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https://www.readbyqxmd.com/read/29345938/pso-method-for-fitting-analytic-potential-energy-functions-application-to-i-h2o
#1
Hum N Bandari, Xinyou Ma, Amit Kumar Paul, Philip Smith, William Louis Hase
In this work a Particle Swarm Optimization (PSO) algorithm was used to fit an analytic potential energy function to I-(H2O) intermolecular potential energy curves calculated with DFT/B97-1 theory. The analytic function is a sum of two-body terms, each written as a generalized sum of Buckingham and Lennard-Jones terms with only six parameters. Two models were used to describe the two-body terms between I- and H2O: a 3-site model H2O; and a 4-site model including a ghost atom. The fits are compared with those obtained with a genetic/non-linear least-squares algorithm...
January 18, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29345630/completely-flat-two-dimensional-zn-sub-3-sub-o-sub-2-sub-monolayer-with-triangle-and-pentangle-coordinated-networks
#2
Lingbiao Meng, Yingjuan Zhang, Jicheng Zhang, Weidong Wu
Two-dimensional (2D) materials with strictly planar hyper-coordinated motifs are of great importance in fundamental science and potential applications but extremely rare. Here we theoretically design a novel 2D IIB-VIA inorganic system, namely Zn3O2 monolayer, by comprehensive first-principles computations. This Zn3O2 monolayer is composed from highly symmetrical tri-coordinated oxygen and tetra-coordinated zinc, featuring planar and peculiar triangle and pentangle combined bonded network. The newly predicted Zn3O2 monolayer possesses excellent dynamic and thermal stabilities and is also the lowest-energy structure of its 2D space indicated by particle swarm search, supporting its experimentally synthetic viability...
January 18, 2018: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/29342942/a-sensor-dynamic-measurement-error-prediction-model-based-on-napso-svm
#3
Minlan Jiang, Lan Jiang, Dingde Jiang, Fei Li, Houbing Song
Dynamic measurement error correction is an effective way to improve sensor precision. Dynamic measurement error prediction is an important part of error correction, and support vector machine (SVM) is often used for predicting the dynamic measurement errors of sensors. Traditionally, the SVM parameters were always set manually, which cannot ensure the model's performance. In this paper, a SVM method based on an improved particle swarm optimization (NAPSO) is proposed to predict the dynamic measurement errors of sensors...
January 15, 2018: Sensors
https://www.readbyqxmd.com/read/29339510/artificial-intelligence-exploration-of-unstable-protocells-leads-to-predictable-properties-and-discovery-of-collective-behavior
#4
Laurie J Points, James Ward Taylor, Jonathan Grizou, Kevin Donkers, Leroy Cronin
Protocell models are used to investigate how cells might have first assembled on Earth. Some, like oil-in-water droplets, can be seemingly simple models, while able to exhibit complex and unpredictable behaviors. How such simple oil-in-water systems can come together to yield complex and life-like behaviors remains a key question. Herein, we illustrate how the combination of automated experimentation and image processing, physicochemical analysis, and machine learning allows significant advances to be made in understanding the driving forces behind oil-in-water droplet behaviors...
January 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29339231/respiratory-patterns-in-field-collected-brown-locust-locustana-pardalina-in-the-gregarious-phase
#5
Frances D Duncan, Shirley A Hanrahan
In this paper we report on the metabolic rates and respiratory patterns measured from gregarious brown locusts, Locustana pardalina, collected from the Nama Karoo region in South Africa. All five instar hopper stages and adults were collected over a three year period when significant numbers of locust swarms were seen. Flow-through respirometry was used to measure the CO2 emission from individual locusts from all the developmental stages and adults within a week of collection. Carbon dioxide emission scaled hypometrically with mass, 0...
January 12, 2018: Journal of Insect Physiology
https://www.readbyqxmd.com/read/29336514/machine-learned-analysis-of-quantitative-sensory-testing-responses-to-noxious-cold-stimulation-in-healthy-subjects
#6
I Weyer-Menkhoff, M C Thrun, J Lötsch
BACKGROUND: Pain in response to noxious cold has a complex molecular background probably involving several types of sensors. A recent observation has been the multimodal distribution of human cold pain thresholds. This study aimed at analysing reproducibility and stability of this observation and further exploration of data patterns supporting a complex background. METHOD: Pain thresholds to noxious cold stimuli (range 32-0 °C, tonic: temperature decrease -1 °C/s, phasic: temperature decrease -8 °C/s) were acquired in 148 healthy volunteers...
January 16, 2018: European Journal of Pain: EJP
https://www.readbyqxmd.com/read/29332979/standardized-maximim-d-optimal-designs-for-enzyme-kinetic-inhibition-models
#7
Ping-Yang Chen, Ray-Bing Chen, Heng-Chin Tung, Weng Kee Wong
Locally optimal designs for nonlinear models require a single set of nominal values for the unknown parameters. An alternative is the maximin approach that allows the user to specify a range of values for each parameter of interest. However, the maximin approach is difficult because we first have to determine the locally optimal design for each set of nominal values before maximin types of optimal designs can be found via a nested optimization process. We show that particle swarm optimization (PSO) techniques can solve such complex optimization problems effectively...
October 15, 2017: Chemometrics and Intelligent Laboratory Systems
https://www.readbyqxmd.com/read/29330449/lithium-chloride-effectively-kills-the-honey-bee-parasite-varroa-destructor-by-a-systemic-mode-of-action
#8
Bettina Ziegelmann, Elisabeth Abele, Stefan Hannus, Michaela Beitzinger, Stefan Berg, Peter Rosenkranz
Honey bees are increasingly important in the pollination of crops and wild plants. Recent reports of the weakening and periodical high losses of managed honey bee colonies have alarmed beekeeper, farmers and scientists. Infestations with the ectoparasitic mite Varroa destructor in combination with its associated viruses have been identified as a crucial driver of these health problems. Although yearly treatments are required to prevent collapses of honey bee colonies, the number of effective acaricides is small and no new active compounds have been registered in the past 25 years...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29326977/monitoring-reservoir-response-to-earthquakes-and-fluid-extraction-salton-sea-geothermal-field-california
#9
Taka'aki Taira, Avinash Nayak, Florent Brenguier, Michael Manga
Continuous monitoring of in situ reservoir responses to stress transients provides insights into the evolution of geothermal reservoirs. By exploiting the stress dependence of seismic velocity changes, we investigate the temporal evolution of the reservoir stress state of the Salton Sea geothermal field (SSGF), California. We find that the SSGF experienced a number of sudden velocity reductions (~0.035 to 0.25%) that are most likely caused by openings of fractures due to dynamic stress transients (as small as 0...
January 2018: Science Advances
https://www.readbyqxmd.com/read/29324230/neutrophils-cause-an-intravascular-traffic-jam
#10
Martin S Minns, Eric Pearlman
Neutrophil swarming is defined by large numbers of cells simultaneously and rapidly migrating to a site of injury or infection. In this issue of Cell Host & Microbe, Lee et al. (2018) demonstrate that intravascular swarming of neutrophils occurs in response to Candida albicans infection and causes vascular occlusion and pathological sequelae.
January 10, 2018: Cell Host & Microbe
https://www.readbyqxmd.com/read/29321600/fis-is-a-global-regulator-critical-for-modulation-of-virulence-factor-production-and-pathogenicity-of-dickeya-zeae
#11
Mingfa Lv, Yufan Chen, Lisheng Liao, Zhibin Liang, Zurong Shi, Yingxin Tang, Sixuan Ye, Jianuan Zhou, Lianhui Zhang
Dickeya zeae is the causal agent of rice foot rot disease, which has recently become a great threat to rice planting countries and regions. The pathogen produces a family of phytotoxins named zeamines that is critical for bacterial virulence, but little is known about the signaling pathways and regulatory mechanisms that govern zeamine production. In this study, we showed that a conserved transcriptional regulator Fis is involved in the regulation of zeamine production in D. zeae strain EC1. Deletion mutants were markedly attenuated in the virulence against rice seed germination...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29318462/long-term-response-to-recombinant-human-growth-hormone-treatment-a-new-predictive-mathematical-method
#12
G Migliaretti, S Ditaranto, C Guiot, S Vannelli, P Matarazzo, N Cappello, I Stura, F Cavallo
INTRODUCTION: Recombinant GH has been offered to GH-deficient (GHD) subjects for more than 30 years, in order to improve height and growth velocity in children and to enhance metabolic effects in adults. AIM: The aim of our work is to describe the long-term effect of rhGH treatment in GHD pediatric patients, suggesting a growth prediction model. MATERIAL AND METHODS: A homogeneous database is defined for diagnosis and treatment modalities, based on GHD patients afferent to Hospital Regina Margherita in Turin (Italy)...
January 9, 2018: Journal of Endocrinological Investigation
https://www.readbyqxmd.com/read/29316459/a-discrete-particle-model-reproducing-collective-dynamics-of-a-bee-swarm
#13
Sara Bernardi, Annachiara Colombi, Marco Scianna
In this article, we present a microscopic discrete mathematical model describing collective dynamics of a bee swarm. More specifically, each bee is set to move according to individual strategies and social interactions, the former involving the desire to reach a target destination, the latter accounting for repulsive/attractive stimuli and for alignment processes. The insects tend in fact to remain sufficiently close to the rest of the population, while avoiding collisions, and they are able to track and synchronize their movement to the flight of a given set of neighbors within their visual field...
January 2, 2018: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/29311555/swarm-incursions-of-reassortants-of-highly-pathogenic-avian-influenza-virus-strains-h5n8-and-h5n5-clade-2-3-4-4b-germany-winter-2016-17
#14
Anne Pohlmann, Elke Starick, Christian Grund, Dirk Höper, Günter Strebelow, Anja Globig, Christoph Staubach, Franz J Conraths, Thomas C Mettenleiter, Timm Harder, Martin Beer
The outbreak of highly pathogenic avian influenza H5Nx viruses in winter 2016/2017 was the most severe HPAI epizootic ever reported in Germany. The H5N8 and H5N5 viruses detected in birds in Germany in 2016/2017 represent a reassortant swarm of at least five distinct genotypes, which carried closely related HA segments derived from clade 2.3.4.4b. The genotypes of these viruses and their spatio-temporal distribution indicated a unique situation with multiple independent entries of HPAIV into Germany.
January 8, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29311275/the-c-terminal-region-of-bacillus-subtilis-swra-is-required-for-activity-and-adaptor-dependent-lona-proteolysis
#15
Anna C Hughes, Sundharraman Subramanian, Charles E Dann, Daniel B Kearns
SwrA is the master activator of flagellar biosynthesis in Bacillus subtilis and SwrA activity is restricted by regulatory proteolysis in liquid environments. SwrA is proteolyzed by the LonA protease but requires a proteolytic adaptor protein, SmiA. Here we show that SwrA and SmiA interact directly. To better understand SwrA activity, SwrA was randomly mutagenized and loss-of-function and gain-of-function mutants were localized primarily to the predicted unstructured C-terminal region. Loss-of-function mutations impaired swarming motility and activation from the Pfla-che promoter...
January 8, 2018: Journal of Bacteriology
https://www.readbyqxmd.com/read/29310699/planning-a-sports-training-program-using-adaptive-particle-swarm-optimization-with-emphasis-on-physiological-constraints
#16
Nattapon Kumyaito, Preecha Yupapin, Kreangsak Tamee
OBJECTIVE: An effective training plan is an important factor in sports training to enhance athletic performance. A poorly considered training plan may result in injury to the athlete, and overtraining. Good training plans normally require expert input, which may have a cost too great for many athletes, particularly amateur athletes. The objectives of this research were to create a practical cycling training plan that substantially improves athletic performance while satisfying essential physiological constraints...
January 8, 2018: BMC Research Notes
https://www.readbyqxmd.com/read/29305504/an-igaa-umob-family-protein-from-serratia-marcescens-regulates-motility-capsular-polysaccharide-and-secondary-metabolite-production
#17
Nicholas A Stella, Kimberly M Brothers, Jake D Callaghan, Angelina M Passerini, Cihad Sigindere, Preston J Hill, Xinyu Liu, Daniel J Wozniak, Robert M Q Shanks
Secondary metabolites are an important source of pharmaceuticals and key modulators of microbe-microbe interactions. The bacterium Serratia marcescens is part of the Enterobacteriaceae family of eubacteria and produces a number of biologically active secondary metabolites. In this study, we screened for novel regulators of secondary metabolites synthesized by a clinical isolate of S. marcescens and found mutations in a gene for an uncharacterized UmoB/IgaA family member here named gumB Mutation of gumB conferred a severe loss of secondary metabolites prodigiosin and serratamolide...
January 5, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29298958/langevin-dynamics-encapsulate-the-microscopic-and-emergent-macroscopic-properties-of-midge-swarms
#18
A M Reynolds
In contrast to bird flocks, fish schools and animal herds, midge swarms maintain cohesion but do not possess global order. High-speed imaging techniques are now revealing that these swarms have surprising properties. Here, I show that simple models found on the Langevin equation are consistent with this wealth of recent observations. The models predict correctly that large accelerations, exceeding 10 g, will be common and they predict correctly the coexistence of core condensed phases surrounded by dilute vapour phases...
January 2018: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/29297344/ioptics-gso-for-identifying-protein-complexes-from-dynamic-ppi-networks
#19
Xiujuan Lei, Huan Li, Aidong Zhang, Fang-Xiang Wu
BACKGROUND: Identifying protein complexes plays an important role for understanding cellular organization and functional mechanisms. As plenty of evidences have indicated that dense sub-networks in dynamic protein-protein interaction network (DPIN) usually correspond to protein complexes, identifying protein complexes is formulated as density-based clustering. METHODS: In this paper, a new approach named iOPTICS-GSO is developed, which is the improved Ordering Points to Identify the Clustering Structure (OPTICS) algorithm with Glowworm swarm optimization algorithm (GSO) to optimize the parameters in OPTICS when finding dense sub-networks...
December 28, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29297287/scaling-bioinformatics-applications-on-hpc
#20
Mike Mikailov, Fu-Jyh Luo, Stuart Barkley, Lohit Valleru, Stephen Whitney, Zhichao Liu, Shraddha Thakkar, Weida Tong, Nicholas Petrick
BACKGROUND: Recent breakthroughs in molecular biology and next generation sequencing technologies have led to the expenential growh of the sequence databases. Researchrs use BLAST for processing these sequences. However traditional software parallelization techniques (threads, message passing interface) applied in newer versios of BLAST are not adequate for processing these sequences in timely manner. METHODS: A new method for array job parallelization has been developed which offers O(T) theoretical speed-up in comparison to multi-threading and MPI techniques...
December 28, 2017: BMC Bioinformatics
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