Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
xet
 Community
1
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DISCUSSION
1
8
[ "r8", "r9" ]
19,056,608
pmid-17065355|pmid-18539917
Furthermore, and perhaps of mechanistic importance, although the relative risk of nonfatal myocardial infarction is lower in the intensively treated group, all cause mortality and mortality from cardiovascular causes is greater.
[ "8", "9" ]
228
37,016
0
false
Furthermore, and perhaps of mechanistic importance, although the relative risk of nonfatal myocardial infarction is lower in the intensively treated group, all cause mortality and mortality from cardiovascular causes is greater.
[]
Furthermore, and perhaps of mechanistic importance, although the relative risk of nonfatal myocardial infarction is lower in the intensively treated group, all cause mortality and mortality from cardiovascular causes is greater.
true
true
true
true
true
6,351
8
DISCUSSION
1
8
[ "r8", "r9" ]
19,056,608
pmid-17065355|pmid-18539917
The effect of antecedent hypoglycemia on autonomic cardiovascular function in individuals with diabetes and in vulnerable diabetic subpopulations, such as critically ill patients or patients with cardiovascular disease, is an important area for additional study.
[ "8", "9" ]
262
37,017
0
false
The effect of antecedent hypoglycemia on autonomic cardiovascular function in individuals with diabetes and in vulnerable diabetic subpopulations, such as critically ill patients or patients with cardiovascular disease, is an important area for additional study.
[]
The effect of antecedent hypoglycemia on autonomic cardiovascular function in individuals with diabetes and in vulnerable diabetic subpopulations, such as critically ill patients or patients with cardiovascular disease, is an important area for additional study.
true
true
true
true
true
6,351
9
DISCUSSION
0
null
null
19,056,608
null
The randomized cross-over design of this study provides the advantage of each subject serving as his/her own control.
null
117
37,018
0
false
null
null
The randomized cross-over design of this study provides the advantage of each subject serving as his/her own control.
true
true
true
true
true
6,352
9
DISCUSSION
0
null
null
19,056,608
null
Additionally, subjects were exposed to similar insulin levels during the hypoglycemic and euglycemic clamp procedures.
null
118
37,019
0
false
null
null
Additionally, subjects were exposed to similar insulin levels during the hypoglycemic and euglycemic clamp procedures.
true
true
true
true
true
6,352
9
DISCUSSION
0
null
null
19,056,608
null
However, this trial design also imposed a potential limitation of residual effects from exposure to hypoglycemia/euglycemia during the first study visit.
null
153
37,020
0
false
null
null
However, this trial design also imposed a potential limitation of residual effects from exposure to hypoglycemia/euglycemia during the first study visit.
true
true
true
true
true
6,352
9
DISCUSSION
0
null
null
19,056,608
null
Therefore, we reevaluated subjects at least 1 and up to 3 months after the initial study visit.
null
95
37,021
0
false
null
null
Therefore, we reevaluated subjects at least 1 and up to 3 months after the initial study visit.
true
true
true
true
true
6,352
9
DISCUSSION
0
null
null
19,056,608
null
To ensure no interval change in autonomic function between clamps, baseline autonomic testing was performed before each clamp.
null
126
37,022
0
false
null
null
To ensure no interval change in autonomic function between clamps, baseline autonomic testing was performed before each clamp.
true
true
true
true
true
6,352
9
DISCUSSION
0
null
null
19,056,608
null
Furthermore, physical activity and dietary intake (including electrolytes) were rigorously controlled.
null
102
37,023
0
false
null
null
Furthermore, physical activity and dietary intake (including electrolytes) were rigorously controlled.
true
true
true
true
true
6,352
10
DISCUSSION
0
null
null
19,056,608
null
In summary, these data suggest that cardiovascular autonomic function, specifically, baroreflex sensitivity and the sympathetic response to a hypotensive stress, is attenuated after antecedent hypoglycemia.
null
206
37,024
0
false
null
null
In summary, these data suggest that cardiovascular autonomic function, specifically, baroreflex sensitivity and the sympathetic response to a hypotensive stress, is attenuated after antecedent hypoglycemia.
true
true
true
true
true
6,353
10
DISCUSSION
0
null
null
19,056,608
null
Attenuation of cardiac vagal baroreflex sensitivity is an independent predictor of mortality in postmyocardial infarction patients.
null
131
37,025
0
false
null
null
Attenuation of cardiac vagal baroreflex sensitivity is an independent predictor of mortality in postmyocardial infarction patients.
true
true
true
true
true
6,353
10
DISCUSSION
0
null
null
19,056,608
null
Because our findings have potential implications for rigorous glycemic control in diabetes, studies are needed to determine the effects of antecedent hypoglycemia on autonomic cardiovascular function in individuals with type 1 and type 2 diabetes.
null
247
37,026
0
false
null
null
Because our findings have potential implications for rigorous glycemic control in diabetes, studies are needed to determine the effects of antecedent hypoglycemia on autonomic cardiovascular function in individuals with type 1 and type 2 diabetes.
true
true
true
true
true
6,353
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B1", "B2", "B8", "B9", "B10", "B11" ]
19,736,212
pmid-15933209|pmid-16449500|pmid-19151090|pmid-12626739|pmid-16855295|pmid-18006571|pmid-16381825|pmid-15933209|pmid-16449500|pmid-14988425|pmid-19073590|pmid-16809671|pmid-17098775
How cells establish and maintain their transcriptome remains one of the fundamental questions in cell biology.
[ "1", "2", "3", "4", "5", "6", "7", "1", "2", "8", "9", "10", "11" ]
110
37,027
0
false
How cells establish and maintain their transcriptome remains one of the fundamental questions in cell biology.
[]
How cells establish and maintain their transcriptome remains one of the fundamental questions in cell biology.
true
true
true
true
true
6,354
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B1", "B2", "B8", "B9", "B10", "B11" ]
19,736,212
pmid-15933209|pmid-16449500|pmid-19151090|pmid-12626739|pmid-16855295|pmid-18006571|pmid-16381825|pmid-15933209|pmid-16449500|pmid-14988425|pmid-19073590|pmid-16809671|pmid-17098775
Transcription factors together with DNA-methylation, histone modifications and micro RNAs are the key components of the regulatory repertoire of the cell.
[ "1", "2", "3", "4", "5", "6", "7", "1", "2", "8", "9", "10", "11" ]
154
37,028
0
false
Transcription factors together with DNA-methylation, histone modifications and micro RNAs are the key components of the regulatory repertoire of the cell.
[]
Transcription factors together with DNA-methylation, histone modifications and micro RNAs are the key components of the regulatory repertoire of the cell.
true
true
true
true
true
6,354
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B1", "B2", "B8", "B9", "B10", "B11" ]
19,736,212
pmid-15933209|pmid-16449500|pmid-19151090|pmid-12626739|pmid-16855295|pmid-18006571|pmid-16381825|pmid-15933209|pmid-16449500|pmid-14988425|pmid-19073590|pmid-16809671|pmid-17098775
Detection of transcription factor (TF)-binding site motifs common to a set of co-expressed genes is a central component of the in silico characterization of transcriptional regulation and transcriptional regulatory networks.
[ "1", "2", "3", "4", "5", "6", "7", "1", "2", "8", "9", "10", "11" ]
224
37,029
0
false
Detection of transcription factor (TF)-binding site motifs common to a set of co-expressed genes is a central component of the in silico characterization of transcriptional regulation and transcriptional regulatory networks.
[]
Detection of transcription factor (TF)-binding site motifs common to a set of co-expressed genes is a central component of the in silico characterization of transcriptional regulation and transcriptional regulatory networks.
true
true
true
true
true
6,354
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B1", "B2", "B8", "B9", "B10", "B11" ]
19,736,212
pmid-15933209|pmid-16449500|pmid-19151090|pmid-12626739|pmid-16855295|pmid-18006571|pmid-16381825|pmid-15933209|pmid-16449500|pmid-14988425|pmid-19073590|pmid-16809671|pmid-17098775
In the absence of comprehensive genome-wide experimental TF-binding data, the standard bioinformatics procedure starts with the extraction of putative promoter sequences for the co-expressed genes.
[ "1", "2", "3", "4", "5", "6", "7", "1", "2", "8", "9", "10", "11" ]
197
37,030
0
false
In the absence of comprehensive genome-wide experimental TF-binding data, the standard bioinformatics procedure starts with the extraction of putative promoter sequences for the co-expressed genes.
[]
In the absence of comprehensive genome-wide experimental TF-binding data, the standard bioinformatics procedure starts with the extraction of putative promoter sequences for the co-expressed genes.
true
true
true
true
true
6,354
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B1", "B2", "B8", "B9", "B10", "B11" ]
19,736,212
pmid-15933209|pmid-16449500|pmid-19151090|pmid-12626739|pmid-16855295|pmid-18006571|pmid-16381825|pmid-15933209|pmid-16449500|pmid-14988425|pmid-19073590|pmid-16809671|pmid-17098775
The sequences are sometimes further refined by phylogenetic footprinting (1,2).
[ "1", "2", "3", "4", "5", "6", "7", "1", "2", "8", "9", "10", "11" ]
79
37,031
0
false
The sequences are sometimes further refined by phylogenetic footprinting.
[ "1,2" ]
The sequences are sometimes further refined by phylogenetic footprinting.
true
true
true
true
true
6,354
0
INTRODUCTION
1
5
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B1", "B2", "B8", "B9", "B10", "B11" ]
19,736,212
pmid-15933209|pmid-16449500|pmid-19151090|pmid-12626739|pmid-16855295|pmid-18006571|pmid-16381825|pmid-15933209|pmid-16449500|pmid-14988425|pmid-19073590|pmid-16809671|pmid-17098775
Subsequently, algorithms are applied that either try to find new DNA sequence motifs overrepresented in the promoters (3,4), or that search the sequence space for occurrences of known TF-binding motifs (5).
[ "1", "2", "3", "4", "5", "6", "7", "1", "2", "8", "9", "10", "11" ]
206
37,032
1
false
Subsequently, algorithms are applied that either try to find new DNA sequence motifs overrepresented in the promoters, or that search the sequence space for occurrences of known TF-binding motifs.
[ "3,4", "5" ]
Subsequently, algorithms are applied that either try to find new DNA sequence motifs overrepresented in the promoters, or that search the sequence space for occurrences of known TF-binding motifs.
true
true
true
true
true
6,354
0
INTRODUCTION
1
6
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B1", "B2", "B8", "B9", "B10", "B11" ]
19,736,212
pmid-15933209|pmid-16449500|pmid-19151090|pmid-12626739|pmid-16855295|pmid-18006571|pmid-16381825|pmid-15933209|pmid-16449500|pmid-14988425|pmid-19073590|pmid-16809671|pmid-17098775
The latter approach relies on databases like JASPAR (6) and Transfac (7) to provide motif descriptions for the TFs involved in the regulation of the genes of interest.
[ "1", "2", "3", "4", "5", "6", "7", "1", "2", "8", "9", "10", "11" ]
167
37,033
1
false
The latter approach relies on databases like JASPAR and Transfac to provide motif descriptions for the TFs involved in the regulation of the genes of interest.
[ "6", "7" ]
The latter approach relies on databases like JASPAR and Transfac to provide motif descriptions for the TFs involved in the regulation of the genes of interest.
true
true
true
true
true
6,354
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B1", "B2", "B8", "B9", "B10", "B11" ]
19,736,212
pmid-15933209|pmid-16449500|pmid-19151090|pmid-12626739|pmid-16855295|pmid-18006571|pmid-16381825|pmid-15933209|pmid-16449500|pmid-14988425|pmid-19073590|pmid-16809671|pmid-17098775
With the ever growing number of characterized binding motifs such approaches are becoming increasingly popular.
[ "1", "2", "3", "4", "5", "6", "7", "1", "2", "8", "9", "10", "11" ]
111
37,034
0
false
With the ever growing number of characterized binding motifs such approaches are becoming increasingly popular.
[]
With the ever growing number of characterized binding motifs such approaches are becoming increasingly popular.
true
true
true
true
true
6,354
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B1", "B2", "B8", "B9", "B10", "B11" ]
19,736,212
pmid-15933209|pmid-16449500|pmid-19151090|pmid-12626739|pmid-16855295|pmid-18006571|pmid-16381825|pmid-15933209|pmid-16449500|pmid-14988425|pmid-19073590|pmid-16809671|pmid-17098775
For a number of applications, overrepresentation calculations based on the annotation of discrete-binding sites (1) are being complemented with affinity based approaches, which avoid the artificial separation between binding sites and non-binding sites in the prediction of TF target promoters but instead assign continu...
[ "1", "2", "3", "4", "5", "6", "7", "1", "2", "8", "9", "10", "11" ]
421
37,035
1
false
For a number of applications, overrepresentation calculations based on the annotation of discrete-binding sites are being complemented with affinity based approaches, which avoid the artificial separation between binding sites and non-binding sites in the prediction of TF target promoters but instead assign continuous ...
[ "1", "2,8,9" ]
For a number of applications, overrepresentation calculations based on the annotation of discrete-binding sites are being complemented with affinity based approaches, which avoid the artificial separation between binding sites and non-binding sites in the prediction of TF target promoters but instead assign continuous ...
true
true
true
true
true
6,354
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B1", "B2", "B8", "B9", "B10", "B11" ]
19,736,212
pmid-15933209|pmid-16449500|pmid-19151090|pmid-12626739|pmid-16855295|pmid-18006571|pmid-16381825|pmid-15933209|pmid-16449500|pmid-14988425|pmid-19073590|pmid-16809671|pmid-17098775
Such affinity based methods were shown to emulate the in vivo TF-binding behavior more quantitatively than hit-based approaches (10,11).
[ "1", "2", "3", "4", "5", "6", "7", "1", "2", "8", "9", "10", "11" ]
136
37,036
0
false
Such affinity based methods were shown to emulate the in vivo TF-binding behavior more quantitatively than hit-based approaches.
[ "10,11" ]
Such affinity based methods were shown to emulate the in vivo TF-binding behavior more quantitatively than hit-based approaches.
true
true
true
true
true
6,354
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B1", "B2", "B8", "B9", "B10", "B11" ]
19,736,212
pmid-15933209|pmid-16449500|pmid-19151090|pmid-12626739|pmid-16855295|pmid-18006571|pmid-16381825|pmid-15933209|pmid-16449500|pmid-14988425|pmid-19073590|pmid-16809671|pmid-17098775
When applied to sets of tissue-specific genes overrepresentation analyses and affinity based approaches were able to identifying key regulators for a limited number of gene sets derived from e.g.
[ "1", "2", "3", "4", "5", "6", "7", "1", "2", "8", "9", "10", "11" ]
195
37,037
0
false
When applied to sets of tissue-specific genes overrepresentation analyses and affinity based approaches were able to identifying key regulators for a limited number of gene sets derived from e.g.
[]
When applied to sets of tissue-specific genes overrepresentation analyses and affinity based approaches were able to identifying key regulators for a limited number of gene sets derived from e.g.
true
true
true
true
true
6,354
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B1", "B2", "B8", "B9", "B10", "B11" ]
19,736,212
pmid-15933209|pmid-16449500|pmid-19151090|pmid-12626739|pmid-16855295|pmid-18006571|pmid-16381825|pmid-15933209|pmid-16449500|pmid-14988425|pmid-19073590|pmid-16809671|pmid-17098775
muscle and liver while they largely fail to produce meaningful results for many other tissues such as lung and brain.
[ "1", "2", "3", "4", "5", "6", "7", "1", "2", "8", "9", "10", "11" ]
117
37,038
0
false
muscle and liver while they largely fail to produce meaningful results for many other tissues such as lung and brain.
[]
muscle and liver while they largely fail to produce meaningful results for many other tissues such as lung and brain.
false
true
true
true
false
6,354
1
INTRODUCTION
1
12
[ "B12", "B13", "B14" ]
19,736,212
pmid-18436437|pmid-14744435|pmid-16432200
To understand the source of the underlying difficulties for enrichment testing more deeply, we need to look at what is known about promoters and their binding site content.
[ "12", "13", "14" ]
172
37,039
0
false
To understand the source of the underlying difficulties for enrichment testing more deeply, we need to look at what is known about promoters and their binding site content.
[]
To understand the source of the underlying difficulties for enrichment testing more deeply, we need to look at what is known about promoters and their binding site content.
true
true
true
true
true
6,355
1
INTRODUCTION
1
12
[ "B12", "B13", "B14" ]
19,736,212
pmid-18436437|pmid-14744435|pmid-16432200
The classical textbook depiction of a eukaryotic proximal promoter shows the core promoter flanked by tissue-specific regulatory inputs.
[ "12", "13", "14" ]
136
37,040
0
false
The classical textbook depiction of a eukaryotic proximal promoter shows the core promoter flanked by tissue-specific regulatory inputs.
[]
The classical textbook depiction of a eukaryotic proximal promoter shows the core promoter flanked by tissue-specific regulatory inputs.
true
true
true
true
true
6,355
1
INTRODUCTION
1
12
[ "B12", "B13", "B14" ]
19,736,212
pmid-18436437|pmid-14744435|pmid-16432200
The eukaryotic RNA polymerase II core promoter thereby typically includes several sequence elements such as an initiator signal coinciding with the transcription start site (TSS), a TATA box and two or three other motifs such as a CAAT or GC-box [for a review of these elements, see e.g.
[ "12", "13", "14" ]
287
37,041
0
false
The eukaryotic RNA polymerase II core promoter thereby typically includes several sequence elements such as an initiator signal coinciding with the transcription start site (TSS), a TATA box and two or three other motifs such as a CAAT or GC-box [for a review of these elements, see e.g.
[]
The eukaryotic RNA polymerase II core promoter thereby typically includes several sequence elements such as an initiator signal coinciding with the transcription start site (TSS), a TATA box and two or three other motifs such as a CAAT or GC-box [for a review of these elements, see e.g.
true
true
true
true
true
6,355
1
INTRODUCTION
1
12
[ "B12", "B13", "B14" ]
19,736,212
pmid-18436437|pmid-14744435|pmid-16432200
Alternatively, the whole promoter can either be partially or completely overlapped by a CpG island.
[ "12", "13", "14" ]
99
37,042
0
false
Alternatively, the whole promoter can either be partially or completely overlapped by a CpG island.
[]
Alternatively, the whole promoter can either be partially or completely overlapped by a CpG island.
true
true
true
true
true
6,355
1
INTRODUCTION
1
14
[ "B12", "B13", "B14" ]
19,736,212
pmid-18436437|pmid-14744435|pmid-16432200
In line with this model, Saxonov (14) made the striking observation that the CpG content of vertebrate promoters shows a distinct bimodal distribution.
[ "12", "13", "14" ]
151
37,043
1
false
In line with this model, Saxonov made the striking observation that the CpG content of vertebrate promoters shows a distinct bimodal distribution.
[ "14" ]
In line with this model, Saxonov made the striking observation that the CpG content of vertebrate promoters shows a distinct bimodal distribution.
true
true
true
true
true
6,355
1
INTRODUCTION
1
12
[ "B12", "B13", "B14" ]
19,736,212
pmid-18436437|pmid-14744435|pmid-16432200
Using the central dip in this distribution as demarcation line about half of the promoters can be classified as having high CpG content (HCPs) while the others are considered to have low CpG content (LCPs).
[ "12", "13", "14" ]
206
37,044
0
false
Using the central dip in this distribution as demarcation line about half of the promoters can be classified as having high CpG content (HCPs) while the others are considered to have low CpG content (LCPs).
[]
Using the central dip in this distribution as demarcation line about half of the promoters can be classified as having high CpG content (HCPs) while the others are considered to have low CpG content (LCPs).
true
true
true
true
true
6,355
2
INTRODUCTION
1
15
[ "B15", "B16", "B17", "B18", "B19", "B20" ]
19,736,212
pmid-12651739|pmid-15784181|pmid-16645617|pmid-15833120|pmid-19074369|pmid-19088187|pmid-19374772|pmid-17210927|pmid-17387144|pmid-16954542
Many pioneering vertebrate enrichment analyses used promoters of genes expressed at a high level in a terminally differentiated tissue.
[ "15", "16", "17", "18", "19", "20" ]
135
37,045
0
false
Many pioneering vertebrate enrichment analyses used promoters of genes expressed at a high level in a terminally differentiated tissue.
[]
Many pioneering vertebrate enrichment analyses used promoters of genes expressed at a high level in a terminally differentiated tissue.
true
true
true
true
true
6,356
2
INTRODUCTION
1
15
[ "B15", "B16", "B17", "B18", "B19", "B20" ]
19,736,212
pmid-12651739|pmid-15784181|pmid-16645617|pmid-15833120|pmid-19074369|pmid-19088187|pmid-19374772|pmid-17210927|pmid-17387144|pmid-16954542
Those promoters were typically of the LCP class and had a landmark TATA box about 30-bp upstream of TSSs (15).
[ "15", "16", "17", "18", "19", "20" ]
110
37,046
1
false
Those promoters were typically of the LCP class and had a landmark TATA box about 30-bp upstream of TSSs.
[ "15" ]
Those promoters were typically of the LCP class and had a landmark TATA box about 30-bp upstream of TSSs.
true
true
true
true
true
6,356
2
INTRODUCTION
1
15
[ "B15", "B16", "B17", "B18", "B19", "B20" ]
19,736,212
pmid-12651739|pmid-15784181|pmid-16645617|pmid-15833120|pmid-19074369|pmid-19088187|pmid-19374772|pmid-17210927|pmid-17387144|pmid-16954542
On the other hand, ubiquitously expressed (‘housekeeping’) genes and developmental regulators, typically lack a TATA box but overlap with a CpG island thus falling in the HCP class.
[ "15", "16", "17", "18", "19", "20" ]
181
37,047
0
false
On the other hand, ubiquitously expressed (‘housekeeping’) genes and developmental regulators, typically lack a TATA box but overlap with a CpG island thus falling in the HCP class.
[]
On the other hand, ubiquitously expressed (‘housekeeping’) genes and developmental regulators, typically lack a TATA box but overlap with a CpG island thus falling in the HCP class.
true
true
true
true
true
6,356
2
INTRODUCTION
1
15
[ "B15", "B16", "B17", "B18", "B19", "B20" ]
19,736,212
pmid-12651739|pmid-15784181|pmid-16645617|pmid-15833120|pmid-19074369|pmid-19088187|pmid-19374772|pmid-17210927|pmid-17387144|pmid-16954542
This broad dichotomy is statistically very convincing, but by no means perfect.
[ "15", "16", "17", "18", "19", "20" ]
79
37,048
0
false
This broad dichotomy is statistically very convincing, but by no means perfect.
[]
This broad dichotomy is statistically very convincing, but by no means perfect.
true
true
true
true
true
6,356
2
INTRODUCTION
1
18
[ "B15", "B16", "B17", "B18", "B19", "B20" ]
19,736,212
pmid-12651739|pmid-15784181|pmid-16645617|pmid-15833120|pmid-19074369|pmid-19088187|pmid-19374772|pmid-17210927|pmid-17387144|pmid-16954542
More recent genome-wide studies revealed that a TATA box is present in only a minority of tissue-specific promoters (16,17) and together with other elements can occur also in CpG-rich promoters (18).
[ "15", "16", "17", "18", "19", "20" ]
199
37,049
1
false
More recent genome-wide studies revealed that a TATA box is present in only a minority of tissue-specific promoters and together with other elements can occur also in CpG-rich promoters.
[ "16,17", "18" ]
More recent genome-wide studies revealed that a TATA box is present in only a minority of tissue-specific promoters and together with other elements can occur also in CpG-rich promoters.
true
true
true
true
true
6,356
2
INTRODUCTION
1
19
[ "B15", "B16", "B17", "B18", "B19", "B20" ]
19,736,212
pmid-12651739|pmid-15784181|pmid-16645617|pmid-15833120|pmid-19074369|pmid-19088187|pmid-19374772|pmid-17210927|pmid-17387144|pmid-16954542
In accordance with this, many tissue-specific genes from brain (19) and testis (20) do not have TATA-box containing promoters characteristic of genes expressed specifically in liver or muscle.
[ "15", "16", "17", "18", "19", "20" ]
192
37,050
1
false
In accordance with this, many tissue-specific genes from brain and testis do not have TATA-box containing promoters characteristic of genes expressed specifically in liver or muscle.
[ "19", "20" ]
In accordance with this, many tissue-specific genes from brain and testis do not have TATA-box containing promoters characteristic of genes expressed specifically in liver or muscle.
true
true
true
true
true
6,356
3
INTRODUCTION
0
null
null
19,736,212
pmid-16141072|pmid-16645617
In this article we show that, while most sets of tissue-specific genes contain a considerable percentage of CpG-rich promoters, the observable tissue-specific motif overrepresentation information within proximal promoters is coming almost exclusively from CpG-depleted promoters.
null
279
37,051
0
false
null
null
In this article we show that, while most sets of tissue-specific genes contain a considerable percentage of CpG-rich promoters, the observable tissue-specific motif overrepresentation information within proximal promoters is coming almost exclusively from CpG-depleted promoters.
true
true
true
true
true
6,357
3
INTRODUCTION
0
null
null
19,736,212
pmid-16141072|pmid-16645617
In contrast, CpG-rich promoters turn out to be of little or no utility for this type of analysis, even when the genes driven by them have clear tissue preference.
null
162
37,052
0
false
null
null
In contrast, CpG-rich promoters turn out to be of little or no utility for this type of analysis, even when the genes driven by them have clear tissue preference.
true
true
true
true
true
6,357
3
INTRODUCTION
0
null
null
19,736,212
pmid-16141072|pmid-16645617
We show that an a priori separation of the two promoter classes (LCP and HCP) gives a stronger, more robust, and spatially constrained binding affinity signal in the CpG-depleted promoters, and therefore recommend this as a general approach for the analysis of motif enrichment in co-regulated gene sets.
null
304
37,053
0
false
null
null
We show that an a priori separation of the two promoter classes (LCP and HCP) gives a stronger, more robust, and spatially constrained binding affinity signal in the CpG-depleted promoters, and therefore recommend this as a general approach for the analysis of motif enrichment in co-regulated gene sets.
true
true
true
true
true
6,357
0
DISCUSSION
0
null
null
19,736,212
pmid-15933209|pmid-16449500|pmid-19151090|pmid-12626739|pmid-16855295|pmid-18006571|pmid-16381825|pmid-15933209|pmid-16449500|pmid-14988425|pmid-19073590|pmid-16809671|pmid-17098775
Traditionally, vertebrate genes are being divided into two distinct classes based on the CpG content of their promoters.
null
120
37,054
0
false
null
null
Traditionally, vertebrate genes are being divided into two distinct classes based on the CpG content of their promoters.
true
true
true
true
true
6,358
0
DISCUSSION
0
null
null
19,736,212
pmid-15933209|pmid-16449500|pmid-19151090|pmid-12626739|pmid-16855295|pmid-18006571|pmid-16381825|pmid-15933209|pmid-16449500|pmid-14988425|pmid-19073590|pmid-16809671|pmid-17098775
While tissue-specific genes tend to possess CpG-depleted promoters, housekeeping genes (broadly expressed) usually have CpG-rich promoters.
null
139
37,055
0
false
null
null
While tissue-specific genes tend to possess CpG-depleted promoters, housekeeping genes (broadly expressed) usually have CpG-rich promoters.
true
true
true
true
true
6,358
0
DISCUSSION
0
null
null
19,736,212
pmid-15933209|pmid-16449500|pmid-19151090|pmid-12626739|pmid-16855295|pmid-18006571|pmid-16381825|pmid-15933209|pmid-16449500|pmid-14988425|pmid-19073590|pmid-16809671|pmid-17098775
However, as shown here, this picture is less clear-cut than generally assumed with many tissue-specific genes falling into the HCP rather than the LCP class.
null
157
37,056
0
false
null
null
However, as shown here, this picture is less clear-cut than generally assumed with many tissue-specific genes falling into the HCP rather than the LCP class.
true
true
true
true
true
6,358
0
DISCUSSION
0
null
null
19,736,212
pmid-15933209|pmid-16449500|pmid-19151090|pmid-12626739|pmid-16855295|pmid-18006571|pmid-16381825|pmid-15933209|pmid-16449500|pmid-14988425|pmid-19073590|pmid-16809671|pmid-17098775
We find that the amount of tissue-specific regulatory TF-binding signals around the TSS is thereby vastly different for LCP and HCP promoters.
null
142
37,057
0
false
null
null
We find that the amount of tissue-specific regulatory TF-binding signals around the TSS is thereby vastly different for LCP and HCP promoters.
true
true
true
true
true
6,358
0
DISCUSSION
0
null
null
19,736,212
pmid-15933209|pmid-16449500|pmid-19151090|pmid-12626739|pmid-16855295|pmid-18006571|pmid-16381825|pmid-15933209|pmid-16449500|pmid-14988425|pmid-19073590|pmid-16809671|pmid-17098775
Consequently, any promoter content analysis assessing the overrepresentation of TF motifs should start by separate the two promoter classes.
null
140
37,058
0
false
null
null
Consequently, any promoter content analysis assessing the overrepresentation of TF motifs should start by separate the two promoter classes.
true
true
true
true
true
6,358
1
DISCUSSION
0
null
null
19,736,212
pmid-18436437|pmid-14744435|pmid-16432200
In accordance with this paradigm, for set of tissue-specific genes with CpG-depleted promoters we find many well characterized TF-tissue associations such as hepatocyte nuclear factor (HNF1) with liver, and pancreas specific TF (PTF1) with pancreas.
null
249
37,059
0
false
null
null
In accordance with this paradigm, for set of tissue-specific genes with CpG-depleted promoters we find many well characterized TF-tissue associations such as hepatocyte nuclear factor (HNF1) with liver, and pancreas specific TF (PTF1) with pancreas.
true
true
true
true
true
6,359
1
DISCUSSION
0
null
null
19,736,212
pmid-18436437|pmid-14744435|pmid-16432200
Successful predictions thereby stem from cis-regulatory elements located usually within only 200-bp upstream of the TSS.
null
120
37,060
0
false
null
null
Successful predictions thereby stem from cis-regulatory elements located usually within only 200-bp upstream of the TSS.
true
true
true
true
true
6,359
1
DISCUSSION
0
null
null
19,736,212
pmid-18436437|pmid-14744435|pmid-16432200
Analyzing HCP promoters proved to be much less successful.
null
58
37,061
0
false
null
null
Analyzing HCP promoters proved to be much less successful.
true
true
true
true
true
6,359
1
DISCUSSION
0
null
null
19,736,212
pmid-18436437|pmid-14744435|pmid-16432200
A notable exception is the association of neuron-restrictive silencing factor, NRSF, with brain specific genes of the HCP class.
null
128
37,062
0
false
null
null
A notable exception is the association of neuron-restrictive silencing factor, NRSF, with brain specific genes of the HCP class.
true
true
true
true
true
6,359
1
DISCUSSION
0
null
null
19,736,212
pmid-18436437|pmid-14744435|pmid-16432200
Interestingly, this association is not detected in the corresponding LCP class and also appears less significant when combining CpG-rich and CpG-depleted promoters indicating that NRSF acts preferentially on the transcription of CpG-rich promoters.
null
248
37,063
0
false
null
null
Interestingly, this association is not detected in the corresponding LCP class and also appears less significant when combining CpG-rich and CpG-depleted promoters indicating that NRSF acts preferentially on the transcription of CpG-rich promoters.
true
true
true
true
true
6,359
1
DISCUSSION
0
null
null
19,736,212
pmid-18436437|pmid-14744435|pmid-16432200
In general, while the overall enrichment scores across all HCP categories are weak, motifs overrepresentation analysis of the HCP genes revealed an accumulation of core promoter elements in tissue-specific genes with CpG-rich promoters.
null
236
37,064
0
false
null
null
In general, while the overall enrichment scores across all HCP categories are weak, motifs overrepresentation analysis of the HCP genes revealed an accumulation of core promoter elements in tissue-specific genes with CpG-rich promoters.
true
true
true
true
true
6,359
1
DISCUSSION
0
null
null
19,736,212
pmid-18436437|pmid-14744435|pmid-16432200
For instance, within 200-bp upstream of the TSS we found NFY as the most enriched motif in liver and muscle, TATA in intestine and stomach and the CAAT box in lung.
null
164
37,065
0
false
null
null
For instance, within 200-bp upstream of the TSS we found NFY as the most enriched motif in liver and muscle, TATA in intestine and stomach and the CAAT box in lung.
true
true
true
true
true
6,359
1
DISCUSSION
0
null
null
19,736,212
pmid-18436437|pmid-14744435|pmid-16432200
While these motifs represent the very opposite to tissue-specific signals, they demonstrate a general enrichment of such core promoter elements in CpG-rich promoters of tissue-specific genes.
null
191
37,066
0
false
null
null
While these motifs represent the very opposite to tissue-specific signals, they demonstrate a general enrichment of such core promoter elements in CpG-rich promoters of tissue-specific genes.
true
true
true
true
true
6,359
1
DISCUSSION
0
null
null
19,736,212
pmid-18436437|pmid-14744435|pmid-16432200
This suggests that such promoters might tend to be activated differently from CpG-rich promoters of broadly expressed genes.
null
124
37,067
0
false
null
null
This suggests that such promoters might tend to be activated differently from CpG-rich promoters of broadly expressed genes.
true
true
true
true
true
6,359
2
DISCUSSION
1
42
[ "B42", "B31", "B43", "B44" ]
19,736,212
pmid-12651739|pmid-15784181|pmid-16645617|pmid-15833120|pmid-19074369|pmid-19088187|pmid-19374772|pmid-17210927|pmid-17387144|pmid-16954542
A plausible explanation for the weak enrichment scores across HCP genes is that regulatory elements driving expression in these contexts are more likely to be outside of ‘conventional’ promoter regions, and a typical analysis in which a fixed sequence range around the TSS is analyzed either misses them or drowns them i...
[ "42", "31", "43", "44" ]
354
37,068
1
false
A plausible explanation for the weak enrichment scores across HCP genes is that regulatory elements driving expression in these contexts are more likely to be outside of ‘conventional’ promoter regions, and a typical analysis in which a fixed sequence range around the TSS is analyzed either misses them or drowns them i...
[ "42" ]
A plausible explanation for the weak enrichment scores across HCP genes is that regulatory elements driving expression in these contexts are more likely to be outside of ‘conventional’ promoter regions, and a typical analysis in which a fixed sequence range around the TSS is analyzed either misses them or drowns them i...
true
true
true
true
true
6,360
2
DISCUSSION
1
42
[ "B42", "B31", "B43", "B44" ]
19,736,212
pmid-12651739|pmid-15784181|pmid-16645617|pmid-15833120|pmid-19074369|pmid-19088187|pmid-19374772|pmid-17210927|pmid-17387144|pmid-16954542
An increasing amount of evidence indicates that many genes have key regulatory elements at large distances in both directions from the core promoter (31,43)—too large, in fact, for any approach that takes a fixed amount of upstream and/or downstream sequence to work.
[ "42", "31", "43", "44" ]
267
37,069
0
false
An increasing amount of evidence indicates that many genes have key regulatory elements at large distances in both directions from the core promoter —too large, in fact, for any approach that takes a fixed amount of upstream and/or downstream sequence to work.
[ "31,43" ]
An increasing amount of evidence indicates that many genes have key regulatory elements at large distances in both directions from the core promoter —too large, in fact, for any approach that takes a fixed amount of upstream and/or downstream sequence to work.
true
true
true
true
true
6,360
2
DISCUSSION
1
42
[ "B42", "B31", "B43", "B44" ]
19,736,212
pmid-12651739|pmid-15784181|pmid-16645617|pmid-15833120|pmid-19074369|pmid-19088187|pmid-19374772|pmid-17210927|pmid-17387144|pmid-16954542
For these, the only hope for finding regulatory elements might come in the form of exhaustive genome-wide experimental TF-binding data from ChIP-seq and related technologies combined with e.g.
[ "42", "31", "43", "44" ]
192
37,070
0
false
For these, the only hope for finding regulatory elements might come in the form of exhaustive genome-wide experimental TF-binding data from ChIP-seq and related technologies combined with e.g.
[]
For these, the only hope for finding regulatory elements might come in the form of exhaustive genome-wide experimental TF-binding data from ChIP-seq and related technologies combined with e.g.
true
true
true
true
true
6,360
2
DISCUSSION
1
44
[ "B42", "B31", "B43", "B44" ]
19,736,212
pmid-12651739|pmid-15784181|pmid-16645617|pmid-15833120|pmid-19074369|pmid-19088187|pmid-19374772|pmid-17210927|pmid-17387144|pmid-16954542
chromatin capture assays (44).
[ "42", "31", "43", "44" ]
30
37,071
1
false
chromatin capture assays.
[ "44" ]
chromatin capture assays.
false
true
true
true
false
6,360
3
DISCUSSION
1
45
[ "B45", "B17" ]
19,736,212
pmid-16141072|pmid-16645617
Another problem with enrichment testing in proximal promoters might be caused by the presence of multiple alternative promoters as expression data often does not reveal which of them is used in a given context (45).
[ "45", "17" ]
215
37,072
1
false
Another problem with enrichment testing in proximal promoters might be caused by the presence of multiple alternative promoters as expression data often does not reveal which of them is used in a given context.
[ "45" ]
Another problem with enrichment testing in proximal promoters might be caused by the presence of multiple alternative promoters as expression data often does not reveal which of them is used in a given context.
true
true
true
true
true
6,361
3
DISCUSSION
1
17
[ "B45", "B17" ]
19,736,212
pmid-16141072|pmid-16645617
Similarly, in a large subset of individual vertebrate core promoters, typically those overlapping a CpG island, TSS positions are not unique but rather broadly distributed (17).
[ "45", "17" ]
177
37,073
1
false
Similarly, in a large subset of individual vertebrate core promoters, typically those overlapping a CpG island, TSS positions are not unique but rather broadly distributed.
[ "17" ]
Similarly, in a large subset of individual vertebrate core promoters, typically those overlapping a CpG island, TSS positions are not unique but rather broadly distributed.
true
true
true
true
true
6,361
3
DISCUSSION
1
45
[ "B45", "B17" ]
19,736,212
pmid-16141072|pmid-16645617
Therefore, taking a fixed amount of sequence around any given TSS is likely to result in a functionally heterogeneous set, on which the interpretation of TF content and their position relative to TSS becomes ambiguous.
[ "45", "17" ]
218
37,074
0
false
Therefore, taking a fixed amount of sequence around any given TSS is likely to result in a functionally heterogeneous set, on which the interpretation of TF content and their position relative to TSS becomes ambiguous.
[]
Therefore, taking a fixed amount of sequence around any given TSS is likely to result in a functionally heterogeneous set, on which the interpretation of TF content and their position relative to TSS becomes ambiguous.
true
true
true
true
true
6,361
3
DISCUSSION
1
45
[ "B45", "B17" ]
19,736,212
pmid-16141072|pmid-16645617
However, since the typical CpG-rich promoters have TSS positions spread over a span of only 50–200 bp, this imprecision cannot by itself account for the lack of tissue-specific signals reported here.
[ "45", "17" ]
199
37,075
0
false
However, since the typical CpG-rich promoters have TSS positions spread over a span of only 50–200 bp, this imprecision cannot by itself account for the lack of tissue-specific signals reported here.
[]
However, since the typical CpG-rich promoters have TSS positions spread over a span of only 50–200 bp, this imprecision cannot by itself account for the lack of tissue-specific signals reported here.
true
true
true
true
true
6,361
3
DISCUSSION
1
45
[ "B45", "B17" ]
19,736,212
pmid-16141072|pmid-16645617
In the worst case, it would result in a slightly weaker association due to the ambiguous determination of TSS position, and not the almost complete absence of it that is observed.
[ "45", "17" ]
179
37,076
0
false
In the worst case, it would result in a slightly weaker association due to the ambiguous determination of TSS position, and not the almost complete absence of it that is observed.
[]
In the worst case, it would result in a slightly weaker association due to the ambiguous determination of TSS position, and not the almost complete absence of it that is observed.
true
true
true
true
true
6,361
4
DISCUSSION
1
46
[ "B46", "B47", "B48" ]
19,736,212
pmid-17068082|pmid-17989259|pmid-17274809
CpG islands are relatively easy to find in genomes of tetrapod vertebrates; in many fish genomes, however, they are much smaller and more difficult to detect, although the main distinction between CpG-depleted promoters with well defined TSSs and CpG-rich promoters with ambiguous start positions still holds (A.C. Previ...
[ "46", "47", "48" ]
357
37,077
0
false
CpG islands are relatively easy to find in genomes of tetrapod vertebrates; in many fish genomes, however, they are much smaller and more difficult to detect, although the main distinction between CpG-depleted promoters with well defined TSSs and CpG-rich promoters with ambiguous start positions still holds (A.C. Previ...
[]
CpG islands are relatively easy to find in genomes of tetrapod vertebrates; in many fish genomes, however, they are much smaller and more difficult to detect, although the main distinction between CpG-depleted promoters with well defined TSSs and CpG-rich promoters with ambiguous start positions still holds (A.C. Previ...
true
true
true
true
true
6,362
4
DISCUSSION
1
46
[ "B46", "B47", "B48" ]
19,736,212
pmid-17068082|pmid-17989259|pmid-17274809
Of invertebrates, Drosophila species were shown to have multiple types of core promoters (46) that are associated with different responsiveness to long-range enhancers and different level of tissue-specificity (47).
[ "46", "47", "48" ]
215
37,078
1
false
Of invertebrates, Drosophila species were shown to have multiple types of core promoters that are associated with different responsiveness to long-range enhancers and different level of tissue-specificity.
[ "46", "47" ]
Of invertebrates, Drosophila species were shown to have multiple types of core promoters that are associated with different responsiveness to long-range enhancers and different level of tissue-specificity.
true
true
true
true
true
6,362
4
DISCUSSION
1
46
[ "B46", "B47", "B48" ]
19,736,212
pmid-17068082|pmid-17989259|pmid-17274809
It remains to be seen if genome compaction has led to more of the promoters having the majority of their regulatory elements close to the TSS.
[ "46", "47", "48" ]
142
37,079
0
false
It remains to be seen if genome compaction has led to more of the promoters having the majority of their regulatory elements close to the TSS.
[]
It remains to be seen if genome compaction has led to more of the promoters having the majority of their regulatory elements close to the TSS.
true
true
true
true
true
6,362
4
DISCUSSION
1
48
[ "B46", "B47", "B48" ]
19,736,212
pmid-17068082|pmid-17989259|pmid-17274809
Other model invertebrates were also shown to have a distinct subset of genes responsive to long range enhancers (48).
[ "46", "47", "48" ]
117
37,080
1
false
Other model invertebrates were also shown to have a distinct subset of genes responsive to long range enhancers.
[ "48" ]
Other model invertebrates were also shown to have a distinct subset of genes responsive to long range enhancers.
true
true
true
true
true
6,362
4
DISCUSSION
1
46
[ "B46", "B47", "B48" ]
19,736,212
pmid-17068082|pmid-17989259|pmid-17274809
It is tempting to conclude that the distinction between promoters responding to proximal and distal signals could be found in most metazoan genomes.
[ "46", "47", "48" ]
148
37,081
0
false
It is tempting to conclude that the distinction between promoters responding to proximal and distal signals could be found in most metazoan genomes.
[]
It is tempting to conclude that the distinction between promoters responding to proximal and distal signals could be found in most metazoan genomes.
true
true
true
true
true
6,362
5
DISCUSSION
0
null
null
19,736,212
null
The specific enrichment of regulatory sequence elements in only CpG-depleted promoters points to the potential involvement of alternative mechanisms in the regulation of tissue-specific expression of HCP genes.
null
210
37,082
0
false
null
null
The specific enrichment of regulatory sequence elements in only CpG-depleted promoters points to the potential involvement of alternative mechanisms in the regulation of tissue-specific expression of HCP genes.
true
true
true
true
true
6,363
5
DISCUSSION
0
null
null
19,736,212
null
These mechanisms likely include DNA methylation and distinct histone modifications.
null
83
37,083
0
false
null
null
These mechanisms likely include DNA methylation and distinct histone modifications.
true
true
true
true
true
6,363
5
DISCUSSION
0
null
null
19,736,212
null
With the recent advent of technologies such as ChIP-seq new large-scale data will become available soon that will allow to associate specific histone modifications with specific expression patterns across a variety of different tissues.
null
236
37,084
0
false
null
null
With the recent advent of technologies such as ChIP-seq new large-scale data will become available soon that will allow to associate specific histone modifications with specific expression patterns across a variety of different tissues.
true
true
true
true
true
6,363
0
INTRODUCTION
1
Rios and Pizarro, 1991
[ "bib41" ]
16,735,751
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
It is generally accepted that skeletal muscle type excitation–contraction coupling involves complex mechanisms by which Ca2+ ions are released from the terminal cisternae of the SR in response to an action potential (AP) stimulation.
[ "Rios and Pizarro, 1991" ]
233
37,085
0
false
It is generally accepted that skeletal muscle type excitation–contraction coupling involves complex mechanisms by which Ca2+ ions are released from the terminal cisternae of the SR in response to an action potential (AP) stimulation.
[]
It is generally accepted that skeletal muscle type excitation–contraction coupling involves complex mechanisms by which Ca2+ ions are released from the terminal cisternae of the SR in response to an action potential stimulation.
true
true
true
true
true
6,364
0
INTRODUCTION
1
Rios and Pizarro, 1991
[ "bib41" ]
16,735,751
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
It is currently believed that voltage transduction at the dihydropyridine receptors, located at the transverse tubule (T-tubule) membranes leads to the activation of the RyRs, located at junctional membranes of the SR, by means of a direct interaction between both channels (Rios and Pizarro, 1991).
[ "Rios and Pizarro, 1991" ]
299
37,086
1
false
It is currently believed that voltage transduction at the dihydropyridine receptors, located at the transverse tubule (T-tubule) membranes leads to the activation of the RyRs, located at junctional membranes of the SR, by means of a direct interaction between both channels.
[ "Rios and Pizarro, 1991" ]
It is currently believed that voltage transduction at the dihydropyridine receptors, located at the transverse tubule (T-tubule) membranes leads to the activation of the RyRs, located at junctional membranes of the SR, by means of a direct interaction between both channels.
true
true
true
true
true
6,364
0
INTRODUCTION
1
Rios and Pizarro, 1991
[ "bib41" ]
16,735,751
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
The resulting increase in free Ca2+ concentration ([Ca2+]) is in turn sensed by the regulatory protein troponin and this serves as a signal for activation of the contractile proteins.
[ "Rios and Pizarro, 1991" ]
183
37,087
0
false
The resulting increase in free Ca2+ concentration ([Ca2+]) is in turn sensed by the regulatory protein troponin and this serves as a signal for activation of the contractile proteins.
[]
The resulting increase in free Ca2+ concentration is in turn sensed by the regulatory protein troponin and this serves as a signal for activation of the contractile proteins.
true
true
true
true
true
6,364
1
INTRODUCTION
1
Vergara et al., 1991
[ "bib46", "bib45", "bib8", "bib28", "bib1", "bib50", "bib49", "bib17", "bib39", "bib21", "bib17", "bib47", "bib12", "bib37" ]
16,735,751
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
In both frog and mammalian skeletal muscle, the amplitude and time course of AP-evoked average increases in [Ca2+] occurring throughout multisarcomeric regions of a muscle fiber (global Ca2+ transients) have been mostly measured using fluorescence microscopy and Ca2+ indicators (Vergara et al., 1991; Vergara and DiFran...
[ "Vergara et al., 1991", "Vergara and DiFranco, 1992", "Delbono and Stefani, 1993", "Kim and Vergara, 1998a", "Baylor and Hollingworth, 2003", "Woods et al., 2004", "Woods et al., 2005", "Escobar et al., 1994", "Peachey, 1965", "Franzini-Armstrong, 1972", "Escobar et al., 1994", "Vergara et al....
452
37,088
0
false
In both frog and mammalian skeletal muscle, the amplitude and time course of AP-evoked average increases in [Ca2+] occurring throughout multisarcomeric regions of a muscle fiber (global Ca2+ transients) have been mostly measured using fluorescence microscopy and Ca2+ indicators.
[ "Vergara et al., 1991; Vergara and DiFranco, 1992; Delbono and Stefani, 1993; Kim and Vergara, 1998a; Baylor and Hollingworth, 2003; Woods et al., 2004; Woods et al., 2005" ]
In both frog and mammalian skeletal muscle, the amplitude and time course of AP-evoked average increases in occurring throughout multisarcomeric regions of a muscle fiber have been mostly measured using fluorescence microscopy and Ca2+ indicators.
true
true
true
true
true
6,365
1
INTRODUCTION
1
Vergara et al., 1991
[ "bib46", "bib45", "bib8", "bib28", "bib1", "bib50", "bib49", "bib17", "bib39", "bib21", "bib17", "bib47", "bib12", "bib37" ]
16,735,751
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
However, due to their inherent mix of fluorescence contributions from different regions of the sarcomere, the properties of global transients do not provide information about the existence of intrasarcomeric [Ca2+] gradients.
[ "Vergara et al., 1991", "Vergara and DiFranco, 1992", "Delbono and Stefani, 1993", "Kim and Vergara, 1998a", "Baylor and Hollingworth, 2003", "Woods et al., 2004", "Woods et al., 2005", "Escobar et al., 1994", "Peachey, 1965", "Franzini-Armstrong, 1972", "Escobar et al., 1994", "Vergara et al....
225
37,089
0
false
However, due to their inherent mix of fluorescence contributions from different regions of the sarcomere, the properties of global transients do not provide information about the existence of intrasarcomeric [Ca2+] gradients.
[]
However, due to their inherent mix of fluorescence contributions from different regions of the sarcomere, the properties of global transients do not provide information about the existence of intrasarcomeric gradients.
true
true
true
true
true
6,365
1
INTRODUCTION
1
Escobar et al., 1994
[ "bib46", "bib45", "bib8", "bib28", "bib1", "bib50", "bib49", "bib17", "bib39", "bib21", "bib17", "bib47", "bib12", "bib37" ]
16,735,751
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
Detailed studies about the spatiotemporal distribution of [Ca2+] changes within a sarcomere of frog skeletal muscle fibers was obtained for the first time with a confocal spot detection technique that demonstrated that Ca2+ sources were colocalized with the Z-lines (Escobar et al., 1994) where the triads, structural as...
[ "Vergara et al., 1991", "Vergara and DiFranco, 1992", "Delbono and Stefani, 1993", "Kim and Vergara, 1998a", "Baylor and Hollingworth, 2003", "Woods et al., 2004", "Woods et al., 2005", "Escobar et al., 1994", "Peachey, 1965", "Franzini-Armstrong, 1972", "Escobar et al., 1994", "Vergara et al....
461
37,090
1
false
Detailed studies about the spatiotemporal distribution of [Ca2+] changes within a sarcomere of frog skeletal muscle fibers was obtained for the first time with a confocal spot detection technique that demonstrated that Ca2+ sources were colocalized with the Z-lines where the triads, structural assemblies consisting of ...
[ "Escobar et al., 1994", "Peachey, 1965; Franzini-Armstrong, 1972" ]
Detailed studies about the spatiotemporal distribution of changes within a sarcomere of frog skeletal muscle fibers was obtained for the first time with a confocal spot detection technique that demonstrated that Ca2+ sources were colocalized with the Z-lines where the triads, structural assemblies consisting of one T-t...
true
true
true
true
true
6,365
1
INTRODUCTION
1
Escobar et al., 1994
[ "bib46", "bib45", "bib8", "bib28", "bib1", "bib50", "bib49", "bib17", "bib39", "bib21", "bib17", "bib47", "bib12", "bib37" ]
16,735,751
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
Subsequent refinements of the spot detection methodology allowing to record localized transients at consecutive positions 200 nm apart with spatial and temporal resolutions of 0.3 μm and 30 μs, respectively, confirmed the suggestion (Escobar et al., 1994) that in frog fibers the Ca2+ release sources, though centered at...
[ "Vergara et al., 1991", "Vergara and DiFranco, 1992", "Delbono and Stefani, 1993", "Kim and Vergara, 1998a", "Baylor and Hollingworth, 2003", "Woods et al., 2004", "Woods et al., 2005", "Escobar et al., 1994", "Peachey, 1965", "Franzini-Armstrong, 1972", "Escobar et al., 1994", "Vergara et al....
510
37,091
1
false
Subsequent refinements of the spot detection methodology allowing to record localized transients at consecutive positions 200 nm apart with spatial and temporal resolutions of 0.3 μm and 30 μs, respectively, confirmed the suggestion that in frog fibers the Ca2+ release sources, though centered at the Z-lines, were broa...
[ "Escobar et al., 1994", "Vergara et al., 2001; DiFranco et al., 2002; Novo et al., 2003" ]
Subsequent refinements of the spot detection methodology allowing to record localized transients at consecutive positions 200 nm apart with spatial and temporal resolutions of 0.3 μm and 30 μs, respectively, confirmed the suggestion that in frog fibers the Ca2+ release sources, though centered at the Z-lines, were broa...
true
true
true
true
true
6,365
2
INTRODUCTION
1
Revel, 1962
[ "bib40", "bib22", "bib15", "bib33", "bib49", "bib11", "bib17", "bib32", "bib28", "bib29", "bib33", "bib24", "bib20", "bib3", "bib20", "bib23", "bib19" ]
16,735,751
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
Comparable studies of the Ca2+ release domains in mammalian muscle, though only preliminarily reported (Vergara, J.L., M. DiFranco, and D. Novo.
[ "Revel, 1962", "Franzini-Armstrong et al., 1988", "Dulhunty, 1989", "Lannergren et al., 1999", "Woods et al., 2005", "DiFranco et al., 2006", "Escobar et al., 1994", "Krolenko et al., 1995", "Kim and Vergara, 1998a", "b", "Lannergren et al., 1999", "Giannini et al., 1995", "Flucher and Franz...
144
37,092
0
false
Comparable studies of the Ca2+ release domains in mammalian muscle, though only preliminarily reported (Vergara, J.L., M. DiFranco, and D. Novo.
[]
Comparable studies of the Ca2+ release domains in mammalian muscle, though only preliminarily reported (Vergara, J.L., M. DiFranco, and D. Novo.
true
true
true
true
true
6,366
2
INTRODUCTION
1
Revel, 1962
[ "bib40", "bib22", "bib15", "bib33", "bib49", "bib11", "bib17", "bib32", "bib28", "bib29", "bib33", "bib24", "bib20", "bib3", "bib20", "bib23", "bib19" ]
16,735,751
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
82:642a), are extremely important since there are structural and molecular differences between frog and mammalian fibers that might entail disparities in the Ca2+ release process.
[ "Revel, 1962", "Franzini-Armstrong et al., 1988", "Dulhunty, 1989", "Lannergren et al., 1999", "Woods et al., 2005", "DiFranco et al., 2006", "Escobar et al., 1994", "Krolenko et al., 1995", "Kim and Vergara, 1998a", "b", "Lannergren et al., 1999", "Giannini et al., 1995", "Flucher and Franz...
179
37,093
0
false
82:642a), are extremely important since there are structural and molecular differences between frog and mammalian fibers that might entail disparities in the Ca2+ release process.
[]
82:642a), are extremely important since there are structural and molecular differences between frog and mammalian fibers that might entail disparities in the Ca2+ release process.
false
false
true
true
false
6,366
2
INTRODUCTION
1
Revel, 1962
[ "bib40", "bib22", "bib15", "bib33", "bib49", "bib11", "bib17", "bib32", "bib28", "bib29", "bib33", "bib24", "bib20", "bib3", "bib20", "bib23", "bib19" ]
16,735,751
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
Electron microscopical evidence has shown that in unstretched mammalian fibers the triads are located at both sides of the Z-line at the A-I junction of the sarcomere (Revel, 1962; Franzini-Armstrong et al., 1988; Dulhunty, 1989).
[ "Revel, 1962", "Franzini-Armstrong et al., 1988", "Dulhunty, 1989", "Lannergren et al., 1999", "Woods et al., 2005", "DiFranco et al., 2006", "Escobar et al., 1994", "Krolenko et al., 1995", "Kim and Vergara, 1998a", "b", "Lannergren et al., 1999", "Giannini et al., 1995", "Flucher and Franz...
230
37,094
0
false
Electron microscopical evidence has shown that in unstretched mammalian fibers the triads are located at both sides of the Z-line at the A-I junction of the sarcomere.
[ "Revel, 1962; Franzini-Armstrong et al., 1988; Dulhunty, 1989" ]
Electron microscopical evidence has shown that in unstretched mammalian fibers the triads are located at both sides of the Z-line at the A-I junction of the sarcomere.
true
true
true
true
true
6,366
2
INTRODUCTION
1
Revel, 1962
[ "bib40", "bib22", "bib15", "bib33", "bib49", "bib11", "bib17", "bib32", "bib28", "bib29", "bib33", "bib24", "bib20", "bib3", "bib20", "bib23", "bib19" ]
16,735,751
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
This evidence has been confirmed by in vivo fluorescence imaging of mammalian skeletal muscle fibers stained with styryl dyes (e.g., di-8-ANEPPS or RH-414), which show double rows of T-tubules per sarcomere as a distinctive feature (Lannergren et al., 1999; Woods et al., 2005; DiFranco et al., 2006), in contrast with t...
[ "Revel, 1962", "Franzini-Armstrong et al., 1988", "Dulhunty, 1989", "Lannergren et al., 1999", "Woods et al., 2005", "DiFranco et al., 2006", "Escobar et al., 1994", "Krolenko et al., 1995", "Kim and Vergara, 1998a", "b", "Lannergren et al., 1999", "Giannini et al., 1995", "Flucher and Franz...
459
37,095
0
false
This evidence has been confirmed by in vivo fluorescence imaging of mammalian skeletal muscle fibers stained with styryl dyes (e.g., di-8-ANEPPS or RH-414), which show double rows of T-tubules per sarcomere as a distinctive feature, in contrast with the single row distribution in frog fibers.
[ "Lannergren et al., 1999; Woods et al., 2005; DiFranco et al., 2006", "Escobar et al., 1994; Krolenko et al., 1995; Kim and Vergara, 1998a,b; Lannergren et al., 1999" ]
This evidence has been confirmed by in vivo fluorescence imaging of mammalian skeletal muscle fibers stained with styryl dyes, which show double rows of T-tubules per sarcomere as a distinctive feature, in contrast with the single row distribution in frog fibers.
true
true
true
true
true
6,366
2
INTRODUCTION
1
Revel, 1962
[ "bib40", "bib22", "bib15", "bib33", "bib49", "bib11", "bib17", "bib32", "bib28", "bib29", "bib33", "bib24", "bib20", "bib3", "bib20", "bib23", "bib19" ]
16,735,751
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
In addition, mammalian muscle expresses two isoforms of the ryanodine receptor (RyR1 and RyR3).
[ "Revel, 1962", "Franzini-Armstrong et al., 1988", "Dulhunty, 1989", "Lannergren et al., 1999", "Woods et al., 2005", "DiFranco et al., 2006", "Escobar et al., 1994", "Krolenko et al., 1995", "Kim and Vergara, 1998a", "b", "Lannergren et al., 1999", "Giannini et al., 1995", "Flucher and Franz...
95
37,096
0
false
In addition, mammalian muscle expresses two isoforms of the ryanodine receptor (RyR1 and RyR3).
[]
In addition, mammalian muscle expresses two isoforms of the ryanodine receptor.
true
true
true
true
true
6,366
2
INTRODUCTION
1
Revel, 1962
[ "bib40", "bib22", "bib15", "bib33", "bib49", "bib11", "bib17", "bib32", "bib28", "bib29", "bib33", "bib24", "bib20", "bib3", "bib20", "bib23", "bib19" ]
16,735,751
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
It has been reported that adult skeletal muscle displays a low RyR3/RyR1 ratio (Giannini et al., 1995; Flucher and Franzini-Armstrong, 1996); so it is believed that the Ca2+ release process depends mainly on the activity of RyR1, which is localized at junctional positions of the triads (Block et al., 1988;
[ "Revel, 1962", "Franzini-Armstrong et al., 1988", "Dulhunty, 1989", "Lannergren et al., 1999", "Woods et al., 2005", "DiFranco et al., 2006", "Escobar et al., 1994", "Krolenko et al., 1995", "Kim and Vergara, 1998a", "b", "Lannergren et al., 1999", "Giannini et al., 1995", "Flucher and Franz...
307
37,097
0
false
It has been reported that adult skeletal muscle displays a low RyR3/RyR1 ratio ; so it is believed that the Ca2+ release process depends mainly on the activity of RyR1, which is localized at junctional positions of the triads (Block et al., 1988;
[ "Giannini et al., 1995; Flucher and Franzini-Armstrong, 1996" ]
It has been reported that adult skeletal muscle displays a low RyR3/RyR1 ratio ; so it is believed that the Ca2+ release process depends mainly on the activity of RyR1, which is localized at junctional positions of the triads (Block et al., 1988;
true
true
false
true
false
6,366
2
INTRODUCTION
1
Revel, 1962
[ "bib40", "bib22", "bib15", "bib33", "bib49", "bib11", "bib17", "bib32", "bib28", "bib29", "bib33", "bib24", "bib20", "bib3", "bib20", "bib23", "bib19" ]
16,735,751
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
Flucher and Franzini-Armstrong, 1996; Franzini-Armstrong and Protasi, 1997).
[ "Revel, 1962", "Franzini-Armstrong et al., 1988", "Dulhunty, 1989", "Lannergren et al., 1999", "Woods et al., 2005", "DiFranco et al., 2006", "Escobar et al., 1994", "Krolenko et al., 1995", "Kim and Vergara, 1998a", "b", "Lannergren et al., 1999", "Giannini et al., 1995", "Flucher and Franz...
76
37,098
0
false
Flucher and Franzini-Armstrong, 1996; Franzini-Armstrong and Protasi, 1997).
[]
Flucher and Franzini-Armstrong, 1996; Franzini-Armstrong and Protasi, 1997).
true
true
true
true
true
6,366
2
INTRODUCTION
1
Felder and Franzini-Armstrong, 2002
[ "bib40", "bib22", "bib15", "bib33", "bib49", "bib11", "bib17", "bib32", "bib28", "bib29", "bib33", "bib24", "bib20", "bib3", "bib20", "bib23", "bib19" ]
16,735,751
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
This is contrary to the case of frog skeletal muscle, where similar amounts of the RyR isoforms α and β (equivalent to RyR1 and RyR3, respectively) are found, and the β isoform is distributed in extrajunctional regions of the triads (Felder and Franzini-Armstrong, 2002).
[ "Revel, 1962", "Franzini-Armstrong et al., 1988", "Dulhunty, 1989", "Lannergren et al., 1999", "Woods et al., 2005", "DiFranco et al., 2006", "Escobar et al., 1994", "Krolenko et al., 1995", "Kim and Vergara, 1998a", "b", "Lannergren et al., 1999", "Giannini et al., 1995", "Flucher and Franz...
271
37,099
1
false
This is contrary to the case of frog skeletal muscle, where similar amounts of the RyR isoforms α and β (equivalent to RyR1 and RyR3, respectively) are found, and the β isoform is distributed in extrajunctional regions of the triads.
[ "Felder and Franzini-Armstrong, 2002" ]
This is contrary to the case of frog skeletal muscle, where similar amounts of the RyR isoforms α and β are found, and the β isoform is distributed in extrajunctional regions of the triads.
true
true
true
true
true
6,366
3
INTRODUCTION
1
Denk et al., 1990
[ "bib9", "bib6", "bib48", "bib36", "bib47", "bib12" ]
16,735,751
NA|NA|NA|NA|NA|NA|NA|NA
The primary goal of the current experiments is to investigate the spatiotemporal properties of the AP-evoked Ca2+ release domains in mouse fast twitch skeletal fibers.
[ "Denk et al., 1990", "Centonze and White, 1998", "Wier et al., 2000", "Nguyen et al., 2001", "Vergara et al., 2001", "DiFranco et al., 2002" ]
167
37,100
0
false
The primary goal of the current experiments is to investigate the spatiotemporal properties of the AP-evoked Ca2+ release domains in mouse fast twitch skeletal fibers.
[]
The primary goal of the current experiments is to investigate the spatiotemporal properties of the AP-evoked Ca2+ release domains in mouse fast twitch skeletal fibers.
true
true
true
true
true
6,367
3
INTRODUCTION
1
Denk et al., 1990
[ "bib9", "bib6", "bib48", "bib36", "bib47", "bib12" ]
16,735,751
NA|NA|NA|NA|NA|NA|NA|NA
To this end, we built a custom-made two-photon laser system with laser scanning imaging (Denk et al., 1990; Centonze and White, 1998; Wier et al., 2000; Nguyen et al., 2001) and stage scanning (spot detection) capabilities (Vergara et al., 2001; DiFranco et al., 2002).
[ "Denk et al., 1990", "Centonze and White, 1998", "Wier et al., 2000", "Nguyen et al., 2001", "Vergara et al., 2001", "DiFranco et al., 2002" ]
269
37,101
0
false
To this end, we built a custom-made two-photon laser system with laser scanning imaging and stage scanning (spot detection) capabilities.
[ "Denk et al., 1990; Centonze and White, 1998; Wier et al., 2000; Nguyen et al., 2001", "Vergara et al., 2001; DiFranco et al., 2002" ]
To this end, we built a custom-made two-photon laser system with laser scanning imaging and stage scanning capabilities.
true
true
true
true
true
6,367
4
INTRODUCTION
1
Denk et al., 1990
[ "bib9", "bib14", "bib13", "bib12", "bib28", "bib29", "bib49" ]
16,735,751
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
Two-photon excitation of fluorescent molecules, achieved by using femtosecond pulsed lasers, provides an inherent optical sectioning that minimizes out-of-focus fluorescence contributions (Denk et al., 1990).
[ "Denk et al., 1990", "DiGregorio and Vergara, 1997", "DiGregorio et al., 1999", "DiFranco et al., 2002", "Kim and Vergara, 1998a", "b", "Woods et al., 2005" ]
208
37,102
1
false
Two-photon excitation of fluorescent molecules, achieved by using femtosecond pulsed lasers, provides an inherent optical sectioning that minimizes out-of-focus fluorescence contributions.
[ "Denk et al., 1990" ]
Two-photon excitation of fluorescent molecules, achieved by using femtosecond pulsed lasers, provides an inherent optical sectioning that minimizes out-of-focus fluorescence contributions.
true
true
true
true
true
6,368
4
INTRODUCTION
1
Denk et al., 1990
[ "bib9", "bib14", "bib13", "bib12", "bib28", "bib29", "bib49" ]
16,735,751
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
We used the low-affinity calcium indicator Oregon green 488 BAPTA-5N (OGB-5N), which affords minimal distortion of the kinetic features of the localized Ca2+ transients (DiGregorio and Vergara, 1997; DiGregorio et al., 1999; DiFranco et al., 2002).
[ "Denk et al., 1990", "DiGregorio and Vergara, 1997", "DiGregorio et al., 1999", "DiFranco et al., 2002", "Kim and Vergara, 1998a", "b", "Woods et al., 2005" ]
248
37,103
0
false
We used the low-affinity calcium indicator Oregon green 488 BAPTA-5N (OGB-5N), which affords minimal distortion of the kinetic features of the localized Ca2+ transients.
[ "DiGregorio and Vergara, 1997; DiGregorio et al., 1999; DiFranco et al., 2002" ]
We used the low-affinity calcium indicator Oregon green 488 BAPTA-5N (OGB-5N), which affords minimal distortion of the kinetic features of the localized Ca2+ transients.
true
true
true
true
true
6,368
4
INTRODUCTION
1
Denk et al., 1990
[ "bib9", "bib14", "bib13", "bib12", "bib28", "bib29", "bib49" ]
16,735,751
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
In addition, by labeling the T-tubules with the fluorescent indicator di-8-ANEPPS (Kim and Vergara, 1998a,b; Woods et al., 2005), we mapped the sarcomeric distribution of Ca2+ release domains to that of the T-tubules.
[ "Denk et al., 1990", "DiGregorio and Vergara, 1997", "DiGregorio et al., 1999", "DiFranco et al., 2002", "Kim and Vergara, 1998a", "b", "Woods et al., 2005" ]
217
37,104
0
false
In addition, by labeling the T-tubules with the fluorescent indicator di-8-ANEPPS, we mapped the sarcomeric distribution of Ca2+ release domains to that of the T-tubules.
[ "Kim and Vergara, 1998a,b; Woods et al., 2005" ]
In addition, by labeling the T-tubules with the fluorescent indicator di-8-ANEPPS, we mapped the sarcomeric distribution of Ca2+ release domains to that of the T-tubules.
true
true
true
true
true
6,368
4
INTRODUCTION
1
Denk et al., 1990
[ "bib9", "bib14", "bib13", "bib12", "bib28", "bib29", "bib49" ]
16,735,751
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
One of the main findings of this work is that, in AP stimulated fibers, two Ca2+ release domains per sarcomere can be observed, which flank the Z-lines, and are confined to the immediate surrounding of the junctional SR.
[ "Denk et al., 1990", "DiGregorio and Vergara, 1997", "DiGregorio et al., 1999", "DiFranco et al., 2002", "Kim and Vergara, 1998a", "b", "Woods et al., 2005" ]
220
37,105
0
false
One of the main findings of this work is that, in AP stimulated fibers, two Ca2+ release domains per sarcomere can be observed, which flank the Z-lines, and are confined to the immediate surrounding of the junctional SR.
[]
One of the main findings of this work is that, in AP stimulated fibers, two Ca2+ release domains per sarcomere can be observed, which flank the Z-lines, and are confined to the immediate surrounding of the junctional SR.
true
true
true
true
true
6,368
0
DISCUSSION
1
Escobar et al., 1994
[ "bib17", "bib13", "bib12", "bib37", "bib9", "bib6", "bib4", "bib9", "bib51", "bib4" ]
16,735,751
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
In this article we describe the properties of AP-evoked Ca2+ release domains in mouse skeletal muscle fibers measured using a custom-built two-photon laser microscope system.
[ "Escobar et al., 1994", "DiGregorio et al., 1999", "DiFranco et al., 2002", "Novo et al., 2003", "Denk et al., 1990", "Centonze and White, 1998", "Cahalan et al., 2002", "Denk et al., 1990", "Yuste and Denk, 1995", "Cahalan et al., 2002" ]
174
37,106
0
false
In this article we describe the properties of AP-evoked Ca2+ release domains in mouse skeletal muscle fibers measured using a custom-built two-photon laser microscope system.
[]
In this article we describe the properties of AP-evoked Ca2+ release domains in mouse skeletal muscle fibers measured using a custom-built two-photon laser microscope system.
true
true
true
true
true
6,369
0
DISCUSSION
1
Escobar et al., 1994
[ "bib17", "bib13", "bib12", "bib37", "bib9", "bib6", "bib4", "bib9", "bib51", "bib4" ]
16,735,751
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
This system affords important technical advances for the detection and identification of AP-evoked Ca2+ microdomains in this preparation since it was designed to combine the high spatiotemporal resolution of the spot detection method (Escobar et al., 1994; DiGregorio et al., 1999; DiFranco et al., 2002; Novo et al., 20...
[ "Escobar et al., 1994", "DiGregorio et al., 1999", "DiFranco et al., 2002", "Novo et al., 2003", "Denk et al., 1990", "Centonze and White, 1998", "Cahalan et al., 2002", "Denk et al., 1990", "Yuste and Denk, 1995", "Cahalan et al., 2002" ]
454
37,107
0
false
This system affords important technical advances for the detection and identification of AP-evoked Ca2+ microdomains in this preparation since it was designed to combine the high spatiotemporal resolution of the spot detection method with the obviously advantageous imaging capabilities of TPLSM.
[ "Escobar et al., 1994; DiGregorio et al., 1999; DiFranco et al., 2002; Novo et al., 2003", "Denk et al., 1990; Centonze and White, 1998; Cahalan et al., 2002" ]
This system affords important technical advances for the detection and identification of AP-evoked Ca2+ microdomains in this preparation since it was designed to combine the high spatiotemporal resolution of the spot detection method with the obviously advantageous imaging capabilities of TPLSM.
true
true
true
true
true
6,369
0
DISCUSSION
1
Escobar et al., 1994
[ "bib17", "bib13", "bib12", "bib37", "bib9", "bib6", "bib4", "bib9", "bib51", "bib4" ]
16,735,751
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
In other words, by switching from laser scanning mode (e.g., using the SCH in Fig.
[ "Escobar et al., 1994", "DiGregorio et al., 1999", "DiFranco et al., 2002", "Novo et al., 2003", "Denk et al., 1990", "Centonze and White, 1998", "Cahalan et al., 2002", "Denk et al., 1990", "Yuste and Denk, 1995", "Cahalan et al., 2002" ]
82
37,108
0
false
In other words, by switching from laser scanning mode (e.g., using the SCH in Fig.
[]
In other words, by switching from laser scanning mode (e.g., using the SCH in Fig.
true
true
true
true
true
6,369
0
DISCUSSION
1
Escobar et al., 1994
[ "bib17", "bib13", "bib12", "bib37", "bib9", "bib6", "bib4", "bib9", "bib51", "bib4" ]
16,735,751
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
1) to stage scanning mode (with X and Y nanotranslator motors) it was possible to alternatively acquire high resolution images of the steady-state subsarcomeric distribution of fluorescent probes (e.g., Fig.
[ "Escobar et al., 1994", "DiGregorio et al., 1999", "DiFranco et al., 2002", "Novo et al., 2003", "Denk et al., 1990", "Centonze and White, 1998", "Cahalan et al., 2002", "Denk et al., 1990", "Yuste and Denk, 1995", "Cahalan et al., 2002" ]
207
37,109
0
false
1) to stage scanning mode (with X and Y nanotranslator motors) it was possible to alternatively acquire high resolution images of the steady-state subsarcomeric distribution of fluorescent probes (e.g., Fig.
[]
1) to stage scanning mode it was possible to alternatively acquire high resolution images of the steady-state subsarcomeric distribution of fluorescent probes (e.g., Fig.
false
false
true
true
false
6,369
0
DISCUSSION
1
Escobar et al., 1994
[ "bib17", "bib13", "bib12", "bib37", "bib9", "bib6", "bib4", "bib9", "bib51", "bib4" ]
16,735,751
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
2) or position-dependent AP-evoked Ca2+ transients (e.g., Fig.
[ "Escobar et al., 1994", "DiGregorio et al., 1999", "DiFranco et al., 2002", "Novo et al., 2003", "Denk et al., 1990", "Centonze and White, 1998", "Cahalan et al., 2002", "Denk et al., 1990", "Yuste and Denk, 1995", "Cahalan et al., 2002" ]
62
37,110
0
false
2) or position-dependent AP-evoked Ca2+ transients (e.g., Fig.
[]
2) or position-dependent AP-evoked Ca2+ transients (e.g., Fig.
false
false
true
true
false
6,369
0
DISCUSSION
1
Escobar et al., 1994
[ "bib17", "bib13", "bib12", "bib37", "bib9", "bib6", "bib4", "bib9", "bib51", "bib4" ]
16,735,751
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
3) from the same live muscle fiber preparation.
[ "Escobar et al., 1994", "DiGregorio et al., 1999", "DiFranco et al., 2002", "Novo et al., 2003", "Denk et al., 1990", "Centonze and White, 1998", "Cahalan et al., 2002", "Denk et al., 1990", "Yuste and Denk, 1995", "Cahalan et al., 2002" ]
47
37,111
0
false
3) from the same live muscle fiber preparation.
[]
3) from the same live muscle fiber preparation.
false
false
true
true
false
6,369
0
DISCUSSION
1
Escobar et al., 1994
[ "bib17", "bib13", "bib12", "bib37", "bib9", "bib6", "bib4", "bib9", "bib51", "bib4" ]
16,735,751
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
Furthermore, by using a near infrared pulsed laser (Ti:Sapphire), two-photon microscopy allows for localized fluorescence detection with minimal phototoxicity (Denk et al., 1990; Yuste and Denk, 1995; Cahalan et al., 2002).
[ "Escobar et al., 1994", "DiGregorio et al., 1999", "DiFranco et al., 2002", "Novo et al., 2003", "Denk et al., 1990", "Centonze and White, 1998", "Cahalan et al., 2002", "Denk et al., 1990", "Yuste and Denk, 1995", "Cahalan et al., 2002" ]
223
37,112
0
false
Furthermore, by using a near infrared pulsed laser (Ti:Sapphire), two-photon microscopy allows for localized fluorescence detection with minimal phototoxicity.
[ "Denk et al., 1990; Yuste and Denk, 1995; Cahalan et al., 2002" ]
Furthermore, by using a near infrared pulsed laser, two-photon microscopy allows for localized fluorescence detection with minimal phototoxicity.
true
true
true
true
true
6,369
0
DISCUSSION
1
Escobar et al., 1994
[ "bib17", "bib13", "bib12", "bib37", "bib9", "bib6", "bib4", "bib9", "bib51", "bib4" ]
16,735,751
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
This latter feature is relevant for the current studies because we could demonstrate that 15 illuminating periods of ∼80 ms, required to record 15 individual AP-evoked Ca2+ transients, while maintaining the spot at the same location, did not induce detectable distortions in the signals (unpublished data).
[ "Escobar et al., 1994", "DiGregorio et al., 1999", "DiFranco et al., 2002", "Novo et al., 2003", "Denk et al., 1990", "Centonze and White, 1998", "Cahalan et al., 2002", "Denk et al., 1990", "Yuste and Denk, 1995", "Cahalan et al., 2002" ]
306
37,113
0
false
This latter feature is relevant for the current studies because we could demonstrate that 15 illuminating periods of ∼80 ms, required to record 15 individual AP-evoked Ca2+ transients, while maintaining the spot at the same location, did not induce detectable distortions in the signals (unpublished data).
[]
This latter feature is relevant for the current studies because we could demonstrate that 15 illuminating periods of ∼80 ms, required to record 15 individual AP-evoked Ca2+ transients, while maintaining the spot at the same location, did not induce detectable distortions in the signals.
true
true
true
true
true
6,369
0
DISCUSSION
1
Escobar et al., 1994
[ "bib17", "bib13", "bib12", "bib37", "bib9", "bib6", "bib4", "bib9", "bib51", "bib4" ]
16,735,751
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
Consequently, Ca2+ transients recorded from neighboring positions (even as close as 20 nm apart) along a spot scan are expected to remain unaffected by potential photodynamic damage induced by laser illumination during the acquisition of data at previous locations.
[ "Escobar et al., 1994", "DiGregorio et al., 1999", "DiFranco et al., 2002", "Novo et al., 2003", "Denk et al., 1990", "Centonze and White, 1998", "Cahalan et al., 2002", "Denk et al., 1990", "Yuste and Denk, 1995", "Cahalan et al., 2002" ]
265
37,114
0
false
Consequently, Ca2+ transients recorded from neighboring positions (even as close as 20 nm apart) along a spot scan are expected to remain unaffected by potential photodynamic damage induced by laser illumination during the acquisition of data at previous locations.
[]
Consequently, Ca2+ transients recorded from neighboring positions along a spot scan are expected to remain unaffected by potential photodynamic damage induced by laser illumination during the acquisition of data at previous locations.
true
true
true
true
true
6,369
0
DISCUSSION
1
Escobar et al., 1994
[ "bib17", "bib13", "bib12", "bib37", "bib9", "bib6", "bib4", "bib9", "bib51", "bib4" ]
16,735,751
NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA
This problem is more likely to occur in single-photon systems (either laser scanning microscopes or confocal spot detection methods) because the regions of localized illumination (at effective excitation wavelengths) are not as narrowly constrained, particularly in the Z-axis of the microscope (depth of the preparation...
[ "Escobar et al., 1994", "DiGregorio et al., 1999", "DiFranco et al., 2002", "Novo et al., 2003", "Denk et al., 1990", "Centonze and White, 1998", "Cahalan et al., 2002", "Denk et al., 1990", "Yuste and Denk, 1995", "Cahalan et al., 2002" ]
322
37,115
0
false
This problem is more likely to occur in single-photon systems (either laser scanning microscopes or confocal spot detection methods) because the regions of localized illumination (at effective excitation wavelengths) are not as narrowly constrained, particularly in the Z-axis of the microscope (depth of the preparation...
[]
This problem is more likely to occur in single-photon systems because the regions of localized illumination are not as narrowly constrained, particularly in the Z-axis of the microscope.
true
true
true
true
true
6,369