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Stochastic modeling

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https://www.readbyqxmd.com/read/28350546/comparing-stochastic-proton-interactions-simulated-using-topas-nbio-to-experimental-data-from-fluorescent-nuclear-track-detectors
#1
T S A Underwood, W Sung, C H McFadden, S J McMahon, D C Hall, A L McNamara, H Paganetti, G O Sawakuchi, J Schuemann
Whilst Monte Carlo (MC) simulations of proton energy deposition have been well-validated at the macroscopic level, their microscopic validation remains lacking. Equally, no gold-standard yet exists for experimental metrology of individual proton tracks. In this work we compare the distributions of stochastic proton interactions simulated using the TOPAS-nBio MC platform against confocal microscope data for Al2O3:C,Mg fluorescent nuclear track detectors (FNTDs). We irradiated [Formula: see text] mm(3) FNTD chips inside a water phantom, positioned at seven positions along a pristine proton Bragg peak with a range in water of 12 cm...
April 21, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28343023/classification-of-footwear-outsole-patterns-using-fourier-transform-and-local-interest-points
#2
Nicole Richetelli, Mackenzie C Lee, Carleen A Lasky, Madison E Gump, Jacqueline A Speir
Successful classification of questioned footwear has tremendous evidentiary value; the result can minimize the potential suspect pool and link a suspect to a victim, a crime scene, or even multiple crime scenes to each other. With this in mind, several different automated and semi-automated classification models have been applied to the forensic footwear recognition problem, with superior performance commonly associated with two different approaches: correlation of image power (magnitude) or phase, and the use of local interest points transformed using the Scale Invariant Feature Transform (SIFT) and compared using Random Sample Consensus (RANSAC)...
March 4, 2017: Forensic Science International
https://www.readbyqxmd.com/read/28342787/forecasting-ebola-with-a-regression-transmission-model
#3
Jason Asher
We describe a relatively simple stochastic model of Ebola transmission that was used to produce forecasts with the lowest mean absolute error among Ebola Forecasting Challenge participants. The model enabled prediction of peak incidence, the timing of this peak, and final size of the outbreak. The underlying discrete-time compartmental model used a time-varying reproductive rate modeled as a multiplicative random walk driven by the number of infectious individuals. This structure generalizes traditional Susceptible-Infected-Recovered (SIR) disease modeling approaches and allows for the flexible consideration of outbreaks with complex trajectories of disease dynamics...
February 27, 2017: Epidemics
https://www.readbyqxmd.com/read/28341596/application-of-an-nlme-stochastic-deconvolution-approach-to-level-a-ivivc-modeling
#4
Maziar Kakhi, Sandra Suarez-Sharp, Terry Shepard, Jason Chittenden
Stochastic deconvolution is a parameter estimation method that calculates drug absorption using a non-linear mixed effects model in which the random effects associated with absorption represent a Wiener process. The present work compares, 1) stochastic deconvolution, and 2) numerical deconvolution, using clinical pharmacokinetic data generated for an IVIVC study of extended release (ER) formulations of a BCS class III drug substance. The preliminary analysis found that numerical and stochastic deconvolution yielded superimposable fraction absorbed (Fabs) versus time profiles when supplied with exactly the same externally-determined unit impulse response parameters...
March 21, 2017: Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/28341584/development-of-videogrammetry-as-a-tool-for-gas-particle-fluidization-research
#5
S Anweiler
Many industries use fluidization of solid particles for energy efficiency or environmental friendly process development, and this paper introduces research techniques developed for investigating gas-particle systems At present there is plenty of room for refining gas-particle fluidization process. With the rapidly rising application of mathematical modelling, real time visualization of processes will be widely used for validation of those models in the near future. In presented research, photogrammetry, as a part of close range vision metrology, has been expanded to allow dynamic space and time analysis of the phase concentration distribution inside fluidization devices...
March 21, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/28341132/stochastic-modeling-and-numerical-simulation-of-gene-regulatory-networks-with-protein-bursting
#6
Manuel Pájaro, Antonio A Alonso, Irene Otero-Muras, C Vázquez
Gene expression is inherently stochastic. Advanced single-cell microscopy techniques together with mathematical models for single gene expression led to important insights in elucidating the sources of intrinsic noise in prokaryotic and eukaryotic cells. In addition to the finite size effects due to low copy numbers, translational bursting is a dominant source of stochasticity in cell scenarios involving few short lived mRNA transcripts with high translational efficiency (as is typically the case for prokaryotes), causing protein synthesis to occur in random bursts...
March 21, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28340415/uncertainty-analysis-for-effluent-trading-planning-using-a-bayesian-estimation-based-simulation-optimization-modeling-approach
#7
J L Zhang, Y P Li, G H Huang, B W Baetz, J Liu
In this study, a Bayesian estimation-based simulation-optimization modeling approach (BESMA) is developed for identifying effluent trading strategies. BESMA incorporates nutrient fate modeling with soil and water assessment tool (SWAT), Bayesian estimation, and probabilistic-possibilistic interval programming with fuzzy random coefficients (PPI-FRC) within a general framework. Based on the water quality protocols provided by SWAT, posterior distributions of parameters can be analyzed through Bayesian estimation; stochastic characteristic of nutrient loading can be investigated which provides the inputs for the decision making...
March 6, 2017: Water Research
https://www.readbyqxmd.com/read/28339783/a-stochastic-model-for-tumour-control-probability-that-accounts-for-repair-from-sublethal-damage
#8
Ana Victoria Ponce Bobadilla, Philip K Maini, Helen Byrne
The tumour control probability (TCP) is the probability that a treatment regimen of radiation therapy (RT) eradicates all tumour cells in a given tissue. To decrease the toxic effects on healthy cells, RT is usually delivered over a period of weeks in a series of fractions. This allows tumour cells to repair sublethal damage (RSD) caused by radiation. In this article, we introduce a stochastic model for tumour response to radiotherapy which accounts for the effects of RSD. The tumour is subdivided into two cell types: 'affected' cells which have been damaged by RT and 'unaffected' cells which have not...
February 26, 2017: Mathematical Medicine and Biology: a Journal of the IMA
https://www.readbyqxmd.com/read/28334452/quantitative-assessment-of-the-risk-of-release-of-foot-and-mouth-disease-virus-via-export-of-bull-semen-from-israel
#9
A Meyer, L Zamir, A Ben Yair Gilboa, B Gelman, D U Pfeiffer, T Vergne
Various foot-and-mouth disease (FMD) virus strains circulate in the Middle East, causing frequent episodes of FMD outbreaks among Israeli livestock. Since the virus is highly resistant in semen, artificial insemination with contaminated bull semen may lead to the infection of the receiver cow. As a non-FMD-free country with vaccination, Israel is currently engaged in trading bull semen only with countries of the same status. The purpose of this study was to assess the risk of release of FMD virus through export of bull semen in order to estimate the risk for FMD-free countries considering purchasing Israeli bull semen...
March 23, 2017: Risk Analysis: An Official Publication of the Society for Risk Analysis
https://www.readbyqxmd.com/read/28334409/siapopr-a-computational-method-to-simulate-evolutionary-branching-trees-for-analysis-of-tumor-clonal-evolution
#10
Thomas O McDonald, Franziska Michor
Summary: SIApopr (Simulating Infinite-Allele populations) is an R package to simulate homogeneous and inhomogeneous stochastic branching processes under a very flexible set of assumptions using the speed of C ++. The software simulates clonal evolution with the emergence of driver and passenger mutations under the infinite-allele assumption. The software is an application of the Gillespie Stochastic Simulation Algorithm expanded to a large number of cell types and scenarios, with the intention of allowing users to easily modify existing models or create their own...
March 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334085/environmental-niche-divergence-among-three-dune-shrub-sister-species-with-parapatric-distributions
#11
Sergio Chozas, Rosa M Chefaoui, Otília Correia, Raúl Bonal, Joaquín Hortal
Background and Aims: The geographical distributions of species are constrained by their ecological requirements. The aim of this work was to analyse the effects of environmental conditions, historical events and biogeographical constraints on the diversification of the three species of the western Mediterranean shrub genus Stauracanthus , which have a parapatric distribution in the Iberian Peninsula. Methods: Ecological niche factor analysis and generalized linear models were used to measure the response of all Stauracanthus species to the environmental gradients and map their potential distributions in the Iberian Peninsula...
February 20, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28333995/better-living-through-conifer-removal-a-demographic-analysis-of-sage-grouse-vital-rates
#12
John P Severson, Christian A Hagen, Jason D Tack, Jeremy D Maestas, David E Naugle, James T Forbes, Kerry P Reese
Sagebrush (Artemisia spp.) obligate wildlife species such as the imperiled greater sage-grouse (Centrocercus urophasianus) face numerous threats including altered ecosystem processes that have led to conifer expansion into shrub-steppe. Conifer removal is accelerating despite a lack of empirical evidence on grouse population response. Using a before-after-control-impact design at the landscape scale, we evaluated effects of conifer removal on two important demographic parameters, annual survival of females and nest survival, by monitoring 219 female sage-grouse and 225 nests in the northern Great Basin from 2010 to 2014...
2017: PloS One
https://www.readbyqxmd.com/read/28333971/a-note-on-contracts-on-quadratic-variation
#13
Carl Lindberg
Given a Black stochastic volatility model for a future F, and a function g, we show that the price of [Formula: see text] can be represented by portfolios of put and call options. This generalizes the classical representation result for the variance swap. Further, in a local volatility model, we give an example based on Dupire's formula which shows how the theorem can be used to design variance related contracts with desirable characteristics.
2017: PloS One
https://www.readbyqxmd.com/read/28332207/the-eyes-and-vision-of-butterflies
#14
Kentaro Arikawa
Butterflies use colour vision when searching for flowers. Unlike the trichromatic retinas of humans (blue, green, and red cones; plus rods) and honeybees (ultraviolet, blue, and green photoreceptors), butterfly retinas typically have six or more photoreceptor classes with distinct spectral sensitivities. The eyes of the Japanese yellow swallowtail (Papilio xuthus) contain ultraviolet, violet, blue, green, red and broad-band receptors, with each ommatidium housing nine photoreceptor cells in one of three fixed combinations...
March 22, 2017: Journal of Physiology
https://www.readbyqxmd.com/read/28332113/the-critical-power-concept-applications-to-sports-performance-with-a-focus-on-intermittent-high-intensity-exercise
#15
REVIEW
Andrew M Jones, Anni Vanhatalo
The curvilinear relationship between power output and the time for which it can be sustained is a fundamental and well-known feature of high-intensity exercise performance. This relationship 'levels off' at a 'critical power' (CP) that separates power outputs that can be sustained with stable values of, for example, muscle phosphocreatine, blood lactate, and pulmonary oxygen uptake ([Formula: see text]), from power outputs where these variables change continuously with time until their respective minimum and maximum values are reached and exercise intolerance occurs...
March 22, 2017: Sports Medicine
https://www.readbyqxmd.com/read/28331189/noise-driven-return-statistics-scaling-and-truncation-in-stochastic-storage-processes
#16
Tomás Aquino, Antoine Aubeneau, Gavan McGrath, Diogo Bolster, Suresh Rao
In countless systems, subjected to variable forcing, a key question arises: how much time will a state variable spend away from a given threshold? When forcing is treated as a stochastic process, this can be addressed with first return time distributions. While many studies suggest exponential, double exponential or power laws as empirical forms, we contend that truncated power laws are natural candidates. To this end, we consider a minimal stochastic mass balance model and identify a parsimonious mechanism for the emergence of truncated power law return times...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28330367/multiscale-simulations-of-anisotropic-particles-combining-molecular-dynamics-and-green-s-function-reaction-dynamics
#17
Adithya Vijaykumar, Thomas E Ouldridge, Pieter Rein Ten Wolde, Peter G Bolhuis
The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Green's Function Reaction Dynamics (GFRD) method with explicit stochastic Brownian, Langevin, or deterministic molecular dynamics to treat reactants at the microscopic scale [A. Vijaykumar, P. G. Bolhuis, and P. R. ten Wolde, J. Chem. Phys. 143, 214102 (2015)]. Here we extend this multiscale MD-GFRD approach to include the orientational dynamics that is crucial to describe the anisotropic interactions often prevalent in biomolecular systems...
March 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28329860/modeling-intraindividual-dynamics-using-stochastic-differential-equations-age-differences-in-affect-regulation
#18
Julie Wood, Zita Oravecz, Nina Vogel, Lizbeth Benson, Sy-Miin Chow, Pamela Cole, David E Conroy, Aaron L Pincus, Nilam Ram
Objectives: Life-span theories of aging suggest improvements and decrements in individuals' ability to regulate affect. Dynamic process models, with intensive longitudinal data, provide new opportunities to articulate specific theories about individual differences in intraindividual dynamics. This paper illustrates a method for operationalizing affect dynamics using a multilevel stochastic differential equation (SDE) model, and examines how those dynamics differ with age and trait-level tendencies to deploy emotion regulation strategies (reappraisal and suppression)...
March 2, 2017: Journals of Gerontology. Series B, Psychological Sciences and Social Sciences
https://www.readbyqxmd.com/read/28329034/use-of-pfhrp2-only-rdts-rapidly-select-for-pfhrp2-negative-parasites-with-serious-implications-for-malaria-case-management-and-control
#19
Michelle L Gatton, Jessica Dunn, Alisha Chaudhry, Sadmir Ciketic, Jane Cunningham, Qin Cheng
Background: Rapid diagnostic tests (RDTs) are an important tool for malaria diagnosis, with most utilising antibodies against histidine-rich protein 2 (PfHRP2). Reports of Plasmodium falciparum lacking this protein are increasing, creating a problem for diagnosis of falciparum malaria in locations without quality microscopy. Methods: An agent-based stochastic simulation model of P.falciparum transmission was used to investigate the selective pressure exerted on parasite populations by use of RDTs for diagnosis of symptomatic cases...
March 8, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28328984/using-simulation-to-aid-trial-design-ring-vaccination-trials
#20
Matt David Thomas Hitchings, Rebecca Freeman Grais, Marc Lipsitch
BACKGROUND: The 2014-6 West African Ebola epidemic highlights the need for rigorous, rapid clinical trial methods for vaccines. A challenge for trial design is making sample size calculations based on incidence within the trial, total vaccine effect, and intracluster correlation, when these parameters are uncertain in the presence of indirect effects of vaccination. METHODS AND FINDINGS: We present a stochastic, compartmental model for a ring vaccination trial. After identification of an index case, a ring of contacts is recruited and either vaccinated immediately or after 21 days...
March 22, 2017: PLoS Neglected Tropical Diseases
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