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Kotsalos C, Latt J, Beny J, Chopard B. Digital blood in massively parallel CPU/GPU systems for the study of platelet transport. Interface Focus 2021; 11:20190116. [PMID: 33335703 PMCID: PMC7739916 DOI: 10.1098/rsfs.2019.0116] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2020] [Indexed: 01/13/2023] Open
Abstract
We propose a highly versatile computational framework for the simulation of cellular blood flow focusing on extreme performance without compromising accuracy or complexity. The tool couples the lattice Boltzmann solver Palabos for the simulation of blood plasma, a novel finite-element method (FEM) solver for the resolution of deformable blood cells, and an immersed boundary method for the coupling of the two phases. The design of the tool supports hybrid CPU-GPU executions (fluid, fluid-solid interaction on CPUs, deformable bodies on GPUs), and is non-intrusive, as each of the three components can be replaced in a modular way. The FEM-based kernel for solid dynamics outperforms other FEM solvers and its performance is comparable to state-of-the-art mass-spring systems. We perform an exhaustive performance analysis on Piz Daint at the Swiss National Supercomputing Centre and provide case studies focused on platelet transport, implicitly validating the accuracy of our tool. The tests show that this versatile framework combines unprecedented accuracy with massive performance, rendering it suitable for upcoming exascale architectures.
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Affiliation(s)
- Christos Kotsalos
- Computer Science Department, University of Geneva, 7 route de Drize, 1227 Carouge, Switzerland
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2
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Vassaux M, Sinclair RC, Richardson RA, Suter JL, Coveney PV. Toward High Fidelity Materials Property Prediction from Multiscale Modeling and Simulation. ADVANCED THEORY AND SIMULATIONS 2019. [DOI: 10.1002/adts.201900122] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Maxime Vassaux
- Centre for Computational SciencesUniversity College London20 Gordon Street London WC1H 0AJ UK
| | - Robert C. Sinclair
- Centre for Computational SciencesUniversity College London20 Gordon Street London WC1H 0AJ UK
| | - Robin A. Richardson
- Centre for Computational SciencesUniversity College London20 Gordon Street London WC1H 0AJ UK
| | - James L. Suter
- Centre for Computational SciencesUniversity College London20 Gordon Street London WC1H 0AJ UK
| | - Peter V. Coveney
- Centre for Computational SciencesUniversity College London20 Gordon Street London WC1H 0AJ UK
- Computational Science LaboratoryInstitute for InformaticsFaculty of ScienceUniversity of Amsterdam Amsterdam 1098XH The Netherlands
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3
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Tawfik MK, Ameen AM. Cardioprotective effect of ranolazine in nondiabetic and diabetic male rats subjected to isoprenaline-induced acute myocardial infarction involves modulation of AMPK and inhibition of apoptosis. Can J Physiol Pharmacol 2019; 97:661-674. [DOI: 10.1139/cjpp-2018-0571] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Diabetes increases the sensitivity of myocardium to ischemic damage and impairs response of the myocardium to cardioprotective interventions. The present study aimed to elucidate the potential cardioprotective effect provided by ranolazine during myocardial infarction in nondiabetic and diabetic male rats. As AMP-activated protein kinase (AMPK) has been shown to be involved in the cellular response to ischemic injury, in this context, the present animal study evaluated the modulating role of ranolazine in the AMPK expression in isoprenaline-induced myocardial ischemic rat model. Male rats were divided into 2 experiments: experiment I and II (nondiabetic and diabetic rats) and assigned to normal control, saline control for isoprenaline, isoprenaline control, and ranolazine-treated groups. Ranolazine administration revealed effectiveness in attenuating the severity of isoprenaline-induced myocardial injury in both nondiabetic and diabetic rats as revealed by ECG signs, histopathological score, and apoptotic markers via abrogating the increments in the inflammatory and oxidative stress markers and modulating AMPK expression. Therefore, the current cardioprotective effect of ranolazine was, at least in part, mediated through inhibition of apoptosis and modulation of AMPK expression, encouraging considering the utility of ranolazine in protection from acute myocardial infarction.
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Affiliation(s)
- Mona K. Tawfik
- Department of Pharmacology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Angie M. Ameen
- Department of Physiology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
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Hoekstra AG, Chopard B, Coster D, Portegies Zwart S, Coveney PV. Multiscale computing for science and engineering in the era of exascale performance. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2019; 377:20180144. [PMID: 30967040 PMCID: PMC6388008 DOI: 10.1098/rsta.2018.0144] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/09/2018] [Indexed: 05/18/2023]
Abstract
In this position paper, we discuss two relevant topics: (i) generic multiscale computing on emerging exascale high-performing computing environments, and (ii) the scaling of such applications towards the exascale. We will introduce the different phases when developing a multiscale model and simulating it on available computing infrastructure, and argue that we could rely on it both on the conceptual modelling level and also when actually executing the multiscale simulation, and maybe should further develop generic frameworks and software tools to facilitate multiscale computing. Next, we focus on simulating multiscale models on high-end computing resources in the face of emerging exascale performance levels. We will argue that although applications could scale to exascale performance relying on weak scaling and maybe even on strong scaling, there are also clear arguments that such scaling may no longer apply for many applications on these emerging exascale machines and that we need to resort to what we would call multi-scaling. This article is part of the theme issue 'Multiscale modelling, simulation and computing: from the desktop to the exascale'.
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Affiliation(s)
- Alfons G. Hoekstra
- Computational Science Laboratory, Institute for Informatics, Faculty of Science, University of Amsterdam, The Netherlands
- High Performance Computing Department, ITMO University, St Petersburg, Russia
| | - Bastien Chopard
- Department of Computer Science, University of Geneva, Switzerland
| | | | | | - Peter V. Coveney
- The Centre for Computational Science, Department of Chemistry, University College London, UK
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Zun PS, Anikina T, Svitenkov A, Hoekstra AG. A Comparison of Fully-Coupled 3D In-Stent Restenosis Simulations to In-vivo Data. Front Physiol 2017; 8:284. [PMID: 28588498 PMCID: PMC5440556 DOI: 10.3389/fphys.2017.00284] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/19/2017] [Indexed: 01/05/2023] Open
Abstract
We describe our fully-coupled 3D multiscale model of in-stent restenosis, with blood flow simulations coupled to smooth muscle cell proliferation, and report results of numerical simulations performed with this model. This novel model is based on several previously reported 2D models. We study the effects of various parameters on the process of restenosis and compare with in vivo porcine data where we observe good qualitative agreement. We study the effects of stent deployment depth (and related injury score), reendothelization speed, and simulate the effect of stent width. Also we demonstrate that we are now capable to simulate restenosis in real-sized (18 mm long, 2.8 mm wide) vessel geometries.
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Affiliation(s)
- Pavel S. Zun
- Saint Petersburg State University of Information Technologies, Mechanics and Optics (ITMO) UniversitySt. Petersburg, Russia
- Computational Science Lab, Faculty of Science, Institute for Informatics, University of AmsterdamAmsterdam, Netherlands
| | - Tatiana Anikina
- Saint Petersburg State University of Information Technologies, Mechanics and Optics (ITMO) UniversitySt. Petersburg, Russia
- Computational Science Lab, Faculty of Science, Institute for Informatics, University of AmsterdamAmsterdam, Netherlands
| | - Andrew Svitenkov
- Saint Petersburg State University of Information Technologies, Mechanics and Optics (ITMO) UniversitySt. Petersburg, Russia
| | - Alfons G. Hoekstra
- Saint Petersburg State University of Information Technologies, Mechanics and Optics (ITMO) UniversitySt. Petersburg, Russia
- Computational Science Lab, Faculty of Science, Institute for Informatics, University of AmsterdamAmsterdam, Netherlands
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6
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Hoekstra AG, Alowayyed S, Lorenz E, Melnikova N, Mountrakis L, van Rooij B, Svitenkov A, Závodszky G, Zun P. Towards the virtual artery: a multiscale model for vascular physiology at the physics-chemistry-biology interface. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2016.0146. [PMID: 27698036 PMCID: PMC5052730 DOI: 10.1098/rsta.2016.0146] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/14/2016] [Indexed: 05/27/2023]
Abstract
This discussion paper introduces the concept of the Virtual Artery as a multiscale model for arterial physiology and pathologies at the physics-chemistry-biology (PCB) interface. The cellular level is identified as the mesoscopic level, and we argue that by coupling cell-based models with other relevant models on the macro- and microscale, a versatile model of arterial health and disease can be composed. We review the necessary ingredients, both models of arteries at many different scales, as well as generic methods to compose multiscale models. Next, we discuss how this can be combined into the virtual artery. Finally, we argue that the concept of models at the PCB interface could or perhaps should become a powerful paradigm, not only as in our case for studying physiology, but also for many other systems that have such PCB interfaces.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.
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Affiliation(s)
- Alfons G Hoekstra
- Computational Science Laboratory, Institute for Informatics, Faculty of Science, University of Amsterdam, Sciencepark 904, 1098 XH Amsterdam, The Netherlands High Performance Computing Department, ITMO University, Saint Petersburg, Russia
| | - Saad Alowayyed
- Computational Science Laboratory, Institute for Informatics, Faculty of Science, University of Amsterdam, Sciencepark 904, 1098 XH Amsterdam, The Netherlands King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Eric Lorenz
- Computational Science Laboratory, Institute for Informatics, Faculty of Science, University of Amsterdam, Sciencepark 904, 1098 XH Amsterdam, The Netherlands Electric Ant Lab BV, Panamalaan 4 K, 1019AZ Amsterdam, The Netherlands
| | - Natalia Melnikova
- High Performance Computing Department, ITMO University, Saint Petersburg, Russia
| | - Lampros Mountrakis
- Computational Science Laboratory, Institute for Informatics, Faculty of Science, University of Amsterdam, Sciencepark 904, 1098 XH Amsterdam, The Netherlands
| | - Britt van Rooij
- Computational Science Laboratory, Institute for Informatics, Faculty of Science, University of Amsterdam, Sciencepark 904, 1098 XH Amsterdam, The Netherlands
| | - Andrew Svitenkov
- High Performance Computing Department, ITMO University, Saint Petersburg, Russia
| | - Gábor Závodszky
- Computational Science Laboratory, Institute for Informatics, Faculty of Science, University of Amsterdam, Sciencepark 904, 1098 XH Amsterdam, The Netherlands
| | - Pavel Zun
- High Performance Computing Department, ITMO University, Saint Petersburg, Russia
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Mizeranschi A, Groen D, Borgdorff J, Hoekstra AG, Chopard B, Dubitzky W. Anatomy and Physiology of Multiscale Modeling and Simulation in Systems Medicine. Methods Mol Biol 2016; 1386:375-404. [PMID: 26677192 DOI: 10.1007/978-1-4939-3283-2_17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Systems medicine is the application of systems biology concepts, methods, and tools to medical research and practice. It aims to integrate data and knowledge from different disciplines into biomedical models and simulations for the understanding, prevention, cure, and management of complex diseases. Complex diseases arise from the interactions among disease-influencing factors across multiple levels of biological organization from the environment to molecules. To tackle the enormous challenges posed by complex diseases, we need a modeling and simulation framework capable of capturing and integrating information originating from multiple spatiotemporal and organizational scales. Multiscale modeling and simulation in systems medicine is an emerging methodology and discipline that has already demonstrated its potential in becoming this framework. The aim of this chapter is to present some of the main concepts, requirements, and challenges of multiscale modeling and simulation in systems medicine.
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Affiliation(s)
- Alexandru Mizeranschi
- Biomedical Sciences Research Institute, University of Ulster, Cromore Road, Coleraine, Co. Londonderry, BT52 1SA, UK
| | - Derek Groen
- Chemistry Department, Centre for Computational Science, University College London, 20 Gordon Street, WC1H 0AJ, London, UK
| | - Joris Borgdorff
- Netherlands eScience Center, Science Park 140, 1098 XG, Amsterdam, The Netherlands
| | - Alfons G Hoekstra
- Computational Science Lab, Institute for Informatics, Faculty of Science, University of Amsterdam, Sciencepark 904, 1098 XH, Amsterdam, The Netherlands
- Advanced Computing Lab, ITMO University, 197101, 49 Kronverkskiy av., St. Petersburg, Russia
| | - Bastien Chopard
- Computer Science Department, University of Geneva, 7 route de Drize, 1227, Carouge, Switzerland
| | - Werner Dubitzky
- Biomedical Sciences Research Institute, University of Ulster, Cromore Road, Coleraine, Co. Londonderry, BT52 1SA, UK.
- School of Biomedical Sciences, University of Ulster, Coleraine campus, Cromore Road, Coleraine, Co. Londonderry, BT52 1SA, UK.
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Knap J, Spear CE, Borodin O, Leiter KW. Advancing a distributed multi-scale computing framework for large-scale high-throughput discovery in materials science. NANOTECHNOLOGY 2015; 26:434004. [PMID: 26443333 DOI: 10.1088/0957-4484/26/43/434004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We describe the development of a large-scale high-throughput application for discovery in materials science. Our point of departure is a computational framework for distributed multi-scale computation. We augment the original framework with a specialized module whose role is to route evaluation requests needed by the high-throughput application to a collection of available computational resources. We evaluate the feasibility and performance of the resulting high-throughput computational framework by carrying out a high-throughput study of battery solvents. Our results indicate that distributed multi-scale computing, by virtue of its adaptive nature, is particularly well-suited for building high-throughput applications.
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Affiliation(s)
- J Knap
- Simulation Sciences Branch, RDRL-CIH-C, US Army Research Laboratory, Aberdeen Proving Ground, MD, 21005-5066, USA
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9
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Cappuccio A, Tieri P, Castiglione F. Multiscale modelling in immunology: a review. Brief Bioinform 2015; 17:408-18. [PMID: 25810307 DOI: 10.1093/bib/bbv012] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 01/30/2015] [Indexed: 01/26/2023] Open
Abstract
One of the greatest challenges in biomedicine is to get a unified view of observations made from the molecular up to the organism scale. Towards this goal, multiscale models have been highly instrumental in contexts such as the cardiovascular field, angiogenesis, neurosciences and tumour biology. More recently, such models are becoming an increasingly important resource to address immunological questions as well. Systematic mining of the literature in multiscale modelling led us to identify three main fields of immunological applications: host-virus interactions, inflammatory diseases and their treatment and development of multiscale simulation platforms for immunological research and for educational purposes. Here, we review the current developments in these directions, which illustrate that multiscale models can consistently integrate immunological data generated at several scales, and can be used to describe and optimize therapeutic treatments of complex immune diseases.
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Affiliation(s)
- Antonio Cappuccio
- Laboratory of Integrative biology of human dendritic cells and T cells, U932 Immunity and cancer, Institut Curie, 26 Rue d`Ulm, 75005 Paris, France
| | - Paolo Tieri
- Institute for Applied Mathematics (IAC), National Research Council of Italy (CNR), Via dei Taurini 19, 00185 Rome, Italy
| | - Filippo Castiglione
- Institute for Applied Mathematics (IAC), National Research Council of Italy (CNR), Via dei Taurini 19, 00185 Rome, Italy
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Suter JL, Groen D, Coveney PV. Chemically specific multiscale modeling of clay-polymer nanocomposites reveals intercalation dynamics, tactoid self-assembly and emergent materials properties. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2015; 27:966-84. [PMID: 25488829 PMCID: PMC4368376 DOI: 10.1002/adma.201403361] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 11/03/2014] [Indexed: 05/23/2023]
Abstract
A quantitative description is presented of the dynamical process of polymer intercalation into clay tactoids and the ensuing aggregation of polymer-entangled tactoids into larger structures, obtaining various characteristics of these nanocomposites, including clay-layer spacings, out-of-plane clay-sheet bending energies, X-ray diffractograms, and materials properties. This model of clay-polymer interactions is based on a three-level approach, which uses quantum mechanical and atomistic descriptions to derive a coarse-grained yet chemically specific representation that can resolve processes on hitherto inaccessible length and time scales. The approach is applied to study collections of clay mineral tactoids interacting with two synthetic polymers, poly(ethylene glycol) and poly(vinyl alcohol). The controlled behavior of layered materials in a polymer matrix is centrally important for many engineering and manufacturing applications. This approach opens up a route to computing the properties of complex soft materials based on knowledge of their chemical composition, molecular structure, and processing conditions.
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Affiliation(s)
- James L Suter
- Centre for Computational Science, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
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Karabasov S, Nerukh D, Hoekstra A, Chopard B, Coveney PV. Multiscale modelling: approaches and challenges. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2014; 372:rsta.2013.0390. [PMID: 24982248 PMCID: PMC4084530 DOI: 10.1098/rsta.2013.0390] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Affiliation(s)
- Sergey Karabasov
- Department of Engineering and Materials Science, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Dmitry Nerukh
- Department of Engineering and Applied Science, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Alfons Hoekstra
- Computational Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands National Research University ITMO, Kronverkskiy Prospekt 49, 197101 St Petersburg, Russia
| | - Bastien Chopard
- Computer Science Department, University of Geneva, 1211 Geneva 4, Switzerland
| | - Peter V Coveney
- Centre for Computational Science, University College London, 20 Gordon Street, London WC1H OAJ, UK
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Chopard B, Borgdorff J, Hoekstra AG. A framework for multi-scale modelling. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2014; 372:rsta.2013.0378. [PMID: 24982249 PMCID: PMC4084523 DOI: 10.1098/rsta.2013.0378] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
We review a methodology to design, implement and execute multi-scale and multi-science numerical simulations. We identify important ingredients of multi-scale modelling and give a precise definition of them. Our framework assumes that a multi-scale model can be formulated in terms of a collection of coupled single-scale submodels. With concepts such as the scale separation map, the generic submodel execution loop (SEL) and the coupling templates, one can define a multi-scale modelling language which is a bridge between the application design and the computer implementation. Our approach has been successfully applied to an increasing number of applications from different fields of science and technology.
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Affiliation(s)
- B Chopard
- Department of Computer Science, University of Geneva, Geneva, Switzerland
| | - Joris Borgdorff
- Department of Computational Science, University of Amsterdam, Amsterdam, The Netherlands
| | - A G Hoekstra
- Department of Computational Science, University of Amsterdam, Amsterdam, The Netherlands National Research University ITMO, Saint-Petersburg, Russia
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