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https://www.readbyqxmd.com/read/28212413/scarless-deletion-of-up-to-seven-methyl-accepting-chemotaxis-genes-with-an-optimized-method-highlights-key-function-of-chem-in-salmonella-typhimurium
#1
Stefanie Hoffmann, Christiane Schmidt, Steffi Walter, Jennifer K Bender, Roman G Gerlach
Site-directed scarless mutagenesis is an essential tool of modern pathogenesis research. We describe an optimized two-step protocol for genome editing in Salmonella enterica serovar Typhimurium to enable multiple sequential mutagenesis steps in a single strain. The system is based on the λ Red recombinase-catalyzed integration of a selectable antibiotics resistance marker followed by replacement of this cassette. Markerless mutants are selected by expressing the meganuclease I-SceI which induces double-strand breaks in bacteria still harboring the resistance locus...
2017: PloS One
https://www.readbyqxmd.com/read/28208820/optimal-resonant-band-demodulation-based-on-an-improved-correlated-kurtosis-and-its-application-in-bearing-fault-diagnosis
#2
Xianglong Chen, Bingzhi Zhang, Fuzhou Feng, Pengcheng Jiang
The kurtosis-based indexes are usually used to identify the optimal resonant frequency band. However, kurtosis can only describe the strength of transient impulses, which cannot differentiate impulse noises and repetitive transient impulses cyclically generated in bearing vibration signals. As a result, it may lead to inaccurate results in identifying resonant frequency bands, in demodulating fault features and hence in fault diagnosis. In view of those drawbacks, this manuscript redefines the correlated kurtosis based on kurtosis and auto-correlative function, puts forward an improved correlated kurtosis based on squared envelope spectrum of bearing vibration signals...
February 13, 2017: Sensors
https://www.readbyqxmd.com/read/28208499/collective-transport-for-active-matter-run-and-tumble-disk-systems-on-a-traveling-wave-substrate
#3
Cs Sándor, A Libál, C Reichhardt, C J Olson Reichhardt
We examine numerically the transport of an assembly of active run-and-tumble disks interacting with a traveling-wave substrate. We show that as a function of substrate strength, wave speed, disk activity, and disk density, a variety of dynamical phases arise that are correlated with the structure and net flux of disks. We find that there is a sharp transition into a state in which the disks are only partially coupled to the substrate and form a phase-separated cluster state. This transition is associated with a drop in the net disk flux, and it can occur as a function of the substrate speed, maximum substrate force, disk run time, and disk density...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28204863/influence-of-twitching-and-swarming-motilities-on-biofilm-formation-in-pseudomonas-strains
#4
Letícia Muner Otton, Marina da Silva Campos, Karine Lena Meneghetti, Gertrudes Corção
The genus Pseudomonas mainly includes opportunistic pathogens that rely on type IV pili as an important virulence factor, which is associated with adherence and biofilm formation. Pseudomonas infections are well known to be persistent and resilient in nature largely because of the tendency of the species to form biofilms. This study aimed at analyzing environmental strains of Pseudomonas genus with respect to their ability to execute twitching and swarming motilities as well as with respect to their ability to form biofilms both in the presence as well as in the absence of furanone, a substance that has the potential to prevent the formation of biofilms...
February 15, 2017: Archives of Microbiology
https://www.readbyqxmd.com/read/28204482/collective-behaviour-and-swarm-intelligence-in-slime-moulds
#5
Chris R Reid, Tanya Latty
No abstract text is available yet for this article.
November 1, 2016: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28194138/phenotypic-microdiversity-and-phylogenetic-signal-analysis-of-traits-related-to-social-interaction-in-bacillus-spp-from-sediment-communities
#6
Dolores María Rodríguez-Torres, África Islas-Robles, Zulema Gómez-Lunar, Luis Delaye, Ismael Hernández-González, Valeria Souza, Michael Travisano, Gabriela Olmedo-Álvarez
Understanding the relationship between phylogeny and predicted traits is important to uncover the dimension of the predictive power of a microbial composition approach. Numerous works have addressed the taxonomic composition of bacteria in communities, but little is known about trait heterogeneity in closely related bacteria that co-occur in communities. We evaluated a sample of 467 isolates from the Churince water system of the Cuatro Cienegas Basin (CCB), enriched for Bacillus spp. The 16S rRNA gene revealed a random distribution of taxonomic groups within this genus among 11 sampling sites...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28193812/coping-with-copepods-do-right-whales-eubalaena-glacialis-forage-visually-in-dark-waters
#7
Thomas W Cronin, Jeffry I Fasick, Lorian E Schweikert, Sönke Johnsen, Lorren J Kezmoh, Mark F Baumgartner
North Atlantic right whales (Eubalaena glacialis) feed during the spring and early summer in marine waters off the northeast coast of North America. Their food primarily consists of planktonic copepods, Calanus finmarchicus, which they consume in large numbers by ram filter feeding. The coastal waters where these whales forage are turbid, but they successfully locate copepod swarms during the day at depths exceeding 100 m, where light is very dim and copepod patches may be difficult to see. Using models of E...
April 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28192508/multiswarm-comprehensive-learning-particle-swarm-optimization-for-solving-multiobjective-optimization-problems
#8
Xiang Yu, Xueqing Zhang
Comprehensive learning particle swarm optimization (CLPSO) is a powerful state-of-the-art single-objective metaheuristic. Extending from CLPSO, this paper proposes multiswarm CLPSO (MSCLPSO) for multiobjective optimization. MSCLPSO involves multiple swarms, with each swarm associated with a separate original objective. Each particle's personal best position is determined just according to the corresponding single objective. Elitists are stored externally. MSCLPSO differs from existing multiobjective particle swarm optimizers in three aspects...
2017: PloS One
https://www.readbyqxmd.com/read/28188589/synergistic-activity-of-sub-inhibitory-concentrations-of-curcumin-with-ceftazidime-and-ciprofloxacin-against-pseudomonas-aeruginosa-quorum-sensing-related-genes-and-virulence-traits
#9
Shekoufeh Roudashti, Habib Zeighami, Hesam Mirshahabi, Shahin Bahari, Ali Soltani, Fakhri Haghi
Quorum sensing (QS) system in Pseudomonas aeruginosa may be an important target for pharmacological intervention. The present study aimed to investigate the synergetic activity of sub-MIC concentrations of curcumin (C) with ceftazidime (CAZ) and ciprofloxacin (CIP) against P. aeroginusa QS system. We determined the MIC and synergistic activity of C, CAZ and CIP against P. aeroginusa PAO1 using broth microdilution and checkerboard titration methods. The activity of sub-MIC (1/4 and 1/16 MIC) concentrations of C on the QS signal molecules was assessed using a reporter strain assay...
March 2017: World Journal of Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28187888/a-survey-of-nature-inspired-algorithms-for-feature-selection-to-identify-parkinson-s-disease
#10
Prashant Shrivastava, Anupam Shukla, Praneeth Vepakomma, Neera Bhansali, Kshitij Verma
BACKGROUND AND OBJECTIVES: Parkinson's disease is a chronic neurological disorder that directly affects human gait. It leads to slowness of movement, causes muscle rigidity and tremors. Analyzing human gait serves to be useful in studies aiming at early recognition of the disease. In this paper we perform a comparative analysis of various nature inspired algorithms to select optimal features/variables required for aiding in the classification of affected patients from the rest. METHODS: For the experiments, we use a real life dataset of 166 people containing both healthy controls and affected people...
February 2017: Computer Methods and Programs in Biomedicine
https://www.readbyqxmd.com/read/28182546/three-dimensional-path-planning-for-uninhabited-combat-aerial-vehicle-based-on-predator-prey-pigeon-inspired-optimization-in-dynamic-environment
#11
Bo Zhang, Haibin Duan
Three-dimension path planning of uninhabited combat aerial vehicle (UCAV) is a complicated optimal problem, which mainly focused on optimizing the flight route considering the different types of constrains under complex combating environment. A novel predator-prey pigeon-inspired optimization (PPPIO) is proposed to solve the UCAV three-dimension path planning problem in dynamic environment. Pigeon-inspired optimization (PIO) is a new bio-inspired optimization algorithm. In this algorithm, map and compass operator model and landmark operator model are used to search the best result of a function...
January 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28182545/a-gene-selection-method-for-microarray-data-based-on-binary-pso-encoding-gene-to-class-sensitivity-information
#12
Fei Han, Chun Yang, Ya-Qi Wu, Jian-Sheng Zhu, Qing-Hua Ling, Yu-Qing Song, De-Shuang Huang
Traditional gene selection methods for microarray data mainly considered the features' relevance by evaluating their utility for achieving accurate predication or exploiting data variance and distribution, and the selected genes were usually poorly explicable. To improve the interpretability of the selected genes as well as prediction accuracy, an improved gene selection method based on binary particle swarm optimization (BPSO) and prior information is proposed in this paper. In the proposed method, BPSO encoding gene-to-class sensitivity (GCS) information is used to perform gene selection...
January 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28182544/a-novel-cluster-head-selection-algorithm-based-on-fuzzy-clustering-and-particle-swarm-optimization
#13
Qingjian Ni, Qianqian Pan, Huimin Du, Cen Cao, Yuqing Zhai
An important objective of wireless sensor network is to prolong the network life cycle, and topology control is of great significance for extending the network life cycle. Based on previous work, for cluster head selection in hierarchical topology control, we propose a solution based on fuzzy clustering preprocessing and particle swarm optimization. More specifically, first, fuzzy clustering algorithm is used to initial clustering for sensor nodes according to geographical locations, where a sensor node belongs to a cluster with a determined probability, and the number of initial clusters is analyzed and discussed...
January 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28182543/an-effective-application-of-bacteria-quorum-sensing-and-circular-elimination-in-mopso
#14
Shan Cheng, Long-Long Zhao, Xiao-Yu Jiang
In this paper, an approach that incorporates a turbulence mechanism and a circular elimination strategy is presented to strengthen the performance of multi-objective particle swarm optimization (MOPSO). For convergence enhancement, the turbulence mechanism derived from bacteria quorum sensing behavior is introduced to MOPSO to preserve the swarm diversity. Meanwhile, the circular elimination strategy is used to select particles for next iteration for better distribution of the Pareto-optimal solutions. The improved MOPSO algorithm has been tested on a set of benchmark functions and compared with representative multi-objective optimization algorithms...
January 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28182542/fireworks-algorithm-with-enhanced-fireworks-interaction
#15
Bei Zhang, Yu-Jun Zheng, Min-Xia Zhang, Sheng-Yong Chen
As a relatively new metaheuristic in swarm intelligence, fireworks algorithm (FWA) has exhibited promising performance on a wide range of optimization problems. This paper aims to improve FWA by enhancing fireworks interaction in three aspects: 1) Developing a new Gaussian mutation operator to make sparks learn from more exemplars; 2) Integrating the regular explosion operator of FWA with the migration operator of biogeography-based optimization (BBO) to increase information sharing; 3) Adopting a new population selection strategy that enables high-quality solutions to have high probabilities of entering the next generation without incurring high computational cost...
January 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28182540/symbiosis-based-alternative-learning-multi-swarm-particle-swarm-optimization
#16
Ben Niu, Huali Huang, Lijing Tan, Qiqi Duan
Inspired by the ideas from the mutual cooperation of symbiosis in natural ecosystem, this paper proposes a new variant of PSO, named Symbiosis-based Alternative Learning Multi-swarm Particle Swarm Optimization (SALMPSO). A learning probability to select one exemplar out of the center positions, the local best position, and the historical best position including the experience of internal and external multiple swarms, is used to keep the diversity of the population. Two different levels of social interaction within and between multiple swarms are proposed...
January 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28181879/parameter-estimation-of-nonlinear-systems-by-dynamic-cuckoo-search
#17
Qixiang Liao, Shudao Zhou, Hanqing Shi, Weilai Shi
In order to address with the problem of the traditional or improved cuckoo search (CS) algorithm, we propose a dynamic adaptive cuckoo search with crossover operator (DACS-CO) algorithm. Normally, the parameters of the CS algorithm are kept constant or adapted by empirical equation that may result in decreasing the efficiency of the algorithm. In order to solve the problem, a feedback control scheme of algorithm parameters is adopted in cuckoo search; Rechenberg's 1/5 criterion, combined with a learning strategy, is used to evaluate the evolution process...
February 9, 2017: Neural Computation
https://www.readbyqxmd.com/read/28181593/ultra-wideband-wide-angle-and-polarization-insensitive-specular-reflection-reduction-by-metasurface-based-on-parameter-adjustable-meta-atoms
#18
Jianxun Su, Yao Lu, Hui Zhang, Zengrui Li, Yaoqing Lamar Yang, Yongxing Che, Kainan Qi
In this paper, an ultra-wideband, wide angle and polarization-insensitive metasurface is designed, fabricated, and characterized for suppressing the specular electromagnetic wave reflection or backward radar cross section (RCS). Square ring structure is chosen as the basic meta-atoms. A new physical mechanism based on size adjustment of the basic meta-atoms is proposed for ultra-wideband manipulation of electromagnetic (EM) waves. Based on hybrid array pattern synthesis (APS) and particle swarm optimization (PSO) algorithm, the selection and distribution of the basic meta-atoms are optimized simultaneously to obtain the ultra-wideband diffusion scattering patterns...
February 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28174308/bacillus-subtilis-swarmer-cells-lead-the-swarm-multiply-and-generate-a-trail-of-quiescent-descendants
#19
Lina Hamouche, Soumaya Laalami, Adrian Daerr, Solène Song, I Barry Holland, Simone J Séror, Kassem Hamze, Harald Putzer
: Bacteria adopt social behavior to expand into new territory, led by specialized swarmers, before forming a biofilm. Such mass migration of Bacillus subtilis on a synthetic medium produces hyperbranching dendrites that transiently (equivalent to 4 to 5 generations of growth) maintain a cellular monolayer over long distances, greatly facilitating single-cell gene expression analysis. Paradoxically, while cells in the dendrites (nonswarmers) might be expected to grow exponentially, the rate of swarm expansion is constant, suggesting that some cells are not multiplying...
February 7, 2017: MBio
https://www.readbyqxmd.com/read/28167523/the-role-of-cyclic-di-gmp-and-exopolysaccharide-in-type-iv-pilus-dynamics
#20
Jan Ribbe, Amy E Baker, Sebstian Euler, George A O'Toole, Berenike Maier
For Pseudomonas aeruginosa the levels of cyclic di-GMP govern the transition from the planktonic state to biofilm formation. Type IV pili (T4P) are crucial determinants of biofilm structure and dynamics, but it is unknown how the levels of c-di-GMP affect pilus dynamics. Here, we scrutinized how c-di-GMP affects molecular motor properties and adhesive behavior of T4P. By means of retraction, T4P generated forces of ∼ 30 pN. Deletion mutants in the proteins with known roles in biofilm formation, swarming motility and exopolysaccharide (EPS) production, specifically, the diguanulate cyclases sadC and roeA or the c-di-GMP phosphodiesterase bifA, showed only modest effects on velocity or force of T4P retraction...
February 6, 2017: Journal of Bacteriology
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