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Stochastic modeling

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https://www.readbyqxmd.com/read/29166093/a-study-of-the-dense-uniform-electron-gas-with-high-orders-of-coupled-cluster
#1
Verena A Neufeld, Alex J W Thom
We investigate the accuracies of different coupled cluster levels in a finite model solid, the 14 electron spin-non-polarised uniform electron gas. For densities between rs = 0.5 a0 and rs = 5 a0, we calculate ground state correlation energies with stochastic coupled cluster ranging from coupled cluster singles and doubles (CCSD) to coupled cluster including all excitations up to quintuples (CCSDTQ5). We find the need to add triple excitations for an accuracy of 0.01 eV/electron beyond rs = 0.5 a0. Quadruple excitations start being significant past rs = 3 a0...
November 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29164716/mechanism-matters-the-cause-of-fluctuations-in-boom-bust-populations-governs-optimal-habitat-restoration-strategy
#2
Gina K Himes Boor, Cheryl B Schultz, Elizabeth E Crone, William F Morris
Many populations exhibit boom-bust dynamics in which abundance fluctuates dramatically over time. Past research has focused on identifying whether the cause of fluctuations is primarily exogenous, e.g., environmental stochasticity coupled with weak density dependence, or endogenous, e.g., over-compensatory density dependence. Far fewer studies have addressed whether the mechanism responsible for boom-bust dynamics matters with respect to at-risk species management. Here, we ask whether the best strategy for restoring habitat across a landscape differs under exogenously versus endogenously driven boom-bust dynamics...
November 21, 2017: Ecological Applications: a Publication of the Ecological Society of America
https://www.readbyqxmd.com/read/29164637/internal-pilot-design-for-balanced-repeated-measures
#3
Xinrui Zhang, Keith E Muller, Maureen M Goodenow, Yueh-Yun Chi
Repeated measures are common in clinical trials and epidemiological studies. Designing studies with repeated measures requires reasonably accurate specifications of the variances and correlations to select an appropriate sample size. Underspecifying the variances leads to a sample size that is inadequate to detect a meaningful scientific difference, while overspecifying the variances results in an unnecessarily large sample size. Both lead to wasting resources and placing study participants in unwarranted risk...
November 21, 2017: Statistics in Medicine
https://www.readbyqxmd.com/read/29164138/modeling-the-costs-of-postpartum-dysgalactia-syndrome-and-locomotory-disorders-on-sow-productivity-and-replacement
#4
Jarkko K Niemi, Paula Bergman, Sami Ovaska, Marja-Liisa Sevón-Aimonen, Mari Heinonen
Postpartum dysgalactia syndrome (PPDS) and locomotory disorders are common health problems in sows. Previous research suggests that they can cause substantial losses, reduce sow welfare, and result in premature removal of the sow from the herd. However, economic consequences of PPDS and locomotory disorders have not been investigated thoroughly. The goal of this study was to examine economic losses caused by PPDS and locomotory disorders and their impacts on sow longevity. A stochastic dynamic programming model, which maximizes return on sow space unit and assesses sow replacement under several scenarios, was developed...
2017: Frontiers in Veterinary Science
https://www.readbyqxmd.com/read/29163310/perception-accuracy-of-affiliative-relationships-in-elementary-school-children-and-young-adolescents
#5
João R Daniel, Rita R Silva, António J Santos, Jordana Cardoso, Leandra Coelho, Miguel Freitas, Olívia Ribeiro
There has been a rapid growth of studies focused on selection and socialization processes of peer groups, mostly due to the development of stochastic actor-based models to analyze longitudinal social network data. One of the core assumptions of these models is that individuals have an accurate knowledge of the dyadic relationships within their network (i.e., who is and is not connected to whom). Recent cross-sectional findings suggest that elementary school children are very inaccurate in perceiving their classmates' dyadic relationships...
2017: Frontiers in Psychology
https://www.readbyqxmd.com/read/29161884/accounting-for-non-gaussian-sources-of-spatial-correlation-in-parametric-fmri-paradigms-ii-a-method-to-obtain-first-level-analysis-residuals-with-uniform-and-gaussian-spatial-autocorrelation-function-and-independent-and-identically-distributed-time-series
#6
Kaundinya Gopinath, Venkatagiri Krishnamurthy, Simon Lacey, K Sathian
A recent study (Eklund et al., 2016) has shown that cluster-wise family-wise error (FWE) rate corrected inferences made in parametric statistical methods based fMRI studies over the past couple of decades may have been invalid, particularly for cluster defining thresholds less stringent than p < 0.001; principally because the spatial autocorrelation functions (sACF) of fMRI data had been modeled incorrectly to follow a Gaussian form, whereas empirical data suggests otherwise (Eklund et al., 2016). Hence the residuals from general linear model (GLM) based fMRI activation estimates in these studies may not have possessed a homogenously Gaussian sACF (Eklund et al...
November 22, 2017: Brain Connectivity
https://www.readbyqxmd.com/read/29161872/asymptotic-behavior-of-a-delayed-stochastic-logistic-model-with-impulsive-perturbations
#7
Sanling Yuan, Xuehui Ji, Huaiping Zhu
In this paper, we investigate the dynamics of a delayed logistic model with both impulsive and stochastic perturbations. The impulse is introduced at fixed moments and the stochastic perturbation is of white noise type which is assumed to be proportional to the population density. We start with the existence and uniqueness of the positive solution of the model, then establish sufficient conditions ensuring its global attractivity. By using the theory of integral Markov semigroups, we further derive sufficient conditions for the existence of the stationary distribution of the system...
October 2017: Mathematical Biosciences and Engineering: MBE
https://www.readbyqxmd.com/read/29161847/formulation-of-the-protein-synthesis-rate-with-sequence-information
#8
Wenjun Xia, Jinzhi Lei
Translation is a central biological process by which proteins are synthesized from genetic information contained within mRNAs. Here, we investigate the kinetics of translation at the molecular level by a stochastic simulation model. The model explicitly includes RNA sequences, ribosome dynamics, the tRNA pool and biochemical reactions involved in the translation elongation. The results show that the translation efficiency is mainly limited by the available ribosome number, translation initiation and the translation elongation time...
April 1, 2018: Mathematical Biosciences and Engineering: MBE
https://www.readbyqxmd.com/read/29160179/the-miage-calculator-a-dna-methylation-based-mitotic-age-calculator-of-human-tissue-types
#9
Ahrim Youn, Shuang Wang
Cell division is important in human aging and cancer. To estimate the number of cell divisions (mitotic age) of a given tissue type between individuals is of great interest as that not only allows to study biological aging using a new molecular aging target but also allows the stratification of prospective cancer risk. Here we introduce the MiAge Calculator, a mitotic age calculator based on a novel statistical framework, the MiAge model. MiAge is designed to quantitatively estimate mitotic age (total number of lifetime cell divisions) of a tissue using the stochastic replication errors accumulated in the epigenetic inheritance process during cell divisions...
November 21, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29159273/a-health-economic-evaluation-of-needle-based-confocal-laser-endomicroscopy-for-the-diagnosis-of-pancreatic-cysts
#10
Claude Le Pen, Laurent Palazzo, Bertrand Napoléon
Background and study aims:  The low sensitivity of endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA), especially for the diagnosis of serous cystadenomas (SCAs), can be associated with diagnostic uncertainty that can regularly lead to unnecessary surgical procedures. Needle-based confocal laser endomicroscopy (nCLE) used with EUS-FNA improves diagnostic accuracy, helping to reduce unnecessary surgery and patient follow-up. This study was conducted to evaluate the economic benefit of EUS-FNA + nCLE...
October 2017: Endoscopy International Open
https://www.readbyqxmd.com/read/29158597/a-new-paradigm-in-modelling-the-evolution-of-a-stand-via-the-distribution-of-tree-sizes
#11
Petras Rupšys, Edmundas Petrauskas
Our study focusses on investigating a modern modelling paradigm, a bivariate stochastic process, that allows us to link individual tree variables with growth and yield stand attributes. In this paper, our aim is to introduce the mathematics of mixed effect parameters in a bivariate stochastic differential equation and to describe how such a model can be used to aid our understanding of the bivariate height and diameter distribution in a stand using a large dataset provided by the Lithuanian National Forest Inventory (LNFI)...
November 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29158403/beating-the-curse-of-dimension-with-accurate-statistics-for-the-fokker-planck-equation-in-complex-turbulent-systems
#12
Nan Chen, Andrew J Majda
Solving the Fokker-Planck equation for high-dimensional complex dynamical systems is an important issue. Recently, the authors developed efficient statistically accurate algorithms for solving the Fokker-Planck equations associated with high-dimensional nonlinear turbulent dynamical systems with conditional Gaussian structures, which contain many strong non-Gaussian features such as intermittency and fat-tailed probability density functions (PDFs). The algorithms involve a hybrid strategy with a small number of samples [Formula: see text], where a conditional Gaussian mixture in a high-dimensional subspace via an extremely efficient parametric method is combined with a judicious Gaussian kernel density estimation in the remaining low-dimensional subspace...
November 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29157873/quantized-filtering-for-t-s-fuzzy-networked-systems-with-saturation-nonlinearities-an-output-dependent-triggering-method
#13
Yushun Tan, Dongsheng Du, Shumin Fei
This paper addresses the problem of H∞ filter design for T-S fuzzy systems with saturation nonlinearities. For the purpose of reducing network burden, an output-dependent triggering scheme and a quantizer are introduced at the same time. The output-dependent triggering scheme is applied to determine whether or not the current instant information should be transmitted to the quantizer. Saturation nonlinearities, as a common phenomenon in networked systems due to the physical or technological constraints, is also considered here...
November 17, 2017: ISA Transactions
https://www.readbyqxmd.com/read/29157376/epidemiological-and-partial-budget-analysis-for-treatment-of-subclinical-staphylococcus-aureus-intramammary-infections-considering-microbiological-and-cytological-scenarios
#14
Inge-Marié Petzer, Eric M C Etter, Edward F Donkin, Edward C Webb, Joanne Karzis
An innovative method was investigated to aid in the elimination of Staphylococcus aureus (S. aureus) intramammary infections (IMI) from dairy herds. A stochastic model explore the economic benefit of three-day or eight-day treatment of subclinical IMI in all S. aureus infected cows or in only those with a somatic cell count (SCC) exceeding 200,000 cells/ml. An epidemiological model was developed to run parallel to the economic model that would predict the S. aureus IMI likely to persist, develop new infections and clinical mastitis...
December 1, 2017: Preventive Veterinary Medicine
https://www.readbyqxmd.com/read/29157246/inferring-gene-regulatory-networks-from-single-cell-data-a-mechanistic-approach
#15
Ulysse Herbach, Arnaud Bonnaffoux, Thibault Espinasse, Olivier Gandrillon
BACKGROUND: The recent development of single-cell transcriptomics has enabled gene expression to be measured in individual cells instead of being population-averaged. Despite this considerable precision improvement, inferring regulatory networks remains challenging because stochasticity now proves to play a fundamental role in gene expression. In particular, mRNA synthesis is now acknowledged to occur in a highly bursty manner. RESULTS: We propose to view the inference problem as a fitting procedure for a mechanistic gene network model that is inherently stochastic and takes not only protein, but also mRNA levels into account...
November 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29157162/discrete-stochastic-analogs-of-erlang-epidemic-models
#16
Wayne M Getz, Eric R Dougherty
Erlang differential equation models of epidemic processes provide more realistic disease-class transition dynamics from susceptible (S) to exposed (E) to infectious (I) and removed (R) categories than the ubiquitous SEIR model. The latter is itself is at one end of the spectrum of Erlang SE[Formula: see text]I[Formula: see text]R models with [Formula: see text] concatenated E compartments and [Formula: see text] concatenated I compartments. Discrete-time models, however, are computationally much simpler to simulate and fit to epidemic outbreak data than continuous-time differential equations, and are also much more readily extended to include demographic and other types of stochasticity...
December 2018: Journal of Biological Dynamics
https://www.readbyqxmd.com/read/29155811/an-efficient-moments-based-inference-method-for-within-host-bacterial-infection-dynamics
#17
David J Price, Alexandre Breuzé, Richard Dybowski, Piero Mastroeni, Olivier Restif
Over the last ten years, isogenic tagging (IT) has revolutionised the study of bacterial infection dynamics in laboratory animal models. However, quantitative analysis of IT data has been hindered by the piecemeal development of relevant statistical models. The most promising approach relies on stochastic Markovian models of bacterial population dynamics within and among organs. Here we present an efficient numerical method to fit such stochastic dynamic models to in vivo experimental IT data. A common approach to statistical inference with stochastic dynamic models relies on producing large numbers of simulations, but this remains a slow and inefficient method for all but simple problems, especially when tracking bacteria in multiple locations simultaneously...
November 20, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29155808/a-hierarchical-stochastic-model-for-bistable-perception
#18
Stefan Albert, Katharina Schmack, Philipp Sterzer, Gaby Schneider
Viewing of ambiguous stimuli can lead to bistable perception alternating between the possible percepts. During continuous presentation of ambiguous stimuli, percept changes occur as single events, whereas during intermittent presentation of ambiguous stimuli, percept changes occur at more or less regular intervals either as single events or bursts. Response patterns can be highly variable and have been reported to show systematic differences between patients with schizophrenia and healthy controls. Existing models of bistable perception often use detailed assumptions and large parameter sets which make parameter estimation challenging...
November 20, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29155604/modelling-evolutionary-algorithms-with-stochastic-differential-equations
#19
Jorge Pérez Heredia
There has been renewed interest in modelling the behaviour of evolutionary algorithms (EAs) by more traditional mathematical objects, such as ordinary differential equations or Markov chains. The advantage is that the analysis becomes greatly facilitated due to the existence of well established methods. However, this typically comes at the cost of disregarding information about the process. Here, we introduce the use of stochastic differential equations (SDEs) for the study of EAs. SDEs can produce simple analytical results for the dynamics of stochastic processes, unlike Markov chains which can produce rigorous but unwieldy expressions about the dynamics...
November 20, 2017: Evolutionary Computation
https://www.readbyqxmd.com/read/29155595/water-wicking-and-droplet-spreading-on-randomly-structured-thin-nanoporous-layers
#20
Claire Kunkle Wemp, Van P Carey
Growing thin, nanostructured layers on metallic surfaces, such as heat exchangers, is an attractive approach to creating thin, superhydrophilic coatings on surfaces to enhance spray cooling heat transfer. This paper presents results of an experimental study of enhanced droplet spreading on zinc oxide, nanostructured surfaces of this type that were thermally grown on a copper substrates. The spreading rate data obtained from experimental high speed videos was used to develop a model specifically for this type of ultra-thin, nano-porous layer...
November 20, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
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