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He Y, Battista NA, Waldrop LD. Mixed uncertainty analysis on pumping by peristaltic hearts using Dempster-Shafer theory. J Math Biol 2024; 89:13. [PMID: 38879850 DOI: 10.1007/s00285-024-02116-6] [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: 02/01/2024] [Revised: 05/22/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024]
Abstract
In this paper, we introduce the numerical strategy for mixed uncertainty propagation based on probability and Dempster-Shafer theories, and apply it to the computational model of peristalsis in a heart-pumping system. Specifically, the stochastic uncertainty in the system is represented with random variables while epistemic uncertainty is represented using non-probabilistic uncertain variables with belief functions. The mixed uncertainty is propagated through the system, resulting in the uncertainty in the chosen quantities of interest (QoI, such as flow volume, cost of transport and work). With the introduced numerical method, the uncertainty in the statistics of QoIs will be represented using belief functions. With three representative probability distributions consistent with the belief structure, global sensitivity analysis has also been implemented to identify important uncertain factors and the results have been compared between different peristalsis models. To reduce the computational cost, physics constrained generalized polynomial chaos method is adopted to construct cheaper surrogates as approximations for the full simulation.
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Affiliation(s)
- Yanyan He
- Department of Mathematics, and of Computer Science and Engineering, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA.
| | - Nicholas A Battista
- Department of Mathematics and Statistics, The College of New Jersey, Pennington Rd, Ewing Township, NJ, 08618, USA
| | - Lindsay D Waldrop
- Schmid College of Science and Technology, Chapman University, One University Drive, Orange, CA, 92866, USA
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Clevenger AJ, Crawford LZ, Noltensmeyer D, Babaei H, Mabbott SB, Avazmohammadi R, Raghavan S. Rapid Prototypable Biomimetic Peristalsis Bioreactor Capable of Concurrent Shear and Multi-Axial Strain. Cells Tissues Organs 2022; 212:96-110. [PMID: 35008089 PMCID: PMC9271135 DOI: 10.1159/000521752] [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: 09/08/2021] [Accepted: 12/31/2021] [Indexed: 11/19/2022] Open
Abstract
Peristalsis is a nuanced mechanical stimulus comprised of multi-axial strain (radial and axial strain) and shear stress. Forces associated with peristalsis regulate diverse biological functions including digestion, reproductive function, and urine dynamics. Given the central role peristalsis plays in physiology and pathophysiology, we were motivated to design a bioreactor capable of holistically mimicking peristalsis. We engineered a novel rotating screw-drive based design combined with a peristaltic pump, in order to deliver multi-axial strain and concurrent shear stress to a biocompatible polydimethylsiloxane (PDMS) membrane "wall." Radial indentation and rotation of the screw drive against the wall demonstrated multi-axial strain evaluated via finite element modeling. Experimental measurements of strain using piezoelectric strain resistors were in close alignment with model-predicted values (15.9 ± 4.2% vs. 15.2% predicted). Modeling of shear stress on the "wall" indicated a uniform velocity profile and a moderate shear stress of 0.4 Pa. Human mesenchymal stem cells (hMSCs) seeded on the PDMS "wall" and stimulated with peristalsis demonstrated dramatic changes in actin filament alignment, proliferation, and nuclear morphology compared to static controls, perfusion, or strain, indicating that hMSCs sensed and responded to peristalsis uniquely. Lastly, significant differences were observed in gene expression patterns of calponin, caldesmon, smooth muscle actin, and transgelin, corroborating the propensity of hMSCs toward myogenic differentiation in response to peristalsis. Collectively, our data suggest that the peristalsis bioreactor is capable of generating concurrent multi-axial strain and shear stress on a "wall." hMSCs experience peristalsis differently than perfusion or strain, resulting in changes in proliferation, actin fiber organization, smooth muscle actin expression, and genetic markers of differentiation. The peristalsis bioreactor device has broad utility in the study of development and disease in several organ systems.
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Affiliation(s)
| | - Logan Z. Crawford
- Department of Biomedical Engineering, Texas A&M University, College Station TX
| | - Dillon Noltensmeyer
- Department of Biomedical Engineering, Texas A&M University, College Station TX
| | - Hamed Babaei
- Department of Biomedical Engineering, Texas A&M University, College Station TX
| | - Samuel B. Mabbott
- Department of Biomedical Engineering, Texas A&M University, College Station TX
- Center for Remote Health Technologies & Systems, Texas A&M Engineering Experiment Station, College Station, TX
| | - Reza Avazmohammadi
- Department of Biomedical Engineering, Texas A&M University, College Station TX
- J. Mike Walker ‘66 Department of Mechanical Engineering, Texas A&M University, College Station TX
- Department of Cardiovascular Sciences, Houston Methodist Academic Institute, Houston TX
| | - Shreya Raghavan
- Department of Biomedical Engineering, Texas A&M University, College Station TX
- Department of Nanomedicine, Houston Methodist Research Institute, Houston TX
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Sharifi A, Gendernalik A, Garrity D, Bark D. Valveless pumping behavior of the simulated embryonic heart tube as a function of contractile patterns and myocardial stiffness. Biomech Model Mechanobiol 2021; 20:2001-2012. [PMID: 34297252 DOI: 10.1007/s10237-021-01489-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 06/29/2021] [Indexed: 10/20/2022]
Abstract
During development, the heart begins pumping as a valveless multilayered tube capable of driving blood flow throughout the embryonic vasculature. The mechanical properties and how they interface with pumping function are not well-defined at this stage. Here, we evaluate pumping patterns using a fluid-structure interaction computational model, combined with experimental data and an energetic analysis to investigate myocardial mechanical properties. Through this work, we propose that a myocardium modeled as a Neo-Hookean material with a material constant on the order of 10 kPa is necessary for the heart tube to function with an optimal pressure and cardiac output.
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Affiliation(s)
- Alireza Sharifi
- Department of Mechanical Engineering, Colorado State University, Fort Collins, CO, USA
| | - Alex Gendernalik
- Department of Biomedical Engineering, Colorado State University, Fort Collins, CO, USA
| | - Deborah Garrity
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - David Bark
- Department of Mechanical Engineering, Colorado State University, Fort Collins, CO, USA. .,Department of Biomedical Engineering, Colorado State University, Fort Collins, CO, USA. .,Department of Pediatrics, Washington University in St. Louis, St. Louis, MO, USA.
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Chatterjee K, Graybill PM, Socha JJ, Davalos RV, Staples AE. Frequency-specific, valveless flow control in insect-mimetic microfluidic devices. BIOINSPIRATION & BIOMIMETICS 2021; 16:036004. [PMID: 33561847 DOI: 10.1088/1748-3190/abe4bc] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
Inexpensive, portable lab-on-a-chip devices would revolutionize fields like environmental monitoring and global health, but current microfluidic chips are tethered to extensive off-chip hardware. Insects, however, are self-contained and expertly manipulate fluids at the microscale using largely unexplored methods. We fabricated a series of microfluidic devices that mimic key features of insect respiratory kinematics observed by synchrotron-radiation imaging, including the collapse of portions of multiple respiratory tracts in response to a single fluctuating pressure signal. In one single-channel device, the flow rate and direction could be controlled by the actuation frequency alone, without the use of internal valves. Additionally, we fabricated multichannel chips whose individual channels responded selectively (on with a variable, frequency-dependent flow rate, or off) to a single, global actuation frequency. Our results demonstrate that insect-mimetic designs have the potential to drastically reduce the actuation overhead for microfluidic chips, and that insect respiratory systems may share features with impedance-mismatch pumps.
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Affiliation(s)
- Krishnashis Chatterjee
- Laboratory for Fluid Dynamics in Nature, Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA, United States of America
- Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA, United States of America
| | - Philip M Graybill
- Bioelectromechanical Systems Laboratory, Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA, United States of America
- Mechanical Engineering, Virginia Tech, Blacksburg, VA, United States of America
| | - John J Socha
- Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA, United States of America
| | - Rafael V Davalos
- Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA, United States of America
- Bioelectromechanical Systems Laboratory, Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA, United States of America
| | - Anne E Staples
- Laboratory for Fluid Dynamics in Nature, Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA, United States of America
- Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA, United States of America
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MHD peristaltic flow of nanofluid in a vertical channel with multiple slip features: an application to chyme movement. Biomech Model Mechanobiol 2021; 20:1047-1067. [PMID: 33656629 DOI: 10.1007/s10237-021-01430-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 02/01/2021] [Indexed: 10/22/2022]
Abstract
The mathematical modelling of biological fluids is of utmost importance due to its applications in various fields of medicine. The peristaltic mechanism plays a crucial role in understanding numerous biological flows. The current paper emphasizes on the MHD peristalsis of Jeffrey nanofluid flowing through a vertical channel when subjected to the combined heat/mass transportation. The equations for the current flow scenario are developed with relevant assumptions for which the perturbation technique is followed to simulate the solution. The expressions of velocity, temperature and concentration are obtained, and the solutions of skin-friction coefficient, Nusselt number and Sherwood number at the wall are acquired. Further, the influence of relevant parameters on various physical quantities for both non-Newtonian Jeffery and viscous fluid is graphically analyzed. The outcomes are deliberated in detail Further, it is renowned that the current study has many biomechanical applications such as the movement of chyme motion in the gastrointestinal tract and during the surgery to take control of the flow of blood by adjusting the magnetic field intensity.
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Senter DM, Douglas DR, Strickland WC, Thomas SG, Talkington AM, Miller LA, Battista NA. A semi-automated finite difference mesh creation method for use with immersed boundary software IB2d and IBAMR. BIOINSPIRATION & BIOMIMETICS 2020; 16:10.1088/1748-3190/ababb0. [PMID: 32746437 PMCID: PMC7970534 DOI: 10.1088/1748-3190/ababb0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
Numerous fluid-structure interaction problems in biology have been investigated using the immersed boundary method. The advantage of this method is that complex geometries, e.g., internal or external morphology, can easily be handled without the need to generate matching grids for both the fluid and the structure. Consequently, the difficulty of modeling the structure lies often in discretizing the boundary of the complex geometry (morphology). Both commercial and open source mesh generators for finite element methods have long been established; however, the traditional immersed boundary method is based on a finite difference discretization of the structure. Here we present a software library for obtaining finite difference discretizations of boundaries for direct use in the 2D immersed boundary method. This library provides tools for extracting such boundaries as discrete mesh points from digital images. We give several examples of how the method can be applied that include passing flow through the veins of insect wings, within lymphatic capillaries, and around starfish using open-source immersed boundary software.
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Affiliation(s)
- D Michael Senter
- Dept. of Mathematics, CB 3250, University of North Carolina, Chapel Hill, NC, 27599, United States of America
- Bioinformatics. and Comp. Biology, CB 7264, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States of America
| | - Dylan R Douglas
- Dept. of Mathematics, CB 3250, University of North Carolina, Chapel Hill, NC, 27599, United States of America
- Department of Mathematics, University of Arizona, 617 N. Santa Rita Ave. P.O. Box 210089 Tucson, AZ 85721-0089, United States of America
| | - W Christopher Strickland
- Dept. of Mathematics, CB 3250, University of North Carolina, Chapel Hill, NC, 27599, United States of America
- Dept. of Mathematics, 1403 Circle Drive, University of Tennessee at Knoxville, Knoxville, TN 37919, United States of America
| | - Steven G Thomas
- Dept. of Mathematics, CB 3250, University of North Carolina, Chapel Hill, NC, 27599, United States of America
| | - Anne M Talkington
- Dept. of Mathematics, CB 3250, University of North Carolina, Chapel Hill, NC, 27599, United States of America
- Bioinformatics. and Comp. Biology, CB 7264, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States of America
| | - Laura A Miller
- Dept. of Mathematics, CB 3250, University of North Carolina, Chapel Hill, NC, 27599, United States of America
- Bioinformatics. and Comp. Biology, CB 7264, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States of America
- Department of Mathematics, University of Arizona, 617 N. Santa Rita Ave. P.O. Box 210089 Tucson, AZ 85721-0089, United States of America
| | - Nicholas A Battista
- Dept. of Mathematics and Statistics, The College of New Jersey, 2000 Pennington Rd., Ewing, NJ 08628, United States of America
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Waldrop LD, He Y, Battista NA, Neary Peterman T, Miller LA. Uncertainty quantification reveals the physical constraints on pumping by peristaltic hearts. J R Soc Interface 2020; 17:20200232. [PMID: 32900306 DOI: 10.1098/rsif.2020.0232] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Most biological functional systems are complex, and this complexity is a fundamental driver of diversity. Because input parameters interact in complex ways, a holistic understanding of functional systems is key to understanding how natural selection produces diversity. We present uncertainty quantification (UQ) as a quantitative analysis tool on computational models to study the interplay of complex systems and diversity. We investigate peristaltic pumping in a racetrack circulatory system using a computational model and analyse the impact of three input parameters (Womersley number, compression frequency, compression ratio) on flow and the energetic costs of circulation. We employed two models of peristalsis (one that allows elastic interactions between the heart tube and fluid and one that does not), to investigate the role of elastic interactions on model output. A computationally cheaper surrogate of the input parameter space was created with generalized polynomial chaos expansion to save computational resources. Sobol indices were then calculated based on the generalized polynomial chaos expansion and model output. We found that all flow metrics were highly sensitive to changes in compression ratio and insensitive to Womersley number and compression frequency, consistent across models of peristalsis. Elastic interactions changed the patterns of parameter sensitivity for energetic costs between the two models, revealing that elastic interactions are probably a key physical metric of peristalsis. The UQ analysis created two hypotheses regarding diversity: favouring high flow rates (where compression ratio is large and highly conserved) and minimizing energetic costs (which avoids combinations of high compression ratios, high frequencies and low Womersley numbers).
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Affiliation(s)
- Lindsay D Waldrop
- Schmid College of Science and Technology, Chapman University, 1 University Drive, Orange, CA 92866, USA
| | - Yanyan He
- Department of Mathematics, University of North Texas, Denton, TX 76203, USA.,Department of Computer Science and Engineering, University of North Texas, Denton, TX 76203, USA
| | - Nicholas A Battista
- Department of Mathematics and Statistics, The College of New Jersey, Ewing Township, NJ 08628, USA
| | - Tess Neary Peterman
- Department of Biology, New Mexico Institute of Mining and Technology, Socorro, NM 87801, USA
| | - Laura A Miller
- Department of Mathematics, University of Arizona, Tuscon, AZ 85721, USA
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Heat transfer analysis of peristaltic flow of a Phan-Thien–Tanner fluid model due to metachronal wave of cilia. Biomech Model Mechanobiol 2020; 19:1925-1933. [DOI: 10.1007/s10237-020-01317-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 02/19/2020] [Indexed: 10/24/2022]
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Kolahdouz EM, Bhalla APS, Craven BA, Griffith BE. An Immersed Interface Method for Discrete Surfaces. JOURNAL OF COMPUTATIONAL PHYSICS 2020; 400:108854. [PMID: 31802781 PMCID: PMC6892596 DOI: 10.1016/j.jcp.2019.07.052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Fluid-structure systems occur in a range of scientific and engineering applications. The immersed boundary (IB) method is a widely recognized and effective modeling paradigm for simulating fluid-structure interaction (FSI) in such systems, but a difficulty of the IB formulation of these problems is that the pressure and viscous stress are generally discontinuous at fluid-solid interfaces. The conventional IB method regularizes these discontinuities, which typically yields low-order accuracy at these interfaces. The immersed interface method (IIM) is an IB-like approach to FSI that sharply imposes stress jump conditions, enabling higher-order accuracy, but prior applications of the IIM have been largely restricted to numerical methods that rely on smooth representations of the interface geometry. This paper introduces an immersed interface formulation that uses only a C 0 representation of the immersed interface, such as those provided by standard nodal Lagrangian finite element methods. Verification examples for models with prescribed interface motion demonstrate that the method sharply resolves stress discontinuities along immersed boundaries while avoiding the need for analytic information about the interface geometry. Our results also demonstrate that only the lowest-order jump conditions for the pressure and velocity gradient are required to realize global second-order accuracy. Specifically, we demonstrate second-order global convergence rates along with nearly second-order local convergence in the Eulerian velocity field, and between first- and second-order global convergence rates along with approximately first-order local convergence for the Eulerian pressure field. We also demonstrate approximately second-order local convergence in the interfacial displacement and velocity along with first-order local convergence in the fluid traction along the interface. As a demonstration of the method's ability to tackle more complex geometries, the present approach is also used to simulate flow in a patient-averaged anatomical model of the inferior vena cava, which is the large vein that carries deoxygenated blood from the lower extremities back to the heart. Comparisons of the general hemodynamics and wall shear stress obtained by the present IIM and a body-fitted discretization approach show that the present method yields results that are in good agreement with those obtained by the body-fitted approach.
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Affiliation(s)
- Ebrahim M Kolahdouz
- Department of Mathematics, University of North Carolina, Chapel Hill, NC, USA
- Division of Applied Mechanics, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, United States Food and Drug Administration, Silver Spring, MD, USA
| | | | - Brent A Craven
- Division of Applied Mechanics, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Boyce E Griffith
- Departments of Mathematics, Applied Physical Sciences, and Biomedical Engineering, University of North Carolina, Chapel Hill, NC, USA
- Carolina Center for Interdisciplinary Applied Mathematics, University of North Carolina, Chapel Hill, NC, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC, USA
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Kinking and Torsion Can Significantly Improve the Efficiency of Valveless Pumping in Periodically Compressed Tubular Conduits. Implications for Understanding of the Form-Function Relationship of Embryonic Heart Tubes. J Cardiovasc Dev Dis 2017; 4:jcdd4040019. [PMID: 29367548 PMCID: PMC5753120 DOI: 10.3390/jcdd4040019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 11/14/2017] [Accepted: 11/15/2017] [Indexed: 01/01/2023] Open
Abstract
Valveless pumping phenomena (peristalsis, Liebau-effect) can generate unidirectional fluid flow in periodically compressed tubular conduits. Early embryonic hearts are tubular conduits acting as valveless pumps. It is unclear whether such hearts work as peristaltic or Liebau-effect pumps. During the initial phase of its pumping activity, the originally straight embryonic heart is subjected to deforming forces that produce bending, twisting, kinking, and coiling. This deformation process is called cardiac looping. Its function is traditionally seen as generating a configuration needed for establishment of correct alignments of pulmonary and systemic flow pathways in the mature heart of lung-breathing vertebrates. This idea conflicts with the fact that cardiac looping occurs in all vertebrates, including gill-breathing fishes. We speculate that looping morphogenesis may improve the efficiency of valveless pumping. To test the physical plausibility of this hypothesis, we analyzed the pumping performance of a Liebau-effect pump in straight and looped (kinked) configurations. Compared to the straight configuration, the looped configuration significantly improved the pumping performance of our pump. This shows that looping can improve the efficiency of valveless pumping driven by the Liebau-effect. Further studies are needed to clarify whether this finding may have implications for understanding of the form-function relationship of embryonic hearts.
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On the Dynamic Suction Pumping of Blood Cells in Tubular Hearts. ASSOCIATION FOR WOMEN IN MATHEMATICS SERIES 2017. [DOI: 10.1007/978-3-319-60304-9_11] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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