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Charlebois DA, Balázsi G. Modeling cell population dynamics. In Silico Biol 2019; 13:21-39. [PMID: 30562900 PMCID: PMC6598210 DOI: 10.3233/isb-180470] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 09/13/2018] [Accepted: 10/16/2018] [Indexed: 12/27/2022]
Abstract
Quantitative modeling is quickly becoming an integral part of biology, due to the ability of mathematical models and computer simulations to generate insights and predict the behavior of living systems. Single-cell models can be incapable or misleading for inferring population dynamics, as they do not consider the interactions between cells via metabolites or physical contact, nor do they consider competition for limited resources such as nutrients or space. Here we examine methods that are commonly used to model and simulate cell populations. First, we cover simple models where analytic solutions are available, and then move on to more complex scenarios where computational methods are required. Overall, we present a summary of mathematical models used to describe cell population dynamics, which may aid future model development and highlights the importance of population modeling in biology.
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Affiliation(s)
- Daniel A. Charlebois
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, NY, USA
- Department of Physics, University of Alberta, Edmonton, AB, Canada
| | - Gábor Balázsi
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, NY, USA
- Department of Biomedical Engineering, Stony Brook University, NY, USA
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2
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Abstract
Quantitative modeling is quickly becoming an integral part of biology, due to the ability of mathematical models and computer simulations to generate insights and predict the behavior of living systems. Single-cell models can be incapable or misleading for inferring population dynamics, as they do not consider the interactions between cells via metabolites or physical contact, nor do they consider competition for limited resources such as nutrients or space. Here we examine methods that are commonly used to model and simulate cell populations. First, we cover simple models where analytic solutions are available, and then move on to more complex scenarios where computational methods are required. Overall, we present a summary of mathematical models used to describe cell population dynamics, which may aid future model development and highlights the importance of population modeling in biology.
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Affiliation(s)
- Daniel A Charlebois
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, NY, USA.,Department of Physics, University of Alberta, Edmonton, AB, Canada
| | - Gábor Balázsi
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, NY, USA.,Department of Biomedical Engineering, Stony Brook University, NY, USA
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3
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Gautam S, Sharma L, Dela Cruz CS, Spiegel DA. A Slick Solution to a Sticky Problem. Biochemistry 2018; 57:5923-5924. [PMID: 30289246 DOI: 10.1021/acs.biochem.8b00916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Samir Gautam
- Internal Medicine, Section of Pulmonary and Critical Care , Yale University School of Medicine , 333 Cedar Street , New Haven , Connecticut 06520 , United States.,Department of Chemistry , Yale University , 225 Prospect Street , P.O. Box 208107, New Haven , Connecticut 06520 , United States
| | - Lokesh Sharma
- Internal Medicine, Section of Pulmonary and Critical Care , Yale University School of Medicine , 333 Cedar Street , New Haven , Connecticut 06520 , United States
| | - Charles S Dela Cruz
- Internal Medicine, Section of Pulmonary and Critical Care , Yale University School of Medicine , 333 Cedar Street , New Haven , Connecticut 06520 , United States
| | - David Adam Spiegel
- Department of Chemistry , Yale University , 225 Prospect Street , P.O. Box 208107, New Haven , Connecticut 06520 , United States
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4
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Schwartz L, da Veiga Moreira J, Jolicoeur M. Physical forces modulate cell differentiation and proliferation processes. J Cell Mol Med 2018; 22:738-745. [PMID: 29193856 PMCID: PMC5783863 DOI: 10.1111/jcmm.13417] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 09/12/2017] [Indexed: 01/06/2023] Open
Abstract
Currently, the predominant hypothesis explains cellular differentiation and behaviour as an essentially genetically driven intracellular process, suggesting a gene-centrism paradigm. However, although many living species genetic has now been described, there is still a large gap between the genetic information interpretation and cell behaviour prediction. Indeed, the physical mechanisms underlying the cell differentiation and proliferation, which are now known or suspected to guide such as the flow of energy through cells and tissues, have been often overlooked. We thus here propose a complementary conceptual framework towards the development of an energy-oriented classification of cell properties, that is, a mitochondria-centrism hypothesis based on physical forces-driven principles. A literature review on the physical-biological interactions in a number of various biological processes is analysed from the point of view of the fluid and solid mechanics, electricity and thermodynamics. There is consistent evidence that physical forces control cell proliferation and differentiation. We propose that physical forces interfere with the cell metabolism mostly at the level of the mitochondria, which in turn control gene expression. The present perspective points towards a paradigm shift complement in biology.
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Affiliation(s)
| | | | - Mario Jolicoeur
- Research Laboratory in Applied Metabolic EngineeringDepartment of Chemical EngineeringÉcole Polytechnique de MontréalMontréalQCCanada
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5
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Cordes T, Metallo CM. Tracing insights into human metabolism using chemical engineering approaches. Curr Opin Chem Eng 2016; 14:72-81. [PMID: 28480159 DOI: 10.1016/j.coche.2016.08.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Metabolism coordinates the conversion of available nutrients toward energy, biosynthetic intermediates, and signaling molecules to mediate virtually all biological functions. Dysregulation of metabolic pathways contributes to many diseases, so a detailed understanding of human metabolism has significant therapeutic implications. Over the last decade major technological advances in the areas of analytical chemistry, computational estimation of intracellular fluxes, and biological engineering have improved our ability to observe and engineer metabolic pathways. These approaches are reminiscent of the design, operation, and control of industrial chemical plants. Immune cells have emerged as an intriguing system in which metabolism influences diverse biological functions. Application of metabolic flux analysis and related approaches to macrophages and T cells offers great therapeutic opportunities to biochemical engineers.
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Affiliation(s)
- Thekla Cordes
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Christian M Metallo
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.,Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA
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6
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Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism. PLoS One 2015; 10:e0139507. [PMID: 26469081 PMCID: PMC4607504 DOI: 10.1371/journal.pone.0139507] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/12/2015] [Indexed: 12/20/2022] Open
Abstract
An understanding of the dynamics of the metabolic profile of a bacterial cell is sought from a dynamical systems analysis of kinetic models. This modelling formalism relies on a deterministic mathematical description of enzyme kinetics and their metabolite regulation. However, it is severely impeded by the lack of available kinetic information, limiting the size of the system that can be modelled. Furthermore, the subsystem of the metabolic network whose dynamics can be modelled is faced with three problems: how to parameterize the model with mostly incomplete steady state data, how to close what is now an inherently open system, and how to account for the impact on growth. In this study we address these challenges of kinetic modelling by capitalizing on multi-‘omics’ steady state data and a genome-scale metabolic network model. We use these to generate parameters that integrate knowledge embedded in the genome-scale metabolic network model, into the most comprehensive kinetic model of the central carbon metabolism of E. coli realized to date. As an application, we performed a dynamical systems analysis of the resulting enriched model. This revealed bistability of the central carbon metabolism and thus its potential to express two distinct metabolic states. Furthermore, since our model-informing technique ensures both stable states are constrained by the same thermodynamically feasible steady state growth rate, the ensuing bistability represents a temporal coexistence of the two states, and by extension, reveals the emergence of a phenotypically heterogeneous population.
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Braun E, Marom S. Universality, complexity and the praxis of biology: Two case studies. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2015; 53:68-72. [PMID: 25903120 DOI: 10.1016/j.shpsc.2015.03.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 03/30/2015] [Indexed: 06/04/2023]
Abstract
The phenomenon of biology provides a prime example for a naturally occurring complex system. The approach to this complexity reflects the tension between a reductionist, reverse-engineering stance, and more abstract, systemic ones. Both of us are reductionists, but our observations challenge reductionism, at least the naive version of it. Here we describe the challenge, focusing on two universal characteristics of biological complexity: two-way microscopic-macroscopic degeneracy, and lack of time scale separation within and between levels of organization. These two features and their consequences for the praxis of experimental biology, reflect inherent difficulties in separating the dynamics of any given level of organization from the coupled dynamics of all other levels, including the environment within which the system is embedded. Where these difficulties are not deeply acknowledged, the impacts of fallacies that are inherent to naive reductionism are significant. In an era where technology enables experimental high-resolution access to numerous observables, the challenge faced by the mature reductionist-identification of relevant microscopic variables-becomes more demanding than ever. The demonstrations provided here are taken from two very different biological realizations: populations of microorganisms and populations of neurons, thus making the lesson potentially general.
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Affiliation(s)
- Erez Braun
- Technion-Israel Institute of Technology, Israel
| | - Shimon Marom
- Technion-Israel Institute of Technology, Israel.
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Fanconi anemia cells with unrepaired DNA damage activate components of the checkpoint recovery process. Theor Biol Med Model 2015; 12:19. [PMID: 26385365 PMCID: PMC4575447 DOI: 10.1186/s12976-015-0011-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 08/12/2015] [Indexed: 12/30/2022] Open
Abstract
Background The FA/BRCA pathway repairs DNA interstrand crosslinks. Mutations in this pathway cause Fanconi anemia (FA), a chromosome instability syndrome with bone marrow failure and cancer predisposition. Upon DNA damage, normal and FA cells inhibit the cell cycle progression, until the G2/M checkpoint is turned off by the checkpoint recovery, which becomes activated when the DNA damage has been repaired. Interestingly, highly damaged FA cells seem to override the G2/M checkpoint. In this study we explored with a Boolean network model and key experiments whether checkpoint recovery activation occurs in FA cells with extensive unrepaired DNA damage. Methods We performed synchronous/asynchronous simulations of the FA/BRCA pathway Boolean network model. FA-A and normal lymphoblastoid cell lines were used to study checkpoint and checkpoint recovery activation after DNA damage induction. The experimental approach included flow cytometry cell cycle analysis, cell division tracking, chromosome aberration analysis and gene expression analysis through qRT-PCR and western blot. Results Computational simulations suggested that in FA mutants checkpoint recovery activity inhibits the checkpoint components despite unrepaired DNA damage, a behavior that we did not observed in wild-type simulations. This result implies that FA cells would eventually reenter the cell cycle after a DNA damage induced G2/M checkpoint arrest, but before the damage has been fixed. We observed that FA-A cells activate the G2/M checkpoint and arrest in G2 phase, but eventually reach mitosis and divide with unrepaired DNA damage, thus resolving the initial checkpoint arrest. Based on our model result we look for ectopic activity of checkpoint recovery components. We found that checkpoint recovery components, such as PLK1, are expressed to a similar extent as normal undamaged cells do, even though FA-A cells harbor highly damaged DNA. Conclusions Our results show that FA cells, despite extensive DNA damage, do not loss the capacity to express the transcriptional and protein components of checkpoint recovery that might eventually allow their division with unrepaired DNA damage. This might allow cell survival but increases the genomic instability inherent to FA individuals and promotes cancer.
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Gut P, Zweckstetter M, Banati RB. Lost in translocation: the functions of the 18-kD translocator protein. Trends Endocrinol Metab 2015; 26:349-56. [PMID: 26026242 PMCID: PMC5654500 DOI: 10.1016/j.tem.2015.04.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 03/31/2015] [Accepted: 04/21/2015] [Indexed: 01/29/2023]
Abstract
Research spanning nearly four decades has assigned to the translocator protein (18 kDa) (TSPO) a critical role, among others, in the mitochondrial import of cholesterol, the subsequent steps of (neuro)steroid production, and systemic endocrine regulation, with implications for the pathophysiology of immune, inflammatory, neurodegenerative, and psychiatric as well as neoplastic diseases. Recent knockout studies in mice unexpectedly report normal or latent phenotypes, raising doubts about the protein's role in steroidogenesis and other previously postulated functions and challenging the validity of earlier data on the selectivity of TSPO-binding drugs. Here we provide a synthesis of the current debate from a structural and molecular biology perspective, discuss the limits of inference in loss-of-function (gene knockout) studies, and suggest new functions of TSPO.
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Affiliation(s)
- Philipp Gut
- Nestlé Institute of Health Sciences, EPFL Innovation Park, Bâtiment H, 1015 Lausanne, Switzerland
| | - Markus Zweckstetter
- Max-Planck-Institut für Biophysikalische Chemie, 37077 Göttingen, Germany; Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 37077 Göttingen, Germany; Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center, 37073 Göttingen, Germany
| | - Richard B Banati
- Life Sciences, Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW 2234, Australia; National Imaging Facility and Ramaciotti Centre for Brain Imaging, Brain and Mind Research Institute, Faculty of Health Sciences, University of Sydney, Sydney, NSW 2006, Australia.
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Vlachos I, Zaytsev YV, Spreizer S, Aertsen A, Kumar A. Neural system prediction and identification challenge. Front Neuroinform 2014; 7:43. [PMID: 24399966 PMCID: PMC3872335 DOI: 10.3389/fninf.2013.00043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Accepted: 12/11/2013] [Indexed: 11/29/2022] Open
Abstract
Can we infer the function of a biological neural network (BNN) if we know the connectivity and activity of all its constituent neurons?This question is at the core of neuroscience and, accordingly, various methods have been developed to record the activity and connectivity of as many neurons as possible. Surprisingly, there is no theoretical or computational demonstration that neuronal activity and connectivity are indeed sufficient to infer the function of a BNN. Therefore, we pose the Neural Systems Identification and Prediction Challenge (nuSPIC). We provide the connectivity and activity of all neurons and invite participants (1) to infer the functions implemented (hard-wired) in spiking neural networks (SNNs) by stimulating and recording the activity of neurons and, (2) to implement predefined mathematical/biological functions using SNNs. The nuSPICs can be accessed via a web-interface to the NEST simulator and the user is not required to know any specific programming language. Furthermore, the nuSPICs can be used as a teaching tool. Finally, nuSPICs use the crowd-sourcing model to address scientific issues. With this computational approach we aim to identify which functions can be inferred by systematic recordings of neuronal activity and connectivity. In addition, nuSPICs will help the design and application of new experimental paradigms based on the structure of the SNN and the presumed function which is to be discovered.
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Affiliation(s)
- Ioannis Vlachos
- Faculty of Biology, Bernstein Center Freiburg, University of Freiburg Freiburg im Breisgau, Germany
| | - Yury V Zaytsev
- Faculty of Biology, Bernstein Center Freiburg, University of Freiburg Freiburg im Breisgau, Germany ; Simulation Laboratory Neuroscience - Bernstein Facility for Simulation and Database Technology, Institute for Advanced Simulation, Jülich Aachen Research Alliance, Jülich Research Center Jülich, Germany
| | - Sebastian Spreizer
- Faculty of Biology, Bernstein Center Freiburg, University of Freiburg Freiburg im Breisgau, Germany
| | - Ad Aertsen
- Faculty of Biology, Bernstein Center Freiburg, University of Freiburg Freiburg im Breisgau, Germany
| | - Arvind Kumar
- Faculty of Biology, Bernstein Center Freiburg, University of Freiburg Freiburg im Breisgau, Germany
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11
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Shultz MD. Setting expectations in molecular optimizations: Strengths and limitations of commonly used composite parameters. Bioorg Med Chem Lett 2013; 23:5980-91. [PMID: 24018190 DOI: 10.1016/j.bmcl.2013.08.029] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 07/25/2013] [Accepted: 08/05/2013] [Indexed: 01/02/2023]
Abstract
Over the past 15years there have been extensive efforts to understand and reduce the high attrition rates of drug candidates with an increased focus on physicochemical properties. The fruits of this labor have been the generation of numerous efficiency indices, metric-based rules and visualization tools to help guide medicinal chemists in the design of new compounds with more favorable properties. This deluge of information may have had the unintended consequence of further obfuscating molecular optimizations by the inability of these scoring functions, rules and guides to reach a consensus on when a particular transformation is identified as beneficial. In this manuscript, several composite parameters, or efficiency indices, are examined utilizing theoretical and experimental matched molecular pair analyses in order to understand the basis for how each will perform under varying scenarios of molecular optimizations. In contrast to empirically derived composite parameters based on heavy atom count, lipophilic efficiency (LipE) sets consistent expectations regardless of molecular weight or relative potency and can be used to generate consistent expectations for any matched molecular pair.
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Affiliation(s)
- Michael D Shultz
- Novartis Institutes for Biomedical Research, Inc., 250 Massachusetts Avenue, Cambridge, MA 02139, USA.
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Saetzler K, Sonnenschein C, Soto AM. Systems biology beyond networks: generating order from disorder through self-organization. Semin Cancer Biol 2011; 21:165-74. [PMID: 21569848 DOI: 10.1016/j.semcancer.2011.04.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2011] [Accepted: 04/26/2011] [Indexed: 12/26/2022]
Abstract
Erwin Schrödinger pointed out in his 1944 book "What is Life" that one defining attribute of biological systems seems to be their tendency to generate order from disorder defying the second law of thermodynamics. Almost parallel to his findings, the science of complex systems was founded based on observations on physical and chemical systems showing that inanimate matter can exhibit complex structures although their interacting parts follow simple rules. This is explained by a process known as self-organization and it is now widely accepted that multi-cellular biological organisms are themselves self-organizing complex systems in which the relations among their parts are dynamic, contextual and interdependent. In order to fully understand such systems, we are required to computationally and mathematically model their interactions as promulgated in systems biology. The preponderance of network models in the practice of systems biology inspired by a reductionist, bottom-up view, seems to neglect, however, the importance of bidirectional interactions across spatial scales and domains. This approach introduces a shortcoming that may hinder research on emergent phenomena such as those of tissue morphogenesis and related diseases, such as cancer. Another hindrance of current modeling attempts is that those systems operate in a parameter space that seems far removed from biological reality. This misperception calls for more tightly coupled mathematical and computational models to biological experiments by creating and designing biological model systems that are accessible to a wide range of experimental manipulations. In this way, a comprehensive understanding of fundamental processes in normal development or of aberrations, like cancer, will be generated.
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Affiliation(s)
- K Saetzler
- School of Biomedical Sciences, University of Ulster, Coleraine, Northern Ireland, United Kingdom.
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Abstract
Systems Biology approaches to drug discovery largely focus on the increasing understanding of intracellular and cellular circuits, by computational representation of a molecular system followed by parameter validation against experimental data. This chapter outlines a universal approach to systems biology that allows the linking of intracellular molecular machinery and cellular activity. This procedure is achieved by applying mathematical modeling to molecular modules of a cell in the light of systems biology techniques.
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