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Stochastic modeling

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https://www.readbyqxmd.com/read/28731794/a-neutral-model-for-the-evolution-of-diet-breadth
#1
Matthew L Forister, Stephen H Jenkins
Variation in diet breadth among organisms is a pervasive feature of the natural world that has resisted general explanation. In particular, trade-offs in the ability to use one resource at the expense of another have been expected but rarely detected. We explore a spatial model for the evolution of specialization, motivated by studies of plant-feeding insects. The model is neutral with respect to the causes and consequences of diet breadth: the number of hosts utilized is not constrained by trade-offs, and specialization or generalization does not confer a direct advantage with respect to the persistence of populations or the probability of diversification...
August 2017: American Naturalist
https://www.readbyqxmd.com/read/28731756/stochastic-chaos-in-a-turbulent-swirling-flow
#2
D Faranda, Y Sato, B Saint-Michel, C Wiertel, V Padilla, B Dubrulle, F Daviaud
We report the experimental evidence of the existence of a random attractor in a fully developed turbulent swirling flow. By defining a global observable which tracks the asymmetry in the flux of angular momentum imparted to the flow, we can first reconstruct the associated turbulent attractor and then follow its route towards chaos. We further show that the experimental attractor can be modeled by stochastic Duffing equations, that match the quantitative properties of the experimental flow, namely, the number of quasistationary states and transition rates among them, the effective dimensions, and the continuity of the first Lyapunov exponents...
July 7, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28731409/assessment-of-the-probability-of-autochthonous-transmission-of-chikungunya-virus-in-canada-under-recent-and-projected-climate-change
#3
Victoria Ng, Aamir Fazil, Philippe Gachon, Guillaume Deuymes, Milka Radojević, Mariola Mascarenhas, Sophiya Garasia, Michael A Johansson, Nicholas H Ogden
BACKGROUND: Chikungunya virus (CHIKV) is a reemerging pathogen transmitted by Aedes aegypti and Aedes albopictus mosquitoes. The ongoing Caribbean outbreak is of concern due to the potential for infected travelers to spread the virus to countries where vectors are present and the population is susceptible. Although there has been no autochthonous transmission of CHIKV in Canada, there is concern that both Ae. albopictus and CHIKV will become established, particularly under projected climate change...
June 5, 2017: Environmental Health Perspectives
https://www.readbyqxmd.com/read/28729840/cardiac-subtype-specific-modeling-of-kv1-5-ion-channel-deficiency-using-human-pluripotent-stem-cells
#4
Maike Marczenke, Ilaria Piccini, Isabella Mengarelli, Jakob Fell, Albrecht Röpke, Guiscard Seebohm, Arie O Verkerk, Boris Greber
The ultrarapid delayed rectifier K(+) current (IKur), mediated by Kv1.5 channels, constitutes a key component of the atrial action potential. Functional mutations in the underlying KCNA5 gene have been shown to cause hereditary forms of atrial fibrillation (AF). Here, we combine targeted genetic engineering with cardiac subtype-specific differentiation of human induced pluripotent stem cells (hiPSCs) to explore the role of Kv1.5 in atrial hiPSC-cardiomyocytes. CRISPR/Cas9-mediated mutagenesis of integration-free hiPSCs was employed to generate a functional KCNA5 knockout...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28729542/reaching-agreement-in-quantum-hybrid-networks
#5
Guodong Shi, Bo Li, Zibo Miao, Peter M Dower, Matthew R James
We consider a basic quantum hybrid network model consisting of a number of nodes each holding a qubit, for which the aim is to drive the network to a consensus in the sense that all qubits reach a common state. Projective measurements are applied serving as control means, and the measurement results are exchanged among the nodes via classical communication channels. In this way the quantum-opeartion/classical-communication nature of hybrid quantum networks is captured, although coherent states and joint operations are not taken into consideration in order to facilitate a clear and explicit analysis...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28728997/sepsis-reconsidered-identifying-novel-metrics-for-behavioral-landscape-characterization-with-a-high-performance-computing-implementation-of-an-agent-based-model
#6
Chase Cockrell, Gary An
OBJECTIVES: Sepsis affects nearly 1 million people in the United States per year, has a mortality rate of 28-50% and requires more than $20 billion a year in hospital costs. Over a quarter century of research has not yielded a single reliable diagnostic test or a directed therapeutic agent for sepsis. Central to this insufficiency is the fact that sepsis remains a clinical/physiological diagnosis representing a multitude of molecularly heterogeneous pathological trajectories. Advances in computational capabilities offered by High Performance Computing (HPC) platforms call for an evolution in the investigation of sepsis to attempt to define the boundaries of traditional research (bench, clinical and computational) through the use of computational proxy models...
July 17, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28727069/system-dynamics-modeling-in-designing-breeding-schemes-the-case-of-menz-sheep-in-ethiopian-highlands
#7
K T Gebre, M Wurzinger, S Gizaw, A Haile, B Rischkowsky, T Getachew, J Sölkner
A comprehensive dynamic simulation model was developed to describe a community-based breeding program for the Menz sheep population of Ethiopia. Selection of male and female animals based on their own and maternal performance was simulated. The breeding goal traits were 6-mo weight, preweaning survival, and fertility rate. The model input data were obtained from the flock book, questionnaires, and references. The simulation model used a mix of deterministic and stochastic procedures to model the complex system...
June 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28725390/grazed-wet-meadows-are-sink-habitats-for-the-southern-dunlin-calidris-alpina-schinzii-due-to-nest-trampling-by-cattle
#8
Veli-Matti Pakanen, Sami Aikio, Aappo Luukkonen, Kari Koivula
The effect of habitat management is commonly evaluated by measuring population growth, which does not distinguish changes in reproductive success from changes in survival or the effects of immigration or emigration. Management has rarely been evaluated considering complete life cycle of the target organisms, including also possible negative impacts from management. We evaluated the effectiveness of cattle grazing in the restoration of coastal meadows as a breeding habitat for small and medium-sized ground-nesting birds by examining the size and demography of a southern dunlin (Calidris alpina schinzii) breeding population...
October 2016: Ecology and Evolution
https://www.readbyqxmd.com/read/28725369/adding-energy-gradients-and-long-distance-dispersal-to-a-neutral-model-improves-predictions-of-madagascan-bird-diversity
#9
Falko T Buschke, Luc Brendonck, Bram Vanschoenwinkel
Macroecological patterns are likely the result of both stochastically neutral mechanisms and deterministic differences between species. In Madagascar, the simplest stochastically neutral hypothesis - the mid-domain effects (MDE) hypothesis - has already been rejected. However, rejecting the MDE hypothesis does not necessarily refute the existence of all other neutral mechanisms. Here, we test whether adding complexity to a basic neutral model improves predictions of biodiversity patterns. The simplest MDE model assumes that: (1) species' ranges are continuous and unfragmented, (2) are randomly located throughout the landscape, and (3) can be stacked independently and indefinitely...
October 2016: Ecology and Evolution
https://www.readbyqxmd.com/read/28724978/economic-factors-influencing-zoonotic-disease-dynamics-demand-for-poultry-meat-and-seasonal-transmission-of-avian-influenza-in-vietnam
#10
Alexis Delabouglise, Marc Choisy, Thang D Phan, Nicolas Antoine-Moussiaux, Marisa Peyre, Ton D Vu, Dirk U Pfeiffer, Guillaume Fournié
While climate is often presented as a key factor influencing the seasonality of diseases, the importance of anthropogenic factors is less commonly evaluated. Using a combination of methods - wavelet analysis, economic analysis, statistical and disease transmission modelling - we aimed to explore the influence of climatic and economic factors on the seasonality of H5N1 Highly Pathogenic Avian Influenza in the domestic poultry population of Vietnam. We found that while climatic variables are associated with seasonal variation in the incidence of avian influenza outbreaks in the North of the country, this is not the case in the Centre and the South...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28722734/scavenging-and-recombination-kinetics-in-radiation-chemistry
#11
Eyad H Al-Samra, Nicholas J B Green
This work describes stochastic models developed to study the competition between radical scavenging and recombination for simple model systems typical of radiation chemistry, where the reactive particles are tightly clustered and reactions are assumed fully diffusion limited. Three models are developed: a Monte Carlo random flights model with a periodic boundary condition for scavengers, Monte Carlo simulations in which the scavenging rate is calculated from the Smoluchowski theory for diffusion-limited reactions and a modification of the independent reaction times method where the scavengers close to the spur are explicitly included and the scavengers further away are treated as a continuum...
July 19, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28721470/an-alternative-to-moment-closure
#12
Ingemar Nåsell
Moment closure methods are widely used to analyze mathematical models. They are specifically geared toward derivation of approximations of moments of stochastic models, and of similar quantities in other models. The methods possess several weaknesses: Conditions for validity of the approximations are not known, magnitudes of approximation errors are not easily evaluated, spurious solutions can be generated that require large efforts to eliminate, and expressions for the approximations are in many cases too complex to be useful...
July 18, 2017: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/28719044/symmetry-breaking-in-development-and-stochastic-gene-expression
#13
REVIEW
Jonathan R Chubb
The prevailing emphasis in developmental biology since the expansion of the molecular biology age has been that developmental decisions are instructive. A cell differentiates to become a specific cell type because it receives a signal, whereas its neighbor that does not receive the signal adopts a different fate. This emphasis has been generally accepted, largely because of the success of this view in tractable invertebrate model organisms, and the widespread similarities in molecular regulation to the development of more complex species...
July 18, 2017: Wiley Interdisciplinary Reviews. Developmental Biology
https://www.readbyqxmd.com/read/28718637/non-gaussian-brownian-diffusion-in-dynamically-disordered-thermal-environments
#14
Neha Tyagi, Binny J Cherayil
In this article, we suggest simple alternatives to the methods recently used by Jain and Sebastian [ J. Phys. Chem. B 2016 , 120 , 3988 ] and Chechkin et al. [ Phys. Rev. X 2017 , 7 , 021002 ] to treat a model of non-Gaussian Brownian diffusion based on the dynamics of a particle governed by Ornstein-Uhlenbeck modulated white noise. In addition to substantiating these authors' earlier findings (which show that a particle can execute a simple random walk even when the distribution of its displacements deviates from Gaussianity), our approach identifies another process, two-state white noise, that exhibits the same "anomalous" Brownian behavior...
July 18, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28716198/herd-specific-interventions-to-reduce-antimicrobial-usage-in-pig-production-without-jeopardising-technical-and-economic-performance
#15
L Collineau, C Rojo-Gimeno, A Léger, A Backhans, S Loesken, E Okholm Nielsen, M Postma, U Emanuelson, E Grosse Beilage, M Sjölund, E Wauters, K D C Stärk, J Dewulf, C Belloc, S Krebs
Pig farmers are strongly encouraged to reduce their antimicrobial usage in order to reduce the risk of antimicrobial resistance. Herd-level intervention is needed to achieve national and European reduction targets. Alternative, especially preventive measures, have to be implemented to reduce the need for antimicrobial treatments. However, little is known about the feasibility, effectiveness and return on investment of such measures. The objective of this study was to assess, across four countries, the technical and economic impact of herd-specific interventions aiming at reducing antimicrobial usage in pig production while implementing alternative measures...
September 1, 2017: Preventive Veterinary Medicine
https://www.readbyqxmd.com/read/28714693/stochastic-simulation-of-dopamine-neuromodulation-for-implementation-of-fluorescent-neurochemical-probes-in-the-striatal-extracellular-space
#16
Abraham Beyene, Ian McFarlane, Rebecca Pinals, Markita P Landry
Imaging the dynamic behavior of neuromodulatory neurotransmitters in the extracelluar space arising from individual quantal releases would constitute a major advance in neurochemical imaging. Spatial and temporal resolution of these highly stochastic neuromodulatory events requires concurrent advances in the chemical development of optical nanosensors selective for neuromodulators in concert with advances in imaging methodologies to capture millisecond neurotransmitter release. Herein, we develop and implement a stochastic model to describe dopamine dynamics in the extracellular space (ECS) of the brain dorsal striatum to guide the design and implementation of fluorescent neurochemical probes that record neurotransmitter dynamics in the ECS...
July 17, 2017: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/28713422/computational-analysis-of-lifespan-experiment-reproducibility
#17
Michael Petrascheck, Dana L Miller
Independent reproducibility is essential to the generation of scientific knowledge. Optimizing experimental protocols to ensure reproducibility is an important aspect of scientific work. Genetic or pharmacological lifespan extensions are generally small compared to the inherent variability in mean lifespan even in isogenic populations housed under identical conditions. This variability makes reproducible detection of small but real effects experimentally challenging. In this study, we aimed to determine the reproducibility of C...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28713210/variance-reduction-in-stochastic-gradient-langevin-dynamics
#18
Avinava Dubey, Sashank J Reddi, Barnabás Póczos, Alexander J Smola, Eric P Xing, Sinead A Williamson
Stochastic gradient-based Monte Carlo methods such as stochastic gradient Langevin dynamics are useful tools for posterior inference on large scale datasets in many machine learning applications. These methods scale to large datasets by using noisy gradients calculated using a mini-batch or subset of the dataset. However, the high variance inherent in these noisy gradients degrades performance and leads to slower mixing. In this paper, we present techniques for reducing variance in stochastic gradient Langevin dynamics, yielding novel stochastic Monte Carlo methods that improve performance by reducing the variance in the stochastic gradient...
December 2016: Advances in Neural Information Processing Systems
https://www.readbyqxmd.com/read/28712084/effluent-trading-in-river-systems-through-stochastic-decision-making-process-a-case-study
#19
Mohammad Amin Zolfagharipoor, Azadeh Ahmadi
The objective of this paper is to provide an efficient framework for effluent trading in river systems. The proposed framework consists of two pessimistic and optimistic decision-making models to increase the executability of river water quality trading programs. The models used for this purpose are (1) stochastic fallback bargaining (SFB) to reach an agreement among wastewater dischargers and (2) stochastic multi-criteria decision-making (SMCDM) to determine the optimal treatment strategy. The Monte-Carlo simulation method is used to incorporate the uncertainty into analysis...
July 15, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28711048/beyond-mean-field-approximations-for-accurate-and-computationally-efficient-models-of-on-lattice-chemical-kinetics
#20
M Pineda, M Stamatakis
Modeling the kinetics of surface catalyzed reactions is essential for the design of reactors and chemical processes. The majority of microkinetic models employ mean-field approximations, which lead to an approximate description of catalytic kinetics by assuming spatially uncorrelated adsorbates. On the other hand, kinetic Monte Carlo (KMC) methods provide a discrete-space continuous-time stochastic formulation that enables an accurate treatment of spatial correlations in the adlayer, but at a significant computation cost...
July 14, 2017: Journal of Chemical Physics
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