Subject: Nucleic Acids Research Table of Contents for 04 November 2019 ------=_Part_631394866.1572370959283 Content-Type: text/plain;charset=UTF-8 Oxford Academic *** {Nucleic Acids Research} *** Volume 47, Issue 19, 4 November 2019 Read this issue (https://academic.oup.com/nar/issue/47/19) ============================= Survey and Summary ============================Genome reading by the NF-kappa B transcription factors Maria Carmen Mulero, Vivien Ya-Fan Wang, Tom Huxford, Gourisankar Ghosh (https://academic.oup.com/nar/article/47/19/9967/5566586) ============================= Chemical Biology and Nucleic Acid Chemistry ============================Interbase FRET in RNA: from A to Z Anders F Füchtbauer, Moa S Wranne, Mattias Bood, Erik Weis, Pauline Pfeiffer (https://academic.oup.com/nar/article/47/19/9990/5572572) ============================= Computational Biology ============================Low complexity regions in the proteins of prokaryotes perform important functional roles and are highly conserved Chrysa Ntountoumi, Panayotis Vlastaridis, Dimitris Mossialos, Constantinos Stathopoulos, Ioannis Iliopoulos (https://academic.oup.com/nar/article/47/19/9998/5559688) Signatures of cell death and proliferation in perturbation transcriptomics data---from confounding factor to effective prediction Bence Szalai, Vigneshwari Subramanian, Christian H Holland, Róbert Alföldi, László G Puskás (https://academic.oup.com/nar/article/47/19/10010/5573547) ============================= Data Resources and Analyses ============================Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data Eldad David Shulman, Ran Elkon (https://academic.oup.com/nar/article/47/19/10027/5566587) ============================= Gene Regulation, Chromatin and Epigenetics ============================Post-transcriptional negative feedback regulation of proteostasis through the Dis3 ribonuclease and its disruption by polyQ-expanded Huntingtin Ka-Yiu Edwin Kong, Ting-Ngai Felix Hung, Pui-Hei Marcus Man, Tin-Ning Wong, Tao Cheng (https://academic.oup.com/nar/article/47/19/10040/5552069) Gene silencing by double-stranded RNA from C. elegans neurons reveals functional mosaicism of RNA interference Snusha Ravikumar, Sindhuja Devanapally, Antony M Jose (https://academic.oup.com/nar/article/47/19/10059/5563947) Human mitochondrial DNA is extensively methylated in a non-CpG context Vibha Patil, Cyrille Cuenin, Felicia Chung, Jesus R Rodriguez Aguilera, Nora Fernandez-Jimenez (https://academic.oup.com/nar/article/47/19/10072/5563943) The metabolic sensor PASK is a histone 3 kinase that also regulates H3K4 methylation by associating with H3K4 MLL2 methyltransferase complex Jimsheena V Karakkat, Suneesh Kaimala, Sreejisha P Sreedharan, Princy Jayaprakash, Ernest A Adeghate (https://academic.oup.com/nar/article/47/19/10086/5569988) Molecular determinants for enzalutamide-induced transcription in prostate cancer Fuwen Yuan, William Hankey, Dayong Wu, Hongyan Wang, Jason Somarelli (https://academic.oup.com/nar/article/47/19/10104/5566589) Ash2l interacts with Oct4-stemness circuitry to promote super-enhancer-driven pluripotency network Ping-Hsing Tsai, Yueh Chien, Mong-Lien Wang, Chih-Hung Hsu, Benoit Laurent (https://academic.oup.com/nar/article/47/19/10115/5573952) ============================= Genome Integrity, Repair and Replication ============================Identification of a ligand binding hot spot and structural motifs replicating aspects of tyrosyl-DNA phosphodiesterase I (TDP1) phosphoryl recognition by crystallographic fragment cocktail screening George T Lountos, Xue Zhi Zhao, Evgeny Kiselev, Joseph E Tropea, Danielle Needle (https://academic.oup.com/nar/article/47/19/10134/5519170) The human Shu complex functions with PDS5B and SPIDR to promote homologous recombination Julieta Martino, Gregory J Brunette, Jonathan Barroso-González, Tatiana N Moiseeva, Chelsea M Smith (https://academic.oup.com/nar/article/47/19/10151/5563942) Conserved HORMA domain-containing protein Hop1 stabilizes interaction between proteins of meiotic DNA break hotspots and chromosome axis Ryo Kariyazono, Arisa Oda, Takatomi Yamada, Kunihiro Ohta (https://academic.oup.com/nar/article/47/19/10166/5563950) SLX4IP acts with SLX4 and XPF--ERCC1 to promote interstrand crosslink repair Huimin Zhang, Zhen Chen, Yin Ye, Zu Ye, Dan Cao (https://academic.oup.com/nar/article/47/19/10181/5565288) ============================= Molecular Biology ============================Spacer acquisition from RNA mediated by a natural reverse transcriptase-Cas1 fusion protein associated with a type III-D CRISPR--Cas system in Vibrio vulnificus Alejandro González-Delgado, Mario Rodríguez Mestre, Francisco Martínez-Abarca, Nicolás Toro (https://academic.oup.com/nar/article/47/19/10202/5559687) HIF-transcribed p53 chaperones HIF-1alpha Esha Madan, Taylor M Parker, Christopher J Pelham, Antonio M Palma, Maria L Peixoto (https://academic.oup.com/nar/article/47/19/10212/5563951) Multiple cytosolic DNA sensors bind plasmid DNA after transfection Nina Semenova, Masa Bosnjak, Bostjan Markelc, Katarina Znidar, Maja Cemazar (https://academic.oup.com/nar/article/47/19/10235/5565289) G-quadruplex located in the 5'UTR of the BAG-1 mRNA affects both its cap-dependent and cap-independent translation through global secondary structure maintenance Rachel Jodoin, Julie C Carrier, Nathalie Rivard, Martin Bisaillon, Jean-Pierre Perreault (https://academic.oup.com/nar/article/47/19/10247/5559686) ============================= Nucleic Acid Enzymes ============================METTL15 introduces N4-methylcytidine into human mitochondrial 12S rRNA and is required for mitoribosome biogenesis Lindsey Van Haute, Alan G Hendrick, Aaron R D'Souza, Christopher A Powell, Pedro Rebelo-Guiomar (https://academic.oup.com/nar/article/47/19/10267/5563944) Dynamical ensemble of the active state and transition state mimic for the RNA-cleaving 8--17 DNAzyme in solution Şölen Ekesan, Darrin M York (https://academic.oup.com/nar/article/47/19/10282/5568213) Oxazinomycin arrests RNA polymerase at the polythymidine sequences Ranjit K Prajapati, Petja Rosenqvist, Kaisa Palmu, Janne J Mäkinen, Anssi M Malinen (https://academic.oup.com/nar/article/47/19/10296/5565285) The hRPC62 subunit of human RNA polymerase III displays helicase activity Leyla El Ayoubi, Hélène Dumay-Odelot, Aleksandar Chernev, Fanny Boissier, Lionel Minvielle-Sébastia (https://academic.oup.com/nar/article/47/19/10313/5569986) ============================= RNA and RNA-protein complexes ============================Functional analysis of Cwc24 ZF-domain in 5' splice site selection Nan-Ying Wu, Soo-Chen Cheng (https://academic.oup.com/nar/article/47/19/10327/5555674) Hypertension-associated mitochondrial DNA 4401A>G mutation caused the aberrant processing of tRNAMet, all 8 tRNAs and ND6 mRNA in the light-strand transcript Xiaoxu Zhao, Limei Cui, Yun Xiao, Qin Mao, Maerhaba Aishanjiang (https://academic.oup.com/nar/article/47/19/10340/5555676) LYAR potentiates rRNA synthesis by recruiting BRD2/4 and the MYST-type acetyltransferase KAT7 to rDNA Keiichi Izumikawa, Hideaki Ishikawa, Harunori Yoshikawa, Sally Fujiyama, Akira Watanabe (https://academic.oup.com/nar/article/47/19/10357/5558127) mTOR-regulated U2af1 tandem exon splicing specifies transcriptome features for translational control Jae-Woong Chang, Hsin-Sung Yeh, Meeyeon Park, Luke Erber, Jiao Sun (https://academic.oup.com/nar/article/47/19/10373/5558346) ============================= Structural Biology ============================Molecular basis of abasic site sensing in single-stranded DNA by the SRAP domain of E. coli yedK Na Wang, Hongyu Bao, Liu Chen, Yanhong Liu, Yue Li (https://academic.oup.com/nar/article/47/19/10388/5555671) Monomeric YoeB toxin retains RNase activity but adopts an obligate dimeric form for thermal stability Ian J Pavelich, Tatsuya Maehigashi, Eric D Hoffer, Ajchareeya Ruangprasert, Stacey J Miles (https://academic.oup.com/nar/article/47/19/10400/5566584) Structural consequences of the interaction of RbgA with a 50S ribosomal subunit assembly intermediate Amal Seffouh, Nikhil Jain, Dushyant Jahagirdar, Kaustuv Basu, Aida Razi (https://academic.oup.com/nar/article/47/19/10414/5563945) The internal interaction in RBBP5 regulates assembly and activity of MLL1 methyltransferase complex Jianming Han, Tingting Li, Yanjing Li, Muchun Li, Xiaoman Wang (https://academic.oup.com/nar/article/47/19/10426/5572575) ============================= Synthetic Biology and Bioengineering ============================Fail-safe genetic codes designed to intrinsically contain engineered organisms Jonathan Calles, Isaac Justice, Detravious Brinkley, Alexa Garcia, Drew Endy (https://academic.oup.com/nar/article/47/19/10439/5568210) De novo design of programmable inducible promoters Xiangyang Liu, Sanjan T P Gupta, Devesh Bhimsaria, Jennifer L Reed, José A Rodríguez-Martínez (https://academic.oup.com/nar/article/47/19/10452/5573546) Synthetic metabolic computation in a bioluminescence-sensing system Natalia Barger, Phyana Litovco, Ximing Li, Mouna Habib, Ramez Daniel (https://academic.oup.com/nar/article/47/19/10464/5572567) ============================= Corrigendum ============================The nuclear structural protein NuMA is a negative regulator of 53BP1 in DNA double-strand break repair Naike Salvador Moreno, Jing Liu, Karen M Haas, Laurie L Parker, Chaitali Chakraborty (https://academic.oup.com/nar/article/47/19/10475/5568214) ============================= Methods Online ============================FICC-Seq: a method for enzyme-specified profiling of methyl-5-uridine in cellular RNA Jean-Michel Carter, Warren Emmett, Igor Rdl Mozos, Annika Kotter, Mark Helm (https://academic.oup.com/nar/article/47/19/e113/5541094) Generation of a caged lentiviral vector through an unnatural amino acid for photo-switchable transduction Yan Wang, Shuai Li, Zhenyu Tian, Jiaqi Sun, Shuobin Liang (https://academic.oup.com/nar/article/47/19/e114/5541091) Targeted short read sequencing and assembly of re-arrangements and candidate gene loci provide megabase diplotypes GiWon Shin, Stephanie U Greer, Li C Xia, HoJoon Lee, Jun Zhou (https://academic.oup.com/nar/article/47/19/e115/5539887) Simultaneous precise editing of multiple genes in human cells Stephan Riesenberg, Manjusha Chintalapati, Dominik Macak, Philipp Kanis, Tomislav Maricic (https://academic.oup.com/nar/article/47/19/e116/5545003) Analyzing whole genome bisulfite sequencing data from highly divergent genotypes Phillip Wulfridge, Ben Langmead, Andrew P Feinberg, Kasper D Hansen (https://academic.oup.com/nar/article/47/19/e117/5545001) Efficient inhibition of RNA self-primed extension by addition of competing 3'-capture DNA-improved RNA synthesis by T7 RNA polymerase Yasaman Gholamalipour, William C Johnson, Craig T Martin (https://academic.oup.com/nar/article/47/19/e118/5545017) Polymerization retardation isothermal amplification (PRIA): a strategy enables sensitively quantify genome-wide 5-methylcytosine oxides rapidly on handy instruments with nanoscale sample input Danping Chen, Yang Wang, Mingming Mo, Junjie Zhang, Yanfei Zhang (https://academic.oup.com/nar/article/47/19/e119/5550326) A transient reporter for editing enrichment (TREE) in human cells Kylie Standage-Beier, Stefan J Tekel, Nicholas Brookhouser, Grace Schwarz, Toan Nguyen (https://academic.oup.com/nar/article/47/19/e120/5552066) Global prediction of chromatin accessibility using small-cell-number and single-cell RNA-seq Weiqiang Zhou, Zhicheng Ji, Weixiang Fang, Hongkai Ji (https://academic.oup.com/nar/article/47/19/e121/5552071) DNA Analysis by Restriction Enzyme (DARE) enables concurrent genomic and epigenomic characterization of single cells Ramya Viswanathan, Elsie Cheruba, Lih Feng Cheow (https://academic.oup.com/nar/article/47/19/e122/5550324) Unsubscribe (http://cp20.com/unsubscribe) Manage email alerts (https://academic.oup.com/my-account/email-alerts) Written requests to unsubscribe can be sent to: Journals Marketing, Oxford University Press, Great Clarendon Street, Oxford, OX2 6DP, UK. Our Privacy Policy (http://global.oup.com/privacy) sets out how Oxford University Press handles your personal information. The content of this email is protected by copyright. Oxford University Press This email is intended for bionet@evol.biology.mcmaster.ca. ------=_Part_631394866.1572370959283 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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New issue alert
 
 
 
 
 
 
Nucleic Acids Research  
Volume 47 Issue 19
 
04 November 2019
 
button-issue.png
 
 
Survey and Summary
 
 
 
Genome reading by the NF-kappa B transcription factors 
 
Maria Carmen Mulero; Vivien Ya-Fan Wang; Tom Huxford ; Gourisankar Ghosh
 
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
Interbase FRET in RNA: from A to Z border= 
 
Anders F Füchtbauer; Moa S Wranne ; Mattias Bood; Erik Weis; Pauline Pfeiffer ...
 
 
 
Computational Biology
 
 
 
Low complexity regions in the proteins of prokaryotes perform important functional roles and are highly conserved border= 
 
Chrysa Ntountoumi ; Panayotis Vlastaridis; Dimitris Mossialos; Constantinos Stathopoulos; Ioannis Iliopoulos ...
 
 
Signatures of cell death and proliferation in perturbation transcriptomics data'from confounding factor to effective prediction border= 
 
Bence Szalai ; Vigneshwari Subramanian; Christian H Holland; Róbert Alföldi; László G Puskás ...
 
 
 
Data Resources and Analyses
 
 
 
Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data border= 
 
Eldad David Shulman ; Ran Elkon
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
Post-transcriptional negative feedback regulation of proteostasis through the Dis3 ribonuclease and its disruption by polyQ-expanded Huntingtin border= 
 
Ka-Yiu Edwin Kong ; Ting-Ngai Felix Hung; Pui-Hei Marcus Man; Tin-Ning Wong; Tao Cheng ...
 
 
Gene silencing by double-stranded RNA from C. elegans neurons reveals functional mosaicism of RNA interference border= 
 
Snusha Ravikumar; Sindhuja Devanapally; Antony M Jose
 
 
Human mitochondrial DNA is extensively methylated in a non-CpG context border= 
 
Vibha Patil ; Cyrille Cuenin; Felicia Chung; Jesus R Rodriguez Aguilera; Nora Fernandez-Jimenez ...
 
 
The metabolic sensor PASK is a histone 3 kinase that also regulates H3K4 methylation by associating with H3K4 MLL2 methyltransferase complex border= 
 
Jimsheena V Karakkat ; Suneesh Kaimala; Sreejisha P Sreedharan; Princy Jayaprakash; Ernest A Adeghate ...
 
 
Molecular determinants for enzalutamide-induced transcription in prostate cancer border= 
 
Fuwen Yuan ; William Hankey; Dayong Wu; Hongyan Wang; Jason Somarelli ...
 
 
Ash2l interacts with Oct4-stemness circuitry to promote super-enhancer-driven pluripotency network border= 
 
Ping-Hsing Tsai ; Yueh Chien; Mong-Lien Wang; Chih-Hung Hsu; Benoit Laurent ...
 
 
 
Genome Integrity, Repair and Replication
 
 
 
Identification of a ligand binding hot spot and structural motifs replicating aspects of tyrosyl-DNA phosphodiesterase I (TDP1) phosphoryl recognition by crystallographic fragment cocktail screening 
 
George T Lountos; Xue Zhi Zhao ; Evgeny Kiselev; Joseph E Tropea; Danielle Needle ...
 
 
The human Shu complex functions with PDS5B and SPIDR to promote homologous recombination border= 
 
Julieta Martino ; Gregory J Brunette; Jonathan Barroso-González; Tatiana N Moiseeva; Chelsea M Smith ...
 
 
Conserved HORMA domain-containing protein Hop1 stabilizes interaction between proteins of meiotic DNA break hotspots and chromosome axis border= 
 
Ryo Kariyazono ; Arisa Oda; Takatomi Yamada; Kunihiro Ohta
 
 
SLX4IP acts with SLX4 and XPF'ERCC1 to promote interstrand crosslink repair border= 
 
Huimin Zhang ; Zhen Chen; Yin Ye; Zu Ye; Dan Cao ...
 
 
 
Molecular Biology
 
 
 
Spacer acquisition from RNA mediated by a natural reverse transcriptase-Cas1 fusion protein associated with a type III-D CRISPR'Cas system in Vibrio vulnificus  border= 
 
Alejandro González-Delgado; Mario Rodríguez Mestre ; Francisco Martínez-Abarca; Nicolás Toro
 
 
HIF-transcribed p53 chaperones HIF-1alpha  border=  
 
Esha Madan; Taylor M Parker; Christopher J Pelham ; Antonio M Palma; Maria L Peixoto ...
 
 
Multiple cytosolic DNA sensors bind plasmid DNA after transfection border= 
 
Nina Semenova ; Masa Bosnjak; Bostjan Markelc; Katarina Znidar; Maja Cemazar ...
 
 
G-quadruplex located in the 5UTR of the BAG-1 mRNA affects both its cap-dependent and cap-independent translation through global secondary structure maintenance border= 
 
Rachel Jodoin ; Julie C Carrier; Nathalie Rivard; Martin Bisaillon; Jean-Pierre Perreault
 
 
 
Nucleic Acid Enzymes
 
 
 
METTL15 introduces N4-methylcytidine into human mitochondrial 12S rRNA and is required for mitoribosome biogenesis border= 
 
Lindsey Van Haute ; Alan G Hendrick; Aaron R D'Souza; Christopher A Powell; Pedro Rebelo-Guiomar ...
 
 
Dynamical ensemble of the active state and transition state mimic for the RNA-cleaving 8'17 DNAzyme in solution border= 
 
Şölen Ekesan ; Darrin M York
 
 
Oxazinomycin arrests RNA polymerase at the polythymidine sequences border= 
 
Ranjit K Prajapati ; Petja Rosenqvist; Kaisa Palmu; Janne J Mäkinen; Anssi M Malinen ...
 
 
The hRPC62 subunit of human RNA polymerase III displays helicase activity border= 
 
Leyla El Ayoubi ; Hélène Dumay-Odelot; Aleksandar Chernev; Fanny Boissier; Lionel Minvielle-Sébastia ...
 
 
 
RNA and RNA-protein complexes
 
 
 
Functional analysis of Cwc24 ZF-domain in 5 splice site selection border= 
 
Nan-Ying Wu ; Soo-Chen Cheng
 
 
Hypertension-associated mitochondrial DNA 4401A>G mutation caused the aberrant processing of tRNAMet, all 8 tRNAs and ND6 mRNA in the light-strand transcript border= 
 
Xiaoxu Zhao; Limei Cui; Yun Xiao; Qin Mao; Maerhaba Aishanjiang ...
 
 
LYAR potentiates rRNA synthesis by recruiting BRD2/4 and the MYST-type acetyltransferase KAT7 to rDNA border= 
 
Keiichi Izumikawa ; Hideaki Ishikawa; Harunori Yoshikawa; Sally Fujiyama; Akira Watanabe ...
 
 
mTOR-regulated U2af1 tandem exon splicing specifies transcriptome features for translational control border= 
 
Jae-Woong Chang ; Hsin-Sung Yeh; Meeyeon Park; Luke Erber; Jiao Sun ...
 
 
 
Structural Biology
 
 
 
Molecular basis of abasic site sensing in single-stranded DNA by the SRAP domain of E. coli yedK border= 
 
Na Wang; Hongyu Bao ; Liu Chen; Yanhong Liu; Yue Li ...
 
 
Monomeric YoeB toxin retains RNase activity but adopts an obligate dimeric form for thermal stability border= 
 
Ian J Pavelich ; Tatsuya Maehigashi; Eric D Hoffer; Ajchareeya Ruangprasert; Stacey J Miles ...
 
 
Structural consequences of the interaction of RbgA with a 50S ribosomal subunit assembly intermediate border= 
 
Amal Seffouh ; Nikhil Jain; Dushyant Jahagirdar; Kaustuv Basu; Aida Razi ...
 
 
The internal interaction in RBBP5 regulates assembly and activity of MLL1 methyltransferase complex border= 
 
Jianming Han ; Tingting Li; Yanjing Li; Muchun Li; Xiaoman Wang ...
 
 
 
Synthetic Biology and Bioengineering
 
 
 
Fail-safe genetic codes designed to intrinsically contain engineered organisms border= 
 
Jonathan Calles ; Isaac Justice; Detravious Brinkley; Alexa Garcia; Drew Endy
 
 
De novo design of programmable inducible promoters border= 
 
Xiangyang Liu; Sanjan T P Gupta; Devesh Bhimsaria; Jennifer L Reed; José A Rodríguez-Martínez ...
 
 
Synthetic metabolic computation in a bioluminescence-sensing system border= 
 
Natalia Barger ; Phyana Litovco; Ximing Li; Mouna Habib; Ramez Daniel
 
 
 
Corrigendum
 
 
 
The nuclear structural protein NuMA is a negative regulator of 53BP1 in DNA double-strand break repair border= 
 
Naike Salvador Moreno ; Jing Liu; Karen M Haas; Laurie L Parker; Chaitali Chakraborty ...
 
 
 
Methods Online
 
 
 
FICC-Seq: a method for enzyme-specified profiling of methyl-5-uridine in cellular RNA border= 
 
Jean-Michel Carter ; Warren Emmett; Igor Rdl Mozos; Annika Kotter; Mark Helm ...
 
 
Generation of a caged lentiviral vector through an unnatural amino acid for photo-switchable transduction border= 
 
Yan Wang ; Shuai Li; Zhenyu Tian; Jiaqi Sun; Shuobin Liang ...
 
 
Targeted short read sequencing and assembly of re-arrangements and candidate gene loci provide megabase diplotypes border= 
 
GiWon Shin ; Stephanie U Greer; Li C Xia; HoJoon Lee; Jun Zhou ...
 
 
Simultaneous precise editing of multiple genes in human cells border= 
 
Stephan Riesenberg ; Manjusha Chintalapati; Dominik Macak; Philipp Kanis; Tomislav Maricic ...
 
 
Analyzing whole genome bisulfite sequencing data from highly divergent genotypes border= 
 
Phillip Wulfridge ; Ben Langmead; Andrew P Feinberg; Kasper D Hansen
 
 
Efficient inhibition of RNA self-primed extension by addition of competing 3-capture DNA-improved RNA synthesis by T7 RNA polymerase border= 
 
Yasaman Gholamalipour ; William C Johnson; Craig T Martin
 
 
Polymerization retardation isothermal amplification (PRIA): a strategy enables sensitively quantify genome-wide 5-methylcytosine oxides rapidly on handy instruments with nanoscale sample input border= 
 
Danping Chen ; Yang Wang; Mingming Mo; Junjie Zhang; Yanfei Zhang ...
 
 
A transient reporter for editing enrichment (TREE) in human cells border= 
 
Kylie Standage-Beier ; Stefan J Tekel; Nicholas Brookhouser; Grace Schwarz; Toan Nguyen ...
 
 
Global prediction of chromatin accessibility using small-cell-number and single-cell RNA-seq border= 
 
Weiqiang Zhou ; Zhicheng Ji; Weixiang Fang; Hongkai Ji
 
 
DNA Analysis by Restriction Enzyme (DARE) enables concurrent genomic and epigenomic characterization of single cells border= 
 
Ramya Viswanathan ; Elsie Cheruba; Lih Feng Cheow
 
 
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