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
3	INTRODUCTION	0	null	null	17,485,481	pmid-3034610\|NA	(b) DNA sequence of the transcriptional switches, where the C operators and the start codons of the respective operon are shaded.	null	129	7,400	0	false	null	null	(b) DNA sequence of the transcriptional switches, where the C operators and the start codons of the respective operon are shaded.	false	false	true	true	false	1,201
3	INTRODUCTION	0	null	null	17,485,481	pmid-3034610\|NA	The −10 and −35 regions of the respective promoter are underlined and the transcriptional start sites are indicated by the bent arrows.	null	135	7,401	0	false	null	null	The −10 and −35 regions of the respective promoter are underlined and the transcriptional start sites are indicated by the bent arrows.	true	true	true	true	true	1,201
4	INTRODUCTION	0	null	null	17,485,481	null	To gain further insight into the transcriptional switches of the P2-like phages we have made comparative analyses of the C proteins of the heteroimmune E. coli phages P2 and WΦ.	null	177	7,402	0	false	null	null	To gain further insight into the transcriptional switches of the P2-like phages we have made comparative analyses of the C proteins of the heteroimmune E. coli phages P2 and WΦ.	true	true	true	true	true	1,202
0	DISCUSSION	0	null	null	17,485,481	NA\|NA\|pmid-6363394\|pmid-12949155\|NA\|pmid-16707684	In this work, we have shown that WΦ C, like P2 C, has a strong dimerization activity in vivo, but in solution there are no indications of higher oligomeric forms in the plasmid reporter system used.	null	198	7,403	0	false	null	null	In this work, we have shown that WΦ C, like P2 C, has a strong dimerization activity in vivo, but in solution there are no indications of higher oligomeric forms in the plasmid reporter system used.	true	true	true	true	true	1,203
0	DISCUSSION	0	null	null	17,485,481	NA\|NA\|pmid-6363394\|pmid-12949155\|NA\|pmid-16707684	The repressors might, however, form higher oligomeric structures upon binding to DNA.	null	85	7,404	0	false	null	null	The repressors might, however, form higher oligomeric structures upon binding to DNA.	true	true	true	true	true	1,203
0	DISCUSSION	0	null	null	17,485,481	NA\|NA\|pmid-6363394\|pmid-12949155\|NA\|pmid-16707684	Both C repressors induce bending of its respective DNA target upon binding, and it seems as if P2 C induces a slightly stronger bend in the DNA.	null	144	7,405	0	false	null	null	Both C repressors induce bending of its respective DNA target upon binding, and it seems as if P2 C induces a slightly stronger bend in the DNA.	true	true	true	true	true	1,203
0	DISCUSSION	0	null	null	17,485,481	NA\|NA\|pmid-6363394\|pmid-12949155\|NA\|pmid-16707684	However, this difference may be a consequence of the locations of the operator half-sites, or within the fluctuations caused by the limitations of the determination of the bending angle in the circular permutation analysis.	null	223	7,406	0	false	null	null	However, this difference may be a consequence of the locations of the operator half-sites, or within the fluctuations caused by the limitations of the determination of the bending angle in the circular permutation analysis.	true	true	true	true	true	1,203
1	DISCUSSION	0	null	null	17,485,481	NA\|pmid-8626714\|pmid-8349570\|pmid-11700308\|pmid-12139616\|pmid-14871931\|pmid-16507359\|pmid-10871623\|pmid-11244081	The distance between the operator half-sites in P2 and WΦ differs, but as shown here, a reduction of the distance between the half-sites in WΦ from 3 to 2.5 or 2 turns has no effect of the capacity of WΦ C to repress the early promoter in vivo.	null	244	7,407	0	false	null	null	The distance between the operator half-sites in P2 and WΦ differs, but as shown here, a reduction of the distance between the half-sites in WΦ from 3 to 2.5 or 2 turns has no effect of the capacity of WΦ C to repress the early promoter in vivo.	true	true	true	true	true	1,204
1	DISCUSSION	0	null	null	17,485,481	NA\|pmid-8626714\|pmid-8349570\|pmid-11700308\|pmid-12139616\|pmid-14871931\|pmid-16507359\|pmid-10871623\|pmid-11244081	However, the complexes formed in our electrophoretic mobility shift analysis differ, only the fast migrating complex is formed when the distance is decreased.	null	158	7,408	0	false	null	null	However, the complexes formed in our electrophoretic mobility shift analysis differ, only the fast migrating complex is formed when the distance is decreased.	true	true	true	true	true	1,204
1	DISCUSSION	0	null	null	17,485,481	NA\|pmid-8626714\|pmid-8349570\|pmid-11700308\|pmid-12139616\|pmid-14871931\|pmid-16507359\|pmid-10871623\|pmid-11244081	Possibly this fast migrating band correspond to binding to only one half-site, and that the substrate needs to be supercoiled for binding to both half-sites when the distance between the half-sites is reduced.	null	209	7,409	0	false	null	null	Possibly this fast migrating band correspond to binding to only one half-site, and that the substrate needs to be supercoiled for binding to both half-sites when the distance between the half-sites is reduced.	true	true	true	true	true	1,204
1	DISCUSSION	0	null	null	17,485,481	NA\|pmid-8626714\|pmid-8349570\|pmid-11700308\|pmid-12139616\|pmid-14871931\|pmid-16507359\|pmid-10871623\|pmid-11244081	This possibility is supported by the fact that in constructs containing only one half-site (O1), where O2 has been mutated or in the hybrid promoter/operator constructs, only one retarded protein–DNA complex is formed and the in vivo assays show that C cannot regulate the constructs that lacks the other half-site.	null	315	7,410	0	false	null	null	This possibility is supported by the fact that in constructs containing only one half-site (O1), where O2 has been mutated or in the hybrid promoter/operator constructs, only one retarded protein–DNA complex is formed and the in vivo assays show that C cannot regulate the constructs that lacks the other half-site.	true	true	true	true	true	1,204
2	DISCUSSION	0	null	null	17,485,481	pmid-6330728\|pmid-10559293	The electrophoretic mobility shift analysis performed in this work indicate that P2 and WΦ C have different requirements for DNA binding and that the protein–DNA complexes formed differ.	null	186	7,411	0	false	null	null	The electrophoretic mobility shift analysis performed in this work indicate that P2 and WΦ C have different requirements for DNA binding and that the protein–DNA complexes formed differ.	true	true	true	true	true	1,205
2	DISCUSSION	0	null	null	17,485,481	pmid-6330728\|pmid-10559293	P2 C is unable to bind to one half-site as opposed to WΦ C. Furthermore, WΦ C gives three retarded fragments to its wild-type operator/promoter region, indicating an ability to bind to the half-sites independently.	null	214	7,412	0	false	null	null	P2 C is unable to bind to one half-site as opposed to WΦ C. Furthermore, WΦ C gives three retarded fragments to its wild-type operator/promoter region, indicating an ability to bind to the half-sites independently.	true	true	true	true	true	1,205
2	DISCUSSION	0	null	null	17,485,481	pmid-6330728\|pmid-10559293	However, our analysis shows that the phage sequences upstream of the −35 region and downstream of O2 affects both the promoter activity and the repressor–DNA complexes formed.	null	175	7,413	0	false	null	null	However, our analysis shows that the phage sequences upstream of the −35 region and downstream of O2 affects both the promoter activity and the repressor–DNA complexes formed.	true	true	true	true	true	1,205
2	DISCUSSION	0	null	null	17,485,481	pmid-6330728\|pmid-10559293	Replacing the phage flanking sequences with vector DNA leads to an almost 100-fold increase in the in vivo expression system using the cat reporter gene in the absence of the repressor, indicating an interference of some phage sequences or an enhancement of the vector DNA.	null	273	7,414	0	false	null	null	Replacing the phage flanking sequences with vector DNA leads to an almost 100-fold increase in the in vivo expression system using the cat reporter gene in the absence of the repressor, indicating an interference of some phage sequences or an enhancement of the vector DNA.	true	true	true	true	true	1,205
2	DISCUSSION	0	null	null	17,485,481	pmid-6330728\|pmid-10559293	This is an interesting observation that has not been studied further in this work, since the capacity of the WΦ C to repress both constructs is as efficient, indicating that the flanking sequences do not affect the capacity of C to bind and repress its operator in vivo.	null	270	7,415	0	false	null	null	This is an interesting observation that has not been studied further in this work, since the capacity of the WΦ C to repress both constructs is as efficient, indicating that the flanking sequences do not affect the capacity of C to bind and repress its operator in vivo.	true	true	true	true	true	1,205
2	DISCUSSION	0	null	null	17,485,481	pmid-6330728\|pmid-10559293	However, the repressor–DNA complexes formed in the electrophoretic mobility shift analysis differ.	null	98	7,416	0	false	null	null	However, the repressor–DNA complexes formed in the electrophoretic mobility shift analysis differ.	true	true	true	true	true	1,205
2	DISCUSSION	0	null	null	17,485,481	pmid-6330728\|pmid-10559293	Instead of the three fragments generated by the wild-type operator/promoter region, only two fragments are generated when the phage flanking regions are replaced by vector sequences.	null	182	7,417	0	false	null	null	Instead of the three fragments generated by the wild-type operator/promoter region, only two fragments are generated when the phage flanking regions are replaced by vector sequences.	true	true	true	true	true	1,205
2	DISCUSSION	0	null	null	17,485,481	pmid-6330728\|pmid-10559293	A possible explanation could be that secondary binding sites are present in the flanking sequences.	null	99	7,418	0	false	null	null	A possible explanation could be that secondary binding sites are present in the flanking sequences.	true	true	true	true	true	1,205
2	DISCUSSION	0	null	null	17,485,481	pmid-6330728\|pmid-10559293	However, since both the construct containing multiple mutations in O1 with flanking phage DNA and the hybrid operator/promoter constructs that contain only O1 or O2 generate only one shifted band in our EMSAs secondary binding sites seems very unlikely.	null	253	7,419	0	false	null	null	However, since both the construct containing multiple mutations in O1 with flanking phage DNA and the hybrid operator/promoter constructs that contain only O1 or O2 generate only one shifted band in our EMSAs secondary binding sites seems very unlikely.	true	true	true	true	true	1,205
2	DISCUSSION	0	null	null	17,485,481	pmid-6330728\|pmid-10559293	Our results clearly points to the difficulties in interpretation of the biological significance of complexes formed in vitro using EMSA, and the importance of complementary in vivo analysis.	null	190	7,420	0	false	null	null	Our results clearly points to the difficulties in interpretation of the biological significance of complexes formed in vitro using EMSA, and the importance of complementary in vivo analysis.	true	true	true	true	true	1,205
3	DISCUSSION	1	37	[ "B37", "B36" ]	17,485,481	pmid-3034610\|NA	Localization of the start sites of the P2 Pe and Pc transcripts confirm that the transcripts overlap by ∼35 nt.	[ "37", "36" ]	111	7,421	0	false	Localization of the start sites of the P2 Pe and Pc transcripts confirm that the transcripts overlap by ∼35 nt.	[]	Localization of the start sites of the P2 Pe and Pc transcripts confirm that the transcripts overlap by ∼35 nt.	true	true	true	true	true	1,206
3	DISCUSSION	1	37	[ "B37", "B36" ]	17,485,481	pmid-3034610\|NA	A foot-print analysis of P2 C shows that the C protein covers not only the O1 and O2 region, but also ∼12 nt downstream of O2, i.e.	[ "37", "36" ]	131	7,422	0	false	A foot-print analysis of P2 C shows that the C protein covers not only the O1 and O2 region, but also ∼12 nt downstream of O2, i.e.	[]	A foot-print analysis of P2 C shows that the C protein covers not only the O1 and O2 region, but also ∼12 nt downstream of O2, i.e.	true	true	true	true	true	1,206
3	DISCUSSION	1	37	[ "B37", "B36" ]	17,485,481	pmid-3034610\|NA	to ∼+16 of Pe (37).	[ "37", "36" ]	19	7,423	1	false	to ∼+16 of Pe.	[ "37" ]	to ∼+16 of Pe.	false	true	true	true	false	1,206
3	DISCUSSION	1	37	[ "B37", "B36" ]	17,485,481	pmid-3034610\|NA	The protected region is interrupted by at least three enhanced cleavage sites, giving four short protected sites spaced by enhanced cleavage two of them correspond to O1 and O2, one to the spacer region between the half-sites, and the fourth is located downstream of O2.	[ "37", "36" ]	270	7,424	0	false	The protected region is interrupted by at least three enhanced cleavage sites, giving four short protected sites spaced by enhanced cleavage two of them correspond to O1 and O2, one to the spacer region between the half-sites, and the fourth is located downstream of O2.	[]	The protected region is interrupted by at least three enhanced cleavage sites, giving four short protected sites spaced by enhanced cleavage two of them correspond to O1 and O2, one to the spacer region between the half-sites, and the fourth is located downstream of O2.	true	true	true	true	true	1,206
3	DISCUSSION	1	37	[ "B37", "B36" ]	17,485,481	pmid-3034610\|NA	One way of interpreting this is that four C protein molecules bind to this region.	[ "37", "36" ]	82	7,425	0	false	One way of interpreting this is that four C protein molecules bind to this region.	[]	One way of interpreting this is that four C protein molecules bind to this region.	true	true	true	true	true	1,206
3	DISCUSSION	1	37	[ "B37", "B36" ]	17,485,481	pmid-3034610\|NA	Since RNA polymerase binding to Pc should cover 75–80 nt, (from −60 to +20), i.e.	[ "37", "36" ]	81	7,426	0	false	Since RNA polymerase binding to Pc should cover 75–80 nt, (from −60 to +20), i.e.	[]	Since RNA polymerase binding to Pc should cover 75–80 nt, (from −60 to +20), i.e.	true	true	true	true	true	1,206
3	DISCUSSION	1	37	[ "B37", "B36" ]	17,485,481	pmid-3034610\|NA	P2 C and the polymerase should be very close which can explain the autoregulation of C expression on Pc expression.	[ "37", "36" ]	115	7,427	0	false	P2 C and the polymerase should be very close which can explain the autoregulation of C expression on Pc expression.	[]	P2 C and the polymerase should be very close which can explain the autoregulation of C expression on Pc expression.	true	true	true	true	true	1,206
3	DISCUSSION	1	37	[ "B37", "B36" ]	17,485,481	pmid-3034610\|NA	In WΦ, however, the Pe and Pc promoters are further apart from each other and the transcripts overlap by 82 nt, and O2 is located 60 nt from the start site of Pc.	[ "37", "36" ]	162	7,428	0	false	In WΦ, however, the Pe and Pc promoters are further apart from each other and the transcripts overlap by 82 nt, and O2 is located 60 nt from the start site of Pc.	[]	In WΦ, however, the Pe and Pc promoters are further apart from each other and the transcripts overlap by 82 nt, and O2 is located 60 nt from the start site of Pc.	true	true	true	true	true	1,206
3	DISCUSSION	1	37	[ "B37", "B36" ]	17,485,481	pmid-3034610\|NA	Since it is not known if WΦ C regulates its own Pc promoter, further studies are required before any conclusions can be drawn about the consequences of the difference in distance between the Pe and Pc promoters of the two phages.	[ "37", "36" ]	229	7,429	0	false	Since it is not known if WΦ C regulates its own Pc promoter, further studies are required before any conclusions can be drawn about the consequences of the difference in distance between the Pe and Pc promoters of the two phages.	[]	Since it is not known if WΦ C regulates its own Pc promoter, further studies are required before any conclusions can be drawn about the consequences of the difference in distance between the Pe and Pc promoters of the two phages.	true	true	true	true	true	1,206
3	DISCUSSION	1	37	[ "B37", "B36" ]	17,485,481	pmid-3034610\|NA	The observed difference in spontaneous phage production from strains carrying either P2 or WΦ prophage might reflect differences in the components of the transcriptional switch, such as relative strengths of the Pe and Pc promoters and the kinetics of the interactions between the C and the Cox repressors and their resp...	[ "37", "36" ]	336	7,430	0	false	The observed difference in spontaneous phage production from strains carrying either P2 or WΦ prophage might reflect differences in the components of the transcriptional switch, such as relative strengths of the Pe and Pc promoters and the kinetics of the interactions between the C and the Cox repressors and their resp...	[]	The observed difference in spontaneous phage production from strains carrying either P2 or WΦ prophage might reflect differences in the components of the transcriptional switch, such as relative strengths of the Pe and Pc promoters and the kinetics of the interactions between the C and the Cox repressors and their resp...	true	true	true	true	true	1,206
3	DISCUSSION	1	36	[ "B37", "B36" ]	17,485,481	pmid-3034610\|NA	The kinetics of the interactions between the C proteins to their respective operator has been studied (36), but not the interactions of the Cox proteins with their operators.	[ "37", "36" ]	174	7,431	1	false	The kinetics of the interactions between the C proteins to their respective operator has been studied, but not the interactions of the Cox proteins with their operators.	[ "36" ]	The kinetics of the interactions between the C proteins to their respective operator has been studied, but not the interactions of the Cox proteins with their operators.	true	true	true	true	true	1,206
3	DISCUSSION	1	37	[ "B37", "B36" ]	17,485,481	pmid-3034610\|NA	Other phage or cellular factors could also affect the burst size.	[ "37", "36" ]	65	7,432	0	false	Other phage or cellular factors could also affect the burst size.	[]	Other phage or cellular factors could also affect the burst size.	true	true	true	true	true	1,206
0	INTRODUCTION	1	1	[ "b1", "b4", "b5", "b6", "b7", "b14", "b15", "b5", "b6", "b16", "b19", "b20", "b23", "b12", "b24" ]	16,885,239	pmid-8469282\|pmid-12826250\|pmid-9204689\|pmid-11848927\|pmid-1328155\|pmid-14637244\|pmid-16608160\|pmid-9204689\|pmid-11848927\|pmid-3092878\|NA\|pmid-8127657\|pmid-9520408\|pmid-14637246\|pmid-11848931	Oxidatively generated damage to DNA bases by reactive oxygen species, which is either formed endogenously in cells during aerobic metabolism or following exposure of cells to chemical agents or radiations, can lead to cellular lethality, mutations and diseases such as cancer (1–4).	[ "1", "4", "5", "6", "7", "14", "15", "5", "6", "16", "19", "20", "23", "12", "24" ]	282	7,433	0	false	Oxidatively generated damage to DNA bases by reactive oxygen species, which is either formed endogenously in cells during aerobic metabolism or following exposure of cells to chemical agents or radiations, can lead to cellular lethality, mutations and diseases such as cancer.	[ "1–4" ]	Oxidatively generated damage to DNA bases by reactive oxygen species, which is either formed endogenously in cells during aerobic metabolism or following exposure of cells to chemical agents or radiations, can lead to cellular lethality, mutations and diseases such as cancer.	true	true	true	true	true	1,207
0	INTRODUCTION	1	1	[ "b1", "b4", "b5", "b6", "b7", "b14", "b15", "b5", "b6", "b16", "b19", "b20", "b23", "b12", "b24" ]	16,885,239	pmid-8469282\|pmid-12826250\|pmid-9204689\|pmid-11848927\|pmid-1328155\|pmid-14637244\|pmid-16608160\|pmid-9204689\|pmid-11848927\|pmid-3092878\|NA\|pmid-8127657\|pmid-9520408\|pmid-14637246\|pmid-11848931	Until now, ∼100 oxidized bases and nucleosides have been isolated and characterized in numerous model studies (5,6).	[ "1", "4", "5", "6", "7", "14", "15", "5", "6", "16", "19", "20", "23", "12", "24" ]	116	7,434	0	false	Until now, ∼100 oxidized bases and nucleosides have been isolated and characterized in numerous model studies.	[ "5,6" ]	Until now, ∼100 oxidized bases and nucleosides have been isolated and characterized in numerous model studies.	true	true	true	true	true	1,207
0	INTRODUCTION	1	1	[ "b1", "b4", "b5", "b6", "b7", "b14", "b15", "b5", "b6", "b16", "b19", "b20", "b23", "b12", "b24" ]	16,885,239	pmid-8469282\|pmid-12826250\|pmid-9204689\|pmid-11848927\|pmid-1328155\|pmid-14637244\|pmid-16608160\|pmid-9204689\|pmid-11848927\|pmid-3092878\|NA\|pmid-8127657\|pmid-9520408\|pmid-14637246\|pmid-11848931	The most frequently investigated oxidized lesion is 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxodGuo), a highly mutagenic nucleoside that is formed almost ubiquitously by one-electron oxidants and most of the reactive oxygen and nitrogen species (7–14).	[ "1", "4", "5", "6", "7", "14", "15", "5", "6", "16", "19", "20", "23", "12", "24" ]	251	7,435	0	false	The most frequently investigated oxidized lesion is 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxodGuo), a highly mutagenic nucleoside that is formed almost ubiquitously by one-electron oxidants and most of the reactive oxygen and nitrogen species.	[ "7–14" ]	The most frequently investigated oxidized lesion is 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxodGuo), a highly mutagenic nucleoside that is formed almost ubiquitously by one-electron oxidants and most of the reactive oxygen and nitrogen species.	true	true	true	true	true	1,207
0	INTRODUCTION	1	1	[ "b1", "b4", "b5", "b6", "b7", "b14", "b15", "b5", "b6", "b16", "b19", "b20", "b23", "b12", "b24" ]	16,885,239	pmid-8469282\|pmid-12826250\|pmid-9204689\|pmid-11848927\|pmid-1328155\|pmid-14637244\|pmid-16608160\|pmid-9204689\|pmid-11848927\|pmid-3092878\|NA\|pmid-8127657\|pmid-9520408\|pmid-14637246\|pmid-11848931	8-OxodGuo, currently used as a biomarker of DNA oxidation, is highly susceptible to further reaction with one-electron oxidants agents and singlet oxygen.	[ "1", "4", "5", "6", "7", "14", "15", "5", "6", "16", "19", "20", "23", "12", "24" ]	154	7,436	0	false	8-OxodGuo, currently used as a biomarker of DNA oxidation, is highly susceptible to further reaction with one-electron oxidants agents and singlet oxygen.	[]	8-OxodGuo, currently used as a biomarker of DNA oxidation, is highly susceptible to further reaction with one-electron oxidants agents and singlet oxygen.	false	false	true	true	false	1,207
0	INTRODUCTION	1	1	[ "b1", "b4", "b5", "b6", "b7", "b14", "b15", "b5", "b6", "b16", "b19", "b20", "b23", "b12", "b24" ]	16,885,239	pmid-8469282\|pmid-12826250\|pmid-9204689\|pmid-11848927\|pmid-1328155\|pmid-14637244\|pmid-16608160\|pmid-9204689\|pmid-11848927\|pmid-3092878\|NA\|pmid-8127657\|pmid-9520408\|pmid-14637246\|pmid-11848931	8-OxodGuo-related oxidation products and their potential biological impact, in terms of mutagenicity and repairability, havebeen extensively studied over the last decade [for a recent review see (15) and references cited therein].	[ "1", "4", "5", "6", "7", "14", "15", "5", "6", "16", "19", "20", "23", "12", "24" ]	230	7,437	0	false	8-OxodGuo-related oxidation products and their potential biological impact, in terms of mutagenicity and repairability, havebeen extensively studied over the last decade.	[ "for a recent review see (15) and references cited therein" ]	8-OxodGuo-related oxidation products and their potential biological impact, in terms of mutagenicity and repairability, havebeen extensively studied over the last decade.	false	false	true	true	false	1,207
0	INTRODUCTION	1	1	[ "b1", "b4", "b5", "b6", "b7", "b14", "b15", "b5", "b6", "b16", "b19", "b20", "b23", "b12", "b24" ]	16,885,239	pmid-8469282\|pmid-12826250\|pmid-9204689\|pmid-11848927\|pmid-1328155\|pmid-14637244\|pmid-16608160\|pmid-9204689\|pmid-11848927\|pmid-3092878\|NA\|pmid-8127657\|pmid-9520408\|pmid-14637246\|pmid-11848931	Pyrimidine-oxidation products also present a major interest and therefore have received a large attention in the recent years.	[ "1", "4", "5", "6", "7", "14", "15", "5", "6", "16", "19", "20", "23", "12", "24" ]	126	7,438	0	false	Pyrimidine-oxidation products also present a major interest and therefore have received a large attention in the recent years.	[]	Pyrimidine-oxidation products also present a major interest and therefore have received a large attention in the recent years.	true	true	true	true	true	1,207
0	INTRODUCTION	1	1	[ "b1", "b4", "b5", "b6", "b7", "b14", "b15", "b5", "b6", "b16", "b19", "b20", "b23", "b12", "b24" ]	16,885,239	pmid-8469282\|pmid-12826250\|pmid-9204689\|pmid-11848927\|pmid-1328155\|pmid-14637244\|pmid-16608160\|pmid-9204689\|pmid-11848927\|pmid-3092878\|NA\|pmid-8127657\|pmid-9520408\|pmid-14637246\|pmid-11848931	Thus,cytosine is an efficient target for chemical oxidants such as KMnO4, hydroxyl radical or type I photosensitizers that produce a wide set of base lesions.	[ "1", "4", "5", "6", "7", "14", "15", "5", "6", "16", "19", "20", "23", "12", "24" ]	158	7,439	0	false	Thus,cytosine is an efficient target for chemical oxidants such as KMnO4, hydroxyl radical or type I photosensitizers that produce a wide set of base lesions.	[]	Thus,cytosine is an efficient target for chemical oxidants such as KMnO4, hydroxyl radical or type I photosensitizers that produce a wide set of base lesions.	true	true	true	true	true	1,207
0	INTRODUCTION	1	1	[ "b1", "b4", "b5", "b6", "b7", "b14", "b15", "b5", "b6", "b16", "b19", "b20", "b23", "b12", "b24" ]	16,885,239	pmid-8469282\|pmid-12826250\|pmid-9204689\|pmid-11848927\|pmid-1328155\|pmid-14637244\|pmid-16608160\|pmid-9204689\|pmid-11848927\|pmid-3092878\|NA\|pmid-8127657\|pmid-9520408\|pmid-14637246\|pmid-11848931	Among them, 5-hydroxycytosine and, to a lesser extent, 5-hydroxyuracil (5-ohUra) are abundant degradation products (5,6,16–19).	[ "1", "4", "5", "6", "7", "14", "15", "5", "6", "16", "19", "20", "23", "12", "24" ]	127	7,440	0	false	Among them, 5-hydroxycytosine and, to a lesser extent, 5-hydroxyuracil are abundant degradation products.	[ "5-ohUra", "5,6,16–19" ]	Among them, 5-hydroxycytosine and, to a lesser extent, 5-hydroxyuracil are abundant degradation products.	true	true	true	true	true	1,207
0	INTRODUCTION	1	1	[ "b1", "b4", "b5", "b6", "b7", "b14", "b15", "b5", "b6", "b16", "b19", "b20", "b23", "b12", "b24" ]	16,885,239	pmid-8469282\|pmid-12826250\|pmid-9204689\|pmid-11848927\|pmid-1328155\|pmid-14637244\|pmid-16608160\|pmid-9204689\|pmid-11848927\|pmid-3092878\|NA\|pmid-8127657\|pmid-9520408\|pmid-14637246\|pmid-11848931	The toxicity and mutagenicity of 5-hydroxy-2′-deoxyuridine (5-ohdUrd) are now well established.	[ "1", "4", "5", "6", "7", "14", "15", "5", "6", "16", "19", "20", "23", "12", "24" ]	95	7,441	0	false	The toxicity and mutagenicity of 5-hydroxy-2′-deoxyuridine are now well established.	[ "5-ohdUrd" ]	The toxicity and mutagenicity of 5-hydroxy-2′-deoxyuridine are now well established.	true	true	true	true	true	1,207
0	INTRODUCTION	1	1	[ "b1", "b4", "b5", "b6", "b7", "b14", "b15", "b5", "b6", "b16", "b19", "b20", "b23", "b12", "b24" ]	16,885,239	pmid-8469282\|pmid-12826250\|pmid-9204689\|pmid-11848927\|pmid-1328155\|pmid-14637244\|pmid-16608160\|pmid-9204689\|pmid-11848927\|pmid-3092878\|NA\|pmid-8127657\|pmid-9520408\|pmid-14637246\|pmid-11848931	Indeed, mutations, mainly C>T transitions, are induced when the latter oxidized nucleoside is bypassed by DNA polymerases in vitro and in vivo, proving its high miscoding feature (20–23).	[ "1", "4", "5", "6", "7", "14", "15", "5", "6", "16", "19", "20", "23", "12", "24" ]	187	7,442	0	false	Indeed, mutations, mainly C>T transitions, are induced when the latter oxidized nucleoside is bypassed by DNA polymerases in vitro and in vivo, proving its high miscoding feature.	[ "20–23" ]	Indeed, mutations, mainly C>T transitions, are induced when the latter oxidized nucleoside is bypassed by DNA polymerases in vitro and in vivo, proving its high miscoding feature.	true	true	true	true	true	1,207
0	INTRODUCTION	1	1	[ "b1", "b4", "b5", "b6", "b7", "b14", "b15", "b5", "b6", "b16", "b19", "b20", "b23", "b12", "b24" ]	16,885,239	pmid-8469282\|pmid-12826250\|pmid-9204689\|pmid-11848927\|pmid-1328155\|pmid-14637244\|pmid-16608160\|pmid-9204689\|pmid-11848927\|pmid-3092878\|NA\|pmid-8127657\|pmid-9520408\|pmid-14637246\|pmid-11848931	On the other hand 5-ohdUrd is known to be an efficient substrate for several repair enzymes, namely DNA N-glycosylases, both in eukaryotic and prokaryotic organisms (12,24).	[ "1", "4", "5", "6", "7", "14", "15", "5", "6", "16", "19", "20", "23", "12", "24" ]	173	7,443	0	false	On the other hand 5-ohdUrd is known to be an efficient substrate for several repair enzymes, namely DNA N-glycosylases, both in eukaryotic and prokaryotic organisms.	[ "12,24" ]	On the other hand 5-ohdUrd is known to be an efficient substrate for several repair enzymes, namely DNA N-glycosylases, both in eukaryotic and prokaryotic organisms.	true	true	true	true	true	1,207
1	INTRODUCTION	1	6	[ "b6", "b25", "b25", "b26", "b27", "b29", "b29", "b31", "b32" ]	16,885,239	pmid-11848927\|pmid-15161271\|pmid-15161271\|pmid-16097807\|pmid-3741404\|pmid-10820032\|pmid-10820032\|pmid-8602352\|pmid-15902269	Similar to 8-oxodGuo, 5-ohdUrd exhibits a lower oxidation potential than its unmodified initial nucleoside precursor (6).	[ "6", "25", "25", "26", "27", "29", "29", "31", "32" ]	121	7,444	1	false	Similar to 8-oxodGuo, 5-ohdUrd exhibits a lower oxidation potential than its unmodified initial nucleoside precursor.	[ "6" ]	Similar to 8-oxodGuo, 5-ohdUrd exhibits a lower oxidation potential than its unmodified initial nucleoside precursor.	true	true	true	true	true	1,208
1	INTRODUCTION	1	6	[ "b6", "b25", "b25", "b26", "b27", "b29", "b29", "b31", "b32" ]	16,885,239	pmid-11848927\|pmid-15161271\|pmid-15161271\|pmid-16097807\|pmid-3741404\|pmid-10820032\|pmid-10820032\|pmid-8602352\|pmid-15902269	This property suggests that oxidation of 5-ohdUrd may occur in cellular DNA even if the expected frequency of the event is low.	[ "6", "25", "25", "26", "27", "29", "29", "31", "32" ]	127	7,445	0	false	This property suggests that oxidation of 5-ohdUrd may occur in cellular DNA even if the expected frequency of the event is low.	[]	This property suggests that oxidation of 5-ohdUrd may occur in cellular DNA even if the expected frequency of the event is low.	true	true	true	true	true	1,208
1	INTRODUCTION	1	6	[ "b6", "b25", "b25", "b26", "b27", "b29", "b29", "b31", "b32" ]	16,885,239	pmid-11848927\|pmid-15161271\|pmid-15161271\|pmid-16097807\|pmid-3741404\|pmid-10820032\|pmid-10820032\|pmid-8602352\|pmid-15902269	If this is the case, it is likely that the resulting degradation products may have biological effects.	[ "6", "25", "25", "26", "27", "29", "29", "31", "32" ]	102	7,446	0	false	If this is the case, it is likely that the resulting degradation products may have biological effects.	[]	If this is the case, it is likely that the resulting degradation products may have biological effects.	true	true	true	true	true	1,208
1	INTRODUCTION	1	25	[ "b6", "b25", "b25", "b26", "b27", "b29", "b29", "b31", "b32" ]	16,885,239	pmid-11848927\|pmid-15161271\|pmid-15161271\|pmid-16097807\|pmid-3741404\|pmid-10820032\|pmid-10820032\|pmid-8602352\|pmid-15902269	Recently, Wagner and co-workers (25) reported that oxidation of 5-ohdUrd by Br2, Na2IrBr6 or type I photosensitizers exclusively generates diastereomers of 1-(2-deoxy-β-d-erythro-pentofuranosyl)isodialuric acid (dIdial) as the primary degradation products.	[ "6", "25", "25", "26", "27", "29", "29", "31", "32" ]	256	7,447	1	false	Recently, Wagner and co-workers reported that oxidation of 5-ohdUrd by Br2, Na2IrBr6 or type I photosensitizers exclusively generates diastereomers of 1-(2-deoxy-β-d-erythro-pentofuranosyl)isodialuric acid (dIdial) as the primary degradation products.	[ "25" ]	Recently, Wagner and co-workers reported that oxidation of 5-ohdUrd by Br2, Na2IrBr6 or type I photosensitizers exclusively generates diastereomers of 1-isodialuric acid (dIdial) as the primary degradation products.	true	true	true	true	true	1,208
1	INTRODUCTION	1	6	[ "b6", "b25", "b25", "b26", "b27", "b29", "b29", "b31", "b32" ]	16,885,239	pmid-11848927\|pmid-15161271\|pmid-15161271\|pmid-16097807\|pmid-3741404\|pmid-10820032\|pmid-10820032\|pmid-8602352\|pmid-15902269	Subsequently, diastereoisomeric isodialuric acid nucleosides are converted into 1-(2-deoxy-β-d-erythro-pentofuranosyl)dialuric acid (dDial), 1-(2-deoxy-β-d-erythro-pentofuranosyl)-5-hydroxyhydantoin (5-ohdHyd) diastereomers and 1-(2-deoxy-β-d-erythro-pentofuranosyl)-4-hydroxyimidazolidine-2,5-dione(iso-4-ohdHyd) diaste...	[ "6", "25", "25", "26", "27", "29", "29", "31", "32" ]	347	7,448	0	false	Subsequently, diastereoisomeric isodialuric acid nucleosides are converted into 1-(2-deoxy-β-d-erythro-pentofuranosyl)dialuric acid (dDial), 1-(2-deoxy-β-d-erythro-pentofuranosyl)-5-hydroxyhydantoin (5-ohdHyd) diastereomers and 1-(2-deoxy-β-d-erythro-pentofuranosyl)-4-hydroxyimidazolidine-2,5-dione(iso-4-ohdHyd) diaste...	[ "25,26" ]	Subsequently, diastereoisomeric isodialuric acid nucleosides are converted into 1-(2-deoxy-β-d-erythro-pentofuranosyl)dialuric acid (dDial), 1-(2-deoxy-β-d-erythro-pentofuranosyl)-5-hydroxyhydantoin (5-ohdHyd) diastereomers and 1-(2-deoxy-β-d-erythro-pentofuranosyl)-4-hydroxyimidazolidine-2,5-dione(iso-4-ohdHyd) diaste...	true	true	true	true	true	1,208
1	INTRODUCTION	1	6	[ "b6", "b25", "b25", "b26", "b27", "b29", "b29", "b31", "b32" ]	16,885,239	pmid-11848927\|pmid-15161271\|pmid-15161271\|pmid-16097807\|pmid-3741404\|pmid-10820032\|pmid-10820032\|pmid-8602352\|pmid-15902269	Until now, there was a paucity of information on the formation of Idial and on biochemical features of this oxidatively generated base lesion within DNA.	[ "6", "25", "25", "26", "27", "29", "29", "31", "32" ]	153	7,449	0	false	Until now, there was a paucity of information on the formation of Idial and on biochemical features of this oxidatively generated base lesion within DNA.	[]	Until now, there was a paucity of information on the formation of Idial and on biochemical features of this oxidatively generated base lesion within DNA.	true	true	true	true	true	1,208
1	INTRODUCTION	1	6	[ "b6", "b25", "b25", "b26", "b27", "b29", "b29", "b31", "b32" ]	16,885,239	pmid-11848927\|pmid-15161271\|pmid-15161271\|pmid-16097807\|pmid-3741404\|pmid-10820032\|pmid-10820032\|pmid-8602352\|pmid-15902269	Thus, isodialuric acid base lesion has been detected at significant levels in OsO4-treated isolated DNA, γ-irradiated isolated DNA and H2O2-treated cells, by gas chromatography-mass spectrometry measurements (27–29).	[ "6", "25", "25", "26", "27", "29", "29", "31", "32" ]	216	7,450	0	false	Thus, isodialuric acid base lesion has been detected at significant levels in OsO4-treated isolated DNA, γ-irradiated isolated DNA and H2O2-treated cells, by gas chromatography-mass spectrometry measurements.	[ "27–29" ]	Thus, isodialuric acid base lesion has been detected at significant levels in OsO4-treated isolated DNA, γ-irradiated isolated DNA and H2O2-treated cells, by gas chromatography-mass spectrometry measurements.	true	true	true	true	true	1,208
1	INTRODUCTION	1	6	[ "b6", "b25", "b25", "b26", "b27", "b29", "b29", "b31", "b32" ]	16,885,239	pmid-11848927\|pmid-15161271\|pmid-15161271\|pmid-16097807\|pmid-3741404\|pmid-10820032\|pmid-10820032\|pmid-8602352\|pmid-15902269	The same group has reported that two Escherichia coli enzymes, Nth and Ung, as well as human Ung are able to recognize and excise isodialuric acid from oxidized isolated DNA (29–31).	[ "6", "25", "25", "26", "27", "29", "29", "31", "32" ]	182	7,451	0	false	The same group has reported that two Escherichia coli enzymes, Nth and Ung, as well as human Ung are able to recognize and excise isodialuric acid from oxidized isolated DNA.	[ "29–31" ]	The same group has reported that two Escherichia coli enzymes, Nth and Ung, as well as human Ung are able to recognize and excise isodialuric acid from oxidized isolated DNA.	true	true	true	true	true	1,208
1	INTRODUCTION	1	32	[ "b6", "b25", "b25", "b26", "b27", "b29", "b29", "b31", "b32" ]	16,885,239	pmid-11848927\|pmid-15161271\|pmid-15161271\|pmid-16097807\|pmid-3741404\|pmid-10820032\|pmid-10820032\|pmid-8602352\|pmid-15902269	Recently, Lindahl and co-workers (32) provided some evidence on the toxicity of radiation-induced dIdial in the DNA of mammalian cells deficient in Smug and Ung proteins.	[ "6", "25", "25", "26", "27", "29", "29", "31", "32" ]	170	7,452	1	false	Recently, Lindahl and co-workers provided some evidence on the toxicity of radiation-induced dIdial in the DNA of mammalian cells deficient in Smug and Ung proteins.	[ "32" ]	Recently, Lindahl and co-workers provided some evidence on the toxicity of radiation-induced dIdial in the DNA of mammalian cells deficient in Smug and Ung proteins.	true	true	true	true	true	1,208
2	INTRODUCTION	0	null	null	16,885,239	null	In this article, we report the results of a study dealing with the one-electron oxidation-mediated conversion of 5-ohdUrd residues into dIdial within synthetic single- and double-stranded oligonucleotides.	null	205	7,453	0	false	null	null	In this article, we report the results of a study dealing with the one-electron oxidation-mediated conversion of 5-ohdUrd residues into dIdial within synthetic single- and double-stranded oligonucleotides.	true	true	true	true	true	1,209
2	INTRODUCTION	0	null	null	16,885,239	null	The conversion of dIdial into several degradation products was also investigated in order to further establish the chemistry of the successive steps together with the stability of the resulting modified nucleosides formed within DNA strands.	null	241	7,454	0	false	null	null	The conversion of dIdial into several degradation products was also investigated in order to further establish the chemistry of the successive steps together with the stability of the resulting modified nucleosides formed within DNA strands.	true	true	true	true	true	1,209
2	INTRODUCTION	0	null	null	16,885,239	null	Pulse ESR experiments were performed using the freeze-quench approach in order to gain further insights into the mechanisms of 5-ohdUrd oxidation.	null	146	7,455	0	false	null	null	Pulse ESR experiments were performed using the freeze-quench approach in order to gain further insights into the mechanisms of 5-ohdUrd oxidation.	true	true	true	true	true	1,209
2	INTRODUCTION	0	null	null	16,885,239	null	Finally, information is also provided on the abilities of several prokaryotic and eukaryotic DNA N-glycosylases, involved in the base excision repair (BER) pathway, to remove isodialuric acid from site-specifically modified oligonucleotides.	null	241	7,456	0	false	null	null	Finally, information is also provided on the abilities of several prokaryotic and eukaryotic DNA N-glycosylases, involved in the base excision repair (BER) pathway, to remove isodialuric acid from site-specifically modified oligonucleotides.	true	true	true	true	true	1,209
0	INTRODUCTION	1	1	[ "b1", "b2", "b3", "b4", "b5" ]	17,170,005	pmid-7145702\|pmid-12376375\|pmid-11337476\|NA\|pmid-12209144\|pmid-15342559	Since the first genefinding algorithms such as TESTCODE (1) came onto the scene, their effectiveness have grown with nucleotide sensitivity and specificity now reported in the high 90% range (2,3).	[ "1", "2", "3", "4", "5" ]	197	7,457	1	false	Since the first genefinding algorithms such as TESTCODE came onto the scene, their effectiveness have grown with nucleotide sensitivity and specificity now reported in the high 90% range.	[ "1", "2,3" ]	Since the first genefinding algorithms such as TESTCODE came onto the scene, their effectiveness have grown with nucleotide sensitivity and specificity now reported in the high 90% range.	true	true	true	true	true	1,210
0	INTRODUCTION	1	1	[ "b1", "b2", "b3", "b4", "b5" ]	17,170,005	pmid-7145702\|pmid-12376375\|pmid-11337476\|NA\|pmid-12209144\|pmid-15342559	Despite such nucleotide level results, exon, gene and whole-genome level results still need improvement (4,5).	[ "1", "2", "3", "4", "5" ]	110	7,458	0	false	Despite such nucleotide level results, exon, gene and whole-genome level results still need improvement.	[ "4,5" ]	Despite such nucleotide level results, exon, gene and whole-genome level results still need improvement.	true	true	true	true	true	1,210
0	INTRODUCTION	1	1	[ "b1", "b2", "b3", "b4", "b5" ]	17,170,005	pmid-7145702\|pmid-12376375\|pmid-11337476\|NA\|pmid-12209144\|pmid-15342559	Research presses on towards improving the capabilities of automated gene annotation on the exon and whole-gene levels.	[ "1", "2", "3", "4", "5" ]	118	7,459	0	false	Research presses on towards improving the capabilities of automated gene annotation on the exon and whole-gene levels.	[]	Research presses on towards improving the capabilities of automated gene annotation on the exon and whole-gene levels.	true	true	true	true	true	1,210
0	INTRODUCTION	1	1	[ "b1", "b2", "b3", "b4", "b5" ]	17,170,005	pmid-7145702\|pmid-12376375\|pmid-11337476\|NA\|pmid-12209144\|pmid-15342559	Common among putatively ‘high’ performance genefinders is the implementation of hidden Markov model (HMM) variants.	[ "1", "2", "3", "4", "5" ]	115	7,460	0	false	Common among putatively ‘high’ performance genefinders is the implementation of hidden Markov model (HMM) variants.	[]	Common among putatively ‘high’ performance genefinders is the implementation of hidden Markov model (HMM) variants.	true	true	true	true	true	1,210
0	INTRODUCTION	1	1	[ "b1", "b2", "b3", "b4", "b5" ]	17,170,005	pmid-7145702\|pmid-12376375\|pmid-11337476\|NA\|pmid-12209144\|pmid-15342559	We present an analysis and review of how the contemporary HMM genefinders: Augustus, Genezilla, GenomeScan, GlimmerHMM, SNAP and Twinscan fared on a new dataset (FSH298).	[ "1", "2", "3", "4", "5" ]	170	7,461	0	false	We present an analysis and review of how the contemporary HMM genefinders: Augustus, Genezilla, GenomeScan, GlimmerHMM, SNAP and Twinscan fared on a new dataset.	[ "FSH298" ]	We present an analysis and review of how the contemporary HMM genefinders: Augustus, Genezilla, GenomeScan, GlimmerHMM, SNAP and Twinscan fared on a new dataset.	true	true	true	true	true	1,210
0	INTRODUCTION	1	1	[ "b1", "b2", "b3", "b4", "b5" ]	17,170,005	pmid-7145702\|pmid-12376375\|pmid-11337476\|NA\|pmid-12209144\|pmid-15342559	Building on this, we apply our novel and comprehensive taxonomy of predicted exons to the output of each program tested.	[ "1", "2", "3", "4", "5" ]	120	7,462	0	false	Building on this, we apply our novel and comprehensive taxonomy of predicted exons to the output of each program tested.	[]	Building on this, we apply our novel and comprehensive taxonomy of predicted exons to the output of each program tested.	true	true	true	true	true	1,210
0	INTRODUCTION	1	1	[ "b1", "b2", "b3", "b4", "b5" ]	17,170,005	pmid-7145702\|pmid-12376375\|pmid-11337476\|NA\|pmid-12209144\|pmid-15342559	The purpose of this is to identify patterns of inaccuracy common to all HMM genefinders.	[ "1", "2", "3", "4", "5" ]	88	7,463	0	false	The purpose of this is to identify patterns of inaccuracy common to all HMM genefinders.	[]	The purpose of this is to identify patterns of inaccuracy common to all HMM genefinders.	true	true	true	true	true	1,210
0	INTRODUCTION	1	1	[ "b1", "b2", "b3", "b4", "b5" ]	17,170,005	pmid-7145702\|pmid-12376375\|pmid-11337476\|NA\|pmid-12209144\|pmid-15342559	Subsequently each pattern of inaccuracy can then be addressed hopefully resulting in more accurate genefinders.	[ "1", "2", "3", "4", "5" ]	111	7,464	0	false	Subsequently each pattern of inaccuracy can then be addressed hopefully resulting in more accurate genefinders.	[]	Subsequently each pattern of inaccuracy can then be addressed hopefully resulting in more accurate genefinders.	true	true	true	true	true	1,210
0	INTRODUCTION	1	1	[ "b1", "b2", "b3", "b4", "b5" ]	17,170,005	pmid-7145702\|pmid-12376375\|pmid-11337476\|NA\|pmid-12209144\|pmid-15342559	As this paper specifically evaluates HMM genefinders, a brief review is first provided.	[ "1", "2", "3", "4", "5" ]	87	7,465	0	false	As this paper specifically evaluates HMM genefinders, a brief review is first provided.	[]	As this paper specifically evaluates HMM genefinders, a brief review is first provided.	true	true	true	true	true	1,210
0	DISCUSSION	1	21	[ "b21" ]	17,170,005	pmid-7145702\|pmid-12376375\|pmid-11337476\|NA\|pmid-12209144\|pmid-15342559	The traditional genefinder measurement statistics are presented in Table 1.	[ "21" ]	75	7,466	0	false	The traditional genefinder measurement statistics are presented in Table 1.	[]	The traditional genefinder measurement statistics are presented in Table 1.	true	true	true	true	true	1,211
0	DISCUSSION	1	21	[ "b21" ]	17,170,005	pmid-7145702\|pmid-12376375\|pmid-11337476\|NA\|pmid-12209144\|pmid-15342559	Focusing first at the exon level, GenomeScan seems the decisively best performing program with an average sensitivity and specificity of 0.75.	[ "21" ]	142	7,467	0	false	Focusing first at the exon level, GenomeScan seems the decisively best performing program with an average sensitivity and specificity of 0.75.	[]	Focusing first at the exon level, GenomeScan seems the decisively best performing program with an average sensitivity and specificity of 0.75.	true	true	true	true	true	1,211
0	DISCUSSION	1	21	[ "b21" ]	17,170,005	pmid-7145702\|pmid-12376375\|pmid-11337476\|NA\|pmid-12209144\|pmid-15342559	Issac and Raghava confirmed this result in (21) where GenomeScan fared similarly with an average of 0.74.	[ "21" ]	105	7,468	1	false	Issac and Raghava confirmed this result in where GenomeScan fared similarly with an average of 0.74.	[ "21" ]	Issac and Raghava confirmed this result in where GenomeScan fared similarly with an average of 0.74.	true	true	true	true	true	1,211
0	DISCUSSION	1	21	[ "b21" ]	17,170,005	pmid-7145702\|pmid-12376375\|pmid-11337476\|NA\|pmid-12209144\|pmid-15342559	GlimmerHMM and Augustus converge on a similar performance level of 0.65.	[ "21" ]	72	7,469	0	false	GlimmerHMM and Augustus converge on a similar performance level of 0.65.	[]	GlimmerHMM and Augustus converge on a similar performance level of 0.65.	true	true	true	true	true	1,211
0	DISCUSSION	1	21	[ "b21" ]	17,170,005	pmid-7145702\|pmid-12376375\|pmid-11337476\|NA\|pmid-12209144\|pmid-15342559	A step lower is Twinscan's exon average at 0.55.	[ "21" ]	48	7,470	0	false	A step lower is Twinscan's exon average at 0.55.	[]	A step lower is Twinscan's exon average at 0.55.	true	true	true	true	true	1,211
0	DISCUSSION	1	21	[ "b21" ]	17,170,005	pmid-7145702\|pmid-12376375\|pmid-11337476\|NA\|pmid-12209144\|pmid-15342559	Finally Genezilla and SNAP (Homo sapiens) return an exon level average of 0.44 and 0.38, respectively.	[ "21" ]	102	7,471	0	false	Finally Genezilla and SNAP (Homo sapiens) return an exon level average of 0.44 and 0.38, respectively.	[]	Finally Genezilla and SNAP (Homo sapiens) return an exon level average of 0.44 and 0.38, respectively.	true	true	true	true	true	1,211
1	DISCUSSION	0	null	null	17,170,005	null	At the nucleotide level Twinscan outperformed all the others with 0.88 and 0.89 for AC and CC, respectively.	null	108	7,472	0	false	null	null	At the nucleotide level Twinscan outperformed all the others with 0.88 and 0.89 for AC and CC, respectively.	true	true	true	true	true	1,212
1	DISCUSSION	0	null	null	17,170,005	null	Twinscan's sensitivity and specificity measured 0.90 and 0.95, respectively.	null	76	7,473	0	false	null	null	Twinscan's sensitivity and specificity measured 0.90 and 0.95, respectively.	true	true	true	true	true	1,212
1	DISCUSSION	0	null	null	17,170,005	null	GlimmerHMM, GenomeScan and Augustus all returned AC and CC varying between 0.70 and 0.80.	null	89	7,474	0	false	null	null	GlimmerHMM, GenomeScan and Augustus all returned AC and CC varying between 0.70 and 0.80.	true	true	true	true	true	1,212
1	DISCUSSION	0	null	null	17,170,005	null	Finally SNAP outperformed Genezilla, yet both had an AC and CC value ranging from 0.65 to 0.69.	null	95	7,475	0	false	null	null	Finally SNAP outperformed Genezilla, yet both had an AC and CC value ranging from 0.65 to 0.69.	true	true	true	true	true	1,212
2	DISCUSSION	1	18	[ "b18", "b20", "b22", "b23" ]	17,170,005	pmid-8786136\|pmid-9254694\|NA\|pmid-9012824	It is tempting to state that GenomeScan is the best performing genefinder overall; however, at the whole gene level it rated poorest, not finding 43 genes in the 294 (15%) sequences it successfully completed.	[ "18", "20", "22", "23" ]	208	7,476	0	false	It is tempting to state that GenomeScan is the best performing genefinder overall; however, at the whole gene level it rated poorest, not finding 43 genes in the 294 (15%) sequences it successfully completed.	[]	It is tempting to state that GenomeScan is the best performing genefinder overall; however, at the whole gene level it rated poorest, not finding 43 genes in the 294 sequences it successfully completed.	true	true	true	true	true	1,213
2	DISCUSSION	1	18	[ "b18", "b20", "b22", "b23" ]	17,170,005	pmid-8786136\|pmid-9254694\|NA\|pmid-9012824	Statistically this is worse than any other genefinder in previous independent evaluations (18,20).	[ "18", "20", "22", "23" ]	98	7,477	0	false	Statistically this is worse than any other genefinder in previous independent evaluations.	[ "18,20" ]	Statistically this is worse than any other genefinder in previous independent evaluations.	true	true	true	true	true	1,213
2	DISCUSSION	1	22	[ "b18", "b20", "b22", "b23" ]	17,170,005	pmid-8786136\|pmid-9254694\|NA\|pmid-9012824	Previously Genie (22) and MZEF (23) were the worst performers not finding a gene in 7% of sequences tested.	[ "18", "20", "22", "23" ]	107	7,478	1	false	Previously Genie and MZEF were the worst performers not finding a gene in 7% of sequences tested.	[ "22", "23" ]	Previously Genie and MZEF were the worst performers not finding a gene in 7% of sequences tested.	true	true	true	true	true	1,213
2	DISCUSSION	1	18	[ "b18", "b20", "b22", "b23" ]	17,170,005	pmid-8786136\|pmid-9254694\|NA\|pmid-9012824	Genezilla and Augustus performed best in this area identifying a coding region in every sequence tested.	[ "18", "20", "22", "23" ]	104	7,479	0	false	Genezilla and Augustus performed best in this area identifying a coding region in every sequence tested.	[]	Genezilla and Augustus performed best in this area identifying a coding region in every sequence tested.	true	true	true	true	true	1,213
3	DISCUSSION	0	null	null	17,170,005	null	It is no surprise that the two lowest performing genefinders were those requiring partial or complete training, especially considering the overall lack of documentation and support in the genefinding software development world.	null	227	7,480	0	false	null	null	It is no surprise that the two lowest performing genefinders were those requiring partial or complete training, especially considering the overall lack of documentation and support in the genefinding software development world.	true	true	true	true	true	1,214
3	DISCUSSION	0	null	null	17,170,005	null	Training for SNAP is mostly automated.	null	38	7,481	0	false	null	null	Training for SNAP is mostly automated.	true	true	true	true	true	1,214
3	DISCUSSION	0	null	null	17,170,005	null	Genezilla's complex training regimen however has a larger opportunity for human error.	null	86	7,482	0	false	null	null	Genezilla's complex training regimen however has a larger opportunity for human error.	true	true	true	true	true	1,214
3	DISCUSSION	0	null	null	17,170,005	null	SNAP was designed to perform initial genefinding on sequences for which no organism-specific genefinder exists; furthermore, its state model is not designed specifically for higher eukaryotes.	null	192	7,483	0	false	null	null	SNAP was designed to perform initial genefinding on sequences for which no organism-specific genefinder exists; furthermore, its state model is not designed specifically for higher eukaryotes.	true	true	true	true	true	1,214
3	DISCUSSION	0	null	null	17,170,005	null	Genezilla, however, is a massive system implementing multiple specific sub-model types over a robust state structure.	null	117	7,484	0	false	null	null	Genezilla, however, is a massive system implementing multiple specific sub-model types over a robust state structure.	true	true	true	true	true	1,214
4	DISCUSSION	0	null	null	17,170,005	null	A second explanation for the results of Genezilla and SNAP exists.	null	66	7,485	0	false	null	null	A second explanation for the results of Genezilla and SNAP exists.	true	true	true	true	true	1,215
4	DISCUSSION	0	null	null	17,170,005	null	Each genefinder returned similar results when trained on essentially the same dataset.	null	86	7,486	0	false	null	null	Each genefinder returned similar results when trained on essentially the same dataset.	true	true	true	true	true	1,215
4	DISCUSSION	0	null	null	17,170,005	null	Therefore, it is possible that the training dataset are responsible for their lower results.	null	92	7,487	0	false	null	null	Therefore, it is possible that the training dataset are responsible for their lower results.	true	true	true	true	true	1,215
5	DISCUSSION	1	19	[ "b19", "b19" ]	17,170,005	pmid-11337477\|pmid-11337477	Comparing our results to that of Rogic et al.	[ "19", "19" ]	45	7,488	0	false	Comparing our results to that of Rogic et al.	[]	Comparing our results to that of Rogic et al.	true	true	true	true	true	1,216
5	DISCUSSION	1	19	[ "b19", "b19" ]	17,170,005	pmid-11337477\|pmid-11337477	(19), there does not seem to be a vast improvement in the genefinders tested.	[ "19", "19" ]	77	7,489	1	false	, there does not seem to be a vast improvement in the genefinders tested.	[ "19" ]	, there does not seem to be a vast improvement in the genefinders tested.	false	false	true	true	false	1,216
5	DISCUSSION	1	19	[ "b19", "b19" ]	17,170,005	pmid-11337477\|pmid-11337477	AC varied in (19) from 0.68 to 0.91.	[ "19", "19" ]	36	7,490	1	false	AC varied in from 0.68 to 0.91.	[ "19" ]	AC varied in from 0.68 to 0.91.	true	true	true	true	true	1,216
5	DISCUSSION	1	19	[ "b19", "b19" ]	17,170,005	pmid-11337477\|pmid-11337477	The six programs we tested produced an AC ranging from 0.67 to 0.88.	[ "19", "19" ]	68	7,491	0	false	The six programs we tested produced an AC ranging from 0.67 to 0.88.	[]	The six programs we tested produced an AC ranging from 0.67 to 0.88.	true	true	true	true	true	1,216
5	DISCUSSION	1	19	[ "b19", "b19" ]	17,170,005	pmid-11337477\|pmid-11337477	The mean of exon specificity and sensitivity ranged from 0.43 to 0.76 in Rogic's tests, while most of the genefinders in this evaluation ranged from 0.44 to 0.75.	[ "19", "19" ]	162	7,492	0	false	The mean of exon specificity and sensitivity ranged from 0.43 to 0.76 in Rogic's tests, while most of the genefinders in this evaluation ranged from 0.44 to 0.75.	[]	The mean of exon specificity and sensitivity ranged from 0.43 to 0.76 in Rogic's tests, while most of the genefinders in this evaluation ranged from 0.44 to 0.75.	true	true	true	true	true	1,216
5	DISCUSSION	1	19	[ "b19", "b19" ]	17,170,005	pmid-11337477\|pmid-11337477	Given these results and those at the whole-gene level discussed above, why have genefinders remained stagnant in their performance especially when they have individually published higher results?	[ "19", "19" ]	195	7,493	0	false	Given these results and those at the whole-gene level discussed above, why have genefinders remained stagnant in their performance especially when they have individually published higher results?	[]	Given these results and those at the whole-gene level discussed above, why have genefinders remained stagnant in their performance especially when they have individually published higher results?	true	true	true	true	true	1,216
5	DISCUSSION	1	19	[ "b19", "b19" ]	17,170,005	pmid-11337477\|pmid-11337477	Have HMM genefinders reached their quantum limits?	[ "19", "19" ]	50	7,494	0	false	Have HMM genefinders reached their quantum limits?	[]	Have HMM genefinders reached their quantum limits?	true	true	true	true	true	1,216
5	DISCUSSION	1	19	[ "b19", "b19" ]	17,170,005	pmid-11337477\|pmid-11337477	How can future HMM genefinder development proceed to be more effective in the future?	[ "19", "19" ]	85	7,495	0	false	How can future HMM genefinder development proceed to be more effective in the future?	[]	How can future HMM genefinder development proceed to be more effective in the future?	true	true	true	true	true	1,216
6	DISCUSSION	0	null	null	17,170,005	null	In order to answer these questions we have developed the PET.	null	61	7,496	0	false	null	null	In order to answer these questions we have developed the PET.	true	true	true	true	true	1,217
6	DISCUSSION	0	null	null	17,170,005	null	We submit that every predicted coding sequence must be placed into one of the 13 possible classes, and the patterns (or ratios) between classes considered in future genefinder development.	null	188	7,497	0	false	null	null	We submit that every predicted coding sequence must be placed into one of the 13 possible classes, and the patterns (or ratios) between classes considered in future genefinder development.	true	true	true	true	true	1,217
6	DISCUSSION	0	null	null	17,170,005	null	Similar to the habit of identifying only four classes of coding regions, any classification of predicted exons that is not comprehensive provides inadequate information for properly ascertaining genefinder performance.	null	218	7,498	0	false	null	null	Similar to the habit of identifying only four classes of coding regions, any classification of predicted exons that is not comprehensive provides inadequate information for properly ascertaining genefinder performance.	true	true	true	true	true	1,217
7	DISCUSSION	0	null	null	17,170,005	null	Future techniques must now focus on resolving these patterns of inaccuracy inherent in all HMM-based genefinders.	null	113	7,499	0	false	null	null	Future techniques must now focus on resolving these patterns of inaccuracy inherent in all HMM-based genefinders.	true	true	true	true	true	1,218

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