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Todhanakasem T, Salangsing OL, Koomphongse P, Kaewket S, Kanokratana P, Champreda V. Zymomonas mobilis Biofilm Reactor for Ethanol Production Using Rice Straw Hydrolysate Under Continuous and Repeated Batch Processes. Front Microbiol 2019; 10:1777. [PMID: 31440218 PMCID: PMC6693309 DOI: 10.3389/fmicb.2019.01777] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 07/18/2019] [Indexed: 11/13/2022] Open
Abstract
Plastic composited corn silk was developed as a biotic/abiotic carrier for Zymomonas mobilis biofilm formation for the purpose of ethanol production. Furthermore, we explored the use of rice straw hydrolysate as substrate in both multistage continuous culture and repeated batch processes and compared the ethanol production efficiency by two strains of Z. mobilis. Biofilm formed by bacterial strains Z. mobilis ZM4 and TISTR551 were detected, and its proficiencies were compared under various conditions by scanning electron microscopy (SEM) and crystal violet assays. The greatest biofilm formed by both strains was found on day five after the inoculation. Z. mobilis strain ZM4 grown in repeated batch biofilm reactors produced higher yields of ethanol than TISTR551 grown under the same conditions, while TISTR551 produced higher yields of ethanol in the multistage continuous process. The yields were highly maintained, with no significant differences (p < 0.05) among the three consecutive repeated batches. These experiments highlight exciting uses for agricultural byproducts in the production of ethanol using Z. mobilis biofilm reactors.
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Affiliation(s)
- Tatsaporn Todhanakasem
- Department of Agro-Industry, Faculty of Biotechnology, Assumption University, Bangkok, Thailand
| | - O-Lan Salangsing
- Department of Agro-Industry, Faculty of Biotechnology, Assumption University, Bangkok, Thailand
| | - Piyawit Koomphongse
- National Metal and Materials Technology Center (MTEC), Klong Luang, Thailand
| | - Sanya Kaewket
- National Metal and Materials Technology Center (MTEC), Klong Luang, Thailand
| | - Pattanop Kanokratana
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Klong Luang, Thailand
| | - Verawat Champreda
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Klong Luang, Thailand
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Pineda E, Encalada R, Vázquez C, Néquiz M, Olivos-García A, Moreno-Sánchez R, Saavedra E. In vivoidentification of the steps that control energy metabolism and survival ofEntamoeba histolytica. FEBS J 2014; 282:318-31. [DOI: 10.1111/febs.13131] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 08/29/2014] [Accepted: 10/22/2014] [Indexed: 12/26/2022]
Affiliation(s)
- Erika Pineda
- Departamento de Bioquímica; Instituto Nacional de Cardiología Ignacio Chávez; México D.F México
| | - Rusely Encalada
- Departamento de Bioquímica; Instituto Nacional de Cardiología Ignacio Chávez; México D.F México
| | - Citlali Vázquez
- Departamento de Bioquímica; Instituto Nacional de Cardiología Ignacio Chávez; México D.F México
| | - Mario Néquiz
- Departamento de Medicina Experimental; Facultad de Medicina; Universidad Nacional Autónoma de México; México
| | - Alfonso Olivos-García
- Departamento de Medicina Experimental; Facultad de Medicina; Universidad Nacional Autónoma de México; México
| | - Rafael Moreno-Sánchez
- Departamento de Bioquímica; Instituto Nacional de Cardiología Ignacio Chávez; México D.F México
| | - Emma Saavedra
- Departamento de Bioquímica; Instituto Nacional de Cardiología Ignacio Chávez; México D.F México
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Dynamics of glycolytic regulation during adaptation of Saccharomyces cerevisiae to fermentative metabolism. Appl Environ Microbiol 2008; 74:5710-23. [PMID: 18641162 DOI: 10.1128/aem.01121-08] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ability of baker's yeast (Saccharomyces cerevisiae) to rapidly increase its glycolytic flux upon a switch from respiratory to fermentative sugar metabolism is an important characteristic for many of its multiple industrial applications. An increased glycolytic flux can be achieved by an increase in the glycolytic enzyme capacities (V(max)) and/or by changes in the concentrations of low-molecular-weight substrates, products, and effectors. The goal of the present study was to understand the time-dependent, multilevel regulation of glycolytic enzymes during a switch from fully respiratory conditions to fully fermentative conditions. The switch from glucose-limited aerobic chemostat growth to full anaerobiosis and glucose excess resulted in rapid acceleration of fermentative metabolism. Although the capacities (V(max)) of the glycolytic enzymes did not change until 45 min after the switch, the intracellular levels of several substrates, products, and effectors involved in the regulation of glycolysis did change substantially during the initial 45 min (e.g., there was a buildup of the phosphofructokinase activator fructose-2,6-bisphosphate). This study revealed two distinct phases in the upregulation of glycolysis upon a switch to fermentative conditions: (i) an initial phase, in which regulation occurs completely through changes in metabolite levels; and (ii) a second phase, in which regulation is achieved through a combination of changes in V(max) and metabolite concentrations. This multilevel regulation study qualitatively explains the increase in flux through the glycolytic enzymes upon a switch of S. cerevisiae to fermentative conditions and provides a better understanding of the roles of different regulatory mechanisms that influence the dynamics of yeast glycolysis.
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Albers E, Larsson C, Andlid T, Walsh MC, Gustafsson L. Effect of nutrient starvation on the cellular composition and metabolic capacity of Saccharomyces cerevisiae. Appl Environ Microbiol 2007; 73:4839-48. [PMID: 17545328 PMCID: PMC1951042 DOI: 10.1128/aem.00425-07] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2007] [Accepted: 05/24/2007] [Indexed: 11/20/2022] Open
Abstract
This investigation addresses the following question: what are the important factors for maintenance of a high catabolic capacity under various starvation conditions? Saccharomyces cerevisiae was cultured in aerobic batch cultures, and during the diauxic shift cells were transferred and subjected to 24 h of starvation. The following conditions were used: carbon starvation, nitrogen starvation in the presence of glucose or ethanol, and both carbon starvation and nitrogen starvation. During the starvation period changes in biomass composition (including protein, carbohydrate, lipid, and nucleic acid contents), metabolic activity, sugar transport kinetics, and the levels of selected enzymes were recorded. Subsequent to the starvation period the remaining catabolic capacity was measured by addition of 50 mM glucose. The results showed that the glucose transport capacity is a key factor for maintenance of high metabolic capacity in many, but not all, cases. The results for cells starved of carbon, carbon and nitrogen, or nitrogen in the presence of glucose all indicated that the metabolic capacity was indeed controlled by the glucose transport ability, perhaps with some influence of hexokinase, phosphofructokinase, aldolase, and enolase levels. However, it was also demonstrated that there was no such correlation when nitrogen starvation occurred in the presence of ethanol instead of glucose.
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Affiliation(s)
- Eva Albers
- Department of Chemical and Biological Engineering-Molecular Biotechnology, Chalmers University of Technology, Box 462, SE-405 30 Göteborg, Sweden
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Alberghina L, Colangelo AM. The modular systems biology approach to investigate the control of apoptosis in Alzheimer's disease neurodegeneration. BMC Neurosci 2006; 7 Suppl 1:S2. [PMID: 17118156 PMCID: PMC1775042 DOI: 10.1186/1471-2202-7-s1-s2] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Apoptosis is a programmed cell death that plays a critical role during the development of the nervous system and in many chronic neurodegenerative diseases, including Alzheimer's disease (AD). This pathology, characterized by a progressive degeneration of cholinergic function resulting in a remarkable cognitive decline, is the most common form of dementia with high social and economic impact. Current therapies of AD are only symptomatic, therefore the need to elucidate the mechanisms underlying the onset and progression of the disease is surely needed in order to develop effective pharmacological therapies. Because of its pivotal role in neuronal cell death, apoptosis has been considered one of the most appealing therapeutic targets, however, due to the complexity of the molecular mechanisms involving the various triggering events and the many signaling cascades leading to cell death, a comprehensive understanding of this process is still lacking. Modular systems biology is a very effective strategy in organizing information about complex biological processes and deriving modular and mathematical models that greatly simplify the identification of key steps of a given process. This review aims at describing the main steps underlying the strategy of modular systems biology and briefly summarizes how this approach has been successfully applied for cell cycle studies. Moreover, after giving an overview of the many molecular mechanisms underlying apoptosis in AD, we present both a modular and a molecular model of neuronal apoptosis that suggest new insights on neuroprotection for this disease.
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Affiliation(s)
- Lilia Alberghina
- Department of Biotechnology and Biosciences, Laboratory of Neuroscience R. Levi-Montalcini, University of Milano-Bicocca, 20126 Milan, Italy.
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Rossell S, van der Weijden CC, Lindenbergh A, van Tuijl A, Francke C, Bakker BM, Westerhoff HV. Unraveling the complexity of flux regulation: a new method demonstrated for nutrient starvation in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2006; 103:2166-71. [PMID: 16467155 PMCID: PMC1413710 DOI: 10.1073/pnas.0509831103] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An important question is to what extent metabolic fluxes are regulated by gene expression or by metabolic regulation. There are two distinct aspects to this question: (i) the local regulation of the fluxes through the individual steps in the pathway and (ii) the influence of such local regulation on the pathway's flux. We developed regulation analysis so as to address the former aspect for all steps in a pathway. We demonstrate the method for the issue of how Saccharomyces cerevisiae regulates the fluxes through its individual glycolytic and fermentative enzymes when confronted with nutrient starvation. Regulation was dissected quantitatively into (i) changes in maximum enzyme activity (Vmax, called hierarchical regulation) and (ii) changes in the interaction of the enzyme with the rest of metabolism (called metabolic regulation). Within a single pathway, the regulation of the fluxes through individual steps varied from fully hierarchical to exclusively metabolic. Existing paradigms of flux regulation (such as single- and multisite modulation and exclusively metabolic regulation) were tested for a complete pathway and falsified for a major pathway in an important model organism. We propose a subtler mechanism of flux regulation, with different roles for different enzymes, i.e., "leader," "follower," or "conservative," the latter attempting to hold back the change in flux. This study makes this subtlety, so typical for biological systems, tractable experimentally and invites reformulation of the questions concerning the drives and constraints governing metabolic flux regulation.
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Affiliation(s)
- Sergio Rossell
- *Faculty of Earth and Life Sciences, Department of Molecular Cell Physiology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Coen C. van der Weijden
- *Faculty of Earth and Life Sciences, Department of Molecular Cell Physiology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Alexander Lindenbergh
- *Faculty of Earth and Life Sciences, Department of Molecular Cell Physiology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Arjen van Tuijl
- *Faculty of Earth and Life Sciences, Department of Molecular Cell Physiology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Christof Francke
- *Faculty of Earth and Life Sciences, Department of Molecular Cell Physiology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
- Wageningen Centre for Food Sciences, P.O. Box 557, 6700 AN, Wagenigen, The Netherlands
| | - Barbara M. Bakker
- *Faculty of Earth and Life Sciences, Department of Molecular Cell Physiology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Hans V. Westerhoff
- *Faculty of Earth and Life Sciences, Department of Molecular Cell Physiology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
- Department of Mathematical Biochemistry, BioCentrum Amsterdam, Swammerdam Institute for Life Sciences, Kruislaan 318, 1098 SM, Amsterdam, The Netherlands
- Manchester Centre for Integrative Systems Biology, University of Manchester, P.O. Box 88, Sackville Street, Manchester M60 1QD, United Kingdom; and
- **To whom correspondence should be addressed. E-mail:
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Rossell S, van der Weijden CC, Kruckeberg AL, Bakker BM, Westerhoff HV. Hierarchical and metabolic regulation of glucose influx in starved Saccharomyces cerevisiae. FEMS Yeast Res 2005; 5:611-9. [PMID: 15780660 DOI: 10.1016/j.femsyr.2004.11.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2004] [Revised: 11/01/2004] [Accepted: 11/05/2004] [Indexed: 11/20/2022] Open
Abstract
A novel method dissecting the regulation of a cellular function into direct metabolic regulation and hierarchical (e.g., gene-expression) regulation is applied to yeast starved for nitrogen or carbon. Upon nitrogen starvation glucose influx is down-regulated hierarchically. Upon carbon starvation it is down-regulated both metabolically and hierarchically. The method is expounded in terms of its implications for diverse types of regulation. It is also fine-tuned for cases where isoenzymes catalyze the flux through a single metabolic step.
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Affiliation(s)
- Sergio Rossell
- Department of Molecular Cell Physiology, Faculty of Earth and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, NL-1081 HV Amsterdam, The Netherlands
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A modular systems biology analysis of cell cycle entrance into S-phase. TOPICS IN CURRENT GENETICS 2005. [DOI: 10.1007/b138746] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Abstract
In both industrial fermenters and in their natural habitats, microorganisms often experience an inhomogeneous and fluctuating environment. In this paper we mimicked one aspect of this nonideal behaviour by imposing a low and oscillating extracellular glucose concentration on nonoscillating suspensions of yeast cells. The extracellular dynamics changed the intracellular dynamics--which was monitored through NADH fluorescence--from steady to equally dynamic; the latter followed the extracellular dynamics at the frequency of glucose pulsing. Interestingly, the amplitude of the oscillation of the NADH fluorescence increased with time. This increase in amplitude was sensitive to inhibition of protein synthesis, and was due to a change in the cells rather than in the medium; the cell population was 'trained' to respond to the extracellular dynamics. To examine the mechanism behind this 'training', we subjected the cells to a low and constant extracellular glucose concentration. Seventy-five minutes of adaptation to a low and constant glucose concentration induced the same increase of the amplitude of the forced NADH oscillations as did the train of glucose pulses. Furthermore, 75 min of adaptation to a low (oscillating or continuous) glucose concentration decreased the K(M) of the glucose transporter from 26 mm to 3.5 mm. When subsequently the apparent K(M) was increased by addition of maltose, the amplitude of the forced oscillations dropped to its original value. This demonstrated that the increased affinity of glucose transport was essential for the training of the cells' dynamics.
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Affiliation(s)
- Karin A Reijenga
- Department of Molecular Cell Physiology, CRbCS, BioCentrum Amsterdam, Faculty of Earth and Life Sciences, Vrije Universiteit, Amsterdam, Netherlands
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Alves-Araújo C, Hernandez-Lopez MJ, Prieto JA, Randez-Gil F, Sousa MJ. Isolation and characterization of the LGT1 gene encoding a low-affinity glucose transporter from Torulaspora delbrueckii. Yeast 2005; 22:165-75. [PMID: 15704215 DOI: 10.1002/yea.1192] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Torulaspora delbrueckii PYCC 5321 displayed a mediated glucose transport activity best fitted assuming a biphasic Michaelis-Menten kinetics with a low- and a high-affinity component. A genomic library of this yeast strain was used to transform a mutant of Saccharomyces cerevisiae deficient in glucose transport. Sequence analysis of a DNA fragment cloned, revealed the presence of a 1704 bp length ORF. This ORF, named LGT1, displayed a high homology to yeast glucose transporter genes. Functional characterization of the LGT1 gene product in S. cerevisiae revealed that it encodes a low-affinity transporter, able to mediate the uptake of glucose and fructose. In consonance with this, expression of LGT1 in S. cerevisiae was high in media containing 4% of glucose and almost undetectable in galactose as sole carbon source. In the absence of glucose, repression of LGT1 expression required the transcription factor Rgt1p. However, a functional Rgt1p does not appear to be required for a full induction of LGT1 at high glucose levels. Deletion of the gene coding for the general repressor Mig1p had no effect on LGT1 expression, but additional disruption of MIG2 in a mig1 background indicated that Mig2p or both Mig1p and Mig2p in a redundant way, act as repressors of LGT1 expression at high glucose concentrations. The GeneBank Accession No. for LGT1 is AY598344.
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Affiliation(s)
- Cecília Alves-Araújo
- Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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Reijenga KA, van Megen YMGA, Kooi BW, Bakker BM, Snoep JL, van Verseveld HW, Westerhoff HV. Yeast glycolytic oscillations that are not controlled by a single oscillophore: a new definition of oscillophore strength. J Theor Biol 2005; 232:385-98. [PMID: 15572063 DOI: 10.1016/j.jtbi.2004.08.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2003] [Revised: 07/30/2004] [Accepted: 08/25/2004] [Indexed: 11/27/2022]
Abstract
Biochemical oscillations, such as glycolytic oscillations, are often believed to be caused by a single so-called 'oscillophore'. The main characteristics of yeast glycolytic oscillations, such as frequency and amplitude, are however controlled by several enzymes. In this paper, we develop a method to quantify to which extent any enzyme determines the occurrence of oscillations. Principles extrapolated from metabolic control analysis are applied to calculate the control exerted by individual enzymes on the real and imaginary parts of the eigenvalues of the Jacobian matrix. We propose that the control exerted by an enzyme on the real part of the smallest eigenvalue, in terms of absolute value, quantifies to which extent that enzyme contributes to the emergence of instability. Likewise the control exerted by an enzyme on the imaginary part of complex eigenvalues may serve to quantify the extent to which that enzyme contributes to the tendency of the system to oscillate. The method was applied both to a core model and to a realistic model of yeast glycolytic oscillations. Both the control over stability and the control over oscillatory tendency were distributed among several enzymes, of which glucose transport, pyruvate decarboxylase and ATP utilization were the most important. The distributions of control were different for stability and oscillatory tendency, showing that control of instability does not imply control of oscillatory tendency nor vice versa. The control coefficients summed up to 1, suggesting the existence of a new summation theorem. These results constitute proof that glycolytic oscillations in yeast are not caused by a single oscillophore and provide a new, subtle, definition for the oscillophore strength of an enzyme.
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Affiliation(s)
- Karin A Reijenga
- Department of Molecular Cell Physiology, CRbCS, BioCentrum Amsterdam, Faculty of Earth and Life Sciences, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
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Abstract
Proliferative disorders are a major challenge for human health. The understanding of the organization of cell-cycle events is of the utmost importance to devise effective therapeutic strategies for cancer. The awareness that cells and organisms are complex, modular, hierarchical systems and the availability of genome-wide gene expression and protein analyses, should make it feasible to elucidate human diseases in terms of dysfunctions of molecular systems. Here we review evidence in support of a systems model of the cell cycle, in which two sequential growth-sensitive thresholds control entry into S-phase. The putative molecular determinants that set the threshold for entry into S-phase are consistently altered in cancer cells. Such a framework could be useful in guiding both experimental investigation and data analysis by allowing wiring to other relevant cell modules thereby highlighting the differential responses, or lack of response of cancer cells to intra- and extracellular factors. Pharmacological approaches that take advantage of transformation-induced fragility to glucose shortage are discussed. Extension of this hierarchical, modular approach to tumors as a whole holds promise for the development of effective drug discovery approaches and more efficient therapeutic protocols.
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Affiliation(s)
- Lilia Alberghina
- Department of Biotechnology and Biosciences, Universiy of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy.
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Bibliography. Yeast 2003; 20:185-92. [PMID: 12568102 DOI: 10.1002/yea.941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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