Article
Computer Science, Interdisciplinary Applications
Jianzhen Qian, Hao Pan, Pei Wang
Summary: A new local tensor-type artificial viscosity is proposed for two-dimensional Lagrangian staggered grid hydrodynamics, ensuring dissipation of kinetic energy and damping mesh instabilities. The new viscosity force vanishes in case of expansion, reducing dissipation error, and is demonstrated to be accurate and robust through benchmark tests.
JOURNAL OF COMPUTATIONAL PHYSICS
(2021)
Article
Engineering, Multidisciplinary
Evan J. Lieberman, Xiaodong Liu, Nathaniel R. Morgan, Darby J. Luscher
Summary: A new Lagrangian modal discontinuous Galerkin (DG) hydrodynamic method is presented to support a dynamic dislocation based crystal plasticity model for simulating the mechanical behavior of crystallographic materials under dynamic conditions. The method uses varying the position and material properties of material points within an element to represent the heterogeneous behavior of polycrystalline microstructures.
COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING
(2021)
Article
Computer Science, Interdisciplinary Applications
W. Brent Daniel, Corinne Roth, Xue Li, Cindy Rakowski, Tim McPherson, David Judi
Summary: This article describes a novel rivulet-based 2D flooding model that is computationally much simpler than traditional modeling approaches, while achieving high accuracy in estimating flood inundation areas and depths. The model has been proven to produce accurate results in a wide range of flow depths and can be used for real-time depth estimation, sensitivity analyses, and uncertainty analyses.
ENVIRONMENTAL MODELLING & SOFTWARE
(2023)
Article
Engineering, Chemical
Anjun Li, Zhenbo Wang, Liyun Zhu, Ziyi Wang, Xiaogang Xu, Liang Fang
Summary: The study proposed a down-flow gas-solid cyclone reactor (GSCR) to tackle side reactions in fluidized catalytic cracking process. Three-dimensional numerical models were established to interpret the gas-solid flow features, showing that the four-way approach provided better prediction of the hydrodynamics in GSCR. Most catalysts accumulated on the wall during descent, forming a phase interface structure, where tangential velocity distribution was hump-shaped and tangential and axial kinetic energies dominated. In dilute condition, particle concentration exhibited more severe oscillatory behavior than gas velocities, with both having similar dominant frequency when particle loading increased tenfold.
CANADIAN JOURNAL OF CHEMICAL ENGINEERING
(2021)
Article
Mathematics, Applied
Jin Li, Xiaoning Su, Jinzheng Qu
Summary: This paper presents the linear barycentric rational interpolation collocation method for solving one- and two-dimensional telegraph equations, introducing the barycentric rational interpolation and obtaining the matrix form of the collocation method for easy programming. The convergence rate of the linear barycentric rational interpolation is used to prove the convergence rate of the method for solving telegraph equations, with numerical examples provided to demonstrate convergence rate and verify theoretical analysis.
MATHEMATICAL METHODS IN THE APPLIED SCIENCES
(2021)
Article
Operations Research & Management Science
Shiwei Wang, Chao Ding
Summary: The augmented Lagrangian method (ALM), proposed by Hestenes and Powell in 1969, has gained popularity for its elegant theory and impressive numerical performance. This paper establishes the local (asymptotic Q-superlinear) Q-linear convergence rate of ALM for nonlinear semidefinite programming, without requiring the uniqueness of multipliers. This is done by assuming the second-order sufficient condition and the semi-isolated calmness of the Karush-Kuhn-Tucker solution under mild conditions.
COMPUTATIONAL OPTIMIZATION AND APPLICATIONS
(2023)
Article
Engineering, Civil
Shubin Li, Tao Wang, Hualing Ren, Baiying Shi, Xiangke Kong
Summary: The urban expressway network plays a crucial role in managing traffic pressure in cities, but traditional control methods may be too simplistic. This study proposes an optimal control model based on variable speed limits to minimize delays and maximize traffic flow, effectively improving traffic management strategies for urban expressways.
JOURNAL OF ADVANCED TRANSPORTATION
(2021)
Article
Mathematics, Applied
Jin Li
Summary: The barycentric rational collocation method is presented for solving semi-infinite domain problems. The matrix equation is obtained from the discrete semi-infinite domain problem using the barycentric interpolation method. Truncation and transformation methods are proposed for solving linear and nonlinear differential equations defined on the semi-infinite domains. Finally, numerical examples are provided to validate the theoretical analysis.
Article
Materials Science, Textiles
T. Tetik, R. A. Yildiz, A. R. Labanieh, B. Yoruk, S. Kursun Bahadir, F. Kalaoglu, V Koncar
Summary: This paper examines the washing behavior of fabric using the finite element method and the Coupled Eulerian-Lagrangian approach. It finds that even mild wash cycles can damage conductive yarns and electrical contacts on wearable fabrics. The hydrodynamic simulation method helps investigate the mechanical response of fabric during a washing cycle.
TEXTILE RESEARCH JOURNAL
(2021)
Review
Pharmacology & Pharmacy
Guojun Sun, Dashun Dong, Zuojun Dong, Qian Zhang, Hui Fang, Chaojun Wang, Shaoya Zhang, Shuaijun Wu, Yichen Dong, Yuehua Wan
Summary: Drug repurposing has become an effective approach to drug discovery. This study provides a bibliometric analysis of drug repurposing publications from 2010 to 2020. The findings show that the United States leads in this area of research, followed by China, the United Kingdom, and India. The Chinese Academy of Science published the most research studies, and NIH ranked first on the h-index. COVID-19/SARS-CoV-2/coronavirus is the most popular topic for current drug repurposing research.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Xinghua Zheng, Ming Tang, Yuechang Liu, Zhengzheng Xian, Hankz Hankui Zhuo
Summary: This paper aims to reduce demand loss in bike sharing systems by utilizing both bike trailers and carrier vehicles, and maximize overall profit by considering the sharing economy of bike trailers and fuel cost of carrier vehicles. The experiment shows that this approach outperforms baselines in multiple data sets from bike sharing companies.
APPLIED SCIENCES-BASEL
(2021)
Article
Mathematical & Computational Biology
Jin Li, Yongling Cheng, Zongcheng Li, Zhikang Tian
Summary: In this study, the Poisson equation is solved using the collocation method with linear barycentric rational function. The discrete form of the equation is transformed into matrix form, and the convergence rate of the linear barycentric rational collocation method is analyzed. The domain decomposition method for the barycentric rational collocation method is also introduced, and numerical examples are provided to validate the algorithm.
MATHEMATICAL BIOSCIENCES AND ENGINEERING
(2023)
Article
Polymer Science
Hong He, Jinming Liu, Yaru Zhang, Xue Han, William Mars, Liqun Zhang, Fanzhu Li
Summary: This study used a thermo-mechanical coupling method to predict the steady-state temperature distribution and rolling resistance of solid tires under different loads and rotating speeds. The simulation results were compared with experimental results, and the Lagrangian model showed the highest prediction accuracy. The effectiveness of the thermo-mechanical coupling analysis method was verified through the comparison between simulation and experimental results.
Article
Mathematics, Applied
Jin Li, Yongling Cheng
Summary: This study explores techniques for solving two-dimensional biharmonic boundary-value problems using the linear barycentric rational method to approximate unknown functions and transform the biharmonic equation into two Poisson equations. The linear equations of the discrete biharmonic equation are then converted into matrix form, and the convergence rate of the linear barycentric rational method for the biharmonic equation is analyzed by order reduction. Several numerical examples are provided to demonstrate the theoretical findings.
NUMERICAL METHODS FOR PARTIAL DIFFERENTIAL EQUATIONS
(2021)
Article
Mathematical & Computational Biology
Jin Li
Summary: This paper considers a linear barycentric rational collocation method for equilibrium equations with polar coordinates. The discrete linear equations are transformed into matrix forms. By utilizing the error of barycentric polar coordinate interpolation, the convergence rate of the linear barycentric rational collocation method for equilibrium equations is obtained. Lastly, some numerical examples are presented to validate the proposed theorem.
MATHEMATICAL BIOSCIENCES AND ENGINEERING
(2023)
Article
Ecology
Elyne Dugeny, Julien de Lorgeril, Bruno Petton, Eve Toulza, Yannick Gueguen, Fabrice Pernet
Summary: This study investigates the influence of seaweed living in association with oysters on their response to disease. The results show that different species of seaweeds can alter the bacterial microbiota of oysters and modify their immune response, leading to increased susceptibility to the disease. This study highlights the importance of considering both macrobiotic and microbiotic interactions for the conservation and management of marine ecosystems and resources.
JOURNAL OF ANIMAL ECOLOGY
(2022)
Article
Ecology
Clement Offret, Olivier Gauthier, Garance Despreaux, Adeline Bidault, Charlotte Corporeau, Philippe Miner, Bruno Petton, Fabrice Pernet, Caroline Fabioux, Christine Paillard, Gwenaelle Le Blay
Summary: By studying the behavior of clam digestive glands and extrapallial fluids microbiota, this study found that environmental variations impacted clam microbiota differently according to the tissue considered. Clam tissues could be considered as different microhabitats for bacteria as they showed different responses to small-scale temporal and spatial variabilities in natural conditions.
Article
Microbiology
Marion Soree, Francois Delavat, Christophe Lambert, Solen Lozach, Mathias Papin, Bruno Petton, Delphine Passerini, Lionel Degremont, Dominique Hervio Heath
Summary: The study revealed that oysters grown in controlled environments accumulated more Vibrio parahaemolyticus than those grown in intertidal environments, possibly due to immune priming in the latter. However, both types of oysters showed similar depuration rates for V. parahaemolyticus.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Environmental Sciences
Charlotte Corporeau, Sebastien Petton, Romain Vilaca, Lizenn Delisle, Claudie Quere, Valerian Le Roy, Christine Dubreuil, Sandra Lacas-Gervais, Yann Guitton, Sebastien Artigaud, Benoit Bernay, Vianney Pichereau, Arnaud Huvet, Bruno Petton, Fabrice Pernet, Elodie Fleury, Stephanie Madec, Christophe Brigaudeau, Catherine Brenner, Nathalie M. Mazure
Summary: This study compared intertidal oysters with subtidal oysters and found that intertidal oysters at different depths delayed the onset of mortality associated with POMS. Despite slower growth, intertidal oysters showed increased resistance through metabolic, inflammatory, and immune responses, improving their overall health.
MARINE ENVIRONMENTAL RESEARCH
(2022)
Article
Oceanography
Nicolas Guillou, Georges Chapalain, Sebastien Petton
Summary: Machine learning algorithms have been found to be effective in predicting the salinity of marine ecosystems, especially in estuarine areas. These algorithms can simulate the complex relationships between salinity and factors such as tides, river discharges, and wind velocity, and accurately predict the seasonal and semi-diurnal variations of salinity.
Article
Microbiology
Manon Fallet, Caroline Montagnani, Bruno Petton, Luc Dantan, Julien de Lorgeril, Sebastien Comarmond, Cristian Chaparro, Eve Toulza, Simon Boitard, Jean-Michel Escoubas, Agnes Vergnes, Jacqueline Le Grand, Ingo Bulla, Yannick Gueguen, Jeremie Vidal-Dupiol, Christoph Grunau, Guillaume Mitta, Celine Cosseau
Summary: This study found that early microbial exposure in Pacific oysters can significantly improve their survival rate against a pathogen causing mortality syndrome. The protection provided by microbial exposure is inheritable across generations and is associated with changes in epigenetic marks and immune gene expression. This discovery suggests that microbial exposure may be an important strategy for protecting oyster aquaculture from infectious diseases.
Article
Microbiology
Damien Piel, Maxime Bruto, Yannick Labreuche, Francois Blanquart, David Goudenege, Ruben Barcia-Cruz, Sabine Chenivesse, Sophie Le Panse, Adele James, Javier Dubert, Bruno Petton, Erica Lieberman, K. Mathias Wegner, Fatima A. Hussain, Kathryn M. Kauffman, Martin F. Polz, David Bikard, Sylvain Gandon, Eduardo P. C. Rocha, Frederique Le Roux
Summary: This study investigates the coevolution between bacteriophages and their bacterial hosts, revealing the changes in resistance and counter-resistance mechanisms. The research finds that the adaptation of phages to local hosts is influenced by their ability to infect closely related bacteria and strain-specific defenses. The study further demonstrates the role of genetic exchanges and mobile genetic elements in the evolution of bacterial defenses and phage counter-defenses.
NATURE MICROBIOLOGY
(2022)
Article
Environmental Sciences
Anna Hughes, Kruno Bonacic, Tom Cameron, Ken Collins, Fiz da Costa, Alison Debney, Luca van Duren, Jesper Elzinga, Jose M. Farinas-Franco, Celine Gamble, Luke Helmer, Zoe Holbrook, Eric Holden, Katherine Knight, James A. J. Murphy, Bernadette Pogoda, Stephane Pouvreau, Joanne Preston, Alec Reid, Emilie Reuchlin-Hugenholtz, William G. Sanderson, David Smyth, Brecht Stechele, Asa Strand, John A. Theodorou, Matt Uttley, Ben Wray, Philine S. E. zu Ermgassen
Summary: The European native oyster is a threatened keystone species that historically created biogenic habitats in European seas. Overfishing, habitat destruction, pollution, and other factors have caused the functional extinction of native oyster habitat. However, restoration efforts are gaining momentum, and factors like abiotic, socio-economic, and logistical considerations are important in site selection for restoration projects.
AQUATIC CONSERVATION-MARINE AND FRESHWATER ECOSYSTEMS
(2023)
Article
Immunology
Nicolas Merou, Cyrielle Lecadet, Martin Ubertini, Stephane Pouvreau, Isabelle Arzul
Summary: This study investigated the dynamics of M. refringens and B. ostreae in Rade of Brest, France. M. refringens was found to be present in flat oysters and all sampled environmental compartments, indicating its wider environmental distribution. In contrast, B. ostreae had low prevalence in flat oysters and was rarely detected in planktonic and benthic compartments. Planktonic and benthic compartments play a key role in the transmission and overwintering of M. refringens.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Environmental Sciences
Andreaz Dupoue, Danielle Ferraz Mello, Rafael Trevisan, Christine Dubreuil, Isabelle Queau, Sebastien Petton, Arnaud Huvet, Blandine Guevel, Emmanuelle Com, Fabrice Pernet, Karine Salin, Elodie Fleury, Charlotte Corporeau
Summary: This study investigated the phenotypic plasticity of Pacific oysters in intertidal zones at different foreshore ranges. The findings showed that oysters at the upper limit range exhibited higher energy efficiency and developed antioxidant mechanisms to delay aging, while oysters at the lower limit range showed lower energy efficiency, higher oxidative stress, and shorter telomere length.
MARINE ENVIRONMENTAL RESEARCH
(2023)
Article
Multidisciplinary Sciences
Daniel Oyanedel, Arnaud Lagorce, Maxime Bruto, Philippe Haffner, Amandine Morot, Yannick Labreuche, Yann Dorant, Sebastien de La Forest Divonne, Francois Delavat, Nicolas Inguimbert, Caroline Montagnani, Benjamin Morga, Eve Toulza, Cristian Chaparro, Jean-Michel Escoubas, Yannick Gueguen, Jeremie Vidal-Dupiol, Julien de Lorgeril, Bruno Petton, Lionel Degremont, Delphine Tourbiez, Lea-Lou Pimpare, Marc Leroy, Oceane Romatif, Juliette Pouzadoux, Guillaume Mitta, Frederique Le Roux, Guillaume M. Charriere, Marie-Agnes Travers, Delphine Destoumieux-Garzon
Summary: In Pacific Oyster Mortality Syndrome (POMS), Vibrio harveyi and ostreid herpesvirus 1 (OsHV-1) are the predominant bacteria causing the disease. V. harveyi synergizes with OsHV-1 by promoting mutual growth and inhibiting oyster's cellular defenses. Furthermore, V. harveyi produces metabolites that benefit the growth of coexisting V. rotiferianus.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Fisheries
Stephane Pouvreau, Sylvie Lapegue, Isabelle Arzul, Pierre Boudry
Summary: In the past fifty years, numerous research projects have been conducted in France to revive the aquaculture production of the native European flat oyster Ostrea edulis, as well as to study the ecology of local remnant beds and reefs. These projects have focused on controlled reproduction and hatchery technology, understanding and controlling diseases, and developing resistant lines through genetics. This article provides an overview of the major outcomes of these projects in France and discusses prospects for future work in line with the Native Oyster Restoration Alliance and UN Decade for Ecosystem Restoration.
AQUATIC LIVING RESOURCES
(2023)
Article
Microbiology
Camille Clerissi, Xing Luo, Aude Lucasson, Shogofa Mortaza, Julien de Lorgeril, Eve Toulza, Bruno Petton, Jean-Michel Escoubas, Lionel Degremont, Yannick Gueguen, Delphine Destoumieux-Garzon, Annick Jacq, Guillaume Mitta
Summary: The study used metabarcoding and metatranscriptomic approaches to show that the pathogenesis of POMS is conserved across different infectious environments, and identified a core bacterial consortium that plays a role in POMS pathobiota. The core bacteria have complementary metabolic functions and a low competition for nutrients, which allows them to colonize host tissues and contribute to the conservation of POMS pathobiota.
Article
Geosciences, Multidisciplinary
Sebastien Petton, Valerie Garnier, Matthieu Caillaud, Laurent Debreu, Franck Dumas
Summary: The AGRIF library is used to handle mesoscale or submesoscale structures and coastal processes in the ocean. By solving the hydrodynamic equations at high resolution, these features can be simulated accurately. This paper describes the implementation of AGRIF in the MARS3D model and compares the two-way nesting method with the traditional one-way approach, demonstrating the advantages and increased computational cost of the former. Two application cases illustrate the performance and effectiveness of the MARS3D-AGRIF tool in improving physical hydrodynamics and addressing ecological challenges.
GEOSCIENTIFIC MODEL DEVELOPMENT
(2023)
Article
Virology
Jean Delmotte, Camille Pelletier, Benjamin Morga, Richard Galinier, Bruno Petton, Jean-Baptiste Lamy, Oliver Kaltz, Jean-Christophe Avarre, Maude Jacquot, Caroline Montagnani, Jean-Michel Escoubas
Summary: This study investigated the genetic diversity of the causative agent of Pacific oyster mortality syndrome, OsHV-1, using deep sequencing and bioinformatics tools. The results revealed connectivity between OsHV-1 viral populations in different oyster-farming areas, with oyster transfers in France playing a major role in its dispersal.