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Falque M, Bourgais A, Dumas F, de Carvalho M, Diblasi C. MiniRead: A simple and inexpensive do-it-yourself device for multiple analyses of micro-organism growth kinetics. Yeast 2024; 41:307-314. [PMID: 38380872 DOI: 10.1002/yea.3932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/31/2024] [Accepted: 02/08/2024] [Indexed: 02/22/2024] Open
Abstract
Fitness in micro-organisms can be proxied by growth parameters on different media and/or temperatures. This is achieved by measuring optical density at 600 nm using a spectrophotometer, which measures the effect of absorbance and side scattering due to turbidity of cells suspensions. However, when growth kinetics must be monitored in many 96-well plates at the same time, buying several 96-channel spectrophotometers is often beyond budgets. The MiniRead device presented here is a simple and inexpensive do-it-yourself 96-well temperature-controlled turbidimeter designed to measure the interception of white light via absorption or side scattering through liquid culture medium. Turbidity is automatically recorded in each well at regular time intervals for up to several days or weeks. Output tabulated text files are recorded into a micro-SD memory card to be easily transferred to a computer. We propose also an R package which allows (1) to compute the nonlinear calibration curves required to convert raw readings into cell concentration values, and (2) to analyze growth kinetics output files to automatically estimate proxies of growth parameters such as lag time, maximum growth rate, or cell concentration at the plateau.
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Affiliation(s)
- Matthieu Falque
- GQE-Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Gif-sur-Yvette, France
| | - Aurélie Bourgais
- GQE-Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Gif-sur-Yvette, France
| | - Fabrice Dumas
- GQE-Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Gif-sur-Yvette, France
| | - Mickaël de Carvalho
- GQE-Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Gif-sur-Yvette, France
| | - Célian Diblasi
- GQE-Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Gif-sur-Yvette, France
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2
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Herbst K, Wang T, Forchielli EJ, Thommes M, Paschalidis IC, Segrè D. Multi-Attribute Subset Selection enables prediction of representative phenotypes across microbial populations. Commun Biol 2024; 7:407. [PMID: 38570615 PMCID: PMC10991586 DOI: 10.1038/s42003-024-06093-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 03/22/2024] [Indexed: 04/05/2024] Open
Abstract
The interpretation of complex biological datasets requires the identification of representative variables that describe the data without critical information loss. This is particularly important in the analysis of large phenotypic datasets (phenomics). Here we introduce Multi-Attribute Subset Selection (MASS), an algorithm which separates a matrix of phenotypes (e.g., yield across microbial species and environmental conditions) into predictor and response sets of conditions. Using mixed integer linear programming, MASS expresses the response conditions as a linear combination of the predictor conditions, while simultaneously searching for the optimally descriptive set of predictors. We apply the algorithm to three microbial datasets and identify environmental conditions that predict phenotypes under other conditions, providing biologically interpretable axes for strain discrimination. MASS could be used to reduce the number of experiments needed to identify species or to map their metabolic capabilities. The generality of the algorithm allows addressing subset selection problems in areas beyond biology.
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Affiliation(s)
- Konrad Herbst
- Bioinformatics Program, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
| | - Taiyao Wang
- Division of Systems Engineering, Boston University, Boston, MA, USA
| | - Elena J Forchielli
- Biological Design Center, Boston University, Boston, MA, USA
- Department of Biology, Boston University, Boston, MA, USA
| | - Meghan Thommes
- Biological Design Center, Boston University, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Ioannis Ch Paschalidis
- Division of Systems Engineering, Boston University, Boston, MA, USA.
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
- Faculty of Computing and Data Science, Boston University, Boston, MA, USA.
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA.
| | - Daniel Segrè
- Bioinformatics Program, Boston University, Boston, MA, USA.
- Biological Design Center, Boston University, Boston, MA, USA.
- Department of Biology, Boston University, Boston, MA, USA.
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
- Faculty of Computing and Data Science, Boston University, Boston, MA, USA.
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3
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Lam UTF, Nguyen TTT, Raechell R, Yang J, Singer H, Chen ES. A Normalization Protocol Reduces Edge Effect in High-Throughput Analyses of Hydroxyurea Hypersensitivity in Fission Yeast. Biomedicines 2023; 11:2829. [PMID: 37893202 PMCID: PMC10604075 DOI: 10.3390/biomedicines11102829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/05/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Edge effect denotes better growth of microbial organisms situated at the edge of the solid agar media. Although the precise reason underlying edge effect is unresolved, it is generally attributed to greater nutrient availability with less competing neighbors at the edge. Nonetheless, edge effect constitutes an unavoidable confounding factor that results in misinterpretation of cell fitness, especially in high-throughput screening experiments widely employed for genome-wide investigation using microbial gene knockout or mutant libraries. Here, we visualize edge effect in high-throughput high-density pinning arrays and report a normalization approach based on colony growth rate to quantify drug (hydroxyurea)-hypersensitivity in fission yeast strains. This normalization procedure improved the accuracy of fitness measurement by compensating cell growth rate discrepancy at different locations on the plate and reducing false-positive and -negative frequencies. Our work thus provides a simple and coding-free solution for a struggling problem in robotics-based high-throughput screening experiments.
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Affiliation(s)
- Ulysses Tsz-Fung Lam
- Department of Biochemistry, National University of Singapore, Singapore 117596, Singapore; (U.T.-F.L.); (T.T.T.N.); (R.R.)
| | - Thi Thuy Trang Nguyen
- Department of Biochemistry, National University of Singapore, Singapore 117596, Singapore; (U.T.-F.L.); (T.T.T.N.); (R.R.)
| | - Raechell Raechell
- Department of Biochemistry, National University of Singapore, Singapore 117596, Singapore; (U.T.-F.L.); (T.T.T.N.); (R.R.)
| | - Jay Yang
- Singer Instruments, Roadwater, Watchet TA23 0RE, UK; (J.Y.); (H.S.)
| | - Harry Singer
- Singer Instruments, Roadwater, Watchet TA23 0RE, UK; (J.Y.); (H.S.)
| | - Ee Sin Chen
- Department of Biochemistry, National University of Singapore, Singapore 117596, Singapore; (U.T.-F.L.); (T.T.T.N.); (R.R.)
- NUS Center for Cancer Research, National University of Singapore, Singapore 117599, Singapore
- NUS Synthetic Biology for Clinical & Technological Innovation (SynCTI), Life Science Institute, National University of Singapore, Singapore 117456, Singapore
- National University Health System (NUHS), Singapore 119228, Singapore
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4
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Gyurchev NY, Coral-Medina Á, Weening SM, Almayouf S, Kuijpers NGA, Nevoigt E, Louis EJ. Beyond Saccharomyces pastorianus for modern lager brews: Exploring non- cerevisiae Saccharomyces hybrids with heterotic maltotriose consumption and novel aroma profile. Front Microbiol 2022; 13:1025132. [PMID: 36439845 PMCID: PMC9687090 DOI: 10.3389/fmicb.2022.1025132] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 10/21/2022] [Indexed: 09/11/2024] Open
Abstract
Non-domesticated, wild Saccharomyces yeasts have promising characteristics for beer diversification, particularly when used in the generation of de novo interspecific hybrids. A major motivation for the current work was the question whether attractive novel Saccharomyces interspecific hybrids can be created for the production of exotic lager beers without using the genomic resources of the ale yeast Saccharomyces cerevisiae. Importantly, maltotriose utilization is an essential characteristic typically associated with domesticated ale/lager brewing strains. A high-throughput screening on nearly 200 strains representing all eight species of the Saccharomyces genus was conducted. Three Saccharomyces mikatae strains were able to aerobically grow on maltotriose as the sole carbon source, a trait until recently unidentified for this species. Our screening also confirmed the recently reported maltotriose utilization of the S. jurei strain D5095T. Remarkably, de novo hybrids between a maltotriose-utilizing S. mikatae or S. jurei strain and the maltotriose-negative Saccharomyces eubayanus strain CBS 12357T displayed heterosis and outperformed both parents with regard to aerobically utilizing maltotriose as the sole source of carbon. Indeed, the maximum specific growth rates on this sugar were comparable to the well-known industrial strain, Saccharomyces pastorianus CBS 1513. In lager brewing settings (oxygen-limited), the new hybrids were able to ferment maltose, while maltotriose was not metabolized. Favorable fruity esters were produced, demonstrating that the novel hybrids have the potential to add to the diversity of lager brewing.
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Affiliation(s)
- Nikola Y. Gyurchev
- Centre of Genetic Architecture of Complex Traits, Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- School of Science, Jacobs University Bremen, Bremen, Germany
| | - Ángela Coral-Medina
- SPO, Université de Montpellier, INRAE, Institut Agro, Montpellier, France
- School of Microbiology, University College Cork, Cork, Ireland
| | - Susan M. Weening
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Salwa Almayouf
- Centre of Genetic Architecture of Complex Traits, Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | | | - Elke Nevoigt
- School of Science, Jacobs University Bremen, Bremen, Germany
| | - Edward J. Louis
- Centre of Genetic Architecture of Complex Traits, Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
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Miller JH, Fasanello VJ, Liu P, Longan ER, Botero CA, Fay JC. Using colony size to measure fitness in Saccharomyces cerevisiae. PLoS One 2022; 17:e0271709. [PMID: 36227888 PMCID: PMC9560512 DOI: 10.1371/journal.pone.0271709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/15/2022] [Indexed: 01/05/2023] Open
Abstract
Competitive fitness assays in liquid culture have been a mainstay for characterizing experimental evolution of microbial populations. Growth of microbial strains has also been extensively characterized by colony size and could serve as a useful alternative if translated to per generation measurements of relative fitness. To examine fitness based on colony size, we established a relationship between cell number and colony size for strains of Saccharomyces cerevisiae robotically pinned onto solid agar plates in a high-density format. This was used to measure growth rates and estimate relative fitness differences between evolved strains and their ancestors. After controlling for edge effects through both normalization and agar-trimming, we found that colony size is a sensitive measure of fitness, capable of detecting 1% differences. While fitnesses determined from liquid and solid mediums were not equivalent, our results demonstrate that colony size provides a sensitive means of measuring fitness that is particularly well suited to measurements across many environments.
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Affiliation(s)
- James H. Miller
- Department of Biology, University of Rochester, Rochester, New York, United States of America
| | - Vincent J. Fasanello
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
| | - Ping Liu
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
| | - Emery R. Longan
- Department of Biology, University of Rochester, Rochester, New York, United States of America
| | - Carlos A. Botero
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
| | - Justin C. Fay
- Department of Biology, University of Rochester, Rochester, New York, United States of America
- * E-mail:
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Restoring fertility in yeast hybrids: Breeding and quantitative genetics of beneficial traits. Proc Natl Acad Sci U S A 2021; 118:2101242118. [PMID: 34518218 PMCID: PMC8463882 DOI: 10.1073/pnas.2101242118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2021] [Indexed: 11/18/2022] Open
Abstract
Hybrids between species can harbor a combination of beneficial traits from each parent and may exhibit hybrid vigor, more readily adapting to new harsher environments. Interspecies hybrids are also sterile and therefore an evolutionary dead end unless fertility is restored, usually via auto-polyploidisation events. In the Saccharomyces genus, hybrids are readily found in nature and in industrial settings, where they have adapted to severe fermentative conditions. Due to their hybrid sterility, the development of new commercial yeast strains has so far been primarily conducted via selection methods rather than via further breeding. In this study, we overcame infertility by creating tetraploid intermediates of Saccharomyces interspecies hybrids to allow continuous multigenerational breeding. We incorporated nuclear and mitochondrial genetic diversity within each parental species, allowing for quantitative genetic analysis of traits exhibited by the hybrids and for nuclear-mitochondrial interactions to be assessed. Using pooled F12 generation segregants of different hybrids with extreme phenotype distributions, we identified quantitative trait loci (QTLs) for tolerance to high and low temperatures, high sugar concentration, high ethanol concentration, and acetic acid levels. We identified QTLs that are species specific, that are shared between species, as well as hybrid specific, in which the variants do not exhibit phenotypic differences in the original parental species. Moreover, we could distinguish between mitochondria-type-dependent and -independent traits. This study tackles the complexity of the genetic interactions and traits in hybrid species, bringing hybrids into the realm of full genetic analysis of diploid species, and paves the road for the biotechnological exploitation of yeast biodiversity.
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Balarezo-Cisneros LN, Parker S, Fraczek MG, Timouma S, Wang P, O’Keefe RT, Millar CB, Delneri D. Functional and transcriptional profiling of non-coding RNAs in yeast reveal context-dependent phenotypes and in trans effects on the protein regulatory network. PLoS Genet 2021; 17:e1008761. [PMID: 33493158 PMCID: PMC7886133 DOI: 10.1371/journal.pgen.1008761] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 02/16/2021] [Accepted: 12/19/2020] [Indexed: 12/19/2022] Open
Abstract
Non-coding RNAs (ncRNAs), including the more recently identified Stable Unannotated Transcripts (SUTs) and Cryptic Unstable Transcripts (CUTs), are increasingly being shown to play pivotal roles in the transcriptional and post-transcriptional regulation of genes in eukaryotes. Here, we carried out a large-scale screening of ncRNAs in Saccharomyces cerevisiae, and provide evidence for SUT and CUT function. Phenotypic data on 372 ncRNA deletion strains in 23 different growth conditions were collected, identifying ncRNAs responsible for significant cellular fitness changes. Transcriptome profiles were assembled for 18 haploid ncRNA deletion mutants and 2 essential ncRNA heterozygous deletants. Guided by the resulting RNA-seq data we analysed the genome-wide dysregulation of protein coding genes and non-coding transcripts. Novel functional ncRNAs, SUT125, SUT126, SUT035 and SUT532 that act in trans by modulating transcription factors were identified. Furthermore, we described the impact of SUTs and CUTs in modulating coding gene expression in response to different environmental conditions, regulating important biological process such as respiration (SUT125, SUT126, SUT035, SUT432), steroid biosynthesis (CUT494, SUT053, SUT468) or rRNA processing (SUT075 and snR30). Overall, these data capture and integrate the regulatory and phenotypic network of ncRNAs and protein-coding genes, providing genome-wide evidence of the impact of ncRNAs on cellular homeostasis. A quarter of the yeast genome comprises non-coding RNA molecules (ncRNAs), which do not translate into proteins but are involved in the regulation of gene expression. ncRNAs can affect nearby genes by physically interfering with their transcription (cis mode of action), or they interact with DNA, proteins or other RNAs to regulate the expression of distant genes (trans mode of action). Examples of cis-acting ncRNAs have been broadly described, however, genome-wide studies to identify functional trans-acting ncRNAs involved in global gene regulation are still lacking. Here, we used a ncRNA yeast deletion collection to score ncRNA impact on cellular function in different environmental conditions. A group of 20 ncRNA deletion mutants with broad fitness diversity were selected to investigate the ncRNA effect on the protein and ncRNA expression network. We showed a high correlation between altered phenotypes and global transcriptional changes, in an environmental dependent manner. We confirmed the trans acting regulation of ncRNAs in the genome and their role in altering the expression of transcription factors. These findings support the notion of the involvement of ncRNAs in fine tuning cellular expression via regulation of transcription factors, as an advantageous RNA-mediated mechanism that can be fast and cost-effective for the cells.
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Affiliation(s)
- Laura Natalia Balarezo-Cisneros
- Manchester Institute of Biotechnology, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Steven Parker
- Manchester Institute of Biotechnology, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Marcin G. Fraczek
- Manchester Institute of Biotechnology, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Soukaina Timouma
- Manchester Institute of Biotechnology, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Ping Wang
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Raymond T. O’Keefe
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Catherine B. Millar
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- * E-mail: (CM); (DD)
| | - Daniela Delneri
- Manchester Institute of Biotechnology, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- * E-mail: (CM); (DD)
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Genome-Wide Dynamic Evaluation of the UV-Induced DNA Damage Response. G3-GENES GENOMES GENETICS 2020; 10:2981-2988. [PMID: 32732306 PMCID: PMC7466999 DOI: 10.1534/g3.120.401417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Genetic screens in Saccharomyces cerevisiae have allowed for the identification of many genes as sensors or effectors of DNA damage, typically by comparing the fitness of genetic mutants in the presence or absence of DNA-damaging treatments. However, these static screens overlook the dynamic nature of DNA damage response pathways, missing time-dependent or transient effects. Here, we examine gene dependencies in the dynamic response to ultraviolet radiation-induced DNA damage by integrating ultra-high-density arrays of 6144 diploid gene deletion mutants with high-frequency time-lapse imaging. We identify 494 ultraviolet radiation response genes which, in addition to recovering molecular pathways and protein complexes previously annotated to DNA damage repair, include components of the CCR4-NOT complex, tRNA wobble modification, autophagy, and, most unexpectedly, 153 nuclear-encoded mitochondrial genes. Notably, mitochondria-deficient strains present time-dependent insensitivity to ultraviolet radiation, posing impaired mitochondrial function as a protective factor in the ultraviolet radiation response.
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9
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High-throughput screening for efficient microbial biotechnology. Curr Opin Biotechnol 2020; 64:141-150. [DOI: 10.1016/j.copbio.2020.02.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/21/2020] [Accepted: 02/27/2020] [Indexed: 01/25/2023]
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10
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Femmer C, Bechtold M, Held M, Panke S. In vivo directed enzyme evolution in nanoliter reactors with antimetabolite selection. Metab Eng 2020; 59:15-23. [DOI: 10.1016/j.ymben.2020.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/06/2020] [Accepted: 01/07/2020] [Indexed: 11/16/2022]
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