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Stochastic modeling

Wentao Jing, Mohsen Ramezani, Kun An, Inhi Kim
The path choice behavior of battery electric vehicle (BEV) drivers is influenced by the lack of public charging stations, limited battery capacity, range anxiety and long battery charging time. This paper investigates the congestion/flow pattern captured by stochastic user equilibrium (SUE) traffic assignment problem in transportation networks with BEVs, where the BEV paths are restricted by their battery capacities. The BEV energy consumption is assumed to be a linear function of path length and path travel time, which addresses both path distance limit problem and road congestion effect...
2018: PloS One
Núria Folguera-Blasco, Elisabet Cuyàs, Javier A Menéndez, Tomás Alarcón
Understanding the control of epigenetic regulation is key to explain and modify the aging process. Because histone-modifying enzymes are sensitive to shifts in availability of cofactors (e.g. metabolites), cellular epigenetic states may be tied to changing conditions associated with cofactor variability. The aim of this study is to analyse the relationships between cofactor fluctuations, epigenetic landscapes, and cell state transitions. Using Approximate Bayesian Computation, we generate an ensemble of epigenetic regulation (ER) systems whose heterogeneity reflects variability in cofactor pools used by histone modifiers...
March 15, 2018: PLoS Computational Biology
M R Kholghy, G A Kelesidis, S E Pratsinis
Nucleation is an important, yet poorly understood step in soot formation. Here, the importance of reactive PAH dimerization in reducing soot nucleation reversibility is investigated by simulating soot formation in a so-called "nucleation" flame (P. Desgroux et al., Combust. Flame, 2017, 184, 153-166). There, inception of soot particles is prolonged at minimal subsequent growth. With only reversible PAH dimerization, the simulated soot concentration is negligible. Accounting however for PAH chemical bond formation after physical dimerization, stabilizes dimers by covalent bonds and increases the soot concentration by four orders of magnitude, in good agreement with Laser Induced Incandescence measurements...
March 15, 2018: Physical Chemistry Chemical Physics: PCCP
May Anne Mata, Priscilla Greenwood, Rebecca Tyson
We present an analysis of an avian flu model that yields insight into the roles of different transmission routes in the recurrence of avian influenza epidemics. Recent modelling work suggests that the outbreak periodicity of the disease is mainly determined by the environmental transmission rate. This conclusion, however, is based on a modelling study that only considers a weak between-host transmission rate. We develop an approximate model for stochastic avian flu epidemics, which allows us to determine the relative contribution of environmental and direct transmission routes to the periodicity and intensity of outbreaks over the full range of plausible parameter values for transmission...
March 14, 2018: Bulletin of Mathematical Biology
Balaraju Battu, V S Chandrasekhar Pammi, Narayanan Srinivasan
Conditional cooperation declines over time if heterogeneous ideal conditional agents are involved in repeated interactions. With strict assumptions of rationality and a population consisting of ideal conditional agents who strictly follow a decision rule, cooperation is not expected. However, cooperation is commonly observed in human societies. Hence, we propose a novel evolutionary agent-based model where agents rely on social information. Each agent interacts only once either as a donor or as a receiver. In our model, the population consists of either non-ideal or ideal heterogeneous conditional agents...
March 14, 2018: Scientific Reports
Sherrie L Kelly, Rowan Martin-Hughes, Robyn M Stuart, Xiao F Yap, David J Kedziora, Kelsey L Grantham, S Azfar Hussain, Iyanoosh Reporter, Andrew J Shattock, Laura Grobicki, Hassan Haghparast-Bidgoli, Jolene Skordis-Worrall, Zofia Baranczuk, Olivia Keiser, Janne Estill, Janka Petravic, Richard T Gray, Clemens J Benedikt, Nicole Fraser, Marelize Gorgens, David Wilson, Cliff C Kerr, David P Wilson
BACKGROUND: To move towards ending AIDS by 2030, HIV resources should be allocated cost-effectively. We used the Optima HIV model to estimate how global HIV resources could be retargeted for greatest epidemiological effect and how many additional new infections could be averted by 2030. METHODS: We collated standard data used in country modelling exercises (including demographic, epidemiological, behavioural, programmatic, and expenditure data) from Jan 1, 2000, to Dec 31, 2015 for 44 countries, capturing 80% of people living with HIV worldwide...
March 9, 2018: Lancet HIV
Ilia Korvigo, Andrey Afanasyev, Nikolay Romashchenko, Mikhail Skoblov
Many automatic classifiers were introduced to aid inference of phenotypical effects of uncategorised nsSNVs (nonsynonymous Single Nucleotide Variations) in theoretical and medical applications. Lately, several meta-estimators have been proposed that combine different predictors, such as PolyPhen and SIFT, to integrate more information in a single score. Although many advances have been made in feature design and machine learning algorithms used, the shortage of high-quality reference data along with the bias towards intensively studied in vitro models call for improved generalisation ability in order to further increase classification accuracy and handle records with insufficient data...
2018: PloS One
Samir S Soneji, Hai-Yen Sung, Brian A Primack, John P Pierce, James D Sargent
BACKGROUND: Electronic cigarettes (e-cigarettes) may help cigarette smokers quit smoking, yet they may also facilitate cigarette smoking for never-smokers. We quantify the balance of health benefits and harms associated with e-cigarette use at the population level. METHODS AND FINDINGS: Monte Carlo stochastic simulation model. Model parameters were drawn from census counts, national health and tobacco use surveys, and published literature. We calculate the expected years of life gained or lost from the impact of e-cigarette use on smoking cessation among current smokers and transition to long-term cigarette smoking among never smokers for the 2014 US population cohort...
2018: PloS One
Deepti Chaturvedi, Radhakrishnan Mahalakshmi
Transmembrane β-barrel proteins (OMPs) are highly robust structures for engineering and development of nanopore channels, surface biosensors, and display libraries. Expanding the applications of designed OMPs requires the identification of elements essential for β-barrel scaffold formation and stability. Here, we have designed chimeric 8-stranded OMPs composed of strand hybrids of Escherichia coli OmpX and Yersinia pestis Ail, and identified molecular motifs essential for β-barrel scaffold formation. For the OmpX/Ail chimeras, we find that the central hairpin strands β4-β5 in tandem are vital for β-barrel folding...
March 14, 2018: Biochemistry
Steven R Dolly, Yang Lou, Mark A Anastasio, Hua Li
It is widely known that the optimization of imaging systems based on objective, task-based measures of image quality via computer-simulation requires the use of a stochastic object model (SOM). However, the development of computationally tractable SOMs that can accurately model the statistical variations in human anatomy within a specified ensemble of patients remains a challenging task. Previously reported numerical anatomic models lack the ability to accurately model inter-patient and inter-organ variations in human anatomy among a broad patient population, mainly because they are established on image data corresponding to a few of patients and individual anatomic organs...
March 14, 2018: Physics in Medicine and Biology
Amirhossein Meisami, Jivan Deglise-Hawkinson, Mark E Cowen, Mark P Van Oyen
The decision of whether to admit a patient to a critical care unit is a crucial operational problem that has significant influence on both hospital performance and patient outcomes. Hospitals currently lack a methodology to selectively admit patients to these units in a way that patient health risk metrics can be incorporated while considering the congestion that will occur. The hospital is modeled as a complex loss queueing network with a stochastic model of how long risk-stratified patients spend time in particular units and how they transition between units...
March 13, 2018: Health Care Management Science
Ehsan Shakeri, Gholamreza Latif-Shabgahi, Amir Esmaeili Abharian
In recent years, many efforts have been made to present optimal strategies for cancer therapy through the mathematical modelling of tumour-cell population dynamics and optimal control theory. In many cases, therapy effect is included in the drift term of the stochastic Gompertz model. By fitting the model with empirical data, the parameters of therapy function are estimated. The reported research works have not presented any algorithm to determine the optimal parameters of therapy function. In this study, a logarithmic therapy function is entered in the drift term of the Gompertz model...
April 2018: IET Systems Biology
Greg Keir, Nevenka Bulovic, Neil McIntyre
Setting limits on groundwater extractions is important to ensure sustainable groundwater management. Lack of extraction data can affect interpretations of historical pressure changes, predictions of future impacts, accuracy of groundwater model calibration, and identification of sustainable management options. Yet, many groundwater extractions are unmetered. Therefore, there is a need for models that estimate extraction rates and quantify model outputs uncertainties arising due to a lack of data. This paper develops such a model within the Generalised Linear Modelling (GLM) framework, using a case study of stock and domestic extractions in the Surat Cumulative Management Area, a predominantly cattle farming region in eastern Australia...
March 13, 2018: Ground Water
Matthew Graham, Jonathan E Suk, Saki Takahashi, C Jessica Metcalf, Adela Paez Jimenez, Vladimir Prikazsky, Matthew J Ferrari, Justin Lessler
We report on and evaluate the process and findings of a real-time modeling exercise in response to an outbreak of measles in Lola prefecture, Guinea, in early 2015 in the wake of the Ebola crisis. Multiple statistical methods for the estimation of the size of the susceptible (i.e., unvaccinated) population were applied to weekly reported measles case data on seven subprefectures throughout Lola. Stochastic compartmental models were used to project future measles incidence in each subprefecture in both an initial and a follow-up iteration of forecasting...
March 12, 2018: American Journal of Tropical Medicine and Hygiene
René Bekker, Dennis Moeke, Bas Schmidt
Nursing homes are challenged to develop staffing strategies that enable them to efficiently meet the healthcare demand of their residents. In this study, we investigate how demand for care and support fluctuates over time and during the course of a day, using demand data from three independent nursing home departments of a single Dutch nursing home. This demand data is used as input for an optimization model that provides optimal staffing patterns across the day. For the optimization we use a Lindley-type equation and techniques from stochastic optimization to formulate a Mixed-Integer Linear Programming (MILP) model...
March 12, 2018: Health Care Management Science
Jennifer M SanMiguel, Lara K Abramowitz, Marisa S Bartolomei
Imprinted genes are expressed from one parental allele and regulated by differential DNA methylation at imprinting control regions (ICR). ICRs are reprogrammed in the germline through erasure and reestablishment of DNA methylation. Although much is known about DNA methylation establishment, DNA demethylation is less well understood. Recently, the Ten-Eleven Translocation proteins (TET1-3) have been shown to initiate DNA demethylation, with Tet1 -/- mice exhibiting aberrant levels of imprinted gene expression and ICR methylation...
March 12, 2018: Development
Abi Waqas, Daniele Melati, Paolo Manfredi, Andrea Melloni
Fabrication tolerances can significantly degrade the performance of fabricated photonic circuits and process yield. It is essential to include these stochastic uncertainties in the design phase in order to predict the statistical behaviour of a device before the final fabrication. This paper presents a method to build a novel class of stochastic-based building blocks for the preparation of Process Design Kits for the analysis and design of photonic circuits. The proposed design kits directly store the information on the stochastic behaviour of each building block in the form of a generalized-polynomial-chaos-based augmented macro-model obtained by properly exploiting stochastic collocation and Galerkin methods...
March 5, 2018: Optics Express
Ma'mon M Hatmal, Mutasem O Taha
We previously combined molecular dynamics (classical or simulated annealing) with ligand-receptor contacts analysis as means to extract valid pharmacophore model(s) from single ligand-receptor complexes. However, molecular dynamics methods are computa-tionally expensive and time consuming. Here we describe a novel method for extracting valid pharmacophore model(s) from a single crystallographic structure within reasonable time scale. The new method is based on ligand-receptor contacts analysis following en-ergy relaxation of predetermined set of randomly deformed complexes generated from the targeted crystallographic structure...
March 12, 2018: Journal of Chemical Information and Modeling
Hao Ge, Pingping Wu, Hong Qian, Sunney Xiaoliang Xie
Within an isogenic population, even in the same extracellular environment, individual cells can exhibit various phenotypic states. The exact role of stochastic gene-state switching regulating the transition among these phenotypic states in a single cell is not fully understood, especially in the presence of positive feedback. Recent high-precision single-cell measurements showed that, at least in bacteria, switching in gene states is slow relative to the typical rates of active transcription and translation...
March 12, 2018: PLoS Computational Biology
James Elber Duverger, Vincent Jacquemet, Alain Vinet, Philippe Comtois
The biological pacemaker approach is an alternative to cardiac electronic pacemakers. Its main objective is to create pacemaking activity from added or modified distribution of spontaneous cells in the myocardium. This paper aims to assess how automaticity strength of pacemaker cells (i.e. their ability to maintain robust spontaneous activity with fast rate and to drive neighboring quiescent cells) and structural linear anisotropy, combined with density and spatial distribution of pacemaker cells, may affect the macroscopic behavior of the biological pacemaker...
March 12, 2018: PLoS Computational Biology
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