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Thomas Kovac, Tom Haber, Frank Van Reeth, Niel Hens
BACKGROUND: Over the last years, substantial effort has been put into enhancing our arsenal in fighting epidemics from both technological and theoretical perspectives with scientists from different fields teaming up for rapid assessment of potentially urgent situations. This paper focusses on the computational aspects of infectious disease models and applies commonly available graphics processing units (GPUs) for the simulation of these models. However, fully utilizing the resources of both CPUs and GPUs requires a carefully balanced heterogeneous approach...
March 16, 2018: BMC Bioinformatics
J Harder, A Cacciuto
We use computer simulations to study the behavior of a mixture of large passive charged colloids in a suspension of smaller active dipolar Janus particles. We find that when a single charged colloid is present in solution, it acquires a rotational or translational motion depending on how the active dipoles self-assemble on its surface to form active complexes. The collective behavior of these complexes is quite remarkable, and includes swarming behavior and coherent macroscopic motion. We detail how the variety of different phenomenologies emerging in this system can ultimately be controlled by the strength of the active forces and the relative concentration of the two species...
February 2018: Physical Review. E
Elizabeth A MacDonald, Eric Donovan, Yukitoshi Nishimura, Nathan A Case, D Megan Gillies, Bea Gallardo-Lacourt, William E Archer, Emma L Spanswick, Notanee Bourassa, Martin Connors, Matthew Heavner, Brian Jackel, Burcu Kosar, David J Knudsen, Chris Ratzlaff, Ian Schofield
A glowing ribbon of purple light running east-west in the night sky has recently been observed by citizen scientists. This narrow, subauroral, visible structure, distinct from the traditional auroral oval, was largely undocumented in the scientific literature and little was known about its formation. Amateur photo sequences showed colors distinctly different from common types of aurora and occasionally indicated magnetic field-aligned substructures. Observations from the Swarm satellite as it crossed the arc have revealed an unusual level of electron temperature enhancement and density depletion, along with a strong westward ion flow, indicating that a pronounced subauroral ion drift (SAID) is associated with this structure...
March 2018: Science Advances
Adebayo A Adeleke, Yansun Yao
Experimental studies at finite Pressure-Temperature (P-T) conditions and a theoretical study at 0 K of the phase transition in lead sulphide (PbS) have been inconclusive. Many studies that have been done to understand structural transformation in PbS can broadly be classified into two main ideological streams-one with Pnma and another with Cmcm orthorhombic intermediate phase. To foster better understanding of this phenomenon, we present the result of the first-principles study of phase transition in PbS at finite temperature...
March 14, 2018: Journal of Chemical Physics
Rensheng Cao, Mingyi Fan, Jiwei Hu, Wenqian Ruan, Xianliang Wu, Xionghui Wei
Highly promising artificial intelligence tools, including neural network (ANN), genetic algorithm (GA) and particle swarm optimization (PSO), were applied in the present study to develop an approach for the evaluation of Se(IV) removal from aqueous solutions by reduced graphene oxide-supported nanoscale zero-valent iron (nZVI/rGO) composites. Both GA and PSO were used to optimize the parameters of ANN. The effect of operational parameters (i.e., initial pH, temperature, contact time and initial Se(IV) concentration) on the removal efficiency was examined using response surface methodology (RSM), which was also utilized to obtain a dataset for the ANN training...
March 15, 2018: Materials
Hui Di, Xingpeng Liu, Jiquan Zhang, Zhijun Tong, Meichen Ji
Water environmental risk is the probability of the occurrence of events caused by human activities or the interaction of human activities and natural processes that will damage a water environment. This study proposed a water environmental risk index (WERI) model to assess the water environmental risk in the Yinma River Basin based on hazards, exposure, vulnerability, and regional management ability indicators in a water environment. The data for each indicator were gathered from 2000, 2005, 2010, and 2015 to assess the spatial and temporal variations in water environmental risk using particle swarm optimization and the analytic hierarchy process (PSO-AHP) method...
March 15, 2018: International Journal of Environmental Research and Public Health
Sudhakar Agnihothram, Vineet D Menachery, Boyd L Yount, Lisa C Lindesmith, Trevor Scobey, Alan Whitmore, Alexandra Schäfer, Mark T Heise, Ralph S Baric
Zoonotic viruses circulate as swarms in animal reservoirs and can emerge into human populations causing epidemics that adversely affect public health. Portable, safe, and effective vaccine platforms are needed in the context of these outbreak and emergence situations. In this manuscript, we report the generation and characterization of an alphavirus replicon vaccine platform based on a non-select agent, attenuated Venezuelan equine encephalitis (VEE) virus vaccine strain 3526 (VRP 3526). Using both noroviruses and coronaviruses as model systems, we demonstrate utility of the VRP 3526 platform in generation of recombinant proteins, production of virus like particles, and in vivo efficacy as a vaccine against emergent viruses...
March 14, 2018: Journal of Virology
Marjorie da Silva, Fernando Barbosa Noll, Adriana C Morales-Corrêa E Castro
Swarm-founding wasps are endemic and common representatives of neotropical fauna and compose an interesting social tribe of vespids, presenting both complex social characteristics and uncommon traits for a eusocial group, such as the absence of castes with distinct morphology. The paper wasp Protonectarina sylveirae (Saussure) presents a broad distribution from Brazil, Argentina and Paraguay, occurring widespread in the Atlantic rainforest and arboreal Caatinga, being absent in the Amazon region. Given the peculiar distribution among swarm-founding wasps, an integrative approach to reconstruct the evolutionary history of P...
2018: PloS One
Niloofar Yousefi Moteghaed, Keivan Maghooli, Masoud Garshasbi
Background: Gene expression data are characteristically high dimensional with a small sample size in contrast to the feature size and variability inherent in biological processes that contribute to difficulties in analysis. Selection of highly discriminative features decreases the computational cost and complexity of the classifier and improves its reliability for prediction of a new class of samples. Methods: The present study used hybrid particle swarm optimization and genetic algorithms for gene selection and a fuzzy support vector machine (SVM) as the classifier...
January 2018: Journal of Medical Signals and Sensors
Mingming Pu, Lili Sheng, Sooyeon Song, Ting Gong, Thomas K Wood
Pseudomonas aeruginosa causes many biofilm infections, and the rugose small-colony variants (RSCVs) of this bacterium are important for infection. We found here that inactivation of PA2444, which we determined to be a serine hydroxymethyltransferase (SHMT), leads to the RSCV phenotype of P. aeruginosa PA14. In addition, loss of PA2444 increases biofilm formation by two orders of magnitude, increases exopolysaccharide by 45-fold, and abolishes swarming. The RSCV phenotype is related to higher cyclic diguanylate concentrations due to increased activity of the Wsp chemosensory system, including diguanylate cyclase WspR...
2018: Frontiers in Microbiology
Devin B Holman, Shawn M D Bearson, Bradley L Bearson, Brian W Brunelle
Background: Multidrug-resistant (MDR) Salmonella enterica serovar Typhimurium ( S . Typhimurium) is a serious public health threat as infections caused by these strains are more difficult and expensive to treat. Livestock serve as a reservoir for MDR Salmonella , and the antibiotics chlortetracycline and florfenicol are frequently administrated to food-producing animals to treat and prevent various diseases. Therefore, we evaluated the response of MDR S . Typhimurium after exposure to these two antibiotics...
2018: Gut Pathogens
Yongjin Liu, Steven Kyle, Paul D Straight
Competitive interactions between bacteria reveal physiological adaptations that benefit fitness. Bacillus subtilis is a Gram-positive species with several adaptive mechanisms for competition and environmental stress. Biofilm formation, sporulation, and motility are the outcomes of widespread changes in a population of B. subtilis . These changes emerge from complex, regulated pathways for adapting to external stresses, including competition from other species. To identify competition-specific functions, we cultured B...
January 2018: MSphere
Mengshan Li, Huaijing Zhang, Bingsheng Chen, Yan Wu, Lixin Guan
The pKa value of drugs is an important parameter in drug design and pharmacology. In this paper, an improved particle swarm optimization (PSO) algorithm was proposed based on the population entropy diversity. In the improved algorithm, when the population entropy was higher than the set maximum threshold, the convergence strategy was adopted; when the population entropy was lower than the set minimum threshold the divergence strategy was adopted; when the population entropy was between the maximum and minimum threshold, the self-adaptive adjustment strategy was maintained...
March 5, 2018: Scientific Reports
F Martínez-Pedrero, P Tierno
In this review article, we highlight many recent advances in the field of micromanipulation of colloidal particles using hydrodynamic interactions (HIs), namely solvent mediated long-range interactions. At the micrsocale, the hydrodynamic laws are time reversible and the flow becomes laminar, features that allow precise manipulation and control of colloidal matter. We focus on different strategies where externally operated microstructures generate local flow fields that induce the advection and motion of the surrounding components...
February 21, 2018: Journal of Colloid and Interface Science
Mengmeng Zhang, Mengjia Wang, Xiaocui Zhu, Wengong Yu, Qianhong Gong
OBJECTIVE: To screen for the quorum-sensing (QS) inhibitors from marine-derived fungi and evaluate their anti-QS properties in Pseudomonas aeruginosa. RESULTS: QS inhibitory activity was found in secondary metabolites of a marine fungus Fusarium sp. Z10 using P. aeruginosa QSIS-lasI biosensor. The major active compound of this fungus was isolated by HPLC and identified as equisetin. Subinhibitory concentration of equisetin could inhibit the formation of biofilm, swarming motility, and the production of virulence factors in P...
March 3, 2018: Biotechnology Letters
Hiqmet Kamberaj
In this study, we applied swarm particle-like molecular dynamics (SPMD) approach to enhance conformational sampling of replica exchange simulations. In particular, the approach showed significant improvement in sampling efficiency of conformational phase space when combined with replica exchange method (REM) in computer simulation of peptide/protein folding. First we introduce the augmented dynamical system of equations, and demonstrate the stability of the algorithm. Then, we illustrate the approach by using different fully atomistic and coarse-grained model systems, comparing them with the standard replica exchange method...
February 22, 2018: Journal of Molecular Graphics & Modelling
Li Liu, Tao Li, Xing-Jun Cheng, Cui-Ting Peng, Chang-Cheng Li, Li-Hui He, Si-Min Ju, Ning-Yu Wang, Ting-Hong Ye, Mao Lian, Qing-Jie Xiao, Ying-Jie Song, Yi-Bo Zhu, Luo-Ting Yu, Zhen-Ling Wang, Rui Bao
DspI, a putative enoyl-coenzyme A (CoA) hydratase/isomerase, was proposed to be involved in the synthesis of cis-2-decenoic acid (CDA), a quorum sensing (QS) signal molecule in the pathogen Pseudomonas aeruginosa (P. aeruginosa). The present study provided a structural basis for the dehydration reaction mechanism of DspI during CDA synthesis. Structural analysis reveals that Glu126, Glu146, Cys127, Cys131 and Cys154 are important for its enzymatic function. Moreover, we show that the deletion of dspI results in a remarkable decreased in the pyoverdine production, flagella-dependent swarming motility, and biofilm dispersion as well as attenuated virulence in P...
March 2, 2018: Scientific Reports
Christian Scholz, Michael Engel, Thorsten Pöschel
Biological organisms and artificial active particles self-organize into swarms and patterns. Open questions concern the design of emergent phenomena by choosing appropriate forms of activity and particle interactions. A particularly simple and versatile system are 3D-printed robots on a vibrating table that can perform self-propelled and self-spinning motion. Here we study a mixture of minimalistic clockwise and counter-clockwise rotating robots, called rotors. Our experiments show that rotors move collectively and exhibit super-diffusive interfacial motion and phase separate via spinodal decomposition...
March 2, 2018: Nature Communications
Itshak Tkach, Aleksandar Jevtić, Shimon Y Nof, Yael Edan
Multi-sensor systems can play an important role in monitoring tasks and detecting targets. However, real-time allocation of heterogeneous sensors to dynamic targets/tasks that are unknown a priori in their locations and priorities is a challenge. This paper presents a Modified Distributed Bees Algorithm (MDBA) that is developed to allocate stationary heterogeneous sensors to upcoming unknown tasks using a decentralized, swarm intelligence approach to minimize the task detection times. Sensors are allocated to tasks based on sensors' performance, tasks' priorities, and the distances of the sensors from the locations where the tasks are being executed...
March 2, 2018: Sensors
Linjie Chen, Thibaud Monteiro, Tao Wang, Eric Marcon
Unit-dose drug distribution systems provide optimal choices in terms of medication security and efficiency for organizing the drug-use process in large hospitals. As small hospitals have to share such automatic systems for economic reasons, the structure of their logistic organization becomes a very sensitive issue. In the research reported here, we develop a generalized multi-level optimization method - multi-level particle swarm optimization (MLPSO) - to design a shared unit-dose drug distribution network...
March 1, 2018: Health Care Management Science
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