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  1. Content type: Research article

    The SnRK2s (Plant specific protein kinase) are involved in various biological processes, such as plant defense and environmental challenges. In Arabidopsis, AtSnRK2s regulate the expression of some metal transpor...

    Authors: Ruijiao Wang, Chao Wang, Qin Yao, Xue Xiao, Xing Fan, Lina Sha, Jian Zeng, Houyang Kang, Haiqin Zhang, Yonghong Zhou and Yi Wang

    Citation: BMC Genomics 2019 20:210

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  2. Content type: Research article

    Plants adapted to diverse environments on Earth throughout their evolutionary history, and developed mechanisms to thrive in a variety of terrestrial habitats. When plants are grown in the novel environment of...

    Authors: Mingqi Zhou, Natasha J. Sng, Collin E. LeFrois, Anna-Lisa Paul and Robert J. Ferl

    Citation: BMC Genomics 2019 20:205

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  3. Content type: Research article

    In the summer of 2013, Aedes aegypti Linnaeus was first detected in three cities in central California (Clovis, Madera and Menlo Park). It has now been detected in multiple locations in central and southern CA as...

    Authors: Yoosook Lee, Hanno Schmidt, Travis C. Collier, William R. Conner, Mark J. Hanemaaijer, Montgomery Slatkin, John M. Marshall, Joanna C. Chiu, Chelsea T. Smartt, Gregory C. Lanzaro, F. Steve Mulligan and Anthony J. Cornel

    Citation: BMC Genomics 2019 20:204

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  4. Content type: Research article

    Fungi of the genus Botrytis (presently containing ~ 35 species) are able to infect more than 1400 different plant species and cause losses in a wide range of crops of economic importance. The best studied species...

    Authors: Claudio A. Valero-Jiménez, Javier Veloso, Martijn Staats and Jan A. L. van Kan

    Citation: BMC Genomics 2019 20:203

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  5. Content type: Research article

    Monogenean flatworms are the main fish ectoparasites inflicting serious economic losses in aquaculture. The polyopisthocotylean Sparicotyle chrysophrii parasitizes the gills of gilthead sea bream (GSB, Sparus aur...

    Authors: M. Carla Piazzon, Ivona Mladineo, Fernando Naya-Català, Ron P. Dirks, Susanne Jong-Raadsen, Anamarija Vrbatović, Jerko Hrabar, Jaume Pérez-Sánchez and Ariadna Sitjà-Bobadilla

    Citation: BMC Genomics 2019 20:200

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  6. Content type: Research article

    Peroxisome Proliferator-Activated receptor α (PPARα) and cAMP-Responsive Element Binding Protein 3-Like 3 (CREB3L3) are transcription factors involved in the regulation of lipid metabolism in the liver. The ai...

    Authors: Philip M. M. Ruppert, Jong-Gil Park, Xu Xu, Kyu Yeon Hur, Ann-Hwee Lee and Sander Kersten

    Citation: BMC Genomics 2019 20:199

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  7. Content type: Research article

    Genomes of lethal Amanita and Galerina mushrooms have gradually become available in the past ten years; in contrast the other known amanitin-producing genus, Lepiota, is still vacant in this aspect. A fatal mushr...

    Authors: Yunjiao Lüli, Qing Cai, Zuo H. Chen, Hu Sun, Xue-Tai Zhu, Xuan Li, Zhu L. Yang and Hong Luo

    Citation: BMC Genomics 2019 20:198

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  8. Content type: Research article

    Escherichia coli O157:H7 (O157) has been linked to numerous foodborne disease outbreaks. The ability to rapidly sequence and analyze genomes is important for understanding epidemiology, virulence, survival, and e...

    Authors: Vijay K. Sharma, Suryatej Akavaram, Robert G. Schaut and Darrell O. Bayles

    Citation: BMC Genomics 2019 20:196

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  9. Content type: Research article

    Although the importance of host plant chemistry in plant–insect interactions is widely recognized, our understanding about the genetic basis underlying the relationship between changes in midgut proteins and a...

    Authors: Zehai Hou and Cong Wei

    Citation: BMC Genomics 2019 20:182

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  10. Content type: Research article

    Copy number variations (CNVs) are structural variants consisting of large-scale insertions and deletions of genomic fragments. Exploring CNVs and estimating their effects on phenotypes are useful for genome se...

    Authors: Mei Liu, Lingzhao Fang, Shuli Liu, Michael G. Pan, Eyal Seroussi, John B. Cole, Li Ma, Hong Chen and George E. Liu

    Citation: BMC Genomics 2019 20:181

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  11. Content type: Research article

    After polyploidization, a genome may experience large-scale genome-repatterning, featuring wide-spread DNA rearrangement and loss, and often chromosome number reduction. Grasses share a common tetraploidizatio...

    Authors: Zhenyi Wang, Jinpeng Wang, Yuxin Pan, Tianyu Lei, Weina Ge, Li Wang, Lan Zhang, Yuxian Li, Kanglu Zhao, Tao Liu, Xiaoming Song, Jiaqi Zhang, Jigao Yu, Jingjing Hu and Xiyin Wang

    Citation: BMC Genomics 2019 20:180

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  12. Content type: Research article

    Bioko is one of the few islands that exist around Africa, the most genetically diverse continent on the planet. The native Bantu-speaking inhabitants of Bioko, the Bubi, are believed to have colonized the isla...

    Authors: Pere Gelabert, Manuel Ferrando-Bernal, Toni de-Dios, Benedetta Mattorre, Elena Campoy, Amaya Gorostiza, Etienne Patin, Antonio González-Martín and Carles Lalueza-Fox

    Citation: BMC Genomics 2019 20:179

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  13. Content type: Research article

    The power of genome-wide association studies (GWAS) is often limited by the sample size available for the analysis. Milk fatty acid (FA) traits are scarcely recorded due to expensive and time-consuming analyti...

    Authors: G. Gebreyesus, A. J. Buitenhuis, N. A. Poulsen, M. H. P. W. Visker, Q. Zhang, H. J. F. van Valenberg, D. Sun and H. Bovenhuis

    Citation: BMC Genomics 2019 20:178

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  14. Content type: Database Article

    Non-human primates (NHPs), particularly macaques, serve as critical and highly relevant pre-clinical models of human disease. The similarity in human and macaque natural disease susceptibility, along with para...

    Authors: Benjamin N. Bimber, Melissa Y. Yan, Samuel M. Peterson and Betsy Ferguson

    Citation: BMC Genomics 2019 20:176

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  15. Content type: Research article

    The phyla Cnidaria, Placozoa, Ctenophora, and Porifera emerged before the split of proto- and deuterostome animals, about 600 million years ago. These early metazoans are interesting, because they can give us ...

    Authors: Sofie K. D. Nielsen, Thomas L. Koch, Frank Hauser, Anders Garm and Cornelis J. P. Grimmelikhuijzen

    Citation: BMC Genomics 2019 20:175

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  16. Content type: Research article

    The sample ascertainment bias due to complex population structures remains a major challenge in genome-wide investigations of complex traits. In this study we derived the high-resolution population structure a...

    Authors: Gertrud Grilz-Seger, Thomas Druml, Markus Neuditschko, Max Dobretsberger, Michaela Horna and Gottfried Brem

    Citation: BMC Genomics 2019 20:174

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  17. Content type: Research article

    With the unprecedented rapid growth rate (up to 2.75 cm/day), velvet antler is an invaluable model for the identification of potent growth factors and signaling networks for extremely fast growing tissues, mai...

    Authors: Hengxing Ba, Datao Wang, Tung On Yau, Yudong Shang and Chunyi Li

    Citation: BMC Genomics 2019 20:173

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  18. Content type: Research article

    Diseases on Prunus spp. have been associated with a large number of phylogenetically different pathovars and species within the P. syringae species complex. Despite their economic significance, there is a severe ...

    Authors: Michela Ruinelli, Jochen Blom, Theo H. M. Smits and Joël F. Pothier

    Citation: BMC Genomics 2019 20:172

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  19. Content type: Research article

    Little is understood of the molecular mechanisms involved in the earliest cell fate decision in human development, leading to the establishment of the trophectoderm (TE) and inner cell mass (ICM) stem cell pop...

    Authors: H. L. Smith, A. Stevens, B. Minogue, S. Sneddon, L. Shaw, L. Wood, T. Adeniyi, H. Xiao, P. Lio, S. J. Kimber and D. R. Brison

    Citation: BMC Genomics 2019 20:171

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  20. Content type: Research article

    Intramuscular fat (IMF) content and composition have a strong impact on the nutritional and organoleptic properties of porcine meat. The goal of the current work was to compare the patterns of gene expression ...

    Authors: Rayner González-Prendes, Raquel Quintanilla, Emilio Mármol-Sánchez, Ramona N. Pena, Maria Ballester, Tainã Figueiredo Cardoso, Arianna Manunza, Joaquim Casellas, Ángela Cánovas, Isabel Díaz, José Luis Noguera, Anna Castelló, Anna Mercadé and Marcel Amills

    Citation: BMC Genomics 2019 20:170

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  21. Content type: Research article

    Small RNAs (sRNAs) are short non-coding RNA molecules (20–30 nt) that regulate gene expression at transcriptional or post-transcriptional levels in many eukaryotic organisms, through a mechanism known as RNA i...

    Authors: Alessandro Silvestri, Valentina Fiorilli, Laura Miozzi, Gian Paolo Accotto, Massimo Turina and Luisa Lanfranco

    Citation: BMC Genomics 2019 20:169

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  22. Content type: Research article

    Leptospirosis is an emerging infectious disease worldwide that can cause high morbidity and mortality rates in humans and animals. The causative spirochetes have reservoirs in mammalian hosts, but there has be...

    Authors: Alongkorn Kurilung, Chantisa Keeratipusana, Prapat Suriyaphol, David J. Hampson and Nuvee Prapasarakul

    Citation: BMC Genomics 2019 20:168

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    The Correction to this article has been published in BMC Genomics 2019 20:246

  23. Content type: Research article

    Saliva of mosquitoes contains anti-platelet, anti-clotting, vasodilatory, anti-complement and anti-inflammatory substances that help the blood feeding process. The salivary polypeptides are at a fast pace of e...

    Authors: Vera Margarete Scarpassa, Humbeto Julio Debat, Ronildo Baiatone Alencar, José Ferreira Saraiva, Eric Calvo, Bruno Arcà and José M. C. Ribeiro

    Citation: BMC Genomics 2019 20:166

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  24. Content type: Software Article

    Recent adva1nces in whole genome sequencing (WGS) based technologies have facilitated multi-step applications for predicting antimicrobial resistance (AMR) and investigating the molecular epidemiology of Neisseri...

    Authors: Reema Singh, Jo-Anne R. Dillon, Walter Demczuk and Anthony Kusalik

    Citation: BMC Genomics 2019 20:165

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  25. Content type: Research article

    Microglia are multifunctional cells that are key players in brain development and homeostasis. Recent years have seen tremendous growth in our understanding of the role microglia play in neurodegeneration, CNS...

    Authors: Christine E. Cho, Sagar S. Damle, Edward V. Wancewicz, Swagatam Mukhopadhyay, Christopher E. Hart, Curt Mazur, Eric E. Swayze and Fredrik Kamme

    Citation: BMC Genomics 2019 20:164

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  26. Content type: Research article

    Altered epigenetic profiles are a feature of intestinal diseases, including ulcerative colitis and Crohn’s disease. DNA methylation studies in these diseases have utilised intestinal mucosal tissue or blood wh...

    Authors: Nerissa L. Hearn, Aaron S. Coleman, Vincent Ho, Christine L. Chiu and Joanne M. Lind

    Citation: BMC Genomics 2019 20:163

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  27. Content type: Methodology article

    Understanding how transcription occurs requires the integration of genome-wide and locus-specific information gleaned from robust technologies. Chromatin immunoprecipitation (ChIP) is a staple in gene expressi...

    Authors: Xue Qing David Wang, Christopher J. F. Cameron, Denis Paquette, Dana Segal, Reid Warsaba, Mathieu Blanchette and Josée Dostie

    Citation: BMC Genomics 2019 20:162

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  28. Content type: Research article

    Mermithid nematodes, such as Ovomermis sinensis, display a broad host range including some lepidopteran pests. Infective juveniles penetrate their host through the cuticle, complete their growth within the hemoco...

    Authors: Gui-Jie Wang, Xiao-Rong Zhuo, Wen-Wen Wang, Xu-Sheng Liu, Guo-Xiu Wang and Jia-Lin Wang

    Citation: BMC Genomics 2019 20:161

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  29. Content type: Methodology article

    Single nucleotide polymorphisms (SNP) have been applied as important molecular markers in genetics and breeding studies. The rapid advance of next generation sequencing (NGS) provides a high-throughput means o...

    Authors: Yun Zhao, Ke Wang, Wen-li Wang, Ting-ting Yin, Wei-qi Dong and Chang-jie Xu

    Citation: BMC Genomics 2019 20:160

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  30. Content type: Research article

    Maize is one of the primary crops of genetic manipulation, which provides an excellent means of promoting stress resistance and increasing yield. However, the differences in induction and regeneration capacity...

    Authors: Xiaoling Zhang, Yanli Wang, Yuanyuan Yan, Hua Peng, Yun Long, Yinchao Zhang, Zhou Jiang, Peng Liu, Chaoying Zou, Huanwei Peng, Guangtang Pan and Yaou Shen

    Citation: BMC Genomics 2019 20:159

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  31. Content type: Research article

    Identifying mRNA targets of miRNAs is critical for studying gene expression regulation at the whole-genome level. Multiple computational tools have been developed to predict miRNA:mRNA interactions. Nonetheles...

    Authors: Bi Zhao and Bin Xue

    Citation: BMC Genomics 2019 20:158

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  32. Content type: Research article

    Sclerotinia sclerotiorum is a broad-host range necrotrophic pathogen which is the causative agent of Sclerotinia stem rot (SSR), and a major disease of soybean (Glycine max). A time course transcriptomic analysis...

    Authors: Nathaniel M. Westrick, Ashish Ranjan, Sachin Jain, Craig R. Grau, Damon L. Smith and Mehdi Kabbage

    Citation: BMC Genomics 2019 20:157

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  33. Content type: Research article

    Korean Hanwoo cattle are known for their high meat quality, especially their high intramuscular fat compared to most other cattle breeds. Different muscles have very different meat quality traits and a study o...

    Authors: Sara de las Heras-Saldana, Ki Yong Chung, Seung Hwan Lee and Cedric Gondro

    Citation: BMC Genomics 2019 20:156

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  34. Content type: Research article

    Sequencing-based detection and characterization of viruses in complex samples can suffer from lack of sensitivity due to a variety of factors including, but not limited to, low titer, small genome size, and co...

    Authors: Adrian C. Paskey, Kenneth G. Frey, Gary Schroth, Stephen Gross, Theron Hamilton and Kimberly A. Bishop-Lilly

    Citation: BMC Genomics 2019 20:155

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  35. Content type: Research article

    Incilaria (= Meghimatium) fruhstorferi is an air-breathing land slug found in restricted habitats of Japan, Taiwan and selected provinces of South Korea (Jeju, Chuncheon, Busan, and Deokjeokdo). The species is on...

    Authors: Bharat Bhusan Patnaik, Jong Min Chung, Hee Ju Hwang, Min Kyu Sang, Jie Eun Park, Hye Rin Min, Hang Chul Cho, Neha Dewangan, Snigdha Baliarsingh, Se Won Kang, So Young Park, Yong Hun Jo, Hong Seog Park, Wan Jong Kim, Yeon Soo Han, Jun Sang Lee…

    Citation: BMC Genomics 2019 20:154

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  36. Content type: Research article

    Microsatellites, or Simple Sequence Repeats (SSRs), are short tandem repeats of 1–6 nt motifs present in all genomes. Emerging evidence points to their role in cellular processes and gene regulation. Despite t...

    Authors: Surabhi Srivastava, Akshay Kumar Avvaru, Divya Tej Sowpati and Rakesh K. Mishra

    Citation: BMC Genomics 2019 20:153

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  37. Content type: Research article

    Triple negative breast cancer (TNBC) is a malignancy with very poor prognosis, due to its aggressive clinical characteristics and lack of response to receptor-targeted drug therapy. In TNBC, immune-related pat...

    Authors: Fernando J. Velloso, Alexandre R. Campos, Mari C. Sogayar and Ricardo G. Correa

    Citation: BMC Genomics 2019 20:152

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  38. Content type: Research article

    Meat quality related phenotypes are difficult and expensive to measure and predict but are ideal candidates for genomic selection if genetic markers that account for a worthwhile proportion of the phenotypic v...

    Authors: Joel D. Leal-Gutiérrez, Mauricio A. Elzo, D. Dwain Johnson, Heather Hamblen and Raluca G. Mateescu

    Citation: BMC Genomics 2019 20:151

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  39. Content type: Research article

    Genome-wide association studies (GWAS) are utilized in cattle to identify regions or genetic variants associated with phenotypes of interest, and thus, to identify design strategies that allow for the increase...

    Authors: Luis Orlando Duitama Carreño, Matilde da Conceição Pessoa, Rafael Espigolan, Luciana Takada, Tiago Bresolin, Ligia Cavani, Fernando Baldi, Roberto Carvalheiro, Lucia Galvão de Albuquerque and Ricardo da Fonseca

    Citation: BMC Genomics 2019 20:150

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  40. Content type: Research article

    Glyceollins are isoflavonoid-derived pathogen-inducible defense metabolites (phytoalexins) from soybean (Glycine max L. Merr) that have important roles in providing defense against pathogens. They also have impre...

    Authors: Md Asraful Jahan, Brianna Harris, Matthew Lowery, Katie Coburn, Aniello M. Infante, Ryan J. Percifield, Amanda G. Ammer and Nik Kovinich

    Citation: BMC Genomics 2019 20:149

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  41. Content type: Research article

    Coral reefs can experience salinity fluctuations due to rainfall and runoff; these events can have major impacts on the corals and lead to bleaching and mortality. On the Great Barrier Reef (GBR), low salinity...

    Authors: Catalina Aguilar, Jean-Baptiste Raina, Sylvain Fôret, David C. Hayward, Bruno Lapeyre, David G. Bourne and David J. Miller

    Citation: BMC Genomics 2019 20:148

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  42. Content type: Research article

    Pain is a subjective experience derived from complex interactions among biological, environmental, and psychosocial pathways. Sex differences in pain sensitivity and chronic pain prevalence are well establishe...

    Authors: Kimberly E. Stephens, Weiqiang Zhou, Zhicheng Ji, Zhiyong Chen, Shaoqiu He, Hongkai Ji, Yun Guan and Sean D. Taverna

    Citation: BMC Genomics 2019 20:147

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  43. Content type: Research article

    Prostate cancer (PCa) is the most common malignant neoplasm among men in many countries. Since most precancerous and cancerous tissues show signs of inflammation, chronic bacterial prostatitis has been hypothe...

    Authors: Ye Feng, Varune Rohan Ramnarine, Robert Bell, Stanislav Volik, Elai Davicioni, Vanessa M. Hayes, Shancheng Ren and Colin C. Collins

    Citation: BMC Genomics 2019 20:146

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  44. Content type: Research article

    In wine fermentation starter cultures, the blending of non-Saccharomyces yeast with Saccharomyces cerevisiae to improve the complexity of wine has become common practice, but data regarding the impact of co-culti...

    Authors: Kirti Shekhawat, Hugh Patterton, Florian F. Bauer and Mathabatha E. Setati

    Citation: BMC Genomics 2019 20:145

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  45. Content type: Research article

    Trichoderma spp. are effective biocontrol agents for many plant pathogens, thus the mechanism of Trichoderma-induced plant resistance is not fully understood. In this study, a novel Trichoderma strain was identif...

    Authors: Min Yuan, Yuanyuan Huang, Weina Ge, Zhenhua Jia, Shuishan Song, Lan Zhang and Yali Huang

    Citation: BMC Genomics 2019 20:144

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  46. Content type: Research article

    Genital C. trachomatis infection may cause pelvic inflammatory disease (PID) that can lead to tubal factor infertility (TFI). Understanding the pathogenesis of chlamydial complications including the pathophysiolo...

    Authors: Ifeyinwa Benyeogor, Tankya Simoneaux, Yuehao Wu, Stephanie Lundy, Zenas George, Khamia Ryans, Danielle McKeithen, Roshan Pais, Debra Ellerson, W. Walter Lorenz, Tolulope Omosun, Winston Thompson, Francis O. Eko, Carolyn M. Black, Uriel Blas-Machado, Joseph U. Igietseme…

    Citation: BMC Genomics 2019 20:143

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