Genomic Mutations Within the Host Microbiome: Adaptive Evolution or Purifying Selection

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.

An adaptive genetic algorithm with diversity-guided mutation and its global convergence property

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.

A New Method for Fastening the Convergence of Immune Algorithms Using an Adaptive Mutation Approach

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.

Cell culture-adaptive mutations in hepatitis C virus promote viral production by enhancing viral replication and release

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.

Adaptive mutation sparrow search algorithm-Elman-AdaBoost model for predicting the deformation of subway tunnels

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.

Adaptive immune response during hepatitis C virus infection

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.

An adaptive genetic algorithm for solving bilevel linear programming problem

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.

An improved adaptive differential evolution algorithm for single unmanned aerial vehicle multitasking

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.

基于改进T分布烟花-粒子群算法的AUV全局路径规划

针对传统粒子群算法在处理自主水下机器人(Autonomous Underwater Vehicle,AUV)全局路径规划时面临的寻优时间长、能耗高的问题,本文提出一种改进的T分布烟花-粒子群算法(T-distribution Fireworks-Particle Swarm Optimization Algorithm,TFWA-PSO),该算法融合了烟花算法的高效全局搜索能力和粒子群算法的快速局部寻优特性.在变异阶段,提出自适应T分布变异来扩大搜索范围,并在理论上证明了该变异方式能够使个体在局部最优解附近增强搜索能力.在选择阶段提出了适应度选择策略,淘汰适应度差的个体,解决了传统烟花算法易丢失优秀个体的问题,并对改进的T分布烟花算法与传统烟花算法的收敛速度进行对比.将改进算法的爆炸操作、变异操作和选择策略融合到粒子群算法中,对粒子群算法的速度更新公式进行了改进,同时从理论上对所改进的算法进行了收敛性证明.仿真实验结果表明,TFWA-PSO能够有效规划出一条最短路径,同时与给定的智能优化算法相比,TFWA-PSO在寻找最优路径的时间上平均降低了24.72%,能耗平均降低了17.33%,路径长度平均降低了16.96%.

复杂多方向威胁下的导弹预警雷达优化部署方法

针对现有导弹预警雷达部署相对独立、协同困难,难以满足大规模对抗场景的现状,从远程预警雷达、跟踪识别雷达、机动式预警雷达不同的任务特点出发,建立应对复杂多方向威胁的多型导弹预警雷达优化部署模型,在满足最优覆盖、协同交接、目标识别等任务约束下,解决雷达协同部署问题。针对所提模型设计了一种基于云自适应的分区优化离散粒子群(CPBPSO)算法,通过设计分区编码策略缩减算法求解空间、加入云自适应变异算子提高算法全局寻优和局部跳出能力,使算法更适用于导弹预警雷达部署问题的处理。实例验证了所提模型在求解单方向、多方向威胁场景部署问题的可行性,对比分析了CPBPSO算法的有效性,基本满足导弹预警雷达最优化协同部署的需求。

基于改进遗传算法的钢筋混凝土框架优化设计

为改善标准遗传算法(SGA)在离散变量结构优化设计中的早熟问题,提出一种新自适应交叉、变异算子,并结合罚函数改进措施,以改善SGA的不足。自适应改进措施通过迭代数和个体优秀程度进行共同把控,做到前期有较大交叉概率,丰富种群,后期有较大变异概率,增进局部寻优,并通过正交试验测试得出改进SGA最优的控制参数。采用改进SGA对不同的钢筋混凝土框架结构算例进行验证,结果表明:改进SGA的计算结果比传统设计方法、SGA、拟满内力算法更优,说明了改进SGA的适用性和有效性。从整体结果分析可知,改进SGA可以更好的发挥其自身的全局优化性能,可解决多工况、多单元的钢筋混凝土框架结构优化问题,是一种较为高效的方法。

基于自适应变异粒子群的风光储微网调度

为克服传统粒子群算法(particle swarm optimization,PSO)在求解时容易形成局部最优,求解精度低的不足,提出了一种基于自适应变异粒子群优化(adaptive mutation particle swarm optimization,AMPSO)的微电网调度求解方法。AMPSO惯性权重采用自适应正态分布递减,随着迭代次数的增加更新粒子位置的移动策略,并且在算法后期引入变异环节。为验证算法的有效性,该算法与其他改进算法进行收敛性能对比,并对4种典型天气情况下的微网运行成本模型仿真求解,得到最优调度。算例仿真结果表明,AMPSO能够对粒子全局最优搜索优化,在解决微网经济性运行问题上效果优于其他算法,可合理调配各微电源出力时段,具有良好的灵活性和可行性。

基于NSGA-III算法求解柔性作业车间调度问题

针对多目标柔性作业车间调度问题,提出一种改进NSGA-Ⅲ算法,以完工时间、机器总负荷、瓶颈机器负荷为目标建立调度模型。首先,为提高种群的多样性,提出一种基于惩罚的边界相交距离定义关联操作中种群个体与参考向量之间的距离;其次,为提高环境选择的计算效率,利用基于惩罚的边界相交距离消除机制来保护个体,降低了个体保护策略的计算成本;最后,为避免种群陷入局部最优,在遗传算子中采用一种改进的变异策略。运用两个评价指标与NSGA-Ⅲ算法进行比较,其收敛性与多样性均由于NSGA-Ⅲ算法。同时在4个Kacem算例上进行测试得出改进NSGA-Ⅲ算法解的质量较高,最后通过实际的生产实例证明改进的NSGA-Ⅲ算法优于或等同于现存在的方法,也证明了该方法在解决多目标柔性作业车间调度难题上的可操作性。

基于自适应变异粒子群算法的装配式建筑施工安全投入优化

针对装配式建筑施工安全投入问题,以实际工程项目为例,对装配式建筑施工风险因素进行了二级分解;基于数学规划理论建立了非线性规划模型,并引入3种函数关系进行拟合;采用自适应变异粒子群算法在Matlab中进行求解,得到了相对较优方案。结果表明:在安全风险主要因素中,物的风险因素对安全投入最为敏感;在二级风险因素中,预制构件吊装器具的选择最为敏感,该结论可为日后施工安全投入的方向提供参考依据。

基于AM-PSO-BP神经网络的打印路径规划

为提高弧焊焊接效果,提出一种基于AM-PSO-BP神经网络的弧焊打印路径规划方法。方法采用基于自适应方差的自适应变异操作(AM)消除粒子群优化算法(PSO)后期迭代效率低的问题,然后利用AM-PSO算法优化BP(back propagation)神经网络的权重和阈值,实现BP神经网络参数的优化;最后将AM-PSO-BP神经网络算法对弧焊打印工艺参数进行预测,获取更准确的弧焊打印工艺参数。仿真结果表明:所提方法可精确预测弧焊打印工艺参数,在该工艺参数下,弧焊打印的六边形柱体、圆柱体、正方体预测值与实测值相差较小,且在误差允许范围内,具有较高的准确性。以上方法可为精确弧焊打印提供依据。

基于概率精英差分和自适应黄金正弦的鲸鱼优化算法

针对鲸鱼优化算法收敛速度慢和寻优精度低的缺点,提出一种基于概率精英差分和自适应黄金正弦的鲸鱼优化算法。基于最大最小思想优化拉丁超立方体抽样来初始化鲸鱼种群,使初始种群分布更加均匀,拥有更好的全局搜索能力;提出融合余弦自适应算子的黄金正弦算法改进鲸鱼的螺旋更新,加快收敛速度,提高收敛精度;设计概率精英差分变异方法并进行贪婪选择,优化算法流程,增强算法跳出陷入局部最优的能力。选取4个单峰测试函数、4个多峰测试函数和5个多最优解的多模态测试函数与主流优化算法进行对比实验,实验结果表明,该算法具有更高的寻优精度、更快的收敛速度以及更优的全局搜索能力,通过消融实验验证了该算法改进策略的有效性。

多策略融合改进的自适应蜉蝣算法

为改进蜉蝣算法全局搜索能力较差、种群多样性较小和自适应能力弱等问题,提出一种多策略融合改进的自适应蜉蝣算法(MIMA)。采用Sin混沌映射初始化蜉蝣种群,使种群能够均匀分布在解空间中,提高初始种群质量,增强全局搜索能力;引入Tent混沌映射和高斯变异对种群个体进行调节,增加种群多样性的同时调控种群密度,增强局部最优逃逸能力;引入不完全伽马函数,重构自适应动态调节的重力系数,建立全局搜索和局部开发能力之间更好的平衡,进而提升算法收敛精度,有利于提高全局搜索能力;采用随机反向学习(ROBL)策略,增强全局搜索能力,提高收敛速度并增强稳定性。利用经典测试函数集进行算法对比,并利用Wilcoxon秩和检验分析算法的优化效果,证明改进的有效性和可靠性。实验结果表明:所提算法与其他算法相比,寻优精度、收敛速度、稳定性都取得了较大提升。

多策略改进的蜜獾优化算法

针对标准蜜獾算法存在的易陷入局部最优值、目标精度低、局部搜索能力不足等问题,提出了一种多策略改进的蜜獾算法.在种群初始化阶段,使用Chebyshev混沌映射初始化种群,保证随机性的同时提高种群的均衡性;在局部挖掘阶段加入莱维飞行,使寻找最优值到确定最优值的过程更加平稳,避免算法陷入局部最优;在最优个体确定阶段上引入最优个体自适应变异策略,来提高算法局部搜索能力以及收敛精度,避免算法个体早熟.选取18个基准测试函数进行仿真,同时结合秩和检验、实际工程应用对该算法进行多维度评估,实验证明改进的蜜獾算法与标准蜜獾算法相比,在收敛速度、目标精度以及寻优搜索能力均有明显改善,表现出较好的鲁棒性.

引入精英反向学习和柯西变异的混沌蜉蝣算法

为提高蜉蝣算法的收敛速度,提升算法寻优能力,提出一种引入精英反向学习和柯西变异的混沌蜉蝣算法。利用Circle混沌映射序列优化初始种群使种群分布更加均匀,提高种群多样性。在蜉蝣更新阶段,对蜉蝣中的精英个体进行反向学习策略,防止算法陷入局部最优,提高算法收敛速度。为保证种群进化方向和扩大寻优范围,将自适应概率阈值和柯西变异的扰动机制相结合,对劣势蜉蝣个体附近生成更大的扰动。通过8个基准测试函数实验对比和Wilcoxon秩和检验,实验结果表明,混沌蜉蝣算法在收敛速度、求解精度以及稳定性等方面有较大提高。

融入小生境和混合变异策略的鲸鱼优化算法

鲸鱼优化算法作为一种结构简单的先进优化算法,被用于解决各类学科问题。通过对鲸鱼优化算法进行深入研究,发现该算法存在收敛速度慢、无法跳出局部最优、收敛精度低以及无法平衡全局勘探与局部开发能力等问题。为解决上述问题,提出一种融入小生境和混合变异策略的鲸鱼优化算法(whale optimization algorithm integrating niche and hybrid mutation strategy,NHWOA)。该算法通过引入自适应权重,平衡算法全局勘探与局部开发能力,并加快收敛速度;将种群按照相同规模划分成三个小生境并独立寻优,提高种群多样性;采用混合变异策略对种群进行随机扰动,帮助算法跳出局部最优。通过在CEC2017测试套件上对NHWOA进行仿真实验,并将其应用于特征选择问题,验证了NHWOA的先进性和有效性。NHWOA的收敛速度更快,收敛精度更高,并且鲁棒性更好。