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Stochastic modeling

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https://www.readbyqxmd.com/read/28431361/uncertainty-quantification-and-validation-of-3d-lattice-scaffolds-for-computer-aided-biomedical-applications
#1
Recep M Gorguluarslan, Seung-Kyum Choi, Christopher J Saldana
A methodology is proposed for uncertainty quantification and validation to accurately predict the mechanical response of lattice structures used in the design of scaffolds. Effective structural properties of the scaffolds are characterized using a developed multi-level stochastic upscaling process that propagates the quantified uncertainties at strut level to the lattice structure level. To obtain realistic simulation models for the stochastic upscaling process and minimize the experimental cost, high-resolution finite element models of individual struts were reconstructed from the micro-CT scan images of lattice structures which are fabricated by selective laser melting...
April 12, 2017: Journal of the Mechanical Behavior of Biomedical Materials
https://www.readbyqxmd.com/read/28429787/heat-temperature-and-clausius-inequality-in-a-model-for-active-brownian-particles
#2
Umberto Marini Bettolo Marconi, Andrea Puglisi, Claudio Maggi
Methods of stochastic thermodynamics and hydrodynamics are applied to a recently introduced model of active particles. The model consists of an overdamped particle subject to Gaussian coloured noise. Inspired by stochastic thermodynamics, we derive from the system's Fokker-Planck equation the average exchanges of heat and work with the active bath and the associated entropy production. We show that a Clausius inequality holds, with the local (non-uniform) temperature of the active bath replacing the uniform temperature usually encountered in equilibrium systems...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28429013/a-stochastic-model-for-directional-changes-of-swimming-bacteria
#3
G Fier, D Hansmann, R C Buceta
In this work we introduce a stochastic model to describe directional changes in the movement of swimming bacteria. We use the probability density function (PDF) of turn angles, measured on tumbling wild-type E. coli, to build a Langevin equation for the deflection of the bacterial body swimming in isotropic media. We have solved this equation analytically by means of the Green function method and shown that three parameters are sufficient to describe the movement: the characteristic time, the steady-state solution and the control parameter...
April 21, 2017: Soft Matter
https://www.readbyqxmd.com/read/28428850/shortcuts-in-biodiversity-research-what-determines-the-performance-of-higher-taxa-as-surrogates-for-species
#4
Neil Rosser
Biodiversity research is often impeded by the time and resources required to identify species. One possible solution is to use higher taxa to predict species richness and community composition. However, previous studies have shown that the performance of higher taxa as surrogates for species is highly variable, making it difficult to predict whether the method will be reliable for a particular objective. Using 8 independent datasets, I tested whether higher taxa accurately characterize the responses of beetle and ant communities to environmental drivers...
April 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28428446/the-finite-state-projection-approach-to-analyze-dynamics-of-heterogeneous-populations
#5
Rob Johnson, Brian Munsky
Population modeling aims to capture and predict the dynamics of cell populations in constant or fluctuating environments. At the elementary level, population growth proceeds through sequential divisions of individual cells. Due to stochastic effects, populations of cells are inherently heterogeneous in phenotype, and some phenotypic variables have an effect on division or survival rates, as can be seen in partial drug resistance. Therefore, when modeling population dynamics where the control of growth and division is phenotype dependent, the corresponding model must take account of the underlying cellular heterogeneity...
April 21, 2017: Physical Biology
https://www.readbyqxmd.com/read/28426763/individual-based-modelling-of-population-growth-and-diffusion-in-discrete-time
#6
Natalie Tkachenko, John D Weissmann, Wesley P Petersen, George Lake, Christoph P E Zollikofer, Simone Callegari
Individual-based models (IBMs) of human populations capture spatio-temporal dynamics using rules that govern the birth, behavior, and death of individuals. We explore a stochastic IBM of logistic growth-diffusion with constant time steps and independent, simultaneous actions of birth, death, and movement that approaches the Fisher-Kolmogorov model in the continuum limit. This model is well-suited to parallelization on high-performance computers. We explore its emergent properties with analytical approximations and numerical simulations in parameter ranges relevant to human population dynamics and ecology, and reproduce continuous-time results in the limit of small transition probabilities...
2017: PloS One
https://www.readbyqxmd.com/read/28425140/response-of-parasitoid-egg-load-to-host-dynamics-and-implications-for-egg-load-evolution
#7
Craig B Phillips, John M Kean
A theoretical debate about whether parasitoids should be time- or egg-limited now recognises both as feasible, and interest has turned to determining the circumstances under which each might arise in the field, and their implications for parasitoid behaviour and evolution. Egg loads of parasitoids sampled from the field are predicted to show a negative response to host availability, but empirical support for this relationship is scarce. We measured how a parasitoid's egg load responded to seasonal fluctuations in host population density and recorded the predicted correlation...
April 20, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/28425119/mean-intercept-anisotropy-analysis-of-porous-media-i-analytic-formulae-for-anisotropic-boolean-models
#8
Michael A Klatt, Gerd E Schröder-Turk, Klaus Mecke
PURPOSE: Structure-property relations, which relate the shape of the microstructure to physical properties such as transport or mechanical properties, need sensitive measures of structure. What are suitable fabric tensors to quantify the shape of anisotropic heterogeneous materials? The mean intercept length is among the most commonly used characteristics of anisotropy in porous media, for example, of trabecular bone in medical physics. METHODS: We analyze the orientation-biased Boolean model, a versatile stochastic model that represents microstructures as overlapping grains with an orientation bias towards a preferred direction...
April 20, 2017: Medical Physics
https://www.readbyqxmd.com/read/28424892/bayesian-characterization-of-uncertainty-in-species-interaction-strengths
#9
Christopher Wolf, Mark Novak, Alix I Gitelman
Considerable effort has been devoted to the estimation of species interaction strengths. This effort has focused primarily on statistical significance testing and obtaining point estimates of parameters that contribute to interaction strength magnitudes, leaving the characterization of uncertainty associated with those estimates unconsidered. We consider a means of characterizing the uncertainty of a generalist predator's interaction strengths by formulating an observational method for estimating a predator's prey-specific per capita attack rates as a Bayesian statistical model...
April 19, 2017: Oecologia
https://www.readbyqxmd.com/read/28424606/bifurcation-analysis-on-phase-amplitude-cross-frequency-coupling-in-neural-networks-with-dynamic-synapses
#10
Takumi Sase, Yuichi Katori, Motomasa Komuro, Kazuyuki Aihara
We investigate a discrete-time network model composed of excitatory and inhibitory neurons and dynamic synapses with the aim at revealing dynamical properties behind oscillatory phenomena possibly related to brain functions. We use a stochastic neural network model to derive the corresponding macroscopic mean field dynamics, and subsequently analyze the dynamical properties of the network. In addition to slow and fast oscillations arising from excitatory and inhibitory networks, respectively, we show that the interaction between these two networks generates phase-amplitude cross-frequency coupling (CFC), in which multiple different frequency components coexist and the amplitude of the fast oscillation is modulated by the phase of the slow oscillation...
2017: Frontiers in Computational Neuroscience
https://www.readbyqxmd.com/read/28423770/epidemiological-models-lacking-process-noise-can-be-overconfident
#11
Lavi Shpigelman, Michal Chorev, Zeev Waks, Ya'ara Goldschmidt, Edwin Michael
Mathematic models of epidemics are the key tool for predicting future course of disease in a population and analyzing the effects of possible intervention policies. Typically, models that produce deterministic are applied for making predictions and reaching decisions. Stochastic modeling methods present an alternative. Here, we demonstrate by example why it is important that stochastic modeling be used in population health decision support systems.
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28422957/towards-a-theory-of-cortical-columns-from-spiking-neurons-to-interacting-neural-populations-of-finite-size
#12
Tilo Schwalger, Moritz Deger, Wulfram Gerstner
Neural population equations such as neural mass or field models are widely used to study brain activity on a large scale. However, the relation of these models to the properties of single neurons is unclear. Here we derive an equation for several interacting populations at the mesoscopic scale starting from a microscopic model of randomly connected generalized integrate-and-fire neuron models. Each population consists of 50-2000 neurons of the same type but different populations account for different neuron types...
April 19, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28422610/joint-bent-cable-tobit-models-for-longitudinal-and-time-to-event-data
#13
Getachew A Dagne
In this article, we show how to estimate a transition period for the evolvement of drug resistance to antiretroviral (ARV) drug or other related treatments in the framework of developing a Bayesian method for jointly analyzing time to event and longitudinal data. For HIV/AIDS longitudinal data, developmental trajectories of viral loads tend to show a gradual change from a declining trend after initiation of treatment to an increasing trend without an abrupt change. Such characteristics of trajectories are also associated with a time-to-event process...
April 19, 2017: Journal of Biopharmaceutical Statistics
https://www.readbyqxmd.com/read/28420215/a-phonocardiographic-based-fiber-optic-sensor-and-adaptive-filtering-system-for-noninvasive-continuous-fetal-heart-rate-monitoring
#14
Radek Martinek, Jan Nedoma, Marcel Fajkus, Radana Kahankova, Jaromir Konecny, Petr Janku, Stanislav Kepak, Petr Bilik, Homer Nazeran
This paper focuses on the design, realization, and verification of a novel phonocardiographic- based fiber-optic sensor and adaptive signal processing system for noninvasive continuous fetal heart rate (fHR) monitoring. Our proposed system utilizes two Mach-Zehnder interferometeric sensors. Based on the analysis of real measurement data, we developed a simplified dynamic model for the generation and distribution of heart sounds throughout the human body. Building on this signal model, we then designed, implemented, and verified our adaptive signal processing system by implementing two stochastic gradient-based algorithms: the Least Mean Square Algorithm (LMS), and the Normalized Least Mean Square (NLMS) Algorithm...
April 18, 2017: Sensors
https://www.readbyqxmd.com/read/28419511/analysis-of-the-variability-of-food-texture-properties-application-to-the-fracturability-of-dry-pet-food
#15
B Gouriou, Ph Bressolette, Ch Vial
An original Stochastic Finite Element Method (SFEM) is proposed for the texture analysis of food products for which samples cannot be standardized. SFEM is able to distinguish shape and texture variability. As an illustration, the methodology is applied to dry cat food using compression testing. First, a deterministic damage elastic model depending on six mechanical and three size parameters is shown to fit adequately experimental data. Then, Morris screening method is applied to FEM data: this highlights that the variability of compression tests is significantly affected by two mechanical and two size parameters...
April 17, 2017: Journal of Texture Studies
https://www.readbyqxmd.com/read/28419148/how-long-to-rest-in-unpredictably-changing-habitats
#16
Mirosław Slusarczyk, Jacek Starzyński, Piotr Bernatowicz
In the present study, we investigated the optimum length of prolonged dormancy (developmental arrest extending over favourable periods) of organisms under uncertain environmental conditions. We used an artificial life model to simulate the evolution of suspended development in the ontogenesis of organisms inhabiting unpredictably changing habitats. A virtual population of semelparous parthenogenetic individuals that varied in a duration of developmental arrest competed for limited resources. At a constant level of available resources, uninterrupted development was the superior life strategy...
2017: PloS One
https://www.readbyqxmd.com/read/28418824/financial-forecasting-and-stochastic-modeling-predicting-the-impact-of-business-decisions
#17
REVIEW
Geoffrey D Rubin, Bhavik N Patel
In health care organizations, effective investment of precious resources is critical to assure that the organization delivers high-quality and sustainable patient care within a supportive environment for patients, their families, and the health care providers. This holds true for organizations independent of size, from small practices to large health systems. For radiologists whose role is to oversee the delivery of imaging services and the interpretation, communication, and curation of imaging-informed information, business decisions influence where and how they practice, the tools available for image acquisition and interpretation, and ultimately their professional satisfaction...
May 2017: Radiology
https://www.readbyqxmd.com/read/28416680/using-microsecond-single-molecule-fret-to-determine-the-assembly-pathways-of-t4-ssdna-binding-protein-onto-model-dna-replication-forks
#18
Carey Phelps, Brett Israels, Davis Jose, Morgan C Marsh, Peter H von Hippel, Andrew H Marcus
DNA replication is a core biological process that occurs in prokaryotic cells at high speeds (∼1 nucleotide residue added per millisecond) and with high fidelity (fewer than one misincorporation event per 10(7) nucleotide additions). The ssDNA binding protein [gene product 32 (gp32)] of the T4 bacteriophage is a central integrating component of the replication complex that must continuously bind to and unbind from transiently exposed template strands during DNA synthesis. We here report microsecond single-molecule FRET (smFRET) measurements on Cy3/Cy5-labeled primer-template (p/t) DNA constructs in the presence of gp32...
April 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28415353/noise-induced-symmetry-breaking-far-from-equilibrium-and-the-emergence-of-biological-homochirality
#19
Farshid Jafarpour, Tommaso Biancalani, Nigel Goldenfeld
The origin of homochirality, the observed single-handedness of biological amino acids and sugars, has long been attributed to autocatalysis, a frequently assumed precursor for early life self-replication. However, the stability of homochiral states in deterministic autocatalytic systems relies on cross-inhibition of the two chiral states, an unlikely scenario for early life self-replicators. Here we present a theory for a stochastic individual-level model of autocatalytic prebiotic self-replicators that are maintained out of thermal equilibrium...
March 2017: Physical Review. E
https://www.readbyqxmd.com/read/28415350/simple-unified-view-of-branching-process-statistics-random-walks-in-balanced-logarithmic-potentials
#20
Serena di Santo, Pablo Villegas, Raffaella Burioni, Miguel A Muñoz
We revisit the problem of deriving the mean-field values of avalanche exponents in systems with absorbing states. These are well known to coincide with those of unbiased branching processes. Here we show that for at least four different universality classes (directed percolation, dynamical percolation, the voter model or compact directed percolation class, and the Manna class of stochastic sandpiles) this common result can be obtained by mapping the corresponding Langevin equations describing each of them into a random walker confined to the origin by a logarithmic potential...
March 2017: Physical Review. E
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