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Virus-like nanoparticle vaccines for inducing long-lasting immunity against infectious diseases

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National Science Review 2024年第4期11卷 13-15页

作者： Yi-Nan Zhang Sarah Auclair Jiang Zhu department of Integrative Structural and computational Biology The Scripps Research Institute department of Immunology and Microbiology The Scripps Research Institute

Prophylactic vaccines that can generate long-lasting protective immune responses are needed for many infectious diseases. Efficient vaccination requires vaccine antigens to be retained and presented to B cells in lymp...

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Sparse-Grid Implementation of Fixed-Point Fast Sweeping WENO Schemes for Eikonal Equations

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Communications on Applied Mathematics and Computation 2024年第1期6卷 3-29页

作者： Zachary M.Miksis Yong-Tao Zhang department of Applied and computational Mathematics and Statistics University of Notre DameNotre DameIN46556USA

Fixed-point fast sweeping methods are a class of explicit iterative methods developed in the literature to efficiently solve steady-state solutions of hyperbolic partial differential equations(PDEs).As other types of fast sweeping schemes,fixed-point fast sweeping methods use the Gauss-Seidel iterations and alternating sweeping strategy to cover characteristics of hyperbolic PDEs in a certain direction simultaneously in each sweeping order.The resulting iterative schemes have a fast convergence rate to steady-state solutions.Moreover,an advantage of fixed-point fast sweeping methods over other types of fast sweeping methods is that they are explicit and do not involve the inverse operation of any nonlinear local system.Hence,they are robust and flexible,and have been combined with high-order accurate weighted essentially non-oscillatory(WENO)schemes to solve various hyperbolic PDEs in the literature.For multidimensional nonlinear problems,high-order fixed-point fast sweeping WENO methods still require quite a large amount of computational costs.In this technical note,we apply sparse-grid techniques,an effective approximation tool for multidimensional problems,to fixed-point fast sweeping WENO methods for reducing their computational costs.Here,we focus on fixed-point fast sweeping WENO schemes with third-order accuracy(Zhang et al.2006[41]),for solving Eikonal equations,an important class of static Hamilton-Jacobi(H-J)equations.Numerical experiments on solving multidimensional Eikonal equations and a more general static H-J equation are performed to show that the sparse-grid computations of the fixed-point fast sweeping WENO schemes achieve large savings of CPU times on refined meshes,and at the same time maintain comparable accuracy and resolution with those on corresponding regular single grids.

关键词： Fixed-point fast sweeping methods Weighted essentially non-oscillatory(WENO)schemes Sparse grids Static Hamilton-Jacobi(H-J)equations Eikonal equations

Spatial search weighting information contained in cell velocity distribution

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Chinese Physics B 2024年第2期33卷 522-528页

作者：马一凯李娜陈唯 State Key Laboratory of Surface Physics and department of Physics Fudan UniversityShanghai 200438China China National Center for Bioinformation Beijing 100101China National genomics Data Center Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China

Cell migration plays a significant role in physiological and pathological processes.Understanding the characteristics of cell movement is crucial for comprehending biological processes such as cell functionality,cell migration,and cell–cell interactions.One of the fundamental characteristics of cell movement is the specific distribution of cell speed,containing valuable information that still requires comprehensive understanding.This article investigates the distribution of mean velocities along cell trajectories,with a focus on optimizing the efficiency of cell food search in the context of the entire colony.We confirm that the specific velocity distribution in the experiments corresponds to an optimal search efficiency when spatial weighting is considered.The simulation results indicate that the distribution of average velocity does not align with the optimal search efficiency when employing average spatial weighting.However,when considering the distribution of central spatial weighting,the specific velocity distribution in the experiment is shown to correspond to the optimal search efficiency.Our simulations reveal that for any given distribution of average velocity,a specific central spatial weighting can be identified among the possible central spatial weighting that aligns with the optimal search strategy.Additionally,our work presents a method for determining the spatial weights embedded in the velocity distribution of cell movement.Our results have provided new avenues for further investigation of significant topics,such as relationship between cell behavior and environmental conditions throughout their evolutionary history,and how cells achieve collective cooperation through cell-cell communication.

关键词： cell migration foraging efficiency random walk spatial search weight

Characteristics of cell motility during cell collision

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Chinese Physics B 2024年第2期33卷 72-77页

Quantitative examination of cellular motion and intercellullar interactions possesses substantial relevance for both biology and medicine.However,the effects of intercellular interactions during cellular locomotion remain under-explored in experimental research.As such,this study seeks to bridge this research gap,adopting Dictyostelium discoideum(Dicty)cells as a paradigm to investigate variations in cellular motion during reciprocal collisions.We aim to attain a comprehensive understanding of how cell interactions influence cell motion.By observing and processing the motion trajectories of colliding cells under diverse chemical environments,we calculated the diffusion coefficient(D)and the persistence time(τ),using mean square displacement.Our analysis of the relationship dynamics between D andτprior to the collisions reveals intricate and non-monotonic alterations in cell movements during collisions.By quantitatively scrutinizing theτtrend,we were able to categorize the cellular responses to interactions under different conditions.Importantly,we ascertained that the effect of cell interactions during collisions in Dicty cells emulates a classical sigmoid function.This discovery suggests that cellular responses might comply with a pattern akin to the Weber–Fechner law.

关键词： cell migration random walk cell-cell interaction

Insufficient TRPM5 Mediates Lipotoxicity-induced Pancreaticβ-cell Dysfunction

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Current Medical Science 2024年第2期44卷 346-354页

作者： Kai-yuan WANG Shi-mei WU Zheng-jian YAO Yun-xia ZHU Xiao HAN Key Laboratory of Human Functional genomics of Jiangsu Province Department of Biochemistry and Molecular BiologyNanjing Medical UniversityNanjing 211166China

Objective:While the reduction of transient receptor potential channel subfamily M member 5(TRPM5)has been reported in islet cells from type 2 diabetic(T2D)mouse models,its role in lipotoxicity-induced pancreaticβ-cell dysfunction remains unclear.This study aims to study its role.Methods:Pancreas slices were prepared from mice subjected to a high-fat-diet(HFD)at different time points,and TRPM5 expression in the pancreaticβcells was examined using immunofluorescence staining.Glucose-stimulated insulin secretion(GSIS)defects caused by lipotoxicity were mimicked by saturated fatty acid palmitate(Palm).Primary mouse islets and mouse insulinoma MIN6 cells were treated with Palm,and the TRPM5 expression was detected using qRT-PCR and Western blotting.Palm-induced GSIS defects were measured following siRNA-based Trpm5 knockdown.The detrimental effects of Palm on primary mouse islets were also assessed after overexpressing Trpm5 via an adenovirus-derived Trpm5(Ad-Trpm5).Results:HFD feeding decreased the mRNA levels and protein expression of TRPM5 in mouse pancreatic islets.Palm reduced TRPM5 protein expression in a time-and dose-dependent manner in MIN6 cells.Palm also inhibited TRPM5 expression in primary mouse islets.Knockdown of Trpm5 inhibited insulin secretion upon high glucose stimulation but had little effect on insulin biosynthesis.Overexpression of Trpm5 reversed Palm-induced GSIS defects and the production of functional maturation molecules unique toβcells.Conclusion:Our findings suggest that lipotoxicity inhibits TRPM5 expression in pancreaticβcells both in vivo and in vitro and,in turn,drivesβ-cell dysfunction.

关键词： type 2 diabetes β-cell dysfunction lipotoxicity TRPM5

Praseodymium metal nanorods as a 5-fluorouracil carrier

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Journal of Rare Earths 2024年第7期42卷 1328-1336页

作者： Varnitha Manikantan Govindaraj Sri Varalakshmi Ujma Ashapak Tamboli Archana Sumohan Pillai Aleyamma Alexander Anushka Lucas Bose Allben Akash Israel V.M.V.Enoch Centre for Nanoscience and genomics Karunya Institute of Technology and Sciences (Deemed University) department of Applied Chemistry Karunya Institute of Technology and Sciences (Deemed University)

Interest in metal nanoparticles as nanoscale drug-carrying vehicles has been increasing.In such an aspect,lanthanide metal nanoparticles are particularly intriguing.Herein,we report praseodymium nanoparticles as a novel anticancer therapeutic transporting agent.The material was made as a composite with the supramolecular host polymer,poly-β-cyclodextrin.The praseodymium nanorods were characterized using standard analytical techniques,including X-ray diffraction（XRD）,X-ray photoelectron spectroscopy（XPS）,and thermogravimetric analysis（TGA）.In addition,they were imaged using transmission electron microscopy.The nanostructures are a long rod-shaped material with 2.0±0.1 μm in length and 230±10 nm in width.The material shows a saturation magnetization value above 30 emu/g with a coercivity value of 130 Oe.The nanocarrier is freighted with the drug 5-fluorouracil,and the encapsulation efficiency is 76.09%.The drug release is continuous from the nanocarrier（polymer-containing praseodymium nanoparticles） and proceeds for above 250 h.The in vitro cytotoxicities of the blank nanocarrier and the 5-fluorouracil-loaded one are deduced by testing them on MCF-7 and Vero（non-cancerous） cell lines.The cytotoxicity on the cancerous cell lines is observed,whereas the noncancerous cells are unaffected.The IC50values on the cell lines are reported.

关键词： Anticancer activity Drug delivery Metal nanoparticles Poly-cyclodextrin Praseodymium Rare earths

Recent advances in protein conformation sampling by combining machine learning with molecular simulation

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Chinese Physics B 2024年第3期33卷 80-87页

作者：唐一鸣杨中元姚逸飞周运谈圆王子超潘瞳熊瑞孙俊力韦广红 department of Physics State Key Laboratory of Surface Physicsand Key Laboratory for Computational Physical Sciences (Ministry of Education)Shanghai 200438China

The rapid advancement and broad application of machine learning(ML)have driven a groundbreaking revolution in computational biology.One of the most cutting-edge and important applications of ML is its integration with molecular simulations to improve the sampling efficiency of the vast conformational space of large biomolecules.This review focuses on recent studies that utilize ML-based techniques in the exploration of protein conformational landscape.We first highlight the recent development of ML-aided enhanced sampling methods,including heuristic algorithms and neural networks that are designed to refine the selection of reaction coordinates for the construction of bias potential,or facilitate the exploration of the unsampled region of the energy landscape.Further,we review the development of autoencoder based methods that combine molecular simulations and deep learning to expand the search for protein conformations.Lastly,we discuss the cutting-edge methodologies for the one-shot generation of protein conformations with precise Boltzmann weights.Collectively,this review demonstrates the promising potential of machine learning in revolutionizing our insight into the complex conformational ensembles of proteins.

关键词： machine learning molecular simulation protein conformational space enhanced sampling

FedDAA:a robust federated learning framework to protect privacy and defend against adversarial attack

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Frontiers of Computer Science 2024年第2期18卷 107-122页

作者： Shiwei LU Ruihu LI Wenbin LIU Fundamentals department Air Force Engineering UniversityXi’an 710051China Institute of Advanced computational Science and Technology Guangzhou UniversityGuangzhou 510006China

Federated learning(FL)has emerged to break data-silo and protect clients’privacy in the field of artificial intelligence.However,deep leakage from gradient(DLG)attack can fully reconstruct clients’data from the submitted gradient,which threatens the fundamental privacy of FL.Although cryptology and differential privacy prevent privacy leakage from gradient,they bring negative effect on communication overhead or model performance.Moreover,the original distribution of local gradient has been changed in these schemes,which makes it difficult to defend against adversarial attack.In this paper,we propose a novel federated learning framework with model decomposition,aggregation and assembling(FedDAA),along with a training algorithm,to train federated model,where local gradient is decomposed into multiple blocks and sent to different proxy servers to complete aggregation.To bring better privacy protection performance to FedDAA,an indicator is designed based on image structural similarity to measure privacy leakage under DLG attack and an optimization method is given to protect privacy with the least proxy servers.In addition,we give defense schemes against adversarial attack in FedDAA and design an algorithm to verify the correctness of aggregated results.Experimental results demonstrate that FedDAA can reduce the structural similarity between the reconstructed image and the original image to 0.014 and remain model convergence accuracy as 0.952,thus having the best privacy protection performance and model training effect.More importantly,defense schemes against adversarial attack are compatible with privacy protection in FedDAA and the defense effects are not weaker than those in the traditional FL.Moreover,verification algorithm of aggregation results brings about negligible overhead to FedDAA.

关键词： federated learning privacy protection adversarial attacks aggregated rule correctness verification

Primary lateral sclerosis:more than just an upper motor neuron disease

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Neural Regeneration Research 2024年第9期19卷 1881-1882页

作者： Ee Ling Tan Jasmin Lope Peter Bede computational Neuroimaging Group(CNG) School of MedicineTrinity College DublinIreland department of Neurology St James’s HospitalDublinIreland

Advances in clinical care and recent research achievements:Primary lateral sclerosis(PLS)has traditionally been regarded as a pure upper motor neuron condition,a view perpetuated by most medical textbooks.

关键词： sclerosis clinical traditionally