The honey badger algorithm(HBA),as a new swarm intelligence(SI)optimization algorithm,has shown certain effectiveness in its applications.Aiming at the problems of unsatisfactory initial population distribution of HBA...The honey badger algorithm(HBA),as a new swarm intelligence(SI)optimization algorithm,has shown certain effectiveness in its applications.Aiming at the problems of unsatisfactory initial population distribution of HBA,poor ability to avoid local optimum,and slow convergence speed,this paper proposes a multi-strategy improved HBA based on periodical mutation and t-distribution perturbation,called MHBA.Firstly,a good point set population initialization is introduced to get a uniform initial population.Secondly,periodic mutation and t-distribution perturbation are successively used to improve the algorithm’s ability to avoid local optimum.Finally,the density factor is improved for balancing exploration and exploitation.By comparing MHBA with HBA and 7 other SIs on 6 benchmark functions,it is evident that the performance of MHBA is far superior to HBA.In addition,by applying MHBA to robot path planning,MHBA can identify the shortest path more quickly and consistently compared with competitors.展开更多
Accurate forecasting of wind power is crucial for ensuring the reliable operation of the electrical grid.Due to the impact of various factors,wind power forecasting presents a significant challenge.This paper presents...Accurate forecasting of wind power is crucial for ensuring the reliable operation of the electrical grid.Due to the impact of various factors,wind power forecasting presents a significant challenge.This paper presents the model that integrates Osprey and adaptive T-distribution dung beetle algorithm for optimizing a convolutional neural network.The CNN-BiLSTM-Attention model combines bidirectional long short-term memory neural networks with an attention mechanism,thereby improving the accuracy of wind power generation predictions.The original data is subjected to Variational Mode Decomposition(VMD)for analysis,taking into account the fluctuations in wind power across different periods.The BiLSTM network with short-term memory processes time-series wind power data,yielding an optimal predictive performance.The integration of the osprey algorithm and adaptive T-distribution within the Dung Beetle Optimization Algorithm was utilized to optimize the hyperparameters of the CNN-BiLSTM-Attention model,thereby enhancing its predictive performance.To assess the efficacy of the CNN-BiLSTM-Attention algorithm,enhanced by Ospreys and adaptive T-distributed dung beetle algorithm,we conducted experiments using the CEC2021 benchmark function.The integrated Osprey and adaptive T-distribution Dung Beetle algorithm has excellent global optimization performance when dealing with complex optimization problems.The fusion of Osprey and the adaptive T-distribution Dung beetle algorithm optimized the CNN-BiLSTM-Attention algorithm as well as other optimization algorithms for ablation experiments.The results show that the improved algorithm performs well in predicting wind power.The experimental findings suggest that the model’s predictive efficiency has enhanced by a minimum of 17.74%.展开更多
An adaptive genetic algorithm with diversity-guided mutation, which combines adaptive probabilities of crossover and mutation was proposed. By means of homogeneous finite Markov chains, it is proved that adaptive gene...An adaptive genetic algorithm with diversity-guided mutation, which combines adaptive probabilities of crossover and mutation was proposed. By means of homogeneous finite Markov chains, it is proved that adaptive genetic algorithm with diversity-guided mutation and genetic algorithm with diversity-guided mutation converge to the global optimum if they maintain the best solutions, and the convergence of adaptive genetic algorithms with adaptive probabilities of crossover and mutation was studied. The performances of the above algorithms in optimizing several unimodal and multimodal functions were compared. The results show that for multimodal functions the average convergence generation of the adaptive genetic algorithm with diversity-guided mutation is about 900 less than that of (adaptive) genetic algorithm with adaptive probabilities and genetic algorithm with diversity-guided mutation, and the adaptive genetic algorithm with diversity-guided mutation does not lead to premature convergence. It is also shown that the better balance between overcoming premature convergence and quickening convergence speed can be gotten.展开更多
This paper presents a new adaptive mutation approach for fastening the convergence of immune algorithms (IAs). This method is adopted to realize the twin goals of maintaining diversity in the population and sustaining...This paper presents a new adaptive mutation approach for fastening the convergence of immune algorithms (IAs). This method is adopted to realize the twin goals of maintaining diversity in the population and sustaining the convergence capacity of the IA. In this method, the mutation rate (pm) is adaptively varied depending on the fitness values of the solutions. Solutions of high fitness are protected, while solutions with sub-average fitness are totally disrupted. A solution to the problem of deciding the optimal value of pm is obtained. Experiments are carried out to compare the proposed approach to traditional one on a set of optimization problems. These are namely: 1) an exponential multi-variable function;2) a rapidly varying multimodal function and 3) design of a second order 2-D narrow band recursive LPF. Simulation results show that the proposed method efficiently improves IA’s performance and prevents it from getting stuck at a local optimum.展开更多
AIM To explore hepatitis C virus(HCV) adaptive mutations or combinations thereof responsible for enhanced viral production and investigate the underlying mechanisms.METHODS A series of plasmids with adaptive mutations...AIM To explore hepatitis C virus(HCV) adaptive mutations or combinations thereof responsible for enhanced viral production and investigate the underlying mechanisms.METHODS A series of plasmids with adaptive mutations were constructed. After the plasmids were transfected into Huh7.5 cells, we determined the infectious HCV particle titers by NS5 A immunofluorescence assays, and detected HCV RNA replication by real-time PCR and protein expression by Western blot. Then we carried out immunoblotting of supernatants and celllysates with anti-NS3 to analyze the virus release level. In addition, co-localization of lipid droplets(LDs) with NS5 A was measured using confocal laser scanning microscopy. The ratio between the p56 and p58 phosphoforms of NS5 A was analyzed further.RESULTS The plasmids named JFH1-m E2, JFH1-mp7, JFH1-m NS4 B, JFH1-m NS5 A, JFH1-m E2/NS5 A, JFH1-mp7/NS5 A, JFH1-m NS4 B/NS5 A, JFH1-m E2/p7/NS5 A, and m JFH1 were constructed successfully. This study generated infectious HCV particles with a robust titer of 1.61 × 106 focus-forming units(FFUs)/m L. All of the six adaptive mutations increased the HCV particle production at varying levels. The NS5 A(C2274 R, I2340 T, and V2440 L) and p7(H781 Y) were critical adaptive mutations. The effect of NS5 A(C2274 R, I2340 T, and V2440 L), p7(H781 Y), and NS4 B(N1931 S) on infectious HCV titers was investigated by measuring the HCV RNA replication, protein expression, and virion release. However, the six adaptive mutations were not required for the LD localization of NS5 A proteins or the phosphorylation of NS5 A.CONCLUSION In this study, we generated infectious HCV particles with a robust titer of 1.61 × 106 FFUs/m L, and found that the viral replication and release levels could be enhanced by some of the adaptive mutations.展开更多
Next-generation sequencing technology has transformed our ability to assess the taxonomic composition functions of host-associated microbiota and microbiomes. More human microbiome research projects—particularly thos...Next-generation sequencing technology has transformed our ability to assess the taxonomic composition functions of host-associated microbiota and microbiomes. More human microbiome research projects—particularly those that explore genomic mutations within the microbiome—will be launched in the next decade. This review focuses on the coevolution of microbes within a microbiome, which shapes strain-level diversity both within and between host species. We also explore the correlation between microbial genomic mutations and common metabolic diseases, and the adaptive evolution of pathogens and probiotics during invasion and colonization. Finally, we discuss advances in methods and algorithms for annotating and analyzing microbial genomic mutations.展开更多
The live attenuated hepatitis A virus vaccine H2 strain was developed by passaging a wild-type H2w isolate in cell cultures.Currently,the mechanism underlying its attenuation phenotype remain largely unknown.In this s...The live attenuated hepatitis A virus vaccine H2 strain was developed by passaging a wild-type H2w isolate in cell cultures.Currently,the mechanism underlying its attenuation phenotype remain largely unknown.In this study,we generated a full-length infectious cDNA clone of the H2 strain using in-fusion techniques.The recovered H2 strain(H2ic)from the cDNA clone exhibited an efficient replication in both the hepatoma cell line Huh7.5.1 and the 2BS cell line used for vaccine production,similar to the parental H2 strain.Additionally,H2ic did not cause disease in Ifnar1-/- C57 mice,consistent with the H2 strain.To explore the cell-adaptive mutations of the H2 strain,chimeric viruses were generated by replacing its non-structural proteins with corresponding regions from H2w using the infectious cDNA clone as a genetic backbone.The chimeric viruses carrying the 3C or 3D proteins from H2w showed decreased replication in Huh7.5.1 and 2BS cell lines compared to H2ic.Other chimeric viruses containing the 2B,2C,or 3A proteins from H2w failed to be recovered.Furthermore,there were no significant differences in disease manifestation in mice between H2ic and the recovered chimeric viruses.These results demonstrate that adaptive mutations in the 2B,2C,and 3A proteins are essential for efficient replication of the H2 strain in cell cultures.Mutations in the 3C and 3D proteins contribute to enhanced replication in cell cultures but did not influence the attenuated phenotypes in mice.Together,this study presents the first reverse genetic system of the H2 strain and identifies viral proteins essential for adaptation to cell cultures.展开更多
Single unmanned aerial vehicle(UAV)multitasking plays an important role in multiple UAVs cooperative control,which is as well as the most complicated and hardest part.This paper establishes a threedimensional topograp...Single unmanned aerial vehicle(UAV)multitasking plays an important role in multiple UAVs cooperative control,which is as well as the most complicated and hardest part.This paper establishes a threedimensional topographical map,and an improved adaptive differential evolution(IADE)algorithm is proposed for single UAV multitasking.As an optimized problem,the efficiency of using standard differential evolution to obtain the global optimal solution is very low to avoid this problem.Therefore,the algorithm adopts the mutation factor and crossover factor into dynamic adaptive functions,which makes the crossover factor and variation factor can be adjusted with the number of population iteration and individual fitness value,letting the algorithm exploration and development more reasonable.The experimental results implicate that the IADE algorithm has better performance,higher convergence and efficiency to solve the multitasking problem compared with other algorithms.展开更多
Hepatitis C virus(HCV)infection affects about 170 million people worldwide and it is a major cause of liver cirrhosis and hepatocellular carcinoma.HCV is a hepatotropic non-cytopathic virus able to persist in a great ...Hepatitis C virus(HCV)infection affects about 170 million people worldwide and it is a major cause of liver cirrhosis and hepatocellular carcinoma.HCV is a hepatotropic non-cytopathic virus able to persist in a great percentage of infected hosts due to its ability to escape from the immune control.Liver damage and disease progression during HCV infection are driven by both viral and host factors.Specifically,adaptive immune response carries out an essential task in controllingnon-cytopathic viruses because of its ability to recognize infected cells and to destroy them by cytopathic mechanisms and to eliminate the virus by non-cytolytic machinery.HCV is able to impair this response by several means such as developing escape mutations in neutralizing antibodies and in T cell receptor viral epitope recognition sites and inducing HCV-specific cytotoxic T cell anergy and deletion.To impair HCV-specific T cell reactivity,HCV affects effector T cell regulation by modulating T helper and Treg response and by impairing the balance between positive and negative co-stimulatory molecules and between pro-and antiapoptotic proteins.In this review,the role of adaptive immune response in controlling HCV infection and the HCV mechanisms to evade this response are reviewed.展开更多
Bilevel linear programming, which consists of the objective functions of the upper level and lower level, is a useful tool for modeling decentralized decision problems. Various methods are proposed for solving this pr...Bilevel linear programming, which consists of the objective functions of the upper level and lower level, is a useful tool for modeling decentralized decision problems. Various methods are proposed for solving this problem. Of all the algorithms, the ge- netic algorithm is an alternative to conventional approaches to find the solution of the bilevel linear programming. In this paper, we describe an adaptive genetic algorithm for solving the bilevel linear programming problem to overcome the difficulty of determining the probabilities of crossover and mutation. In addition, some techniques are adopted not only to deal with the difficulty that most of the chromosomes maybe infeasible in solving constrained optimization problem with genetic algorithm but also to improve the efficiency of the algorithm. The performance of this proposed algorithm is illustrated by the examples from references.展开更多
Curvature lines are special and important curves on surfaces.It is of great significance to construct developable surface interpolated on curvature lines in engineering applications.In this paper,the shape optimizatio...Curvature lines are special and important curves on surfaces.It is of great significance to construct developable surface interpolated on curvature lines in engineering applications.In this paper,the shape optimization of generalized cubic ball developable surface interpolated on the curvature line is studied by using the improved reptile search algorithm.Firstly,based on the curvature line of generalized cubic ball curve with shape adjustable,this paper gives the construction method of SGC-Ball developable surface interpolated on the curve.Secondly,the feedback mechanism,adaptive parameters and mutation strategy are introduced into the reptile search algorithm,and the Feedback mechanism-driven improved reptile search algorithm effectively improves the solving precision.On IEEE congress on evolutionary computation 2014,2017,2019 and four engineering design problems,the feedback mechanism-driven improved reptile search algorithm is compared with other representative methods,and the result indicates that the solution performance of the feedback mechanism-driven improved reptile search algorithm is competitive.At last,taking the minimum energy as the evaluation index,the shape optimization model of SGC-Ball interpolation developable surface is established.The developable surface with the minimum energy is achieved with the help of the feedback mechanism-driven improved reptile search algorithm,and the comparison experiment verifies the superiority of the feedback mechanism-driven improved reptile search algorithm for the shape optimization problem.展开更多
Since its outbreak in 2019,Severe Acute Respiratory Syndrome Coronavirus 2(SARS-Co V-2)keeps surprising the medical community by evolving diverse immune escape mutations in a rapid and effective manner.To gain deeper ...Since its outbreak in 2019,Severe Acute Respiratory Syndrome Coronavirus 2(SARS-Co V-2)keeps surprising the medical community by evolving diverse immune escape mutations in a rapid and effective manner.To gain deeper insight into mutation frequency and dynamics,we isolated ten ancestral strains of SARS-Co V-2 and performed consecutive serial incubation in ten replications in a suitable and common cell line and subsequently analysed them using RT-q PCR and whole genome sequencing.Along those lines we hoped to gain fundamental insights into the evolutionary capacity of SARS-Co V-2 in vitro.Our results identified a series of adaptive genetic changes,ranging from unique convergent substitutional mutations and hitherto undescribed insertions.The region coding for spike proved to be a mutational hotspot,evolving a number of mutational changes including the already known substitutions at positions S:484 and S:501.We discussed the evolution of all specific adaptations as well as possible reasons for the seemingly inhomogeneous potential of SARS-Co V-2 in the adaptation to cell culture.The combination of serial passage in vitro with whole genome sequencing uncovers the immense mutational potential of some SARS-Co V-2 strains.The observed genetic changes of SARS-Co V-2 in vitro could not be explained solely by selectively neutral mutations but possibly resulted from the action of directional selection accumulating favourable genetic changes in the evolving variants,along the path of increasing potency of the strain.Competition among a high number of quasi-species in the SARS-Co V-2 in vitro population gene pool may reinforce directional selection and boost the speed of evolutionary change.展开更多
Introduction:Chikungunya virus(CHIKV),transmitted by Aedes aegypti and Aedes albopictus,causes chikungunya fever.Since its 2005 re-emergence,it has become endemic in 119 countries across Africa,Asia,the Americas,Europ...Introduction:Chikungunya virus(CHIKV),transmitted by Aedes aegypti and Aedes albopictus,causes chikungunya fever.Since its 2005 re-emergence,it has become endemic in 119 countries across Africa,Asia,the Americas,Europe,and Oceania.An outbreak in China’s Guangdong Province(July 2025)led to more than 15,000 cases by August 20,straining public health systems and highlighting the need to strengthen viral mutation surveillance.However,the precise genomic characteristics of this prevalent virus remain unknown,and this study aims to fill this critical knowledge gap through high-throughput sequencing technology.Methods:This study collected two serum samples from this epidemic,extracting and sequencing total nucleic acids via an MGISEQ-G99 sequencer.Complete viral genomes were generated via a consensus reference assembly;they were phylogenetically analyzed and comparatively assessed to identify viral nucleotide variations and protein amino acid substitutions.Results:Phylogenetic analysis confirmed that both research strains belong to the East/Central/South African genotype,clustering within the Middle African Lineage and sharing the highest identity with currently circulating CHIKV isolates from Réunion Island.The circulating strain carries adaptive mutation sites such as E1-A226V,E2-L210Q,and E2-I211T,significantly enhancing viral replication efficiency in Ae.albopictus.Conclusions:Understanding viral etiology is essential for controlling outbreaks.The current epidemic strain carries mutations adaptive to Ae.albopictus,increasing transmission risk.Guangdong’s mosquito population—predominantly Ae.albopictus with limited Ae.aegypti presence—facilitates efficient virus import and spread.展开更多
A novel coupled model integrating Elman-AdaBoost with adaptive mutation sparrow search algorithm(AM-SSA),called AMSSAElman-AdaBoost,is proposed for predicting the existing metro tunnel deformation induced by adjacent ...A novel coupled model integrating Elman-AdaBoost with adaptive mutation sparrow search algorithm(AM-SSA),called AMSSAElman-AdaBoost,is proposed for predicting the existing metro tunnel deformation induced by adjacent deep excavations in soft ground.The novelty is that the modified SSA proposes adaptive adjustment strategy to create a balance between the capacity of exploitation and exploration.In AM-SSA,firstly,the population is initialized by cat mapping chaotic sequences to improve the ergodicity and randomness of the individual sparrow,enhancing the global search ability.Then the individuals are adjusted by Tent chaotic disturbance and Cauchy mutation to avoid the population being too concentrated or scattered,expanding the local search ability.Finally,the adaptive producer-scrounger number adjustment formula is introduced to balance the ability to seek the global and local optimal.In addition,it leads to the improved algorithm achieving a better accuracy level and convergence speed compared with the original SSA.To demonstrate the effectiveness and reliability of AM-SSA,23 classical benchmark functions and 25 IEEE Congress on Evolutionary Computation benchmark test functions(CEC2005),are employed as the numerical examples and investigated in comparison with some wellknown optimization algorithms.The statistical results indicate the promising performance of AM-SSA in a variety of optimization with constrained and unknown search spaces.By utilizing the AdaBoost algorithm,multiple sets of weak AMSSA-Elman predictor functions are restructured into one strong predictor by successive iterations for the tunnel deformation prediction output.Additionally,the on-site monitoring data acquired from a deep excavation project in Ningbo,China,were selected as the training and testing sample.Meanwhile,the predictive outcomes are compared with those of other different optimization and machine learning techniques.In the end,the obtained results in this real-world geotechnical engineering field reveal the feasibility of the proposed hybrid algorithm model,illustrating its power and superiority in terms of computational efficiency,accuracy,stability,and robustness.More critically,by observing data in real time on daily basis,the structural safety associated with metro tunnels could be supervised,which enables decision-makers to take concrete control and protection measures.展开更多
A new adaptive mutation particle swarm optimizer,which is based on the variance of the population's fitness,is presented in this paper.During the running time,the mutation probability for the current best particle...A new adaptive mutation particle swarm optimizer,which is based on the variance of the population's fitness,is presented in this paper.During the running time,the mutation probability for the current best particle is determined by two factors:the variance of the population's fitness and the current optimal solution.The ability of particle swarm optimization(PSO)algorithm to break away from the local optimum is greatly improved by the mutation.The experimental results show that the new algorithm not only has great advantage of convergence property over genetic algorithm and PSO,but can also avoid the premature convergence problem effectively.展开更多
A super-repressed mutant of purR (purRs), which encodes a repressor protein controlling expression of purine biosynthetic genes in Salmonella typhimurium, grew very slowly on NCE medium with 10 μg/mL Ade and lactose ...A super-repressed mutant of purR (purRs), which encodes a repressor protein controlling expression of purine biosynthetic genes in Salmonella typhimurium, grew very slowly on NCE medium with 10 μg/mL Ade and lactose as sole carbon source (cannot form colonies). However, a phenomenon of late-arising mutations was observed when purRs mutants were spread on NCE+lactose plates and subjected to a prolonged non-lethal selection. The reconstruction experiments of revertants showed that the late-arising 'lac+' mutants are not slow growing mutants. Statistical analysis indicated that the distribution of late-arising mutants is Poisson distribution, showing that reversion occurred after plating. The result of co-transductional analysis preliminarily showed that late-arising mutation occurred at selected gene purR or 16 bp PUR box, cis element of structural gene purD. The above results suggest that the phenomenon of late-arising mutation observed by our system is a result of adaptive mutations which are different from random mutations. This is the first time to extend target genes at which adaptive mutations could occur from structural genes involved in carbon metabolism and amino acid biosynthesis to trans regulatory gene coding represser protein. Our results have provided not only a new proof for generality of adaptive mutations but also a new system for study on adaptive mutations.展开更多
基金Supported by the National Key Research and Development Program of China(No.2022ZD0119001)。
文摘The honey badger algorithm(HBA),as a new swarm intelligence(SI)optimization algorithm,has shown certain effectiveness in its applications.Aiming at the problems of unsatisfactory initial population distribution of HBA,poor ability to avoid local optimum,and slow convergence speed,this paper proposes a multi-strategy improved HBA based on periodical mutation and t-distribution perturbation,called MHBA.Firstly,a good point set population initialization is introduced to get a uniform initial population.Secondly,periodic mutation and t-distribution perturbation are successively used to improve the algorithm’s ability to avoid local optimum.Finally,the density factor is improved for balancing exploration and exploitation.By comparing MHBA with HBA and 7 other SIs on 6 benchmark functions,it is evident that the performance of MHBA is far superior to HBA.In addition,by applying MHBA to robot path planning,MHBA can identify the shortest path more quickly and consistently compared with competitors.
基金supported by the National Natural Science Foundation of China[Grant No.12371378]the Fujian Natural Science Foundation[Grant No.2022J01378,Grant No.2023J011127].
文摘Accurate forecasting of wind power is crucial for ensuring the reliable operation of the electrical grid.Due to the impact of various factors,wind power forecasting presents a significant challenge.This paper presents the model that integrates Osprey and adaptive T-distribution dung beetle algorithm for optimizing a convolutional neural network.The CNN-BiLSTM-Attention model combines bidirectional long short-term memory neural networks with an attention mechanism,thereby improving the accuracy of wind power generation predictions.The original data is subjected to Variational Mode Decomposition(VMD)for analysis,taking into account the fluctuations in wind power across different periods.The BiLSTM network with short-term memory processes time-series wind power data,yielding an optimal predictive performance.The integration of the osprey algorithm and adaptive T-distribution within the Dung Beetle Optimization Algorithm was utilized to optimize the hyperparameters of the CNN-BiLSTM-Attention model,thereby enhancing its predictive performance.To assess the efficacy of the CNN-BiLSTM-Attention algorithm,enhanced by Ospreys and adaptive T-distributed dung beetle algorithm,we conducted experiments using the CEC2021 benchmark function.The integrated Osprey and adaptive T-distribution Dung Beetle algorithm has excellent global optimization performance when dealing with complex optimization problems.The fusion of Osprey and the adaptive T-distribution Dung beetle algorithm optimized the CNN-BiLSTM-Attention algorithm as well as other optimization algorithms for ablation experiments.The results show that the improved algorithm performs well in predicting wind power.The experimental findings suggest that the model’s predictive efficiency has enhanced by a minimum of 17.74%.
文摘An adaptive genetic algorithm with diversity-guided mutation, which combines adaptive probabilities of crossover and mutation was proposed. By means of homogeneous finite Markov chains, it is proved that adaptive genetic algorithm with diversity-guided mutation and genetic algorithm with diversity-guided mutation converge to the global optimum if they maintain the best solutions, and the convergence of adaptive genetic algorithms with adaptive probabilities of crossover and mutation was studied. The performances of the above algorithms in optimizing several unimodal and multimodal functions were compared. The results show that for multimodal functions the average convergence generation of the adaptive genetic algorithm with diversity-guided mutation is about 900 less than that of (adaptive) genetic algorithm with adaptive probabilities and genetic algorithm with diversity-guided mutation, and the adaptive genetic algorithm with diversity-guided mutation does not lead to premature convergence. It is also shown that the better balance between overcoming premature convergence and quickening convergence speed can be gotten.
文摘This paper presents a new adaptive mutation approach for fastening the convergence of immune algorithms (IAs). This method is adopted to realize the twin goals of maintaining diversity in the population and sustaining the convergence capacity of the IA. In this method, the mutation rate (pm) is adaptively varied depending on the fitness values of the solutions. Solutions of high fitness are protected, while solutions with sub-average fitness are totally disrupted. A solution to the problem of deciding the optimal value of pm is obtained. Experiments are carried out to compare the proposed approach to traditional one on a set of optimization problems. These are namely: 1) an exponential multi-variable function;2) a rapidly varying multimodal function and 3) design of a second order 2-D narrow band recursive LPF. Simulation results show that the proposed method efficiently improves IA’s performance and prevents it from getting stuck at a local optimum.
基金Beijing Natural Science Foundation,No.7161006Beijing Municipal Administration of Hospitals’ Youth Program,No.QML20161801 and No.QML20171801
文摘AIM To explore hepatitis C virus(HCV) adaptive mutations or combinations thereof responsible for enhanced viral production and investigate the underlying mechanisms.METHODS A series of plasmids with adaptive mutations were constructed. After the plasmids were transfected into Huh7.5 cells, we determined the infectious HCV particle titers by NS5 A immunofluorescence assays, and detected HCV RNA replication by real-time PCR and protein expression by Western blot. Then we carried out immunoblotting of supernatants and celllysates with anti-NS3 to analyze the virus release level. In addition, co-localization of lipid droplets(LDs) with NS5 A was measured using confocal laser scanning microscopy. The ratio between the p56 and p58 phosphoforms of NS5 A was analyzed further.RESULTS The plasmids named JFH1-m E2, JFH1-mp7, JFH1-m NS4 B, JFH1-m NS5 A, JFH1-m E2/NS5 A, JFH1-mp7/NS5 A, JFH1-m NS4 B/NS5 A, JFH1-m E2/p7/NS5 A, and m JFH1 were constructed successfully. This study generated infectious HCV particles with a robust titer of 1.61 × 106 focus-forming units(FFUs)/m L. All of the six adaptive mutations increased the HCV particle production at varying levels. The NS5 A(C2274 R, I2340 T, and V2440 L) and p7(H781 Y) were critical adaptive mutations. The effect of NS5 A(C2274 R, I2340 T, and V2440 L), p7(H781 Y), and NS4 B(N1931 S) on infectious HCV titers was investigated by measuring the HCV RNA replication, protein expression, and virion release. However, the six adaptive mutations were not required for the LD localization of NS5 A proteins or the phosphorylation of NS5 A.CONCLUSION In this study, we generated infectious HCV particles with a robust titer of 1.61 × 106 FFUs/m L, and found that the viral replication and release levels could be enhanced by some of the adaptive mutations.
基金supported by the National Natural Science Foundation of China(31701577).
文摘Next-generation sequencing technology has transformed our ability to assess the taxonomic composition functions of host-associated microbiota and microbiomes. More human microbiome research projects—particularly those that explore genomic mutations within the microbiome—will be launched in the next decade. This review focuses on the coevolution of microbes within a microbiome, which shapes strain-level diversity both within and between host species. We also explore the correlation between microbial genomic mutations and common metabolic diseases, and the adaptive evolution of pathogens and probiotics during invasion and colonization. Finally, we discuss advances in methods and algorithms for annotating and analyzing microbial genomic mutations.
基金funding from the National Key Research and Development Project of China(2021YFC2300202)the National Natural Science Foundation of China(82171820)+2 种基金C.-F.Q.received support from the National Science Fund for Distinguished Young Scholar(81925025)the Innovative Research Group(81621005)from the National Natural Science Foundation Chinathe Innovation Fund for Medical Sciences(No.2019-I2M-5-049)from the Chinese Academy of Medical Sciences.
文摘The live attenuated hepatitis A virus vaccine H2 strain was developed by passaging a wild-type H2w isolate in cell cultures.Currently,the mechanism underlying its attenuation phenotype remain largely unknown.In this study,we generated a full-length infectious cDNA clone of the H2 strain using in-fusion techniques.The recovered H2 strain(H2ic)from the cDNA clone exhibited an efficient replication in both the hepatoma cell line Huh7.5.1 and the 2BS cell line used for vaccine production,similar to the parental H2 strain.Additionally,H2ic did not cause disease in Ifnar1-/- C57 mice,consistent with the H2 strain.To explore the cell-adaptive mutations of the H2 strain,chimeric viruses were generated by replacing its non-structural proteins with corresponding regions from H2w using the infectious cDNA clone as a genetic backbone.The chimeric viruses carrying the 3C or 3D proteins from H2w showed decreased replication in Huh7.5.1 and 2BS cell lines compared to H2ic.Other chimeric viruses containing the 2B,2C,or 3A proteins from H2w failed to be recovered.Furthermore,there were no significant differences in disease manifestation in mice between H2ic and the recovered chimeric viruses.These results demonstrate that adaptive mutations in the 2B,2C,and 3A proteins are essential for efficient replication of the H2 strain in cell cultures.Mutations in the 3C and 3D proteins contribute to enhanced replication in cell cultures but did not influence the attenuated phenotypes in mice.Together,this study presents the first reverse genetic system of the H2 strain and identifies viral proteins essential for adaptation to cell cultures.
文摘Single unmanned aerial vehicle(UAV)multitasking plays an important role in multiple UAVs cooperative control,which is as well as the most complicated and hardest part.This paper establishes a threedimensional topographical map,and an improved adaptive differential evolution(IADE)algorithm is proposed for single UAV multitasking.As an optimized problem,the efficiency of using standard differential evolution to obtain the global optimal solution is very low to avoid this problem.Therefore,the algorithm adopts the mutation factor and crossover factor into dynamic adaptive functions,which makes the crossover factor and variation factor can be adjusted with the number of population iteration and individual fitness value,letting the algorithm exploration and development more reasonable.The experimental results implicate that the IADE algorithm has better performance,higher convergence and efficiency to solve the multitasking problem compared with other algorithms.
基金Grants from"Instituto de Salud Carlos Ⅲ",Spain and"European Regional Development Fund(ERDF),a way of making Europe",E.U.,No.PI12/00130"Fundacion de In-vestigacion Medica Mutua Madrilena",Spain,No.8922/2011Lokhande MU was funded by a research grant from"Asoci-acion de Hepatologia Translacional"No.AHT-2010/01,Spain
文摘Hepatitis C virus(HCV)infection affects about 170 million people worldwide and it is a major cause of liver cirrhosis and hepatocellular carcinoma.HCV is a hepatotropic non-cytopathic virus able to persist in a great percentage of infected hosts due to its ability to escape from the immune control.Liver damage and disease progression during HCV infection are driven by both viral and host factors.Specifically,adaptive immune response carries out an essential task in controllingnon-cytopathic viruses because of its ability to recognize infected cells and to destroy them by cytopathic mechanisms and to eliminate the virus by non-cytolytic machinery.HCV is able to impair this response by several means such as developing escape mutations in neutralizing antibodies and in T cell receptor viral epitope recognition sites and inducing HCV-specific cytotoxic T cell anergy and deletion.To impair HCV-specific T cell reactivity,HCV affects effector T cell regulation by modulating T helper and Treg response and by impairing the balance between positive and negative co-stimulatory molecules and between pro-and antiapoptotic proteins.In this review,the role of adaptive immune response in controlling HCV infection and the HCV mechanisms to evade this response are reviewed.
基金the National Natural Science Foundation of China(Nos.60574071 and70771080)
文摘Bilevel linear programming, which consists of the objective functions of the upper level and lower level, is a useful tool for modeling decentralized decision problems. Various methods are proposed for solving this problem. Of all the algorithms, the ge- netic algorithm is an alternative to conventional approaches to find the solution of the bilevel linear programming. In this paper, we describe an adaptive genetic algorithm for solving the bilevel linear programming problem to overcome the difficulty of determining the probabilities of crossover and mutation. In addition, some techniques are adopted not only to deal with the difficulty that most of the chromosomes maybe infeasible in solving constrained optimization problem with genetic algorithm but also to improve the efficiency of the algorithm. The performance of this proposed algorithm is illustrated by the examples from references.
基金supported by the National Natural Science Foundation of China(Grant No.52375264).
文摘Curvature lines are special and important curves on surfaces.It is of great significance to construct developable surface interpolated on curvature lines in engineering applications.In this paper,the shape optimization of generalized cubic ball developable surface interpolated on the curvature line is studied by using the improved reptile search algorithm.Firstly,based on the curvature line of generalized cubic ball curve with shape adjustable,this paper gives the construction method of SGC-Ball developable surface interpolated on the curve.Secondly,the feedback mechanism,adaptive parameters and mutation strategy are introduced into the reptile search algorithm,and the Feedback mechanism-driven improved reptile search algorithm effectively improves the solving precision.On IEEE congress on evolutionary computation 2014,2017,2019 and four engineering design problems,the feedback mechanism-driven improved reptile search algorithm is compared with other representative methods,and the result indicates that the solution performance of the feedback mechanism-driven improved reptile search algorithm is competitive.At last,taking the minimum energy as the evaluation index,the shape optimization model of SGC-Ball interpolation developable surface is established.The developable surface with the minimum energy is achieved with the help of the feedback mechanism-driven improved reptile search algorithm,and the comparison experiment verifies the superiority of the feedback mechanism-driven improved reptile search algorithm for the shape optimization problem.
基金the financial support of the Austrian Research Promotion Agency(FFG),Grant No.35863961。
文摘Since its outbreak in 2019,Severe Acute Respiratory Syndrome Coronavirus 2(SARS-Co V-2)keeps surprising the medical community by evolving diverse immune escape mutations in a rapid and effective manner.To gain deeper insight into mutation frequency and dynamics,we isolated ten ancestral strains of SARS-Co V-2 and performed consecutive serial incubation in ten replications in a suitable and common cell line and subsequently analysed them using RT-q PCR and whole genome sequencing.Along those lines we hoped to gain fundamental insights into the evolutionary capacity of SARS-Co V-2 in vitro.Our results identified a series of adaptive genetic changes,ranging from unique convergent substitutional mutations and hitherto undescribed insertions.The region coding for spike proved to be a mutational hotspot,evolving a number of mutational changes including the already known substitutions at positions S:484 and S:501.We discussed the evolution of all specific adaptations as well as possible reasons for the seemingly inhomogeneous potential of SARS-Co V-2 in the adaptation to cell culture.The combination of serial passage in vitro with whole genome sequencing uncovers the immense mutational potential of some SARS-Co V-2 strains.The observed genetic changes of SARS-Co V-2 in vitro could not be explained solely by selectively neutral mutations but possibly resulted from the action of directional selection accumulating favourable genetic changes in the evolving variants,along the path of increasing potency of the strain.Competition among a high number of quasi-species in the SARS-Co V-2 in vitro population gene pool may reinforce directional selection and boost the speed of evolutionary change.
基金Supported by Shenzhen Medical Research Fund(B2404002)Sanming Project of Medicine in Shenzhen(SZSM202211023)Shenzhen Science and Technology Program(SYSPG20241211173921049,SGDX20240115113259001).
文摘Introduction:Chikungunya virus(CHIKV),transmitted by Aedes aegypti and Aedes albopictus,causes chikungunya fever.Since its 2005 re-emergence,it has become endemic in 119 countries across Africa,Asia,the Americas,Europe,and Oceania.An outbreak in China’s Guangdong Province(July 2025)led to more than 15,000 cases by August 20,straining public health systems and highlighting the need to strengthen viral mutation surveillance.However,the precise genomic characteristics of this prevalent virus remain unknown,and this study aims to fill this critical knowledge gap through high-throughput sequencing technology.Methods:This study collected two serum samples from this epidemic,extracting and sequencing total nucleic acids via an MGISEQ-G99 sequencer.Complete viral genomes were generated via a consensus reference assembly;they were phylogenetically analyzed and comparatively assessed to identify viral nucleotide variations and protein amino acid substitutions.Results:Phylogenetic analysis confirmed that both research strains belong to the East/Central/South African genotype,clustering within the Middle African Lineage and sharing the highest identity with currently circulating CHIKV isolates from Réunion Island.The circulating strain carries adaptive mutation sites such as E1-A226V,E2-L210Q,and E2-I211T,significantly enhancing viral replication efficiency in Ae.albopictus.Conclusions:Understanding viral etiology is essential for controlling outbreaks.The current epidemic strain carries mutations adaptive to Ae.albopictus,increasing transmission risk.Guangdong’s mosquito population—predominantly Ae.albopictus with limited Ae.aegypti presence—facilitates efficient virus import and spread.
基金supported by the National Natural Science Foundation of China(Grant No.52125803).
文摘A novel coupled model integrating Elman-AdaBoost with adaptive mutation sparrow search algorithm(AM-SSA),called AMSSAElman-AdaBoost,is proposed for predicting the existing metro tunnel deformation induced by adjacent deep excavations in soft ground.The novelty is that the modified SSA proposes adaptive adjustment strategy to create a balance between the capacity of exploitation and exploration.In AM-SSA,firstly,the population is initialized by cat mapping chaotic sequences to improve the ergodicity and randomness of the individual sparrow,enhancing the global search ability.Then the individuals are adjusted by Tent chaotic disturbance and Cauchy mutation to avoid the population being too concentrated or scattered,expanding the local search ability.Finally,the adaptive producer-scrounger number adjustment formula is introduced to balance the ability to seek the global and local optimal.In addition,it leads to the improved algorithm achieving a better accuracy level and convergence speed compared with the original SSA.To demonstrate the effectiveness and reliability of AM-SSA,23 classical benchmark functions and 25 IEEE Congress on Evolutionary Computation benchmark test functions(CEC2005),are employed as the numerical examples and investigated in comparison with some wellknown optimization algorithms.The statistical results indicate the promising performance of AM-SSA in a variety of optimization with constrained and unknown search spaces.By utilizing the AdaBoost algorithm,multiple sets of weak AMSSA-Elman predictor functions are restructured into one strong predictor by successive iterations for the tunnel deformation prediction output.Additionally,the on-site monitoring data acquired from a deep excavation project in Ningbo,China,were selected as the training and testing sample.Meanwhile,the predictive outcomes are compared with those of other different optimization and machine learning techniques.In the end,the obtained results in this real-world geotechnical engineering field reveal the feasibility of the proposed hybrid algorithm model,illustrating its power and superiority in terms of computational efficiency,accuracy,stability,and robustness.More critically,by observing data in real time on daily basis,the structural safety associated with metro tunnels could be supervised,which enables decision-makers to take concrete control and protection measures.
基金supported by the Gansu Natural Science Foundation (No.ZS011-A25-016-G).
文摘A new adaptive mutation particle swarm optimizer,which is based on the variance of the population's fitness,is presented in this paper.During the running time,the mutation probability for the current best particle is determined by two factors:the variance of the population's fitness and the current optimal solution.The ability of particle swarm optimization(PSO)algorithm to break away from the local optimum is greatly improved by the mutation.The experimental results show that the new algorithm not only has great advantage of convergence property over genetic algorithm and PSO,but can also avoid the premature convergence problem effectively.
基金the National Natural Science Foundation of China (Grant No. 39970008) and Director Foundation of Institute of Microbiology, Chinese Academy of Sciences.
文摘A super-repressed mutant of purR (purRs), which encodes a repressor protein controlling expression of purine biosynthetic genes in Salmonella typhimurium, grew very slowly on NCE medium with 10 μg/mL Ade and lactose as sole carbon source (cannot form colonies). However, a phenomenon of late-arising mutations was observed when purRs mutants were spread on NCE+lactose plates and subjected to a prolonged non-lethal selection. The reconstruction experiments of revertants showed that the late-arising 'lac+' mutants are not slow growing mutants. Statistical analysis indicated that the distribution of late-arising mutants is Poisson distribution, showing that reversion occurred after plating. The result of co-transductional analysis preliminarily showed that late-arising mutation occurred at selected gene purR or 16 bp PUR box, cis element of structural gene purD. The above results suggest that the phenomenon of late-arising mutation observed by our system is a result of adaptive mutations which are different from random mutations. This is the first time to extend target genes at which adaptive mutations could occur from structural genes involved in carbon metabolism and amino acid biosynthesis to trans regulatory gene coding represser protein. Our results have provided not only a new proof for generality of adaptive mutations but also a new system for study on adaptive mutations.
