Split (1)

train · 816k rows

paragraph_index int64	sec string	p_has_citation int64	cites string	citeids list	pmid int64	cited_id string	sentences string	all_sent_cites list	sent_len int64	sentence_batch_index int64	sent_has_citation float64	qc_fail bool	cited_sentence string	cites_in_sentence list	cln_sentence string	is_cap bool	is_alpha bool	ends_wp bool	cit_qc bool	lgtm bool	__index_level_0__ int64
8	DISCUSSION	1	5	[ "bib5", "bib26", "bib27", "bib31" ]	18,710,933	pmid-15826822\|pmid-17105816\|pmid-17675488\|pmid-17119110	We have included the additional dimension of H-CDR3 repertoire-based selection along the y-axis of this figure.	[ "5", "26", "27", "31" ]	111	41,319	0	false	We have included the additional dimension of H-CDR3 repertoire-based selection along the y-axis of this figure.	[]	We have included the additional dimension of H-CDR3 repertoire-based selection along the y-axis of this figure.	true	true	true	true	true	7,122
9	DISCUSSION	0	null	null	18,710,933	null	In summary, this study uses a novel approach to study the role of BCR repertoire in B cell development and cell fate decisions in polyclonal mice.	null	146	41,320	0	false	null	null	In summary, this study uses a novel approach to study the role of BCR repertoire in B cell development and cell fate decisions in polyclonal mice.	true	true	true	true	true	7,123
9	DISCUSSION	0	null	null	18,710,933	null	The progressive skewing of the repertoire observed at each developmental step confirms that BCR–ligand interactions, and not just constitutive BCR signals, are important throughout immature and mature B cell development.	null	220	41,321	0	false	null	null	The progressive skewing of the repertoire observed at each developmental step confirms that BCR–ligand interactions, and not just constitutive BCR signals, are important throughout immature and mature B cell development.	true	true	true	true	true	7,123
9	DISCUSSION	0	null	null	18,710,933	null	Furthermore, this approach has allowed us to reconsider specific subset relationships in the BM and spleen, leading us to propose a repertoire-based bifurcation into BM and splenic development pathways and also a novel T1→MZ differentiation pathway.	null	249	41,322	0	false	null	null	Furthermore, this approach has allowed us to reconsider specific subset relationships in the BM and spleen, leading us to propose a repertoire-based bifurcation into BM and splenic development pathways and also a novel T1→MZ differentiation pathway.	true	true	true	true	true	7,123
9	DISCUSSION	0	null	null	18,710,933	null	We demonstrate that MZ and FO B subsets in the spleen and mature B cells in the BM each have distinct repertoire profiles, with the MZ exhibiting a unique preference for the restricted N− fetal-type repertoire.	null	210	41,323	0	false	null	null	We demonstrate that MZ and FO B subsets in the spleen and mature B cells in the BM each have distinct repertoire profiles, with the MZ exhibiting a unique preference for the restricted N− fetal-type repertoire.	true	true	true	true	true	7,123
0	INTRODUCTION	1	1	[ "B1", "B2", "B3", "B1 B2 B3 B4 B5 B6", "B4 B5 B6 B7 B8 B9 B10 B11 B12 B13 B14 B15 B16 B17 B18" ]	19,586,935	pmid-17554300\|pmid-17122850\|pmid-17982442\|pmid-17554300\|pmid-17122850\|pmid-17982442\|pmid-18776908\|pmid-18776909\|NA\|pmid-18776908\|pmid-18776909\|NA\|pmid-15657097\|pmid-16322765\|pmid-16024607\|pmid-16252233\|pmid-16936321\|pmid-16504045\|pmid-16809396\|pmid-16267090\|pmid-16787995\|pmid-17459966\|pmid-17189563\|pmid-18204055\|pmid-1...	Human genetic variation studies offer great promise in deciphering the genetics of complex diseases through genome-wide association studies (GWASs) (1), and copy number variation (CNV) studies (2,3), and for both types of study accurate estimation at high resolution of allelic concentration (AC), which refers to the co...	[ "1", "2", "3", "1–6", "4–18" ]	431	41,324	1	false	Human genetic variation studies offer great promise in deciphering the genetics of complex diseases through genome-wide association studies (GWASs), and copy number variation (CNV) studies, and for both types of study accurate estimation at high resolution of allelic concentration (AC), which refers to the concentratio...	[ "1", "2,3" ]	Human genetic variation studies offer great promise in deciphering the genetics of complex diseases through genome-wide association studies (GWASs), and copy number variation (CNV) studies, and for both types of study accurate estimation at high resolution of allelic concentration (AC), which refers to the concentratio...	true	true	true	true	true	7,124
0	INTRODUCTION	1	1–6	[ "B1", "B2", "B3", "B1 B2 B3 B4 B5 B6", "B4 B5 B6 B7 B8 B9 B10 B11 B12 B13 B14 B15 B16 B17 B18" ]	19,586,935	pmid-17554300\|pmid-17122850\|pmid-17982442\|pmid-17554300\|pmid-17122850\|pmid-17982442\|pmid-18776908\|pmid-18776909\|NA\|pmid-18776908\|pmid-18776909\|NA\|pmid-15657097\|pmid-16322765\|pmid-16024607\|pmid-16252233\|pmid-16936321\|pmid-16504045\|pmid-16809396\|pmid-16267090\|pmid-16787995\|pmid-17459966\|pmid-17189563\|pmid-18204055\|pmid-1...	Among current platforms, Affymetrix single-nucleotide polymorphism (SNP) arrays have been widely used for SNP genotype calling and CNV inference with low-cost (1–6).	[ "1", "2", "3", "1–6", "4–18" ]	165	41,325	1	false	Among current platforms, Affymetrix single-nucleotide polymorphism (SNP) arrays have been widely used for SNP genotype calling and CNV inference with low-cost.	[ "1–6" ]	Among current platforms, Affymetrix single-nucleotide polymorphism (SNP) arrays have been widely used for SNP genotype calling and CNV inference with low-cost.	true	true	true	true	true	7,124
0	INTRODUCTION	1	4–18	[ "B1", "B2", "B3", "B1 B2 B3 B4 B5 B6", "B4 B5 B6 B7 B8 B9 B10 B11 B12 B13 B14 B15 B16 B17 B18" ]	19,586,935	pmid-17554300\|pmid-17122850\|pmid-17982442\|pmid-17554300\|pmid-17122850\|pmid-17982442\|pmid-18776908\|pmid-18776909\|NA\|pmid-18776908\|pmid-18776909\|NA\|pmid-15657097\|pmid-16322765\|pmid-16024607\|pmid-16252233\|pmid-16936321\|pmid-16504045\|pmid-16809396\|pmid-16267090\|pmid-16787995\|pmid-17459966\|pmid-17189563\|pmid-18204055\|pmid-1...	Although numerous methods achieve high accuracy (4–18), most studies have paid little attention to the hybridization with mismatch nucleotides (HWMMN) by off-target allele sequences to the probes, which can affect the accuracy, in particular, the accuracy of annotating heterozygous SNPs.	[ "1", "2", "3", "1–6", "4–18" ]	288	41,326	1	false	Although numerous methods achieve high accuracy, most studies have paid little attention to the hybridization with mismatch nucleotides (HWMMN) by off-target allele sequences to the probes, which can affect the accuracy, in particular, the accuracy of annotating heterozygous SNPs.	[ "4–18" ]	Although numerous methods achieve high accuracy, most studies have paid little attention to the hybridization with mismatch nucleotides (HWMMN) by off-target allele sequences to the probes, which can affect the accuracy, in particular, the accuracy of annotating heterozygous SNPs.	true	true	true	true	true	7,124
0	INTRODUCTION	1	1	[ "B1", "B2", "B3", "B1 B2 B3 B4 B5 B6", "B4 B5 B6 B7 B8 B9 B10 B11 B12 B13 B14 B15 B16 B17 B18" ]	19,586,935	pmid-17554300\|pmid-17122850\|pmid-17982442\|pmid-17554300\|pmid-17122850\|pmid-17982442\|pmid-18776908\|pmid-18776909\|NA\|pmid-18776908\|pmid-18776909\|NA\|pmid-15657097\|pmid-16322765\|pmid-16024607\|pmid-16252233\|pmid-16936321\|pmid-16504045\|pmid-16809396\|pmid-16267090\|pmid-16787995\|pmid-17459966\|pmid-17189563\|pmid-18204055\|pmid-1...	In this study, we address this issue and show that HWMMN occurs in all SNP probe-sets and is non-negligible.	[ "1", "2", "3", "1–6", "4–18" ]	108	41,327	0	false	In this study, we address this issue and show that HWMMN occurs in all SNP probe-sets and is non-negligible.	[]	In this study, we address this issue and show that HWMMN occurs in all SNP probe-sets and is non-negligible.	true	true	true	true	true	7,124
0	INTRODUCTION	1	1	[ "B1", "B2", "B3", "B1 B2 B3 B4 B5 B6", "B4 B5 B6 B7 B8 B9 B10 B11 B12 B13 B14 B15 B16 B17 B18" ]	19,586,935	pmid-17554300\|pmid-17122850\|pmid-17982442\|pmid-17554300\|pmid-17122850\|pmid-17982442\|pmid-18776908\|pmid-18776909\|NA\|pmid-18776908\|pmid-18776909\|NA\|pmid-15657097\|pmid-16322765\|pmid-16024607\|pmid-16252233\|pmid-16936321\|pmid-16504045\|pmid-16809396\|pmid-16267090\|pmid-16787995\|pmid-17459966\|pmid-17189563\|pmid-18204055\|pmid-1...	Ignoring it may lead to biased results and inaccuracy, whereas careful modeling of HWMMN leads to accurate copy number (CN) estimation and SNP genotype calling.	[ "1", "2", "3", "1–6", "4–18" ]	160	41,328	0	false	Ignoring it may lead to biased results and inaccuracy, whereas careful modeling of HWMMN leads to accurate copy number (CN) estimation and SNP genotype calling.	[]	Ignoring it may lead to biased results and inaccuracy, whereas careful modeling of HWMMN leads to accurate copy number (CN) estimation and SNP genotype calling.	true	true	true	true	true	7,124
1	INTRODUCTION	1	19–22	[ "B19 B20 B21 B22", "B20" ]	19,586,935	pmid-17169993\|pmid-12794640\|pmid-16723429\|pmid-12808153\|pmid-12794640\|pmid-16322765\|pmid-17169993\|pmid-12794640\|pmid-11134512	Extensive studies have shown that probe intensities are subject to large variability, and depend on not only the quantities of allelic target sequences, but also the probe-binding affinity.	[ "19–22", "20" ]	189	41,329	0	false	Extensive studies have shown that probe intensities are subject to large variability, and depend on not only the quantities of allelic target sequences, but also the probe-binding affinity.	[]	Extensive studies have shown that probe intensities are subject to large variability, and depend on not only the quantities of allelic target sequences, but also the probe-binding affinity.	true	true	true	true	true	7,125
1	INTRODUCTION	1	19–22	[ "B19 B20 B21 B22", "B20" ]	19,586,935	pmid-17169993\|pmid-12794640\|pmid-16723429\|pmid-12808153\|pmid-12794640\|pmid-16322765\|pmid-17169993\|pmid-12794640\|pmid-11134512	Previously, the perfect match binding of probes to their target sequences has been quantitatively characterized with probe sequence through a positional-dependent-nearest-neighbor (PDNN) or similar model (19–22).	[ "19–22", "20" ]	212	41,330	1	false	Previously, the perfect match binding of probes to their target sequences has been quantitatively characterized with probe sequence through a positional-dependent-nearest-neighbor (PDNN) or similar model.	[ "19–22" ]	Previously, the perfect match binding of probes to their target sequences has been quantitatively characterized with probe sequence through a positional-dependent-nearest-neighbor (PDNN) or similar model.	true	true	true	true	true	7,125
1	INTRODUCTION	1	20	[ "B19 B20 B21 B22", "B20" ]	19,586,935	pmid-17169993\|pmid-12794640\|pmid-16723429\|pmid-12808153\|pmid-12794640\|pmid-16322765\|pmid-17169993\|pmid-12794640\|pmid-11134512	Although the PDNN provides a model for probe intensity in perfect match binding and nonspecific binding (20), HWMMN has not been studied thoroughly.	[ "19–22", "20" ]	148	41,331	1	false	Although the PDNN provides a model for probe intensity in perfect match binding and nonspecific binding, HWMMN has not been studied thoroughly.	[ "20" ]	Although the PDNN provides a model for probe intensity in perfect match binding and nonspecific binding, HWMMN has not been studied thoroughly.	true	true	true	true	true	7,125
1	INTRODUCTION	1	19–22	[ "B19 B20 B21 B22", "B20" ]	19,586,935	pmid-17169993\|pmid-12794640\|pmid-16723429\|pmid-12808153\|pmid-12794640\|pmid-16322765\|pmid-17169993\|pmid-12794640\|pmid-11134512	We illustrate in this paper that proper modeling of HWMMN can significantly improve the accuracy of AC estimation.	[ "19–22", "20" ]	114	41,332	0	false	We illustrate in this paper that proper modeling of HWMMN can significantly improve the accuracy of AC estimation.	[]	We illustrate in this paper that proper modeling of HWMMN can significantly improve the accuracy of AC estimation.	true	true	true	true	true	7,125
2	INTRODUCTION	1	19	[ "B19", "B20" ]	19,586,935	pmid-17169993\|pmid-12794640\|pmid-17597783\|pmid-17597776	To characterize the HWMMN, we studied the physico-chemical properties of sequence binding and generalized the PDNN model to a generalized PDNN (GPDNN) model for the binding free energy involving both perfect match hybridization and HWMMN.	[ "19", "20" ]	238	41,333	0	false	To characterize the HWMMN, we studied the physico-chemical properties of sequence binding and generalized the PDNN model to a generalized PDNN (GPDNN) model for the binding free energy involving both perfect match hybridization and HWMMN.	[]	To characterize the HWMMN, we studied the physico-chemical properties of sequence binding and generalized the PDNN model to a generalized PDNN (GPDNN) model for the binding free energy involving both perfect match hybridization and HWMMN.	true	true	true	true	true	7,126
2	INTRODUCTION	1	19	[ "B19", "B20" ]	19,586,935	pmid-17169993\|pmid-12794640\|pmid-17597783\|pmid-17597776	We then developed a probe intensity composite representation (PICR) model based on a Langmuir-like adsorption principle (19,20) and the GPDNN.	[ "19", "20" ]	142	41,334	0	false	We then developed a probe intensity composite representation (PICR) model based on a Langmuir-like adsorption principle and the GPDNN.	[ "19,20" ]	We then developed a probe intensity composite representation (PICR) model based on a Langmuir-like adsorption principle and the GPDNN.	true	true	true	true	true	7,126
2	INTRODUCTION	1	19	[ "B19", "B20" ]	19,586,935	pmid-17169993\|pmid-12794640\|pmid-17597783\|pmid-17597776	In PICR, the intensities of each probe of a given SNP are decomposed into four terms: two terms for specific binding of the two alleles, one term for nonspecific binding and an error term.	[ "19", "20" ]	188	41,335	0	false	In PICR, the intensities of each probe of a given SNP are decomposed into four terms: two terms for specific binding of the two alleles, one term for nonspecific binding and an error term.	[]	In PICR, the intensities of each probe of a given SNP are decomposed into four terms: two terms for specific binding of the two alleles, one term for nonspecific binding and an error term.	true	true	true	true	true	7,126
2	INTRODUCTION	1	19	[ "B19", "B20" ]	19,586,935	pmid-17169993\|pmid-12794640\|pmid-17597783\|pmid-17597776	The specific binding depends on the ACs of both alleles and the binding affinity, and the latter can be calculated with the GPDNN model.	[ "19", "20" ]	136	41,336	0	false	The specific binding depends on the ACs of both alleles and the binding affinity, and the latter can be calculated with the GPDNN model.	[]	The specific binding depends on the ACs of both alleles and the binding affinity, and the latter can be calculated with the GPDNN model.	true	true	true	true	true	7,126
2	INTRODUCTION	1	19	[ "B19", "B20" ]	19,586,935	pmid-17169993\|pmid-12794640\|pmid-17597783\|pmid-17597776	The parameters of the GPDNN model can be trained with only one array, and the PICR leads to a regression model that yields consistent estimation of ACs by regressing the probe intensities of the probe set for a given SNP on the binding affinity.	[ "19", "20" ]	245	41,337	0	false	The parameters of the GPDNN model can be trained with only one array, and the PICR leads to a regression model that yields consistent estimation of ACs by regressing the probe intensities of the probe set for a given SNP on the binding affinity.	[]	The parameters of the GPDNN model can be trained with only one array, and the PICR leads to a regression model that yields consistent estimation of ACs by regressing the probe intensities of the probe set for a given SNP on the binding affinity.	true	true	true	true	true	7,126
3	INTRODUCTION	0	null	null	19,586,935	null	The PICR has the following key features.	null	40	41,338	0	false	null	null	The PICR has the following key features.	true	true	true	true	true	7,127
3	INTRODUCTION	0	null	null	19,586,935	null	It (i) utilizes probe sequence information, which is invariant and independent of particular samples, and thus only requires a single array for model parameter training; (ii) applies to small sample studies and cross-laboratory studies as a consequence of accurate modeling of DNA sequence binding through the physico-ch...	null	800	41,339	0	false	null	null	It (i) utilizes probe sequence information, which is invariant and independent of particular samples, and thus only requires a single array for model parameter training; (ii) applies to small sample studies and cross-laboratory studies as a consequence of accurate modeling of DNA sequence binding through the physico-ch...	true	true	true	true	true	7,127
0	DISCUSSION	1	18	[ "B18", "B25", "B26" ]	19,586,935	pmid-17554300\|pmid-17122850\|pmid-17982442\|pmid-17554300\|pmid-17122850\|pmid-17982442\|pmid-18776908\|pmid-18776909\|NA\|pmid-18776908\|pmid-18776909\|NA\|pmid-15657097\|pmid-16322765\|pmid-16024607\|pmid-16252233\|pmid-16936321\|pmid-16504045\|pmid-16809396\|pmid-16267090\|pmid-16787995\|pmid-17459966\|pmid-17189563\|pmid-18204055\|pmid-1...	Hybridization with mismatch nucleotides by off-target sequences to array probes has been noticed to decrease the accuracy of probe intensity-based CN estimation in various platforms of microarrays (18,25,26).	[ "18", "25", "26" ]	208	41,340	0	false	Hybridization with mismatch nucleotides by off-target sequences to array probes has been noticed to decrease the accuracy of probe intensity-based CN estimation in various platforms of microarrays.	[ "18,25,26" ]	Hybridization with mismatch nucleotides by off-target sequences to array probes has been noticed to decrease the accuracy of probe intensity-based CN estimation in various platforms of microarrays.	true	true	true	true	true	7,128
0	DISCUSSION	1	18	[ "B18", "B25", "B26" ]	19,586,935	pmid-17554300\|pmid-17122850\|pmid-17982442\|pmid-17554300\|pmid-17122850\|pmid-17982442\|pmid-18776908\|pmid-18776909\|NA\|pmid-18776908\|pmid-18776909\|NA\|pmid-15657097\|pmid-16322765\|pmid-16024607\|pmid-16252233\|pmid-16936321\|pmid-16504045\|pmid-16809396\|pmid-16267090\|pmid-16787995\|pmid-17459966\|pmid-17189563\|pmid-18204055\|pmid-1...	Correct modeling of HWMMN is thus critical and can improve the accuracy of copy number estimation.	[ "18", "25", "26" ]	98	41,341	0	false	Correct modeling of HWMMN is thus critical and can improve the accuracy of copy number estimation.	[]	Correct modeling of HWMMN is thus critical and can improve the accuracy of copy number estimation.	true	true	true	true	true	7,128
0	DISCUSSION	1	18	[ "B18", "B25", "B26" ]	19,586,935	pmid-17554300\|pmid-17122850\|pmid-17982442\|pmid-17554300\|pmid-17122850\|pmid-17982442\|pmid-18776908\|pmid-18776909\|NA\|pmid-18776908\|pmid-18776909\|NA\|pmid-15657097\|pmid-16322765\|pmid-16024607\|pmid-16252233\|pmid-16936321\|pmid-16504045\|pmid-16809396\|pmid-16267090\|pmid-16787995\|pmid-17459966\|pmid-17189563\|pmid-18204055\|pmid-1...	In this work, we observed a strong effect of HWMMN and have provided a quantitative characterization.	[ "18", "25", "26" ]	101	41,342	0	false	In this work, we observed a strong effect of HWMMN and have provided a quantitative characterization.	[]	In this work, we observed a strong effect of HWMMN and have provided a quantitative characterization.	true	true	true	true	true	7,128
0	DISCUSSION	1	18	[ "B18", "B25", "B26" ]	19,586,935	pmid-17554300\|pmid-17122850\|pmid-17982442\|pmid-17554300\|pmid-17122850\|pmid-17982442\|pmid-18776908\|pmid-18776909\|NA\|pmid-18776908\|pmid-18776909\|NA\|pmid-15657097\|pmid-16322765\|pmid-16024607\|pmid-16252233\|pmid-16936321\|pmid-16504045\|pmid-16809396\|pmid-16267090\|pmid-16787995\|pmid-17459966\|pmid-17189563\|pmid-18204055\|pmid-1...	We studied oligonucleotide sequence binding through binding free energy with a GPDNN model and binding affinity, based on Zhang's affinity function, and characterized probe intensities in both perfect match hybridization and HWMMN through the PICR model.	[ "18", "25", "26" ]	254	41,343	0	false	We studied oligonucleotide sequence binding through binding free energy with a GPDNN model and binding affinity, based on Zhang's affinity function, and characterized probe intensities in both perfect match hybridization and HWMMN through the PICR model.	[]	We studied oligonucleotide sequence binding through binding free energy with a GPDNN model and binding affinity, based on Zhang's affinity function, and characterized probe intensities in both perfect match hybridization and HWMMN through the PICR model.	true	true	true	true	true	7,128
0	DISCUSSION	1	18	[ "B18", "B25", "B26" ]	19,586,935	pmid-17554300\|pmid-17122850\|pmid-17982442\|pmid-17554300\|pmid-17122850\|pmid-17982442\|pmid-18776908\|pmid-18776909\|NA\|pmid-18776908\|pmid-18776909\|NA\|pmid-15657097\|pmid-16322765\|pmid-16024607\|pmid-16252233\|pmid-16936321\|pmid-16504045\|pmid-16809396\|pmid-16267090\|pmid-16787995\|pmid-17459966\|pmid-17189563\|pmid-18204055\|pmid-1...	We then developed a method of AC estimation based on the PICR through a statistical regression.	[ "18", "25", "26" ]	95	41,344	0	false	We then developed a method of AC estimation based on the PICR through a statistical regression.	[]	We then developed a method of AC estimation based on the PICR through a statistical regression.	true	true	true	true	true	7,128
0	DISCUSSION	1	18	[ "B18", "B25", "B26" ]	19,586,935	pmid-17554300\|pmid-17122850\|pmid-17982442\|pmid-17554300\|pmid-17122850\|pmid-17982442\|pmid-18776908\|pmid-18776909\|NA\|pmid-18776908\|pmid-18776909\|NA\|pmid-15657097\|pmid-16322765\|pmid-16024607\|pmid-16252233\|pmid-16936321\|pmid-16504045\|pmid-16809396\|pmid-16267090\|pmid-16787995\|pmid-17459966\|pmid-17189563\|pmid-18204055\|pmid-1...	We further developed a genotype-calling method based on the estimated ACs from the PICR.	[ "18", "25", "26" ]	88	41,345	0	false	We further developed a genotype-calling method based on the estimated ACs from the PICR.	[]	We further developed a genotype-calling method based on the estimated ACs from the PICR.	true	true	true	true	true	7,128
0	DISCUSSION	1	18	[ "B18", "B25", "B26" ]	19,586,935	pmid-17554300\|pmid-17122850\|pmid-17982442\|pmid-17554300\|pmid-17122850\|pmid-17982442\|pmid-18776908\|pmid-18776909\|NA\|pmid-18776908\|pmid-18776909\|NA\|pmid-15657097\|pmid-16322765\|pmid-16024607\|pmid-16252233\|pmid-16936321\|pmid-16504045\|pmid-16809396\|pmid-16267090\|pmid-16787995\|pmid-17459966\|pmid-17189563\|pmid-18204055\|pmid-1...	The consistent accuracy of our AC-based genotype-calling method across different laboratories and different array platforms suggests that the PICR accurately characterizes the complex oligonucleotide sequence hybridization (see Figures 1 and S1) and yields nearly unbiased estimation of AC.	[ "18", "25", "26" ]	290	41,346	0	false	The consistent accuracy of our AC-based genotype-calling method across different laboratories and different array platforms suggests that the PICR accurately characterizes the complex oligonucleotide sequence hybridization (see Figures 1 and S1) and yields nearly unbiased estimation of AC.	[]	The consistent accuracy of our AC-based genotype-calling method across different laboratories and different array platforms suggests that the PICR accurately characterizes the complex oligonucleotide sequence hybridization and yields nearly unbiased estimation of AC.	true	true	true	true	true	7,128
1	DISCUSSION	1	8	[ "B8", "B19", "B20", "B27" ]	19,586,935	pmid-17169993\|pmid-12794640\|pmid-16723429\|pmid-12808153\|pmid-12794640\|pmid-16322765\|pmid-17169993\|pmid-12794640\|pmid-11134512	Former belief has held that perfect match probe intensities are proportional to the CNs, and has led to their use as a surrogate in many studies.	[ "8", "19", "20", "27" ]	145	41,347	0	false	Former belief has held that perfect match probe intensities are proportional to the CNs, and has led to their use as a surrogate in many studies.	[]	Former belief has held that perfect match probe intensities are proportional to the CNs, and has led to their use as a surrogate in many studies.	true	true	true	true	true	7,129
1	DISCUSSION	1	8	[ "B8", "B19", "B20", "B27" ]	19,586,935	pmid-17169993\|pmid-12794640\|pmid-16723429\|pmid-12808153\|pmid-12794640\|pmid-16322765\|pmid-17169993\|pmid-12794640\|pmid-11134512	However, this notion has been questioned for its accuracy, and a correction has been suggested using the CN and probe-binding affinity (8,19,20,27).	[ "8", "19", "20", "27" ]	148	41,348	0	false	However, this notion has been questioned for its accuracy, and a correction has been suggested using the CN and probe-binding affinity.	[ "8,19,20,27" ]	However, this notion has been questioned for its accuracy, and a correction has been suggested using the CN and probe-binding affinity.	true	true	true	true	true	7,129
1	DISCUSSION	1	8	[ "B8", "B19", "B20", "B27" ]	19,586,935	pmid-17169993\|pmid-12794640\|pmid-16723429\|pmid-12808153\|pmid-12794640\|pmid-16322765\|pmid-17169993\|pmid-12794640\|pmid-11134512	In fact, the PICR is the first model that rigorously formulates the relationship of intensities among perfect match and ‘mismatch’ probes with AC, sequence-specific binding affinity and background nonspecific binding.	[ "8", "19", "20", "27" ]	217	41,349	0	false	In fact, the PICR is the first model that rigorously formulates the relationship of intensities among perfect match and ‘mismatch’ probes with AC, sequence-specific binding affinity and background nonspecific binding.	[]	In fact, the PICR is the first model that rigorously formulates the relationship of intensities among perfect match and ‘mismatch’ probes with AC, sequence-specific binding affinity and background nonspecific binding.	true	true	true	true	true	7,129
1	DISCUSSION	1	8	[ "B8", "B19", "B20", "B27" ]	19,586,935	pmid-17169993\|pmid-12794640\|pmid-16723429\|pmid-12808153\|pmid-12794640\|pmid-16322765\|pmid-17169993\|pmid-12794640\|pmid-11134512	More importantly, the PICR potentially provides a general framework to uncover the hidden and biologically meaningful relative ACs by transforming noisy probe intensity data into unbiased estimation of relative AC data, which can then be used for subsequent analysis, such as genotype calling, as shown in this paper.	[ "8", "19", "20", "27" ]	317	41,350	0	false	More importantly, the PICR potentially provides a general framework to uncover the hidden and biologically meaningful relative ACs by transforming noisy probe intensity data into unbiased estimation of relative AC data, which can then be used for subsequent analysis, such as genotype calling, as shown in this paper.	[]	More importantly, the PICR potentially provides a general framework to uncover the hidden and biologically meaningful relative ACs by transforming noisy probe intensity data into unbiased estimation of relative AC data, which can then be used for subsequent analysis, such as genotype calling, as shown in this paper.	true	true	true	true	true	7,129
2	DISCUSSION	1	28	[ "B28", "B29" ]	19,586,935	pmid-17169993\|pmid-12794640\|pmid-17597783\|pmid-17597776	DNA CN estimation is essential for human genetic variation studies.	[ "28", "29" ]	67	41,351	0	false	DNA CN estimation is essential for human genetic variation studies.	[]	DNA CN estimation is essential for human genetic variation studies.	true	true	true	true	true	7,130
2	DISCUSSION	1	28	[ "B28", "B29" ]	19,586,935	pmid-17169993\|pmid-12794640\|pmid-17597783\|pmid-17597776	In particular, accurate CN estimation and genotype calling play a critical role in CNV studies, in which CNV detection becomes more challenging with the growing number of microarray platforms (28,29).	[ "28", "29" ]	200	41,352	0	false	In particular, accurate CN estimation and genotype calling play a critical role in CNV studies, in which CNV detection becomes more challenging with the growing number of microarray platforms.	[ "28,29" ]	In particular, accurate CN estimation and genotype calling play a critical role in CNV studies, in which CNV detection becomes more challenging with the growing number of microarray platforms.	true	true	true	true	true	7,130
2	DISCUSSION	1	28	[ "B28", "B29" ]	19,586,935	pmid-17169993\|pmid-12794640\|pmid-17597783\|pmid-17597776	While most CNV studies depend on genotype information and require predetermination or simultaneous determination of SNP genotypes, many rely on large sample multiarray training, and therefore may not be suitable for cross-laboratory and small sample studies, particularly so if the given SNP is strongly associated with ...	[ "28", "29" ]	346	41,353	0	false	While most CNV studies depend on genotype information and require predetermination or simultaneous determination of SNP genotypes, many rely on large sample multiarray training, and therefore may not be suitable for cross-laboratory and small sample studies, particularly so if the given SNP is strongly associated with ...	[]	While most CNV studies depend on genotype information and require predetermination or simultaneous determination of SNP genotypes, many rely on large sample multiarray training, and therefore may not be suitable for cross-laboratory and small sample studies, particularly so if the given SNP is strongly associated with ...	true	true	true	true	true	7,130
2	DISCUSSION	1	28	[ "B28", "B29" ]	19,586,935	pmid-17169993\|pmid-12794640\|pmid-17597783\|pmid-17597776	Since large-scale genome-wide studies often involve collaboration among laboratories, the development of robust methods of CN estimation becomes crucial.	[ "28", "29" ]	153	41,354	0	false	Since large-scale genome-wide studies often involve collaboration among laboratories, the development of robust methods of CN estimation becomes crucial.	[]	Since large-scale genome-wide studies often involve collaboration among laboratories, the development of robust methods of CN estimation becomes crucial.	true	true	true	true	true	7,130
3	DISCUSSION	0	null	null	19,586,935	null	Across-array normalization has been widely used in microarray studies to remove the variability from artifacts in array processes that confound biological differences.	null	167	41,355	0	false	null	null	Across-array normalization has been widely used in microarray studies to remove the variability from artifacts in array processes that confound biological differences.	true	true	true	true	true	7,131
3	DISCUSSION	0	null	null	19,586,935	null	However, this practice tends to introduce undesired variability into SNP genotyping, in that an individual's genotype then depends on the data of other individuals, irrespective of the fact that full individual information is available in one single array.	null	256	41,356	0	false	null	null	However, this practice tends to introduce undesired variability into SNP genotyping, in that an individual's genotype then depends on the data of other individuals, irrespective of the fact that full individual information is available in one single array.	true	true	true	true	true	7,131
3	DISCUSSION	0	null	null	19,586,935	null	Our AC-based genotype-calling method through the PICR does not require across-array normalization because this variability is modeled by the intercept, and consequently does not affect the estimation of the relative values of the ACs NA and NB for any given SNP within the same array.	null	284	41,357	0	false	null	null	Our AC-based genotype-calling method through the PICR does not require across-array normalization because this variability is modeled by the intercept, and consequently does not affect the estimation of the relative values of the ACs NA and NB for any given SNP within the same array.	true	true	true	true	true	7,131
3	DISCUSSION	0	null	null	19,586,935	null	Therefore, an SNP genotype is fully determined by the individual's data alone.	null	78	41,358	0	false	null	null	Therefore, an SNP genotype is fully determined by the individual's data alone.	true	true	true	true	true	7,131
4	DISCUSSION	1	30	[ "B30", "B31", "B31" ]	19,586,935	pmid-18784189\|pmid-17961237\|pmid-17961237	Recent studies on the genome-wide CNVs have identified genomic wave—a special pattern in normalized intensities that presents spatial autocorrelation along the chromosomes (30,31).	[ "30", "31", "31" ]	180	41,359	0	false	Recent studies on the genome-wide CNVs have identified genomic wave—a special pattern in normalized intensities that presents spatial autocorrelation along the chromosomes.	[ "30,31" ]	Recent studies on the genome-wide CNVs have identified genomic wave—a special pattern in normalized intensities that presents spatial autocorrelation along the chromosomes.	true	true	true	true	true	7,132
4	DISCUSSION	1	30	[ "B30", "B31", "B31" ]	19,586,935	pmid-18784189\|pmid-17961237\|pmid-17961237	It has been shown that genomic wave is observed consistently across array media (CGH arrays, Affymetrix arrays and Illumina arrays), and is highly correlated with the GC content of the genomic segment.	[ "30", "31", "31" ]	201	41,360	0	false	It has been shown that genomic wave is observed consistently across array media (CGH arrays, Affymetrix arrays and Illumina arrays), and is highly correlated with the GC content of the genomic segment.	[]	It has been shown that genomic wave is observed consistently across array media (CGH arrays, Affymetrix arrays and Illumina arrays), and is highly correlated with the GC content of the genomic segment.	true	true	true	true	true	7,132
4	DISCUSSION	1	31	[ "B30", "B31", "B31" ]	19,586,935	pmid-18784189\|pmid-17961237\|pmid-17961237	Furthermore, adjustment for genomic wave in the CNV algorithms improves the performance of CNV detection (31).	[ "30", "31", "31" ]	110	41,361	1	false	Furthermore, adjustment for genomic wave in the CNV algorithms improves the performance of CNV detection.	[ "31" ]	Furthermore, adjustment for genomic wave in the CNV algorithms improves the performance of CNV detection.	true	true	true	true	true	7,132
4	DISCUSSION	1	30	[ "B30", "B31", "B31" ]	19,586,935	pmid-18784189\|pmid-17961237\|pmid-17961237	Following a reviewer's suggestion, we examined the effect of the genomic wave artifact through the PICR model and observed the genomic wave in the background term of the PICR, positively correlated with the GC content through the 15 HapMap Nsp arrays (data not shown).	[ "30", "31", "31" ]	268	41,362	0	false	Following a reviewer's suggestion, we examined the effect of the genomic wave artifact through the PICR model and observed the genomic wave in the background term of the PICR, positively correlated with the GC content through the 15 HapMap Nsp arrays (data not shown).	[]	Following a reviewer's suggestion, we examined the effect of the genomic wave artifact through the PICR model and observed the genomic wave in the background term of the PICR, positively correlated with the GC content through the 15 HapMap Nsp arrays (data not shown).	true	true	true	true	true	7,132
4	DISCUSSION	1	30	[ "B30", "B31", "B31" ]	19,586,935	pmid-18784189\|pmid-17961237\|pmid-17961237	Since genomic wave is a complicated phenomenon, we believe more work needs to be done to study it with the PICR model.	[ "30", "31", "31" ]	118	41,363	0	false	Since genomic wave is a complicated phenomenon, we believe more work needs to be done to study it with the PICR model.	[]	Since genomic wave is a complicated phenomenon, we believe more work needs to be done to study it with the PICR model.	true	true	true	true	true	7,132
5	DISCUSSION	1	4	[ "B4", "B5", "B1" ]	19,586,935	pmid-18776908\|pmid-18776909\|pmid-17554300	Affymetrix SNP 6.0 arrays have been launched to enter the market and contain more than 906 600 SNPs and more than 946 000 probes for the detection of CNVs (4,5).	[ "4", "5", "1" ]	161	41,364	0	false	Affymetrix SNP 6.0 arrays have been launched to enter the market and contain more than 906 600 SNPs and more than 946 000 probes for the detection of CNVs.	[ "4,5" ]	Affymetrix SNP 6.0 arrays have been launched to enter the market and contain more than 906 600 SNPs and more than 946 000 probes for the detection of CNVs.	true	true	true	true	true	7,133
5	DISCUSSION	1	4	[ "B4", "B5", "B1" ]	19,586,935	pmid-18776908\|pmid-18776909\|pmid-17554300	Although this array has dropped the mismatch probes and usually has six perfect match probe pairs for each SNP, the distortion of HWMMN as summarized above still remains as a major challenge.	[ "4", "5", "1" ]	191	41,365	0	false	Although this array has dropped the mismatch probes and usually has six perfect match probe pairs for each SNP, the distortion of HWMMN as summarized above still remains as a major challenge.	[]	Although this array has dropped the mismatch probes and usually has six perfect match probe pairs for each SNP, the distortion of HWMMN as summarized above still remains as a major challenge.	true	true	true	true	true	7,133
5	DISCUSSION	1	4	[ "B4", "B5", "B1" ]	19,586,935	pmid-18776908\|pmid-18776909\|pmid-17554300	We have found that estimating the background term with the nonspecific-binding hybridization of the PDNN model makes the PICR work well (data not shown).	[ "4", "5", "1" ]	153	41,366	0	false	We have found that estimating the background term with the nonspecific-binding hybridization of the PDNN model makes the PICR work well (data not shown).	[]	We have found that estimating the background term with the nonspecific-binding hybridization of the PDNN model makes the PICR work well (data not shown).	true	true	true	true	true	7,133
5	DISCUSSION	1	4	[ "B4", "B5", "B1" ]	19,586,935	pmid-18776908\|pmid-18776909\|pmid-17554300	With the assistance of proper statistical techniques, the PICR is expected to provide an alternative method for accurate CN estimation and SNP genotype calling for SNP 6.0 arrays without requiring a relatively large number of arrays for genotype calling.	[ "4", "5", "1" ]	254	41,367	0	false	With the assistance of proper statistical techniques, the PICR is expected to provide an alternative method for accurate CN estimation and SNP genotype calling for SNP 6.0 arrays without requiring a relatively large number of arrays for genotype calling.	[]	With the assistance of proper statistical techniques, the PICR is expected to provide an alternative method for accurate CN estimation and SNP genotype calling for SNP 6.0 arrays without requiring a relatively large number of arrays for genotype calling.	true	true	true	true	true	7,133
5	DISCUSSION	1	1	[ "B4", "B5", "B1" ]	19,586,935	pmid-18776908\|pmid-18776909\|pmid-17554300	Furthermore, the Affymetrix GeneChip 500K arrays have been used in a number of large-scale GWASs, including the Wellcome Trust GWAS on seven common disorders (1).	[ "4", "5", "1" ]	162	41,368	1	false	Furthermore, the Affymetrix GeneChip 500K arrays have been used in a number of large-scale GWASs, including the Wellcome Trust GWAS on seven common disorders.	[ "1" ]	Furthermore, the Affymetrix GeneChip 500K arrays have been used in a number of large-scale GWASs, including the Wellcome Trust GWAS on seven common disorders.	true	true	true	true	true	7,133
5	DISCUSSION	1	4	[ "B4", "B5", "B1" ]	19,586,935	pmid-18776908\|pmid-18776909\|pmid-17554300	Given the large scale of these studies, the data obtained with 500K arrays will continue to remain an important resource for studies on human diseases, and the PICR will remain a viable approach to the studies.	[ "4", "5", "1" ]	210	41,369	0	false	Given the large scale of these studies, the data obtained with 500K arrays will continue to remain an important resource for studies on human diseases, and the PICR will remain a viable approach to the studies.	[]	Given the large scale of these studies, the data obtained with 500K arrays will continue to remain an important resource for studies on human diseases, and the PICR will remain a viable approach to the studies.	true	true	true	true	true	7,133
5	DISCUSSION	1	4	[ "B4", "B5", "B1" ]	19,586,935	pmid-18776908\|pmid-18776909\|pmid-17554300	We anticipate that the PICR may provide a new tool for further mining the GWAS data to produce more biological findings.	[ "4", "5", "1" ]	120	41,370	0	false	We anticipate that the PICR may provide a new tool for further mining the GWAS data to produce more biological findings.	[]	We anticipate that the PICR may provide a new tool for further mining the GWAS data to produce more biological findings.	true	true	true	true	true	7,133
0	INTRODUCTION	1	Mohler	[ "B100", "B73", "B41", "B57", "B34", "B131", "B88", "B102", "B103", "B66", "B27", "B60", "B64", "B91", "B1", "B64", "B139", "B75", "B60", "B136", "B4", "B74", "B82", "B112" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	Membrane fusion is among the most fundamental and tightly controlled processes in life.	[ "Mohler ", "Jahn ", "Earp ", "Gruenbaum ", "Dechat ", "Taimen ", "Lohka and Masui, 1983", "Newport, 1987", "Newport and Dunphy, 1992", "Higa ", "D'Angelo and Hetzer, 2006", "Harel ", "Hetzer ", "Macaulay and Forbes, 1996", "Anderson and Hetzer, 2007", "Hetzer ", "Zhang and Clarke, 20...	87	41,371	0	false	Membrane fusion is among the most fundamental and tightly controlled processes in life.	[]	Membrane fusion is among the most fundamental and tightly controlled processes in life.	true	true	true	true	true	7,134
0	INTRODUCTION	1	Mohler	[ "B100", "B73", "B41", "B57", "B34", "B131", "B88", "B102", "B103", "B66", "B27", "B60", "B64", "B91", "B1", "B64", "B139", "B75", "B60", "B136", "B4", "B74", "B82", "B112" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	Membranes merge during intracellular trafficking, organelle biogenesis, tissue formation, fertilization, and viral infection (Mohler et al., 2002; Jahn et al., 2003; Earp et al., 2005).	[ "Mohler ", "Jahn ", "Earp ", "Gruenbaum ", "Dechat ", "Taimen ", "Lohka and Masui, 1983", "Newport, 1987", "Newport and Dunphy, 1992", "Higa ", "D'Angelo and Hetzer, 2006", "Harel ", "Hetzer ", "Macaulay and Forbes, 1996", "Anderson and Hetzer, 2007", "Hetzer ", "Zhang and Clarke, 20...	185	41,372	0	false	Membranes merge during intracellular trafficking, organelle biogenesis, tissue formation, fertilization, and viral infection.	[ "Mohler et al., 2002; Jahn et al., 2003; Earp et al., 2005" ]	Membranes merge during intracellular trafficking, organelle biogenesis, tissue formation, fertilization, and viral infection.	true	true	true	true	true	7,134
0	INTRODUCTION	1	Mohler	[ "B100", "B73", "B41", "B57", "B34", "B131", "B88", "B102", "B103", "B66", "B27", "B60", "B64", "B91", "B1", "B64", "B139", "B75", "B60", "B136", "B4", "B74", "B82", "B112" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	The formation of the eukaryotic nuclear envelope (NE) also requires membrane fusion events.	[ "Mohler ", "Jahn ", "Earp ", "Gruenbaum ", "Dechat ", "Taimen ", "Lohka and Masui, 1983", "Newport, 1987", "Newport and Dunphy, 1992", "Higa ", "D'Angelo and Hetzer, 2006", "Harel ", "Hetzer ", "Macaulay and Forbes, 1996", "Anderson and Hetzer, 2007", "Hetzer ", "Zhang and Clarke, 20...	91	41,373	0	false	The formation of the eukaryotic nuclear envelope (NE) also requires membrane fusion events.	[]	The formation of the eukaryotic nuclear envelope (NE) also requires membrane fusion events.	true	true	true	true	true	7,134
0	INTRODUCTION	1	Mohler	[ "B100", "B73", "B41", "B57", "B34", "B131", "B88", "B102", "B103", "B66", "B27", "B60", "B64", "B91", "B1", "B64", "B139", "B75", "B60", "B136", "B4", "B74", "B82", "B112" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	The nuclear envelope is composed of an outer nuclear membrane and an inner nuclear membrane, both populated with a variety of transmembrane proteins connecting nuclear membrane to cytoskeleton, nuclear lamina and chromatin (Gruenbaum et al., 2005; Dechat et al., 2008; Taimen et al., 2009).	[ "Mohler ", "Jahn ", "Earp ", "Gruenbaum ", "Dechat ", "Taimen ", "Lohka and Masui, 1983", "Newport, 1987", "Newport and Dunphy, 1992", "Higa ", "D'Angelo and Hetzer, 2006", "Harel ", "Hetzer ", "Macaulay and Forbes, 1996", "Anderson and Hetzer, 2007", "Hetzer ", "Zhang and Clarke, 20...	290	41,374	0	false	The nuclear envelope is composed of an outer nuclear membrane and an inner nuclear membrane, both populated with a variety of transmembrane proteins connecting nuclear membrane to cytoskeleton, nuclear lamina and chromatin.	[ "Gruenbaum et al., 2005; Dechat et al., 2008; Taimen et al., 2009" ]	The nuclear envelope is composed of an outer nuclear membrane and an inner nuclear membrane, both populated with a variety of transmembrane proteins connecting nuclear membrane to cytoskeleton, nuclear lamina and chromatin.	true	true	true	true	true	7,134
0	INTRODUCTION	1	Mohler	[ "B100", "B73", "B41", "B57", "B34", "B131", "B88", "B102", "B103", "B66", "B27", "B60", "B64", "B91", "B1", "B64", "B139", "B75", "B60", "B136", "B4", "B74", "B82", "B112" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	The nuclear membranes are separated by a lumen and joined by nuclear pore complexes.	[ "Mohler ", "Jahn ", "Earp ", "Gruenbaum ", "Dechat ", "Taimen ", "Lohka and Masui, 1983", "Newport, 1987", "Newport and Dunphy, 1992", "Higa ", "D'Angelo and Hetzer, 2006", "Harel ", "Hetzer ", "Macaulay and Forbes, 1996", "Anderson and Hetzer, 2007", "Hetzer ", "Zhang and Clarke, 20...	84	41,375	0	false	The nuclear membranes are separated by a lumen and joined by nuclear pore complexes.	[]	The nuclear membranes are separated by a lumen and joined by nuclear pore complexes.	true	true	true	true	true	7,134
0	INTRODUCTION	1	Mohler	[ "B100", "B73", "B41", "B57", "B34", "B131", "B88", "B102", "B103", "B66", "B27", "B60", "B64", "B91", "B1", "B64", "B139", "B75", "B60", "B136", "B4", "B74", "B82", "B112" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	Much of our knowledge of the mechanism of vertebrate nuclear envelope assembly has been gained from a cell-free system derived from Xenopus egg extracts (Lohka and Masui, 1983; Newport, 1987; Newport and Dunphy, 1992; Higa et al., 2006).	[ "Mohler ", "Jahn ", "Earp ", "Gruenbaum ", "Dechat ", "Taimen ", "Lohka and Masui, 1983", "Newport, 1987", "Newport and Dunphy, 1992", "Higa ", "D'Angelo and Hetzer, 2006", "Harel ", "Hetzer ", "Macaulay and Forbes, 1996", "Anderson and Hetzer, 2007", "Hetzer ", "Zhang and Clarke, 20...	237	41,376	0	false	Much of our knowledge of the mechanism of vertebrate nuclear envelope assembly has been gained from a cell-free system derived from Xenopus egg extracts.	[ "Lohka and Masui, 1983; Newport, 1987; Newport and Dunphy, 1992; Higa et al., 2006" ]	Much of our knowledge of the mechanism of vertebrate nuclear envelope assembly has been gained from a cell-free system derived from Xenopus egg extracts.	true	true	true	true	true	7,134
0	INTRODUCTION	1	Mohler	[ "B100", "B73", "B41", "B57", "B34", "B131", "B88", "B102", "B103", "B66", "B27", "B60", "B64", "B91", "B1", "B64", "B139", "B75", "B60", "B136", "B4", "B74", "B82", "B112" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	This has allowed the in vitro dissection of NE formation into distinct steps: recruitment of membrane vesicles or tubules to the chromatin surface, fusion of these vesicles/tubules to form double nuclear membranes, nuclear pore complex (NPC) assembly, and expansion of the NE to its full size (D'Angelo and Hetzer, 2006;...	[ "Mohler ", "Jahn ", "Earp ", "Gruenbaum ", "Dechat ", "Taimen ", "Lohka and Masui, 1983", "Newport, 1987", "Newport and Dunphy, 1992", "Higa ", "D'Angelo and Hetzer, 2006", "Harel ", "Hetzer ", "Macaulay and Forbes, 1996", "Anderson and Hetzer, 2007", "Hetzer ", "Zhang and Clarke, 20...	417	41,377	0	false	This has allowed the in vitro dissection of NE formation into distinct steps: recruitment of membrane vesicles or tubules to the chromatin surface, fusion of these vesicles/tubules to form double nuclear membranes, nuclear pore complex (NPC) assembly, and expansion of the NE to its full size.	[ "D'Angelo and Hetzer, 2006; Harel et al., 2003a; Hetzer et al., 2000; Macaulay and Forbes, 1996; Anderson and Hetzer, 2007" ]	This has allowed the in vitro dissection of NE formation into distinct steps: recruitment of membrane vesicles or tubules to the chromatin surface, fusion of these vesicles/tubules to form double nuclear membranes, nuclear pore complex (NPC) assembly, and expansion of the NE to its full size.	true	true	true	true	true	7,134
0	INTRODUCTION	1	Mohler	[ "B100", "B73", "B41", "B57", "B34", "B131", "B88", "B102", "B103", "B66", "B27", "B60", "B64", "B91", "B1", "B64", "B139", "B75", "B60", "B136", "B4", "B74", "B82", "B112" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	The formation in vitro of a double nuclear membrane around chromatin requires extensive vesicle–vesicle fusion, promoted by the small GTPase Ran, p97, and αSNAP, and regulated by importin β and transportin (Hetzer et al., 2000; Zhang and Clarke, 2000; Kalab et al., 2002; Harel et al., 2003a; Walther et al., 2003b; Baur...	[ "Mohler ", "Jahn ", "Earp ", "Gruenbaum ", "Dechat ", "Taimen ", "Lohka and Masui, 1983", "Newport, 1987", "Newport and Dunphy, 1992", "Higa ", "D'Angelo and Hetzer, 2006", "Harel ", "Hetzer ", "Macaulay and Forbes, 1996", "Anderson and Hetzer, 2007", "Hetzer ", "Zhang and Clarke, 20...	399	41,378	0	false	The formation in vitro of a double nuclear membrane around chromatin requires extensive vesicle–vesicle fusion, promoted by the small GTPase Ran, p97, and αSNAP, and regulated by importin β and transportin.	[ "Hetzer et al., 2000; Zhang and Clarke, 2000; Kalab et al., 2002; Harel et al., 2003a; Walther et al., 2003b; Baur et al., 2007; Kalab and Heald, 2008; Lau et al., 2009; Rafikova et al., 2009" ]	The formation in vitro of a double nuclear membrane around chromatin requires extensive vesicle–vesicle fusion, promoted by the small GTPase Ran, p97, and αSNAP, and regulated by importin β and transportin.	true	true	true	true	true	7,134
1	INTRODUCTION	1	D'Angelo and Hetzer, 2008	[ "B28", "B80", "B91", "B27" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	Nuclear pore complexes form at two times in the vertebrate cell cycle: (1) NPCs double in number in G1-S phase, then (2) disassemble in prophase and reform at the end of mitosis.	[ "D'Angelo and Hetzer, 2008", "Kutay and Hetzer, 2008", "Macaulay and Forbes, 1996", "D'Angelo " ]	178	41,379	0	false	Nuclear pore complexes form at two times in the vertebrate cell cycle: (1) NPCs double in number in G1-S phase, then (2) disassemble in prophase and reform at the end of mitosis.	[]	Nuclear pore complexes form at two times in the vertebrate cell cycle: (1) NPCs double in number in G1-S phase, then disassemble in prophase and reform at the end of mitosis.	true	true	true	true	true	7,135
1	INTRODUCTION	1	D'Angelo and Hetzer, 2008	[ "B28", "B80", "B91", "B27" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	The most current model of postmitotic NPC assembly argues that only the initial steps of NPC assembly occur on chromatin, followed by double nuclear membrane assembly and concurrent nuclear pore assembly in these nuclear membranes (D'Angelo and Hetzer, 2008; Kutay and Hetzer, 2008).	[ "D'Angelo and Hetzer, 2008", "Kutay and Hetzer, 2008", "Macaulay and Forbes, 1996", "D'Angelo " ]	283	41,380	0	false	The most current model of postmitotic NPC assembly argues that only the initial steps of NPC assembly occur on chromatin, followed by double nuclear membrane assembly and concurrent nuclear pore assembly in these nuclear membranes.	[ "D'Angelo and Hetzer, 2008; Kutay and Hetzer, 2008" ]	The most current model of postmitotic NPC assembly argues that only the initial steps of NPC assembly occur on chromatin, followed by double nuclear membrane assembly and concurrent nuclear pore assembly in these nuclear membranes.	true	true	true	true	true	7,135
1	INTRODUCTION	1	D'Angelo and Hetzer, 2008	[ "B28", "B80", "B91", "B27" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	Indeed, cell-free experiments using the NPC assembly inhibitor BAPTA or an NPC insertion assay show that NPCs can form in vitro in completely closed nuclear membranes, presumably through opposing bilayer fusion (Macaulay and Forbes, 1996; D'Angelo et al., 2006).	[ "D'Angelo and Hetzer, 2008", "Kutay and Hetzer, 2008", "Macaulay and Forbes, 1996", "D'Angelo " ]	262	41,381	0	false	Indeed, cell-free experiments using the NPC assembly inhibitor BAPTA or an NPC insertion assay show that NPCs can form in vitro in completely closed nuclear membranes, presumably through opposing bilayer fusion.	[ "Macaulay and Forbes, 1996; D'Angelo et al., 2006" ]	Indeed, cell-free experiments using the NPC assembly inhibitor BAPTA or an NPC insertion assay show that NPCs can form in vitro in completely closed nuclear membranes, presumably through opposing bilayer fusion.	true	true	true	true	true	7,135
1	INTRODUCTION	1	D'Angelo and Hetzer, 2008	[ "B28", "B80", "B91", "B27" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	This in vitro mechanism mirrors the inner/outer nuclear membrane fusion process that occurs in vivo in vertebrate G1-S-phase nuclei, as well as in yeast nuclei at all stages of the cell cycle.	[ "D'Angelo and Hetzer, 2008", "Kutay and Hetzer, 2008", "Macaulay and Forbes, 1996", "D'Angelo " ]	192	41,382	0	false	This in vitro mechanism mirrors the inner/outer nuclear membrane fusion process that occurs in vivo in vertebrate G1-S-phase nuclei, as well as in yeast nuclei at all stages of the cell cycle.	[]	This in vitro mechanism mirrors the inner/outer nuclear membrane fusion process that occurs in vivo in vertebrate G1-S-phase nuclei, as well as in yeast nuclei at all stages of the cell cycle.	true	true	true	true	true	7,135
1	INTRODUCTION	1	D'Angelo and Hetzer, 2008	[ "B28", "B80", "B91", "B27" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	In all of these, new nuclear pores form in pre-existing nuclear membranes.	[ "D'Angelo and Hetzer, 2008", "Kutay and Hetzer, 2008", "Macaulay and Forbes, 1996", "D'Angelo " ]	74	41,383	0	false	In all of these, new nuclear pores form in pre-existing nuclear membranes.	[]	In all of these, new nuclear pores form in pre-existing nuclear membranes.	true	true	true	true	true	7,135
2	INTRODUCTION	1	Blobel	[ "B8", "B96", "B100", "B73", "B123", "B41", "B72", "B78", "B111", "B4" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	It has been shown that the fusion of biological membranes is driven by integral membrane proteins.	[ "Blobel ", "Mayer, 2002", "Mohler ", "Jahn ", "Schwander ", "Earp ", "Jackson and Chapman, 2006", "Kielian and Rey, 2006", "Podbilewicz ", "Baur " ]	98	41,384	0	false	It has been shown that the fusion of biological membranes is driven by integral membrane proteins.	[]	It has been shown that the fusion of biological membranes is driven by integral membrane proteins.	true	true	true	true	true	7,136
2	INTRODUCTION	1	Blobel	[ "B8", "B96", "B100", "B73", "B123", "B41", "B72", "B78", "B111", "B4" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	Examples of this include enveloped virus entry into cells, SNARE-dependent intracellular fusion, and cell–cell fusion as found in myogenesis and sperm/egg fusion (Blobel et al., 1992; Mayer, 2002; Mohler et al., 2002; Jahn et al., 2003; Schwander et al., 2003; Earp et al., 2005; Jackson and Chapman, 2006; Kielian and R...	[ "Blobel ", "Mayer, 2002", "Mohler ", "Jahn ", "Schwander ", "Earp ", "Jackson and Chapman, 2006", "Kielian and Rey, 2006", "Podbilewicz ", "Baur " ]	356	41,385	0	false	Examples of this include enveloped virus entry into cells, SNARE-dependent intracellular fusion, and cell–cell fusion as found in myogenesis and sperm/egg fusion.	[ "Blobel et al., 1992; Mayer, 2002; Mohler et al., 2002; Jahn et al., 2003; Schwander et al., 2003; Earp et al., 2005; Jackson and Chapman, 2006; Kielian and Rey, 2006; Podbilewicz et al., 2006" ]	Examples of this include enveloped virus entry into cells, SNARE-dependent intracellular fusion, and cell–cell fusion as found in myogenesis and sperm/egg fusion.	true	true	true	true	true	7,136
2	INTRODUCTION	1	Blobel	[ "B8", "B96", "B100", "B73", "B123", "B41", "B72", "B78", "B111", "B4" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	A recent study showed that the vesicle–vesicle fusion event required for forming the double nuclear membranes in Xenopus egg extracts is dependent on SNARE proteins (Baur et al., 2007).	[ "Blobel ", "Mayer, 2002", "Mohler ", "Jahn ", "Schwander ", "Earp ", "Jackson and Chapman, 2006", "Kielian and Rey, 2006", "Podbilewicz ", "Baur " ]	185	41,386	0	false	A recent study showed that the vesicle–vesicle fusion event required for forming the double nuclear membranes in Xenopus egg extracts is dependent on SNARE proteins.	[ "Baur et al., 2007" ]	A recent study showed that the vesicle–vesicle fusion event required for forming the double nuclear membranes in Xenopus egg extracts is dependent on SNARE proteins.	true	true	true	true	true	7,136
3	INTRODUCTION	1	Macaulay and Forbes, 1996	[ "B91", "B53", "B61", "B58", "B51", "B59", "B92", "B93", "B127", "B3", "B93", "B127", "B128", "B48" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	In vivo, a second fusion event between the inner and outer nuclear membranes must be required to form the large proteinaceous nuclear pore complex (Macaulay and Forbes, 1996; Goldberg et al., 1997; Harel et al., 2003b; Guttinger et al., 2009).	[ "Macaulay and Forbes, 1996", "Goldberg ", "Harel ", "Guttinger ", "Gerace ", "Hallberg ", "Madrid ", "Mansfeld ", "Stavru ", "Antonin ", "Mansfeld ", "Stavru ", "Stavru ", "Funakoshi " ]	243	41,387	0	false	In vivo, a second fusion event between the inner and outer nuclear membranes must be required to form the large proteinaceous nuclear pore complex.	[ "Macaulay and Forbes, 1996; Goldberg et al., 1997; Harel et al., 2003b; Guttinger et al., 2009" ]	In vivo, a second fusion event between the inner and outer nuclear membranes must be required to form the large proteinaceous nuclear pore complex.	true	true	true	true	true	7,137
3	INTRODUCTION	1	Macaulay and Forbes, 1996	[ "B91", "B53", "B61", "B58", "B51", "B59", "B92", "B93", "B127", "B3", "B93", "B127", "B128", "B48" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	Importantly, the mechanism for and timing of inner/outer nuclear membrane fusion, however, has not been revealed.	[ "Macaulay and Forbes, 1996", "Goldberg ", "Harel ", "Guttinger ", "Gerace ", "Hallberg ", "Madrid ", "Mansfeld ", "Stavru ", "Antonin ", "Mansfeld ", "Stavru ", "Stavru ", "Funakoshi " ]	113	41,388	0	false	Importantly, the mechanism for and timing of inner/outer nuclear membrane fusion, however, has not been revealed.	[]	Importantly, the mechanism for and timing of inner/outer nuclear membrane fusion, however, has not been revealed.	true	true	true	true	true	7,137
3	INTRODUCTION	1	Macaulay and Forbes, 1996	[ "B91", "B53", "B61", "B58", "B51", "B59", "B92", "B93", "B127", "B3", "B93", "B127", "B128", "B48" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	It is likely that one or more integral membrane proteins play a key role in this fusion event.	[ "Macaulay and Forbes, 1996", "Goldberg ", "Harel ", "Guttinger ", "Gerace ", "Hallberg ", "Madrid ", "Mansfeld ", "Stavru ", "Antonin ", "Mansfeld ", "Stavru ", "Stavru ", "Funakoshi " ]	94	41,389	0	false	It is likely that one or more integral membrane proteins play a key role in this fusion event.	[]	It is likely that one or more integral membrane proteins play a key role in this fusion event.	true	true	true	true	true	7,137
3	INTRODUCTION	1	Macaulay and Forbes, 1996	[ "B91", "B53", "B61", "B58", "B51", "B59", "B92", "B93", "B127", "B3", "B93", "B127", "B128", "B48" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	To date, POM121, gp210, and NDC1 are the only known integral membrane pore proteins in metazoans (Gerace et al., 1982; Hallberg et al., 1993; Madrid et al., 2006; Mansfeld et al., 2006; Stavru et al., 2006a).	[ "Macaulay and Forbes, 1996", "Goldberg ", "Harel ", "Guttinger ", "Gerace ", "Hallberg ", "Madrid ", "Mansfeld ", "Stavru ", "Antonin ", "Mansfeld ", "Stavru ", "Stavru ", "Funakoshi " ]	208	41,390	0	false	To date, POM121, gp210, and NDC1 are the only known integral membrane pore proteins in metazoans.	[ "Gerace et al., 1982; Hallberg et al., 1993; Madrid et al., 2006; Mansfeld et al., 2006; Stavru et al., 2006a" ]	To date, POM121, gp210, and NDC1 are the only known integral membrane pore proteins in metazoans.	true	true	true	true	true	7,137
3	INTRODUCTION	1	Macaulay and Forbes, 1996	[ "B91", "B53", "B61", "B58", "B51", "B59", "B92", "B93", "B127", "B3", "B93", "B127", "B128", "B48" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	RNAi depletion of these transmembrane nucleoporins has shown that POM121 and NDC1 are essential for nuclear pore complex assembly (Antonin et al., 2005; Mansfeld et al., 2006; Stavru et al., 2006a; Stavru et al., 2006b; Funakoshi et al., 2007); however, their potential role in inner/outer nuclear membrane fusion has no...	[ "Macaulay and Forbes, 1996", "Goldberg ", "Harel ", "Guttinger ", "Gerace ", "Hallberg ", "Madrid ", "Mansfeld ", "Stavru ", "Antonin ", "Mansfeld ", "Stavru ", "Stavru ", "Funakoshi " ]	340	41,391	0	false	RNAi depletion of these transmembrane nucleoporins has shown that POM121 and NDC1 are essential for nuclear pore complex assembly ; however, their potential role in inner/outer nuclear membrane fusion has not been investigated.	[ "Antonin et al., 2005; Mansfeld et al., 2006; Stavru et al., 2006a; Stavru et al., 2006b; Funakoshi et al., 2007" ]	RNAi depletion of these transmembrane nucleoporins has shown that POM121 and NDC1 are essential for nuclear pore complex assembly ; however, their potential role in inner/outer nuclear membrane fusion has not been investigated.	true	true	true	true	true	7,137
3	INTRODUCTION	1	Macaulay and Forbes, 1996	[ "B91", "B53", "B61", "B58", "B51", "B59", "B92", "B93", "B127", "B3", "B93", "B127", "B128", "B48" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	One possibility is that these proteins may work either alone or together to promote the fusion of the inner and outer nuclear membranes.	[ "Macaulay and Forbes, 1996", "Goldberg ", "Harel ", "Guttinger ", "Gerace ", "Hallberg ", "Madrid ", "Mansfeld ", "Stavru ", "Antonin ", "Mansfeld ", "Stavru ", "Stavru ", "Funakoshi " ]	136	41,392	0	false	One possibility is that these proteins may work either alone or together to promote the fusion of the inner and outer nuclear membranes.	[]	One possibility is that these proteins may work either alone or together to promote the fusion of the inner and outer nuclear membranes.	true	true	true	true	true	7,137
3	INTRODUCTION	1	Macaulay and Forbes, 1996	[ "B91", "B53", "B61", "B58", "B51", "B59", "B92", "B93", "B127", "B3", "B93", "B127", "B128", "B48" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	Alternatively, an as yet unidentified transmembrane protein may mediate inner/outer nuclear membrane fusion in nuclear pore assembly.	[ "Macaulay and Forbes, 1996", "Goldberg ", "Harel ", "Guttinger ", "Gerace ", "Hallberg ", "Madrid ", "Mansfeld ", "Stavru ", "Antonin ", "Mansfeld ", "Stavru ", "Stavru ", "Funakoshi " ]	133	41,393	0	false	Alternatively, an as yet unidentified transmembrane protein may mediate inner/outer nuclear membrane fusion in nuclear pore assembly.	[]	Alternatively, an as yet unidentified transmembrane protein may mediate inner/outer nuclear membrane fusion in nuclear pore assembly.	true	true	true	true	true	7,137
4	INTRODUCTION	1	Kozlov and Markin, 1983	[ "B79", "B20", "B21", "B89", "B116", "B138", "B111", "B118" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	The most accepted molecular model for general membrane fusion events is the “stalk-pore” mechanism.	[ "Kozlov and Markin, 1983", "Chernomordik ", "Chernomordik ", "Lu ", "Reese ", "Xu ", "Podbilewicz ", "Sapir " ]	99	41,394	0	false	The most accepted molecular model for general membrane fusion events is the “stalk-pore” mechanism.	[]	The most accepted molecular model for general membrane fusion events is the “stalk-pore” mechanism.	true	true	true	true	true	7,138
4	INTRODUCTION	1	Kozlov and Markin, 1983	[ "B79", "B20", "B21", "B89", "B116", "B138", "B111", "B118" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	This mechanism was first identified on artificial protein-free bilayers, then later in viral fusion, intracellular fusion and, most recently, developmental cell fusion (Kozlov and Markin, 1983; Chernomordik et al., 1987; Chernomordik et al., 1993; Lu et al., 2005; Reese et al., 2005; Xu et al., 2005; Podbilewicz et al....	[ "Kozlov and Markin, 1983", "Chernomordik ", "Chernomordik ", "Lu ", "Reese ", "Xu ", "Podbilewicz ", "Sapir " ]	348	41,395	0	false	This mechanism was first identified on artificial protein-free bilayers, then later in viral fusion, intracellular fusion and, most recently, developmental cell fusion.	[ "Kozlov and Markin, 1983; Chernomordik et al., 1987; Chernomordik et al., 1993; Lu et al., 2005; Reese et al., 2005; Xu et al., 2005; Podbilewicz et al., 2006; Sapir et al., 2007" ]	This mechanism was first identified on artificial protein-free bilayers, then later in viral fusion, intracellular fusion and, most recently, developmental cell fusion.	true	true	true	true	true	7,138
4	INTRODUCTION	1	Kozlov and Markin, 1983	[ "B79", "B20", "B21", "B89", "B116", "B138", "B111", "B118" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	In the stalk-pore mechanism, membrane fusion begins with the bending of two membranes toward one another and proceeds through a hemifusion intermediate, which consists of a stalk-like connection that involves only the contacting membrane leaflets of the two fusing bilayers (Supplemental Figure 1).	[ "Kozlov and Markin, 1983", "Chernomordik ", "Chernomordik ", "Lu ", "Reese ", "Xu ", "Podbilewicz ", "Sapir " ]	298	41,396	0	false	In the stalk-pore mechanism, membrane fusion begins with the bending of two membranes toward one another and proceeds through a hemifusion intermediate, which consists of a stalk-like connection that involves only the contacting membrane leaflets of the two fusing bilayers (Supplemental Figure 1).	[]	In the stalk-pore mechanism, membrane fusion begins with the bending of two membranes toward one another and proceeds through a hemifusion intermediate, which consists of a stalk-like connection that involves only the contacting membrane leaflets of the two fusing bilayers.	true	true	true	true	true	7,138
4	INTRODUCTION	1	Kozlov and Markin, 1983	[ "B79", "B20", "B21", "B89", "B116", "B138", "B111", "B118" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	Hemifusion proceeds to complete fusion, which involves the progression to a fusion pore that connects all four leaflets (Supplemental Figure 1).	[ "Kozlov and Markin, 1983", "Chernomordik ", "Chernomordik ", "Lu ", "Reese ", "Xu ", "Podbilewicz ", "Sapir " ]	144	41,397	0	false	Hemifusion proceeds to complete fusion, which involves the progression to a fusion pore that connects all four leaflets (Supplemental Figure 1).	[]	Hemifusion proceeds to complete fusion, which involves the progression to a fusion pore that connects all four leaflets.	true	true	true	true	true	7,138
4	INTRODUCTION	1	Kozlov and Markin, 1983	[ "B79", "B20", "B21", "B89", "B116", "B138", "B111", "B118" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	Subsequent expansion of the fusion pore leads to a fully fused entity.	[ "Kozlov and Markin, 1983", "Chernomordik ", "Chernomordik ", "Lu ", "Reese ", "Xu ", "Podbilewicz ", "Sapir " ]	70	41,398	0	false	Subsequent expansion of the fusion pore leads to a fully fused entity.	[]	Subsequent expansion of the fusion pore leads to a fully fused entity.	true	true	true	true	true	7,138
4	INTRODUCTION	1	Kozlov and Markin, 1983	[ "B79", "B20", "B21", "B89", "B116", "B138", "B111", "B118" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	To date, fusion proteins have been found to provide the driving force that induces hemifusion in biological membranes.	[ "Kozlov and Markin, 1983", "Chernomordik ", "Chernomordik ", "Lu ", "Reese ", "Xu ", "Podbilewicz ", "Sapir " ]	118	41,399	0	false	To date, fusion proteins have been found to provide the driving force that induces hemifusion in biological membranes.	[]	To date, fusion proteins have been found to provide the driving force that induces hemifusion in biological membranes.	true	true	true	true	true	7,138
5	INTRODUCTION	1	Chernomordik	[ "B21", "B17", "B97", "B17", "B89", "B116", "B138" ]	20,926,687	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, the fusion reaction also shows a striking sensitivity to membrane lipid composition (Chernomordik et al., 1993).	[ "Chernomordik ", "Chernomordik and Kozlov, 2003", "Melia ", "Chernomordik and Kozlov, 2003", "Lu ", "Reese ", "Xu " ]	121	41,400	0	false	However, the fusion reaction also shows a striking sensitivity to membrane lipid composition.	[ "Chernomordik et al., 1993" ]	However, the fusion reaction also shows a striking sensitivity to membrane lipid composition.	true	true	true	true	true	7,139
5	INTRODUCTION	1	Chernomordik	[ "B21", "B17", "B97", "B17", "B89", "B116", "B138" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	For biological membranes, hemifusion intermediates are strongly sensitive to the shapes of the lipid molecules in the membrane leaflets.	[ "Chernomordik ", "Chernomordik and Kozlov, 2003", "Melia ", "Chernomordik and Kozlov, 2003", "Lu ", "Reese ", "Xu " ]	136	41,401	0	false	For biological membranes, hemifusion intermediates are strongly sensitive to the shapes of the lipid molecules in the membrane leaflets.	[]	For biological membranes, hemifusion intermediates are strongly sensitive to the shapes of the lipid molecules in the membrane leaflets.	true	true	true	true	true	7,139
5	INTRODUCTION	1	Chernomordik	[ "B21", "B17", "B97", "B17", "B89", "B116", "B138" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	Inverted cone-shaped lipids, such as LPC, inhibit bending of leaflets toward one another and thus inhibit hemifusion.	[ "Chernomordik ", "Chernomordik and Kozlov, 2003", "Melia ", "Chernomordik and Kozlov, 2003", "Lu ", "Reese ", "Xu " ]	117	41,402	0	false	Inverted cone-shaped lipids, such as LPC, inhibit bending of leaflets toward one another and thus inhibit hemifusion.	[]	Inverted cone-shaped lipids, such as LPC, inhibit bending of leaflets toward one another and thus inhibit hemifusion.	true	true	true	true	true	7,139
5	INTRODUCTION	1	Chernomordik	[ "B21", "B17", "B97", "B17", "B89", "B116", "B138" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	This is true for both viral and intracellular fusion events (Chernomordik and Kozlov, 2003; Melia et al., 2006).	[ "Chernomordik ", "Chernomordik and Kozlov, 2003", "Melia ", "Chernomordik and Kozlov, 2003", "Lu ", "Reese ", "Xu " ]	112	41,403	0	false	This is true for both viral and intracellular fusion events.	[ "Chernomordik and Kozlov, 2003; Melia et al., 2006" ]	This is true for both viral and intracellular fusion events.	true	true	true	true	true	7,139
5	INTRODUCTION	1	Chernomordik	[ "B21", "B17", "B97", "B17", "B89", "B116", "B138" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	Cone-shaped lipids, such as oleic acid (OA), promote this type of bending, thereby stabilizing hemifusion but blocking full fusion.	[ "Chernomordik ", "Chernomordik and Kozlov, 2003", "Melia ", "Chernomordik and Kozlov, 2003", "Lu ", "Reese ", "Xu " ]	131	41,404	0	false	Cone-shaped lipids, such as oleic acid (OA), promote this type of bending, thereby stabilizing hemifusion but blocking full fusion.	[]	Cone-shaped lipids, such as oleic acid (OA), promote this type of bending, thereby stabilizing hemifusion but blocking full fusion.	true	true	true	true	true	7,139
5	INTRODUCTION	1	Chernomordik	[ "B21", "B17", "B97", "B17", "B89", "B116", "B138" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	When LPC and OA are added together, however, their complementary shapes neutralize one another and fusion occurs unimpeded.	[ "Chernomordik ", "Chernomordik and Kozlov, 2003", "Melia ", "Chernomordik and Kozlov, 2003", "Lu ", "Reese ", "Xu " ]	123	41,405	0	false	When LPC and OA are added together, however, their complementary shapes neutralize one another and fusion occurs unimpeded.	[]	When LPC and OA are added together, however, their complementary shapes neutralize one another and fusion occurs unimpeded.	true	true	true	true	true	7,139
5	INTRODUCTION	1	Chernomordik	[ "B21", "B17", "B97", "B17", "B89", "B116", "B138" ]	20,926,687	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 consequence, lipids such as LPC have been used as a tool to identify when a membrane fusion event occurs, as LPC has been shown to act as a universal inhibitor of hemifusion.	[ "Chernomordik ", "Chernomordik and Kozlov, 2003", "Melia ", "Chernomordik and Kozlov, 2003", "Lu ", "Reese ", "Xu " ]	177	41,406	0	false	In consequence, lipids such as LPC have been used as a tool to identify when a membrane fusion event occurs, as LPC has been shown to act as a universal inhibitor of hemifusion.	[]	In consequence, lipids such as LPC have been used as a tool to identify when a membrane fusion event occurs, as LPC has been shown to act as a universal inhibitor of hemifusion.	true	true	true	true	true	7,139
5	INTRODUCTION	1	Chernomordik	[ "B21", "B17", "B97", "B17", "B89", "B116", "B138" ]	20,926,687	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 contrast, post-hemifusion stages, those that involve opening and expansion of the fusion pore, are found to be more protein dependent (Chernomordik and Kozlov, 2003; Lu et al., 2005; Reese et al., 2005; Xu et al., 2005).	[ "Chernomordik ", "Chernomordik and Kozlov, 2003", "Melia ", "Chernomordik and Kozlov, 2003", "Lu ", "Reese ", "Xu " ]	223	41,407	0	false	In contrast, post-hemifusion stages, those that involve opening and expansion of the fusion pore, are found to be more protein dependent.	[ "Chernomordik and Kozlov, 2003; Lu et al., 2005; Reese et al., 2005; Xu et al., 2005" ]	In contrast, post-hemifusion stages, those that involve opening and expansion of the fusion pore, are found to be more protein dependent.	true	true	true	true	true	7,139
6	INTRODUCTION	1	Chernomordik	[ "B16", "B94", "B62" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	In analysis of nuclear pore assembly, the membrane fusion step has been difficult to biochemically address, and its temporal order with regard to specific vertebrate nucleoporin recruitment has not been demonstrated.	[ "Chernomordik ", "Markosyan ", "Henderson and Hope, 2006" ]	216	41,408	0	false	In analysis of nuclear pore assembly, the membrane fusion step has been difficult to biochemically address, and its temporal order with regard to specific vertebrate nucleoporin recruitment has not been demonstrated.	[]	In analysis of nuclear pore assembly, the membrane fusion step has been difficult to biochemically address, and its temporal order with regard to specific vertebrate nucleoporin recruitment has not been demonstrated.	true	true	true	true	true	7,140
6	INTRODUCTION	1	Chernomordik	[ "B16", "B94", "B62" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	Using experimental approaches used previously to model membrane fusion reactions throughout the cell (Chernomordik et al., 1998; Markosyan et al., 2003; Henderson and Hope, 2006), here we address questions with respect to the fusion event between the inner and outer nuclear membranes during nuclear pore formation.	[ "Chernomordik ", "Markosyan ", "Henderson and Hope, 2006" ]	315	41,409	0	false	Using experimental approaches used previously to model membrane fusion reactions throughout the cell, here we address questions with respect to the fusion event between the inner and outer nuclear membranes during nuclear pore formation.	[ "Chernomordik et al., 1998; Markosyan et al., 2003; Henderson and Hope, 2006" ]	Using experimental approaches used previously to model membrane fusion reactions throughout the cell, here we address questions with respect to the fusion event between the inner and outer nuclear membranes during nuclear pore formation.	true	true	true	true	true	7,140
6	INTRODUCTION	1	Chernomordik	[ "B16", "B94", "B62" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	Specifically, we describe a novel cold- and lipid-sensitive intermediate that occurs in a completely closed nuclear envelope.	[ "Chernomordik ", "Markosyan ", "Henderson and Hope, 2006" ]	125	41,410	0	false	Specifically, we describe a novel cold- and lipid-sensitive intermediate that occurs in a completely closed nuclear envelope.	[]	Specifically, we describe a novel cold- and lipid-sensitive intermediate that occurs in a completely closed nuclear envelope.	true	true	true	true	true	7,140
6	INTRODUCTION	1	Chernomordik	[ "B16", "B94", "B62" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	This intermediate is formed downstream from the acquisition of early nucleoporins on the chromatin surface, but before observation of NPC structures containing channels functional for diffusion and before the recruitment of FG nucleoporins.	[ "Chernomordik ", "Markosyan ", "Henderson and Hope, 2006" ]	240	41,411	0	false	This intermediate is formed downstream from the acquisition of early nucleoporins on the chromatin surface, but before observation of NPC structures containing channels functional for diffusion and before the recruitment of FG nucleoporins.	[]	This intermediate is formed downstream from the acquisition of early nucleoporins on the chromatin surface, but before observation of NPC structures containing channels functional for diffusion and before the recruitment of FG nucleoporins.	true	true	true	true	true	7,140
0	DISCUSSION	0	null	null	20,926,687	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 this study, we used novel assays and the fusion inhibitors LPC and OA (i) to distinguish when fusion between the inner and outer nuclear membranes occurs in nuclear pore assembly in vertebrates and (ii) to begin to determine the molecular components that precede and follow the fusion step.	null	293	41,412	0	false	null	null	In this study, we used novel assays and the fusion inhibitors LPC and OA (i) to distinguish when fusion between the inner and outer nuclear membranes occurs in nuclear pore assembly in vertebrates and (ii) to begin to determine the molecular components that precede and follow the fusion step.	true	true	true	true	true	7,141
0	DISCUSSION	0	null	null	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	We first identified a 14°C cold intermediate that contains POM121 and the Nup107-160 complex present on the inner but not the outer nuclear membrane (Figure 2).	null	160	41,413	0	false	null	null	We first identified a 14°C cold intermediate that contains POM121 and the Nup107-160 complex present on the inner but not the outer nuclear membrane (Figure 2).	true	true	true	true	true	7,141
0	DISCUSSION	0	null	null	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	WT αSNAP experiments showed that this cold intermediate contains a complete set of the integral membrane components needed to eventually assemble mature nuclear pores.	null	167	41,414	0	false	null	null	WT αSNAP experiments showed that this cold intermediate contains a complete set of the integral membrane components needed to eventually assemble mature nuclear pores.	true	true	true	true	true	7,141
0	DISCUSSION	0	null	null	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	A dextran diffusion assay, together with the fusion inhibitors LPC and OA, allowed us to show that diffusion channel formation has not yet occurred in the 30 min cold intermediate.	null	180	41,415	0	false	null	null	A dextran diffusion assay, together with the fusion inhibitors LPC and OA, allowed us to show that diffusion channel formation has not yet occurred in the 30 min cold intermediate.	true	true	true	true	true	7,141
0	DISCUSSION	0	null	null	20,926,687	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 fusion leading to channel formation appears to coincide with or precede recruitment of the FG Nups.	null	110	41,416	0	false	null	null	Subsequent fusion leading to channel formation appears to coincide with or precede recruitment of the FG Nups.	true	true	true	true	true	7,141
1	DISCUSSION	1	Rasala	[ "B114", "B65", "B117", "B1", "B2" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	The early stages of in vitro nuclear reconstitution in Xenopus egg extracts resemble postmitotic nuclear envelope assembly in dividing cells.	[ "Rasala ", "Hetzer and Wente, 2009", "Rotem ", "Anderson and Hetzer, 2007", "Antonin " ]	141	41,417	0	false	The early stages of in vitro nuclear reconstitution in Xenopus egg extracts resemble postmitotic nuclear envelope assembly in dividing cells.	[]	The early stages of in vitro nuclear reconstitution in Xenopus egg extracts resemble postmitotic nuclear envelope assembly in dividing cells.	true	true	true	true	true	7,142
1	DISCUSSION	1	Rasala	[ "B114", "B65", "B117", "B1", "B2" ]	20,926,687	NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA\|NA	Our findings here reinforce previous studies which argue that NPC assembly occurs by fusion between the two nuclear membranes (Rasala et al., 2008; Hetzer and Wente, 2009; Rotem et al., 2009).	[ "Rasala ", "Hetzer and Wente, 2009", "Rotem ", "Anderson and Hetzer, 2007", "Antonin " ]	192	41,418	0	false	Our findings here reinforce previous studies which argue that NPC assembly occurs by fusion between the two nuclear membranes.	[ "Rasala et al., 2008; Hetzer and Wente, 2009; Rotem et al., 2009" ]	Our findings here reinforce previous studies which argue that NPC assembly occurs by fusion between the two nuclear membranes.	true	true	true	true	true	7,142

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