", "B48", "B48", "B49", "B31", "B50", "B51", "B52", "B19", "B53" ]
20,026,682
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
This was also the case in undifferentiated HESCs, where overexpression of MKP1 not only dampened H2O2-induced JNK activation but also prevented an hypersumoylation response and maintained PR-A activity.
[ "(47", ", 48)", "(48", ", 49)", "(31", ", 50", "51", "52)", "(19)", "(53)" ]
202
36,784
0
false
This was also the case in undifferentiated HESCs, where overexpression of MKP1 not only dampened H2O2-induced JNK activation but also prevented an hypersumoylation response and maintained PR-A activity.
[]
This was also the case in undifferentiated HESCs, where overexpression of MKP1 not only dampened H2O2-induced JNK activation but also prevented an hypersumoylation response and maintained PR-A activity.
true
true
true
true
true
6,311
3
DISCUSSION
1
(47
[ "B47", "B48", "B48", "B49", "B31", "B50", "B51", "B52", "B19", "B53" ]
20,026,682
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
Interestingly, silencing of MKP1 using siRNA or expression of Ξ”MEKK1:ER* in decidualizing cells enhanced JNK phosphorylation upon H2O2 or 4-OHT treatment, respectively, but was insufficient to globally enhance SUMO-1 conjugation (data not shown).
[ "(47", ", 48)", "(48", ", 49)", "(31", ", 50", "51", "52)", "(19)", "(53)" ]
246
36,785
0
false
Interestingly, silencing of MKP1 using siRNA or expression of Ξ”MEKK1:ER* in decidualizing cells enhanced JNK phosphorylation upon H2O2 or 4-OHT treatment, respectively, but was insufficient to globally enhance SUMO-1 conjugation (data not shown).
[]
Interestingly, silencing of MKP1 using siRNA or expression of Ξ”MEKK1:ER* in decidualizing cells enhanced JNK phosphorylation upon H2O2 or 4-OHT treatment, respectively, but was insufficient to globally enhance SUMO-1 conjugation (data not shown).
true
true
true
true
true
6,311
3
DISCUSSION
1
(47
[ "B47", "B48", "B48", "B49", "B31", "B50", "B51", "B52", "B19", "B53" ]
20,026,682
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
Why restoring JNK activity fails to elicit an hypersumoylation response in differentiating HESCs is as yet unknown.
[ "(47", ", 48)", "(48", ", 49)", "(31", ", 50", "51", "52)", "(19)", "(53)" ]
115
36,786
0
false
Why restoring JNK activity fails to elicit an hypersumoylation response in differentiating HESCs is as yet unknown.
[]
Why restoring JNK activity fails to elicit an hypersumoylation response in differentiating HESCs is as yet unknown.
true
true
true
true
true
6,311
3
DISCUSSION
1
(47
[ "B47", "B48", "B48", "B49", "B31", "B50", "B51", "B52", "B19", "B53" ]
20,026,682
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
However, decidualization is associated with down-regulation of PIAS1, PIASL, PIASxa, PIASxb, and RanBP2 in concert with induction of SENP2 (19), suggesting that one of these SUMO enzymes may be a downstream target for H2O2-activated JNK and, upon phosphorylation, triggers the global shift in the sumoylation-desumoylati...
[ "(47", ", 48)", "(48", ", 49)", "(31", ", 50", "51", "52)", "(19)", "(53)" ]
361
36,787
0
false
However, decidualization is associated with down-regulation of PIAS1, PIASL, PIASxa, PIASxb, and RanBP2 in concert with induction of SENP2 (19), suggesting that one of these SUMO enzymes may be a downstream target for H2O2-activated JNK and, upon phosphorylation, triggers the global shift in the sumoylation-desumoylati...
[]
However, decidualization is associated with down-regulation of PIAS1, PIASL, PIASxa, PIASxb, and RanBP2 in concert with induction of SENP2 (19), suggesting that one of these SUMO enzymes may be a downstream target for H2O2-activated JNK and, upon phosphorylation, triggers the global shift in the sumoylation-desumoylati...
true
true
true
true
true
6,311
3
DISCUSSION
1
(47
[ "B47", "B48", "B48", "B49", "B31", "B50", "B51", "B52", "B19", "B53" ]
20,026,682
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
Global changes in cellular sumoylation on post-translational modification of a single SUMO enzyme are not without precedent.
[ "(47", ", 48)", "(48", ", 49)", "(31", ", 50", "51", "52)", "(19)", "(53)" ]
124
36,788
0
false
Global changes in cellular sumoylation on post-translational modification of a single SUMO enzyme are not without precedent.
[]
Global changes in cellular sumoylation on post-translational modification of a single SUMO enzyme are not without precedent.
true
true
true
true
true
6,311
3
DISCUSSION
1
(47
[ "B47", "B48", "B48", "B49", "B31", "B50", "B51", "B52", "B19", "B53" ]
20,026,682
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
For example, S-nitrosation of PIAS3 in response nitric oxide promotes its degradation and has been shown to cause global hyposumoylation in mammalian cells (53).
[ "(47", ", 48)", "(48", ", 49)", "(31", ", 50", "51", "52)", "(19)", "(53)" ]
161
36,789
0
false
For example, S-nitrosation of PIAS3 in response nitric oxide promotes its degradation and has been shown to cause global hyposumoylation in mammalian cells (53).
[]
For example, S-nitrosation of PIAS3 in response nitric oxide promotes its degradation and has been shown to cause global hyposumoylation in mammalian cells (53).
true
true
true
true
true
6,311
4
DISCUSSION
0
null
null
20,026,682
null
In summary, maintaining progesterone signaling and cellular homeostasis in the maternal decidua under oxidative stress conditions is essential for survival of the conceptus.
null
173
36,790
0
false
null
null
In summary, maintaining progesterone signaling and cellular homeostasis in the maternal decidua under oxidative stress conditions is essential for survival of the conceptus.
true
true
true
true
true
6,312
4
DISCUSSION
0
null
null
20,026,682
null
Herein, we demonstrate that dampening of the JNK pathway, mediated by induction of MKP1 and altered expression of other pathway intermediates, is a cardinal event on decidual transformation of endometrial cells, which uncouples oxidative stress signals from the SUMO-1 conjugation pathway in general and PR responses in ...
null
329
36,791
0
false
null
null
Herein, we demonstrate that dampening of the JNK pathway, mediated by induction of MKP1 and altered expression of other pathway intermediates, is a cardinal event on decidual transformation of endometrial cells, which uncouples oxidative stress signals from the SUMO-1 conjugation pathway in general and PR responses in ...
true
true
true
true
true
6,312
4
DISCUSSION
0
null
null
20,026,682
null
This hitherto unrecognized mechanism may provide further insights into the pathological processes that underpin obstetrical complications, especially early pregnancy loss.
null
171
36,792
0
false
null
null
This hitherto unrecognized mechanism may provide further insights into the pathological processes that underpin obstetrical complications, especially early pregnancy loss.
true
true
true
true
true
6,312
0
INTRODUCTION
1
Hake, 1998
[ "B13", "B18", "B21", "B12", "B5", "B26" ]
21,123,694
NA|pmid-16341257|NA|pmid-17548875|NA|pmid-19487500
The traditional teaching/learning pattern in a large lecture course begins with faculty introducing new material each class, students reviewing the information at a later time, followed by a summative exam to assess student understanding.
[ "Hake, 1998", "Knight and Wood, 2005", "Michael, 2006", "Freeman ", "Chaplin, 2009", "O'Dowd and Aguilar-Roca, 2009" ]
238
36,793
0
false
The traditional teaching/learning pattern in a large lecture course begins with faculty introducing new material each class, students reviewing the information at a later time, followed by a summative exam to assess student understanding.
[]
The traditional teaching/learning pattern in a large lecture course begins with faculty introducing new material each class, students reviewing the information at a later time, followed by a summative exam to assess student understanding.
true
true
true
true
true
6,313
0
INTRODUCTION
1
Hake, 1998
[ "B13", "B18", "B21", "B12", "B5", "B26" ]
21,123,694
NA|pmid-16341257|NA|pmid-17548875|NA|pmid-19487500
Higher education practices that promote learning through active engagement in class have been shown to improve student performance (Hake, 1998; Knight and Wood, 2005; Michael, 2006; Freeman et al., 2007; Chaplin, 2009).
[ "Hake, 1998", "Knight and Wood, 2005", "Michael, 2006", "Freeman ", "Chaplin, 2009", "O'Dowd and Aguilar-Roca, 2009" ]
219
36,794
0
false
Higher education practices that promote learning through active engagement in class have been shown to improve student performance.
[ "Hake, 1998; Knight and Wood, 2005; Michael, 2006; Freeman et al., 2007; Chaplin, 2009" ]
Higher education practices that promote learning through active engagement in class have been shown to improve student performance.
true
true
true
true
true
6,313
0
INTRODUCTION
1
O'Dowd and Aguilar-Roca, 2009
[ "B13", "B18", "B21", "B12", "B5", "B26" ]
21,123,694
NA|pmid-16341257|NA|pmid-17548875|NA|pmid-19487500
We found that creating a more learner-centered environment in our large introductory biology course by replacing a small amount of new information in each class period with active learning exercises increases student engagement, encourages critical thinking, and has improved student attitudes (O'Dowd and Aguilar-Roca, ...
[ "Hake, 1998", "Knight and Wood, 2005", "Michael, 2006", "Freeman ", "Chaplin, 2009", "O'Dowd and Aguilar-Roca, 2009" ]
326
36,795
1
false
We found that creating a more learner-centered environment in our large introductory biology course by replacing a small amount of new information in each class period with active learning exercises increases student engagement, encourages critical thinking, and has improved student attitudes.
[ "O'Dowd and Aguilar-Roca, 2009" ]
We found that creating a more learner-centered environment in our large introductory biology course by replacing a small amount of new information in each class period with active learning exercises increases student engagement, encourages critical thinking, and has improved student attitudes.
true
true
true
true
true
6,313
0
INTRODUCTION
1
Hake, 1998
[ "B13", "B18", "B21", "B12", "B5", "B26" ]
21,123,694
NA|pmid-16341257|NA|pmid-17548875|NA|pmid-19487500
However, typical of introductory biology courses, we cover a large amount of material and have conformed to the traditional pattern of introducing most of this in lecture, thus limiting the time available for active engagement exercises in class.
[ "Hake, 1998", "Knight and Wood, 2005", "Michael, 2006", "Freeman ", "Chaplin, 2009", "O'Dowd and Aguilar-Roca, 2009" ]
246
36,796
0
false
However, typical of introductory biology courses, we cover a large amount of material and have conformed to the traditional pattern of introducing most of this in lecture, thus limiting the time available for active engagement exercises in class.
[]
However, typical of introductory biology courses, we cover a large amount of material and have conformed to the traditional pattern of introducing most of this in lecture, thus limiting the time available for active engagement exercises in class.
true
true
true
true
true
6,313
0
INTRODUCTION
1
Hake, 1998
[ "B13", "B18", "B21", "B12", "B5", "B26" ]
21,123,694
NA|pmid-16341257|NA|pmid-17548875|NA|pmid-19487500
It is clear that if more knowledge-level information could be moved out of lecture, there would be more time in class for active learning.
[ "Hake, 1998", "Knight and Wood, 2005", "Michael, 2006", "Freeman ", "Chaplin, 2009", "O'Dowd and Aguilar-Roca, 2009" ]
138
36,797
0
false
It is clear that if more knowledge-level information could be moved out of lecture, there would be more time in class for active learning.
[]
It is clear that if more knowledge-level information could be moved out of lecture, there would be more time in class for active learning.
true
true
true
true
true
6,313
0
INTRODUCTION
1
Hake, 1998
[ "B13", "B18", "B21", "B12", "B5", "B26" ]
21,123,694
NA|pmid-16341257|NA|pmid-17548875|NA|pmid-19487500
The question is, do students learn material as effectively if the first exposure is moved out of the classroom and time in lecture is devoted to teaching higher-order thinking?
[ "Hake, 1998", "Knight and Wood, 2005", "Michael, 2006", "Freeman ", "Chaplin, 2009", "O'Dowd and Aguilar-Roca, 2009" ]
176
36,798
0
false
The question is, do students learn material as effectively if the first exposure is moved out of the classroom and time in lecture is devoted to teaching higher-order thinking?
[]
The question is, do students learn material as effectively if the first exposure is moved out of the classroom and time in lecture is devoted to teaching higher-order thinking?
true
true
true
true
true
6,313
1
INTRODUCTION
1
Narloch
[ "B22", "B11", "B14", "B25", "B24", "B23", "B32", "B19", "B15" ]
21,123,694
NA|pmid-19047506|pmid-20046908|NA|NA|NA|NA|NA|NA|pmid-18765754|pmid-18519610|NA|pmid-19119232|NA
There is mounting evidence that a variety of preclass activities that introduce new material can increase student performance compared with traditional lectures.
[ "Narloch ", "Dobson, 2008", "Johnson and Kiviniemi, 2009", "Novak and Patterson, 2000", "Novak ", "2004", "Simkins and Maier, 2004", "Marrs and Novak, 2004", "Justice " ]
161
36,799
0
false
There is mounting evidence that a variety of preclass activities that introduce new material can increase student performance compared with traditional lectures.
[]
There is mounting evidence that a variety of preclass activities that introduce new material can increase student performance compared with traditional lectures.
true
true
true
true
true
6,314
1
INTRODUCTION
1
Narloch
[ "B22", "B11", "B14", "B25", "B24", "B23", "B32", "B19", "B15" ]
21,123,694
NA|pmid-19047506|pmid-20046908|NA|NA|NA|NA|NA|NA|pmid-18765754|pmid-18519610|NA|pmid-19119232|NA
Preclass online quizzes that encourage students to complete preparatory reading have resulted in improved exam performance (Narloch et al., 2006; Dobson, 2008; Johnson and Kiviniemi, 2009).
[ "Narloch ", "Dobson, 2008", "Johnson and Kiviniemi, 2009", "Novak and Patterson, 2000", "Novak ", "2004", "Simkins and Maier, 2004", "Marrs and Novak, 2004", "Justice " ]
189
36,800
0
false
Preclass online quizzes that encourage students to complete preparatory reading have resulted in improved exam performance.
[ "Narloch et al., 2006; Dobson, 2008; Johnson and Kiviniemi, 2009" ]
Preclass online quizzes that encourage students to complete preparatory reading have resulted in improved exam performance.
true
true
true
true
true
6,314
1
INTRODUCTION
1
Novak and Patterson, 2000
[ "B22", "B11", "B14", "B25", "B24", "B23", "B32", "B19", "B15" ]
21,123,694
NA|pmid-19047506|pmid-20046908|NA|NA|NA|NA|NA|NA|pmid-18765754|pmid-18519610|NA|pmid-19119232|NA
β€œJust-in-time teaching” (JiTT), a pedagogical strategy first developed for use in physics, uses preclass assignments to prompt thinking about the upcoming lecture topic (Novak and Patterson, 2000).
[ "Narloch ", "Dobson, 2008", "Johnson and Kiviniemi, 2009", "Novak and Patterson, 2000", "Novak ", "2004", "Simkins and Maier, 2004", "Marrs and Novak, 2004", "Justice " ]
197
36,801
1
false
β€œJust-in-time teaching” (JiTT), a pedagogical strategy first developed for use in physics, uses preclass assignments to prompt thinking about the upcoming lecture topic.
[ "Novak and Patterson, 2000" ]
β€œJust-in-time teaching” (JiTT), a pedagogical strategy first developed for use in physics, uses preclass assignments to prompt thinking about the upcoming lecture topic.
false
false
true
true
false
6,314
1
INTRODUCTION
1
Narloch
[ "B22", "B11", "B14", "B25", "B24", "B23", "B32", "B19", "B15" ]
21,123,694
NA|pmid-19047506|pmid-20046908|NA|NA|NA|NA|NA|NA|pmid-18765754|pmid-18519610|NA|pmid-19119232|NA
Students submit answers to several questions before class, often addressing common misconceptions, and the instructor uses the students' prelecture quiz answers to make last-minute adjustments to the day's lecture material.
[ "Narloch ", "Dobson, 2008", "Johnson and Kiviniemi, 2009", "Novak and Patterson, 2000", "Novak ", "2004", "Simkins and Maier, 2004", "Marrs and Novak, 2004", "Justice " ]
223
36,802
0
false
Students submit answers to several questions before class, often addressing common misconceptions, and the instructor uses the students' prelecture quiz answers to make last-minute adjustments to the day's lecture material.
[]
Students submit answers to several questions before class, often addressing common misconceptions, and the instructor uses the students' prelecture quiz answers to make last-minute adjustments to the day's lecture material.
true
true
true
true
true
6,314
1
INTRODUCTION
1
Narloch
[ "B22", "B11", "B14", "B25", "B24", "B23", "B32", "B19", "B15" ]
21,123,694
NA|pmid-19047506|pmid-20046908|NA|NA|NA|NA|NA|NA|pmid-18765754|pmid-18519610|NA|pmid-19119232|NA
The JiTT strategy has been successfully adopted for use in a broad range of disciplines (Novak et al., 1999, 2004).
[ "Narloch ", "Dobson, 2008", "Johnson and Kiviniemi, 2009", "Novak and Patterson, 2000", "Novak ", "2004", "Simkins and Maier, 2004", "Marrs and Novak, 2004", "Justice " ]
115
36,803
0
false
The JiTT strategy has been successfully adopted for use in a broad range of disciplines.
[ "Novak et al., 1999, 2004" ]
The JiTT strategy has been successfully adopted for use in a broad range of disciplines.
true
true
true
true
true
6,314
1
INTRODUCTION
1
Simkins and Maier, 2004
[ "B22", "B11", "B14", "B25", "B24", "B23", "B32", "B19", "B15" ]
21,123,694
NA|pmid-19047506|pmid-20046908|NA|NA|NA|NA|NA|NA|pmid-18765754|pmid-18519610|NA|pmid-19119232|NA
A study done in an economics course showed that completing JiTT exercises before class resulted in a small positive effect on student exam performance (Simkins and Maier, 2004).
[ "Narloch ", "Dobson, 2008", "Johnson and Kiviniemi, 2009", "Novak and Patterson, 2000", "Novak ", "2004", "Simkins and Maier, 2004", "Marrs and Novak, 2004", "Justice " ]
177
36,804
1
false
A study done in an economics course showed that completing JiTT exercises before class resulted in a small positive effect on student exam performance.
[ "Simkins and Maier, 2004" ]
A study done in an economics course showed that completing JiTT exercises before class resulted in a small positive effect on student exam performance.
true
true
true
true
true
6,314
1
INTRODUCTION
1
Marrs and Novak, 2004
[ "B22", "B11", "B14", "B25", "B24", "B23", "B32", "B19", "B15" ]
21,123,694
NA|pmid-19047506|pmid-20046908|NA|NA|NA|NA|NA|NA|pmid-18765754|pmid-18519610|NA|pmid-19119232|NA
Results from a large nonmajors biology course suggest that students prefer JiTT to traditional lectures (Marrs and Novak, 2004).
[ "Narloch ", "Dobson, 2008", "Johnson and Kiviniemi, 2009", "Novak and Patterson, 2000", "Novak ", "2004", "Simkins and Maier, 2004", "Marrs and Novak, 2004", "Justice " ]
128
36,805
1
false
Results from a large nonmajors biology course suggest that students prefer JiTT to traditional lectures.
[ "Marrs and Novak, 2004" ]
Results from a large nonmajors biology course suggest that students prefer JiTT to traditional lectures.
true
true
true
true
true
6,314
1
INTRODUCTION
1
Narloch
[ "B22", "B11", "B14", "B25", "B24", "B23", "B32", "B19", "B15" ]
21,123,694
NA|pmid-19047506|pmid-20046908|NA|NA|NA|NA|NA|NA|pmid-18765754|pmid-18519610|NA|pmid-19119232|NA
These studies are encouraging but the JiTT strategy, as the name implies, involves substantial investment on the part of the faculty member to evaluate student responses and revise lecture material within hours of lecture.
[ "Narloch ", "Dobson, 2008", "Johnson and Kiviniemi, 2009", "Novak and Patterson, 2000", "Novak ", "2004", "Simkins and Maier, 2004", "Marrs and Novak, 2004", "Justice " ]
222
36,806
0
false
These studies are encouraging but the JiTT strategy, as the name implies, involves substantial investment on the part of the faculty member to evaluate student responses and revise lecture material within hours of lecture.
[]
These studies are encouraging but the JiTT strategy, as the name implies, involves substantial investment on the part of the faculty member to evaluate student responses and revise lecture material within hours of lecture.
true
true
true
true
true
6,314
1
INTRODUCTION
1
Narloch
[ "B22", "B11", "B14", "B25", "B24", "B23", "B32", "B19", "B15" ]
21,123,694
NA|pmid-19047506|pmid-20046908|NA|NA|NA|NA|NA|NA|pmid-18765754|pmid-18519610|NA|pmid-19119232|NA
Faculty teaching large introductory classes, particularly at research universities, have little appetite for making major revisions to their traditional lecture classes in the face of limited time, resources, and reward (Justice et al., 2009).
[ "Narloch ", "Dobson, 2008", "Johnson and Kiviniemi, 2009", "Novak and Patterson, 2000", "Novak ", "2004", "Simkins and Maier, 2004", "Marrs and Novak, 2004", "Justice " ]
243
36,807
0
false
Faculty teaching large introductory classes, particularly at research universities, have little appetite for making major revisions to their traditional lecture classes in the face of limited time, resources, and reward.
[ "Justice et al., 2009" ]
Faculty teaching large introductory classes, particularly at research universities, have little appetite for making major revisions to their traditional lecture classes in the face of limited time, resources, and reward.
true
true
true
true
true
6,314
1
INTRODUCTION
1
Narloch
[ "B22", "B11", "B14", "B25", "B24", "B23", "B32", "B19", "B15" ]
21,123,694
NA|pmid-19047506|pmid-20046908|NA|NA|NA|NA|NA|NA|pmid-18765754|pmid-18519610|NA|pmid-19119232|NA
A less comprehensive but easier to implement alternative is to move some knowledge-level material from lecture to preclass exposure so students arrive prepared to grapple with higher-level concepts during engagement exercises already scheduled into the class.
[ "Narloch ", "Dobson, 2008", "Johnson and Kiviniemi, 2009", "Novak and Patterson, 2000", "Novak ", "2004", "Simkins and Maier, 2004", "Marrs and Novak, 2004", "Justice " ]
259
36,808
0
false
A less comprehensive but easier to implement alternative is to move some knowledge-level material from lecture to preclass exposure so students arrive prepared to grapple with higher-level concepts during engagement exercises already scheduled into the class.
[]
A less comprehensive but easier to implement alternative is to move some knowledge-level material from lecture to preclass exposure so students arrive prepared to grapple with higher-level concepts during engagement exercises already scheduled into the class.
true
true
true
true
true
6,314
1
INTRODUCTION
1
Narloch
[ "B22", "B11", "B14", "B25", "B24", "B23", "B32", "B19", "B15" ]
21,123,694
NA|pmid-19047506|pmid-20046908|NA|NA|NA|NA|NA|NA|pmid-18765754|pmid-18519610|NA|pmid-19119232|NA
Theoretically, this could be accomplished by students completing assigned readings before class but in our experience this rarely occurs, even when coupled with preclass quizzes worth a small number of points.
[ "Narloch ", "Dobson, 2008", "Johnson and Kiviniemi, 2009", "Novak and Patterson, 2000", "Novak ", "2004", "Simkins and Maier, 2004", "Marrs and Novak, 2004", "Justice " ]
209
36,809
0
false
Theoretically, this could be accomplished by students completing assigned readings before class but in our experience this rarely occurs, even when coupled with preclass quizzes worth a small number of points.
[]
Theoretically, this could be accomplished by students completing assigned readings before class but in our experience this rarely occurs, even when coupled with preclass quizzes worth a small number of points.
true
true
true
true
true
6,314
2
INTRODUCTION
0
null
null
21,123,694
null
We therefore created preclass assignments designed to help students learn knowledge-level material in preparation for lecture.
null
126
36,810
0
false
null
null
We therefore created preclass assignments designed to help students learn knowledge-level material in preparation for lecture.
true
true
true
true
true
6,315
2
INTRODUCTION
0
null
null
21,123,694
null
The assignments were presented in one of two formats: a narrated PowerPoint video with a notetaking sheet or a one-page worksheet.
null
130
36,811
0
false
null
null
The assignments were presented in one of two formats: a narrated PowerPoint video with a notetaking sheet or a one-page worksheet.
true
true
true
true
true
6,315
2
INTRODUCTION
0
null
null
21,123,694
null
These had to be turned in but did not involve instructor review of student responses.
null
85
36,812
0
false
null
null
These had to be turned in but did not involve instructor review of student responses.
true
true
true
true
true
6,315
2
INTRODUCTION
0
null
null
21,123,694
null
The learn before lecture (LBL) assignments were coupled with in-class active learning exercises in which students were guided in applying their new knowledge to solve higher-level problems.
null
189
36,813
0
false
null
null
The learn before lecture (LBL) assignments were coupled with in-class active learning exercises in which students were guided in applying their new knowledge to solve higher-level problems.
true
true
true
true
true
6,315
2
INTRODUCTION
0
null
null
21,123,694
null
To determine whether this strategy was effective in increasing learning, LBLs were included in a small number of lectures (three of 30 periods) in 2009 to replace material that was introduced as part of the lecture in 2007/2008.
null
228
36,814
0
false
null
null
To determine whether this strategy was effective in increasing learning, LBLs were included in a small number of lectures (three of 30 periods) in 2009 to replace material that was introduced as part of the lecture in 2007/2008.
true
true
true
true
true
6,315
2
INTRODUCTION
0
null
null
21,123,694
null
Performance of students on LBL-related exam questions, matched by level and format, in 2009 was compared with 2007/8.
null
117
36,815
0
false
null
null
Performance of students on LBL-related exam questions, matched by level and format, in 2009 was compared with 2007/8.
true
true
true
true
true
6,315