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Microbial genetics, genomics and proteomics

Section edited by Hirotada Mori

This section aims to publish studies relating to all aspects of microbial genomics, proteomics, metabolomics and systems biology.

Page 1 of 8

  1. Cadmium (Cd) is a severely toxic heavy metal to most microorganisms. Many bacteria have developed Cd2+ resistance.

    Authors: Xiaoxia Yu, Zundan Ding, Yangyang Ji, Jintong Zhao, Xiaoqing Liu, Jian Tian, Ningfeng Wu and Yunliu Fan

    Citation: BMC Microbiology 2020 20:18

    Content type: Research article

    Published on:

  2. Thaumarchaeota are abundant in the Amazon River, where they are the only ammonia-oxidizing archaea. Despite the importance of Thaumarchaeota, little is known about their physiology, mainly because few isolates...

    Authors: Otávio H. B. Pinto, Thais F. Silva, Carla S. Vizzotto, Renata H. Santana, Fabyano A. C. Lopes, Bruno S. Silva, Fabiano L. Thompson and Ricardo H. Kruger

    Citation: BMC Microbiology 2020 20:13

    Content type: Research article

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  3. The comparisons of molecular characterization and antibiotic resistance of Klebsiella pneumoniae (KP) isolates from humans and other animal hosts are not well studied. Our goal was to compare the molecular epidem...

    Authors: Xue-shan Zhong, Yong-zhi Li, Jing Ge, Gang Xiao, Yun Mo, Yu-qi Wen, Jing-ping Liu, Yi-quan Xiong, Min Qiu, Shu-ting Huo, Ming-ji Cheng and Qing Chen

    Citation: BMC Microbiology 2020 20:12

    Content type: Research article

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  4. Intestinal pathogen infections are widespread among impoverished populations. Enterocytozoon bieneusi is the most common pathogen of intestinal microsporidian species in humans worldwide. However, no epidemiologi...

    Authors: Yujuan Shen, Baiyan Gong, Xiaohua Liu, Yanchen Wu, Fengkun Yang, Jie Xu, Xiaofan Zhang, Jianping Cao and Aiqin Liu

    Citation: BMC Microbiology 2020 20:10

    Content type: Research article

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  5. Interactions between transcription factors and DNA lie at the centre of many biological processes including DNA recombination, replication, repair and transcription. Most bacteria encode diverse proteins that ...

    Authors: Shi-qi An, Miguel A. Valvano, Yan-hua Yu, Jeremy S. Webb and Guillermo Lopez Campos

    Citation: BMC Microbiology 2020 20:1

    Content type: Methodology article

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  6. Some of the spore-forming strains of Bacillus probiotics are marketed commercially as they survive harsh gastrointestinal conditions and bestow health benefits to the host.

    Authors: Indu Khatri, Gaurav Sharma and Srikrishna Subramanian

    Citation: BMC Microbiology 2019 19:307

    Content type: Research article

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  7. Grey mould is an important plant disease worldwide, caused by Botrytis cinerea, resulting in serious economic loss. Wuyiencin, a low toxicity, high efficiency, and broad-spectrum agricultural antibiotic, has been...

    Authors: Liming Shi, Beibei Ge, Jinzi Wang, Binghua Liu, Jinjin Ma, Qiuhe Wei and Kecheng Zhang

    Citation: BMC Microbiology 2019 19:280

    Content type: Research article

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  8. HSV-1 is a common pathogen that infects 50–90% of the human population worldwide. HSV-1 causes numerous infection-related diseases, some of which are severely life-threatening. There are antiviral medications ...

    Authors: Qiang Huang, Jue Hou, Peng Yang, Jun Yan, Xiaoliang Yu, Ying Zhuo, Sudan He and Feng Xu

    Citation: BMC Microbiology 2019 19:274

    Content type: Research article

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  9. Cannas are popular ornamental plants and widely planted for the beautiful foliage and flower. Viral disease is a major threaten to canna horticulture industry. In the city of Beijing, mosaic disease in canna w...

    Authors: Yongqiang Li, Fei Xia, Yixuan Wang, Chenge Yan, Anning Jia and Yongjiang Zhang

    Citation: BMC Microbiology 2019 19:260

    Content type: Research article

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  10. Gene overlapping is a frequent phenomenon in microbial genomes. Excluding so-called “trivial overlapping”, there are significant implications of such genetic arrangements, including regulation of gene expressi...

    Authors: Paweł Wawrzyniak, Agnieszka Sobolewska-Ruta, Piotr Zaleski, Natalia Łukasiewicz, Paulina Kabaj, Piotr Kierył, Agata Gościk, Anna Bierczyńska-Krzysik, Piotr Baran, Anna Mazurkiewicz-Pisarek, Andrzej Płucienniczak and Dariusz Bartosik

    Citation: BMC Microbiology 2019 19:254

    Content type: Research article

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  11. The human small intestine plays a central role in the processes of digestion and nutrient absorption. However, characterizations of the human gut microbiome have largely relied on stool samples, and the associ...

    Authors: Gabriela Guimaraes Sousa Leite, Walter Morales, Stacy Weitsman, Shreya Celly, Gonzalo Parodi, Ruchi Mathur, Rashin Sedighi, Gillian M. Barlow, Ali Rezaie and Mark Pimentel

    Citation: BMC Microbiology 2019 19:239

    Content type: Methodology article

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  12. Co-translational processes in bacteria are attractive drug targets, but while some processes are essential, others are not. The essentiality of Peptide Deformylase (PDF, def) for vitality of mycobacteria was spec...

    Authors: Noga Naor, Omer Gadot, Michal Meir and Daniel Barkan

    Citation: BMC Microbiology 2019 19:232

    Content type: Research article

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  13. TnaphA6-carrying repAci6 plasmids have been detected in Acinetobacter baumannii isolates belonging to global clones, GC1 and GC2, worldwide. Here, we examined whether RepAci6 plasmids family play a role in the di...

    Authors: Parisa Aris, Mohammad Ali Boroumand and Masoumeh Douraghi

    Citation: BMC Microbiology 2019 19:221

    Content type: Research article

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  14. Cellulose is synthesized by an array of bacterial species. Komagataeibacter xylinus is the best characterized as it produces copious amounts of the polymer extracellularly. Despite many advances in the past decad...

    Authors: Luis Salgado, Silvia Blank, Reza Alipour Moghadam Esfahani, Janice L. Strap and Dario Bonetta

    Citation: BMC Microbiology 2019 19:216

    Content type: Research article

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  15. Several serious vegetable-associated outbreaks of enterohemorrhagic Escherichia coli (EHEC) infections have occurred during the last decades. In this context, vegetables have been suggested to function as seconda...

    Authors: Thorsten Bufe, André Hennig, Jochen Klumpp, Agnes Weiss, Kay Nieselt and Herbert Schmidt

    Citation: BMC Microbiology 2019 19:212

    Content type: Research article

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  16. Efflux pump mediated antibiotic resistance is an unnoticed and undetected mechanism in clinical microbiology laboratory. RND efflux systems are known for aminoglycoside and tetracycline resistance whereas thei...

    Authors: Shiela Chetri, Deepshikha Bhowmik, Deepjyoti Paul, Piyush Pandey, Debadatta Dhar Chanda, Atanu Chakravarty, Debajyoti Bora and Amitabha Bhattacharjee

    Citation: BMC Microbiology 2019 19:210

    Content type: Research article

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  17. Plants have evolved intimate interactions with soil microbes for a range of beneficial functions including nutrient acquisition, pathogen resistance and stress tolerance. Further understanding of this system i...

    Authors: Fang Liu, Tarek Hewezi, Sarah L. Lebeis, Vince Pantalone, Parwinder S. Grewal and Margaret E. Staton

    Citation: BMC Microbiology 2019 19:201

    Content type: Research article

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  18. Enterocytozoon bieneusi is one of the commonest microsporidians contributing to human microsporidiosis, and is frequently found in animals in various countries. However, there is limited epidemiological informati...

    Authors: Yan Zhang, Anson V. Koehler, Tao Wang, David Cunliffe and Robin B. Gasser

    Citation: BMC Microbiology 2019 19:183

    Content type: Research article

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  19. Salmonella enterica is regarded as a major public health threat worldwide. Salmonella secretes the novel translocated effector protein K2 (SseK2), but it is unclear whether this protein plays a significant role i...

    Authors: Xiaojie Zhang, Lei He, Chunjie Zhang, Chuan Yu, Yadong Yang, Yanyan Jia, Xiangchao Cheng, Yinju Li, Chengshui Liao, Jing Li, Zuhua Yu and Fuyu Du

    Citation: BMC Microbiology 2019 19:182

    Content type: Research article

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  20. Most species of Shewanella harbor two ferrochelatase paralogues for the biosynthesis of c-type cytochromes, which are crucial for their respiratory versatility. In our previous study of the Shewanella loihica PV-...

    Authors: Jingcheng Dai, Yaqi Liu, Shuangyuan Liu, Shuyang Li, Na Gao, Jing Wang, Jizhong Zhou and Dongru Qiu

    Citation: BMC Microbiology 2019 19:173

    Content type: Research article

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  21. Termites are an important food resource for many human populations around the world, and are a good supply of nutrients. The fungus-farming ‘higher’ termite members of Macrotermitinae are also consumed by mode...

    Authors: Stephanie L. Schnorr, Courtney A. Hofman, Shandukani R. Netshifhefhe, Frances D. Duncan, Tanvi P. Honap, Julie Lesnik and Cecil M. Lewis

    Citation: BMC Microbiology 2019 19:164

    Content type: Research article

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  22. The role of soil microorganisms in plant growth, nutrient utilization, drought tolerance as well as biocontrol activity cannot be over-emphasized, especially in this era when food crisis is a global challenge....

    Authors: Nicholas O. Igiehon, Olubukola O. Babalola and Bukola R. Aremu

    Citation: BMC Microbiology 2019 19:159

    Content type: Research article

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  23. Staphylococcus epidermidis has emerged as an often encountered pathogen responsible for hospital-acquired infections. The aim of present study is to investigate the microbiological characteristic of S. epidermidi...

    Authors: Yinjuan Guo, Yu Ding, Li Liu, Xiaofei Shen, Zhihao Hao, Jingjing Duan, Ye Jin, Zengqiang Chen and Fangyou Yu

    Citation: BMC Microbiology 2019 19:157

    Content type: Research article

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  24. UK public health organisations perform routine antimicrobial susceptibility tests (ASTs) to characterise the potential for antimicrobial resistance in Salmonella enterica serovars. Genetic determinants of these r...

    Authors: Nana Mensah, Yue Tang, Shaun Cawthraw, Manal AbuOun, Jackie Fenner, Nicholas R. Thomson, Alison E. Mather and Liljana Petrovska-Holmes

    Citation: BMC Microbiology 2019 19:148

    Content type: Research article

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  25. The presence and activity of CRISPR-Cas defense systems is a hallmark of many prokaryotic microorganisms. Here, the distribution of sequences related to the highly iterated palindrome 1 (HIP1) element and the ...

    Authors: Ingeborg Scholz, Steffen C. Lott, Juliane Behler, Katrin Gärtner, Martin Hagemann and Wolfgang R. Hess

    Citation: BMC Microbiology 2019 19:147

    Content type: Research article

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  26. Enterococcus faecalis is a major clinically relevant nosocomial bacterial pathogen frequently isolated from polymicrobial infections. The biofilm forming ability of E. faecalis attributes a key role in its virule...

    Authors: Karthika Suryaletha, Lekshmi Narendrakumar, Joby John, Megha Periyappilly Radhakrishnan, Sanil George and Sabu Thomas

    Citation: BMC Microbiology 2019 19:146

    Content type: Research article

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  27. Complete and contiguous genome assemblies greatly improve the quality of subsequent systems-wide functional profiling studies and the ability to gain novel biological insights. While a de novo genome assembly ...

    Authors: Vincent Somerville, Stefanie Lutz, Michael Schmid, Daniel Frei, Aline Moser, Stefan Irmler, Jürg E. Frey and Christian H. Ahrens

    Citation: BMC Microbiology 2019 19:143

    Content type: Research article

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  28. Recently, in India, there has been a shift from NDM to OXA48-like carbapenemases. OXA-181 and OXA-232 are the frequently produced variants of OXA48-like carbapenemases. OXA48-like carbapenemases are also known...

    Authors: Chaitra Shankar, Purva Mathur, Manigandan Venkatesan, Agila Kumari Pragasam, Shalini Anandan, Surbhi Khurana and Balaji Veeraraghavan

    Citation: BMC Microbiology 2019 19:137

    Content type: Research article

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  29. The Latin American & Mediterranean (LAM) spoligotype family is one of the most successful genotype of Mycobacterium tuberculosis worldwide and particularly prevalent in South-America. Within this family, a sublin...

    Authors: Chyntia Carolina Díaz Acosta, Graciela Russomando, Norma Candia, Viviana Ritacco, Sidra E. G. Vasconcellos, Marcia de Berrêdo Pinho Moreira, Nilda J. de Romero, Nora Morcillo, Jacobus Henri De Waard, Harrison Magdinier Gomes and Philip Noel Suffys

    Citation: BMC Microbiology 2019 19:131

    Content type: Research article

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  30. RNA-binding proteins (RBPs) are well known as key factors in gene expression regulation in eukaryotes. These proteins associate with mRNAs and other proteins to form mRNP complexes that ultimately determine th...

    Authors: Helisa Helena Wippel, Juliane Soldi Malgarin, Alexandre Haruo Inoue, Felipe da Veiga Leprevost, Paulo Costa Carvalho, Samuel Goldenberg and Lysangela Ronalte Alves

    Citation: BMC Microbiology 2019 19:128

    Content type: Research article

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  31. Methicillin-resistant Staphylococcus aureus (MRSA) is known as a leading cause of morbidity and mortality. Investigation of the MRSA’s virulence and resistance mechanisms is a continuing concern toward controllin...

    Authors: Mohamed S. Ali, Nurulfiza M. Isa, Faisal M. Abedelrhman, Tahani B. Alyas, Sara E. Mohammed, Abdallah E. Ahmed, Zainab S. A. Ahmed, Nyok-Sean Lau, Mohamed I. Garbi, Abdullah Al-Ashraf Amirul, Almeen O. Seed, Rihab A. Omer and Sofia B. Mohamed

    Citation: BMC Microbiology 2019 19:126

    Content type: Research article

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  32. Pseudorabies virus (PRV, or suid herpesvirus, SuHV-1), a member of the herpesvirus family, has an extremely broad host range and threatens the pig industry in China. PRV can evade host innate immunity and infe...

    Authors: Yi Fan, Ling Zhu, Xiangang Sun, Wenting Lyu, Lei Xu, Yue Yin, Jun Zhao, Jianbo Huang, Yichao Den, Zhiyi Jiang, Shiyao Xu, Xiyu Mao and Zhiwen Xu

    Citation: BMC Microbiology 2019 19:125

    Content type: Research article

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  33. Clostridium cellulovorans is a mesophilic, cellulosome-producing bacterium containing 57 genomic cellulosomal enzyme-encoding genes. In addition to cellulosomal proteins, C. cellulovorans also secretes non-cellul...

    Authors: Shunsuke Aburaya, Wataru Aoki, Kouichi Kuroda, Hiroshi Minakuchi and Mitsuyoshi Ueda

    Citation: BMC Microbiology 2019 19:118

    Content type: Research article

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  34. The Escherichia coli sequence type 131 (ST131) is a well established clone causing significant extraintestinal infections worldwide. However, no studies have been reported the phenotypic and molecular traits of S...

    Authors: Zoya Hojabri, Narges Darabi, Maedeh Arab, Fereshteh Saffari and Omid Pajand

    Citation: BMC Microbiology 2019 19:117

    Content type: Research article

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  35. Methicillin-resistant Staphylococcus aureus (MRSA) biofilm producers represent an important etiological agent of many chronic human infections. Antibiotics and host immune responses are largely ineffective agains...

    Authors: Khulood Hamid Dakheel, Raha Abdul Rahim, Vasantha Kumari Neela, Jameel R. Al-Obaidi, Tan Geok Hun, Mohd Noor Mat Isa and Khatijah Yusoff

    Citation: BMC Microbiology 2019 19:114

    Content type: Research article

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  37. Hfq is a widely conserved bacterial RNA-binding protein which generally mediates the global regulatory activities involv ed in physiological process and virulence. The goal of this study was to characterize th...

    Authors: Xuelu Liu, Yuping Yan, Haodi Wu, Changyong Zhou and Xuefeng Wang

    Citation: BMC Microbiology 2019 19:103

    Content type: Research article

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  38. Burkholderia pseudomallei is a human pathogen causing severe infections in tropical and subtropical regions and is classified as a bio-threat agent. B. thailandensis strain E264 has been proposed as less pathogen...

    Authors: A. Kovacs-Simon, C. M. Hemsley, A. E. Scott, J. L. Prior and R. W. Titball

    Citation: BMC Microbiology 2019 19:97

    Content type: Research article

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  39. Obtaining sufficient RNA yield and quality for comprehensive transcriptomic studies is cumbersome for clinical samples in which RNA from the pathogen is present in low numbers relative to the nucleic acids fro...

    Authors: Antonio Rodríguez and Mario Vaneechoutte

    Citation: BMC Microbiology 2019 19:94

    Content type: Methodology article

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  41. The opportunistic pathogen, Pseudomonas aeruginosa is well known for its environmental and metabolic versatility, yet many of the functions of its gene-products remain to be fully elucidated. This study’s objecti...

    Authors: Bradley W. Wright, Karthik S. Kamath, Christoph Krisp and Mark P. Molloy

    Citation: BMC Microbiology 2019 19:69

    Content type: Research article

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  42. Structured noncoding RNAs (ncRNAs) play essential roles in many biological processes such as gene regulation, signaling, RNA processing, and protein synthesis. Among the most common groups of ncRNAs in bacteri...

    Authors: Shira Stav, Ruben M. Atilho, Gayan Mirihana Arachchilage, Giahoa Nguyen, Gadareth Higgs and Ronald R. Breaker

    Citation: BMC Microbiology 2019 19:66

    Content type: Research article

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  43. Porphyromonas gingivalis, a microorganism residing in the oral cavity within complex multispecies biofilms, is one of the keystone pathogens in the onset and progression of periodontitis. In this in vitro study, ...

    Authors: María C. Sánchez, Patricia Romero-Lastra, Honorato Ribeiro-Vidal, Arancha Llama-Palacios, Elena Figuero, David Herrera and Mariano Sanz

    Citation: BMC Microbiology 2019 19:58

    Content type: Research article

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  44. With the current rise of antibiotic resistance in bacteria, it is important to monitor the efficacy of antimicrobials in clinical use. Paeniclostridium sordellii (previously Clostridium sordellii) is a bacterial ...

    Authors: Callum J. Vidor, Dieter Bulach, Milena Awad and Dena Lyras

    Citation: BMC Microbiology 2019 19:53

    Content type: Research article

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  45. Ornithobacterium (O.) rhinotracheale is an emerging bacterial pathogen in poultry and not fully understood to date. Because of its importance particularly for the global turkey meat industry, reliable diagnostic ...

    Authors: Inês M. B. Veiga, Dörte Lüschow, Stefanie Gutzer, Hafez M. Hafez and Kristin Mühldorfer

    Citation: BMC Microbiology 2019 19:31

    Content type: Methodology article

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  46. Metarhizium robertsii, a widely distributed insect pathogen, is presently used as a natural alternative to chemical insecticides. Unfortunately, its worldwide commercial use has been restricted by a short shelf l...

    Authors: Tian Xie, Yulong Wang, Deshui Yu, Qilin Zhang, Tingting Zhang, Zhangxun Wang and Bo Huang

    Citation: BMC Microbiology 2019 19:25

    Content type: Research article

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  47. Group A Streptococcus (GAS) is a major human pathogen, which is associated with a wide spectrum of invasive diseases, such as pharyngitis, scarlet fever, rheumatic fever, and streptococcal toxic shock syndrome (S...

    Authors: Shunsuke Yamada, Masaki Shibasaki, Kazunori Murase, Takayasu Watanabe, Chihiro Aikawa, Takashi Nozawa and Ichiro Nakagawa

    Citation: BMC Microbiology 2019 19:24

    Content type: Research article

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  49. To describe the temporal dynamics, molecular characterization, clinical and ex vivo virulence of emerging O1:K1 neonatal meningitis Escherichia coli (NMEC) strains of Sequence Type complex (STc) 95 in France.

    Authors: Guillaume Geslain, André Birgy, Sandrine Adiba, Mélanie Magnan, Céline Courroux, Corinne Levy, Robert Cohen, Philippe Bidet and Stéphane Bonacorsi

    Citation: BMC Microbiology 2019 19:17

    Content type: Research article

    Published on:

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