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Stochastic modeling

Ross Wilson, J Haxby Abbott
OBJECTIVE: To describe the construction and preliminary validation of a new population-based microsimulation model developed to analyse the health and economic burden and cost-effectiveness of treatments for knee osteoarthritis (OA) in New Zealand (NZ). METHOD: We developed the New Zealand Management of Osteoarthritis (NZ-MOA) model, a discrete-time state-transition microsimulation model of the natural history of radiographic knee OA. In this article, we report on the model structure, derivation of input data, validation of baseline model parameters against external data sources, and validation of model outputs by comparison of the predicted population health loss with previous estimates...
January 10, 2018: Osteoarthritis and Cartilage
Jinxian Li, Weiqiang Li, Zhen Jin
The spread of an infectious disease may depend on the structure of the network. To study the influence of the structure parameters of the network on the spread of the epidemic, we need to put these parameters into the epidemic model. The method of moment closure introduces structure parameters into the epidemic model. In this paper, we present a new moment closure epidemic model based on the approximation of third-order motifs in networks. The order of a motif defined in this paper is determined by the number of the edges in the motif, rather than by the number of nodes in the motif as defined in the literature...
January 9, 2018: Mathematical Biosciences
Matan Danino, Nadav M Shnerb
A fundamental problem in the fields of population genetics, evolution, and community ecology, is the fate of a single mutant, or invader, introduced in a finite population of wild types. For a fixed-size community of N individuals, with Markovian, zero-sum dynamics driven by stochastic birth-death events, the mutant population eventually reaches either fixation or extinction. The classical analysis, provided by Kimura and his coworkers, is focused on the neutral case, [where the dynamics is only due to demographic stochasticity (drift)], and on time-independent selective forces (deleterious/beneficial mutation)...
January 9, 2018: Journal of Theoretical Biology
Chi Xue, Nigel Goldenfeld
The "kill the winner" hypothesis is an attempt to address the problem of diversity in biology. It argues that host-specific predators control the population of each prey, preventing a winner from emerging and thus maintaining the coexistence of all species in the system. We develop a stochastic model for the kill the winner paradigm and show that the stable coexistence state of the deterministic kill the winner model is destroyed by demographic stochasticity, through a cascade of extinction events. We formulate an individual-level stochastic model in which predator-prey coevolution promotes the high diversity of the ecosystem by generating a persistent population flux of species...
December 29, 2017: Physical Review Letters
Daniel S Calovi, Alexandra Litchinko, Valentin Lecheval, Ugo Lopez, Alfonso Pérez Escudero, Hugues Chaté, Clément Sire, Guy Theraulaz
The development of tracking methods for automatically quantifying individual behavior and social interactions in animal groups has open up new perspectives for building quantitative and predictive models of collective behavior. In this work, we combine extensive data analyses with a modeling approach to measure, disentangle, and reconstruct the actual functional form of interactions involved in the coordination of swimming in Rummy-nose tetra (Hemigrammus rhodostomus). This species of fish performs burst-and-coast swimming behavior that consists of sudden heading changes combined with brief accelerations followed by quasi-passive, straight decelerations...
January 11, 2018: PLoS Computational Biology
Devin W Goodsman, Brian H Aukema, Nate G McDowell, Richard S Middleton, Chonggang Xu
Phenology models are becoming increasingly important tools to accurately predict how climate change will impact the life histories of organisms. We propose a class of integral projection phenology models derived from stochastic individual-based models of insect development and demography. Our derivation, which is based on the rate summation concept, produces integral projection models that capture the effect of phenotypic rate variability on insect phenology, but which are typically more computationally frugal than equivalent individual-based phenology models...
January 2018: Ecology and Evolution
Anja Lück, Lukas Klimmasch, Peter Großmann, Sebastian Germerodt, Christoph Kaleta
Organisms need to adapt to changing environments and they do so by using a broad spectrum of strategies. These strategies include finding the right balance between expressing genes before or when they are needed, and adjusting the degree of noise inherent in gene expression. We investigated the interplay between different nutritional environments and the inhabiting organisms' metabolic and genetic adaptations by applying an evolutionary algorithm to an agent-based model of a concise bacterial metabolism. Our results show that constant environments and rapidly fluctuating environments produce similar adaptations in the organisms, making the predictability of the environment a major factor in determining optimal adaptation...
January 10, 2018: Scientific Reports
Yuta Sakurai, Yutaka Hori
Model-guided design has become a standard approach to engineering biomolecular circuits in synthetic biology. However, the stochastic nature of biomolecular reactions is often overlooked in the design process. As a result, cell-cell heterogeneity causes unexpected deviation of biocircuit behaviours from model predictions and requires additional iterations of design-build-test cycles. To enhance the design process of stochastic biocircuits, this paper presents a computational framework to systematically specify the level of intrinsic noise using well-defined metrics of statistics and design highly heterogeneous biocircuits based on the specifications...
January 2018: Journal of the Royal Society, Interface
Giancarlo De Luca, Kim Van Kerckhove, Pietro Coletti, Chiara Poletto, Nathalie Bossuyt, Niel Hens, Vittoria Colizza
BACKGROUND: School closure is often considered as an option to mitigate influenza epidemics because of its potential to reduce transmission in children and then in the community. The policy is still however highly debated because of controversial evidence. Moreover, the specific mechanisms leading to mitigation are not clearly identified. METHODS: We introduced a stochastic spatial age-specific metapopulation model to assess the role of holiday-associated behavioral changes and how they affect seasonal influenza dynamics...
January 10, 2018: BMC Infectious Diseases
Gustavo J Costa, Antonio Carlos Borin, Rogério Custodio, Luciano N Vidal
A study is presented on the resonance Raman (RR) spectrum based on fully anharmonic wavefunctions and energies obtained from ab initio multireference potential energy curves of diatomic systems. The vibrational problem is numerically solved using a variational stochastic method or the Cooley-Numerov method, as implemented in Le Roy's LEVEL program. Anharmonic Franck-Condon and Herzberg-Teller integrals are numerically evaluated and the RR polarizability is calculated within the time-independent framework of the RR theory...
January 9, 2018: Journal of Chemical Theory and Computation
John D Rice, Brent A Johnson, Robert L Strawderman
Many longitudinal studies with a binary outcome measure involve a fraction of subjects with a homogeneous response profile. In our motivating data set, a study on the rate of human immunodeficiency virus (HIV) self-testing in a population of men who have sex with men (MSM), a substantial proportion of the subjects did not self-test during the follow-up study. The observed data in this context consist of a binary sequence for each subject indicating whether or not that subject experienced any events between consecutive observation time points, so subjects who never self-tested were observed to have a response vector consisting entirely of zeros...
January 4, 2018: Biostatistics
Onur Basak, Teresa G Krieger, Mauro J Muraro, Kay Wiebrands, Daniel E Stange, Javier Frias-Aldeguer, Nicolas C Rivron, Marc van de Wetering, Johan H van Es, Alexander van Oudenaarden, Benjamin D Simons, Hans Clevers
The adult mouse subependymal zone provides a niche for mammalian neural stem cells (NSCs). However, the molecular signature, self-renewal potential, and fate behavior of NSCs remain poorly defined. Here we propose a model in which the fate of active NSCs is coupled to the total number of neighboring NSCs in a shared niche. Using knock-in reporter alleles and single-cell RNA sequencing, we show that the Wnt target Tnfrsf19/Troy identifies both active and quiescent NSCs. Quantitative analysis of genetic lineage tracing of individual NSCs under homeostasis or in response to injury reveals rapid expansion of stem-cell number before some return to quiescence...
January 8, 2018: Proceedings of the National Academy of Sciences of the United States of America
Junjie Jiang, Zi-Gang Huang, Thomas P Seager, Wei Lin, Celso Grebogi, Alan Hastings, Ying-Cheng Lai
Complex networked systems ranging from ecosystems and the climate to economic, social, and infrastructure systems can exhibit a tipping point (a "point of no return") at which a total collapse of the system occurs. To understand the dynamical mechanism of a tipping point and to predict its occurrence as a system parameter varies are of uttermost importance, tasks that are hindered by the often extremely high dimensionality of the underlying system. Using complex mutualistic networks in ecology as a prototype class of systems, we carry out a dimension reduction process to arrive at an effective 2D system with the two dynamical variables corresponding to the average pollinator and plant abundances...
January 8, 2018: Proceedings of the National Academy of Sciences of the United States of America
Hyoshin Park, Ali Haghani, Siby Samuel, Michael A Knodler
According to the Federal Highway Administration, nonrecurring congestion contributes to nearly half of the overall congestion. Temporal disruptions impact the effective use of the complete roadway, due to speed reduction and rubbernecking resulting from primary incidents that in turn provoke secondary incidents. There is an additional reduction of discharge flow caused by secondary incident that significantly increases total delay. Therefore, it is important to sequentially predict the probability of secondary incidents and develop appropriate countermeasures to reduce the associated risk...
January 4, 2018: Accident; Analysis and Prevention
Samit Bhattacharyya, Matthew J Ferrari, Ottar N Bjørnstad
Incidence of whooping cough exhibits variable dynamics across time and space. The periodicity of this disease varies from annual to five years in different geographic regions in both developing and developed countries. Many hypotheses have been put forward to explain this variability such as nonlinearity and seasonality, stochasticity, variable recruitment of susceptible individuals via birth, immunization, and immune boosting. We propose an alternative hypothesis to describe the variability in periodicity - the intricate dynamical variability of whooping cough may arise from interactions between its dominant etiological agents of Bordetella pertussis and Bordetella parapertussis...
December 14, 2017: Epidemics
Chang-Yu Hsieh, Jianshu Cao
We extend a standard stochastic theory to study open quantum systems coupled to a generic quantum environment. We exemplify the general framework by studying a two-level quantum system coupled bilinearly to the three fundamental classes of non-interacting particles: bosons, fermions, and spins. In this unified stochastic approach, the generalized stochastic Liouville equation (SLE) formally captures the exact quantum dissipations when noise variables with appropriate statistics for different bath models are applied...
January 7, 2018: Journal of Chemical Physics
Chang-Yu Hsieh, Jianshu Cao
We use the "generalized hierarchical equation of motion" proposed in Paper I [C.-Y. Hsieh and J. Cao, J. Chem. Phys. 148, 014103 (2018)] to study decoherence in a system coupled to a spin bath. The present methodology allows a systematic incorporation of higher-order anharmonic effects of the bath in dynamical calculations. We investigate the leading order corrections to the linear response approximations for spin bath models. Two kinds of spin-based environments are considered: (1) a bath of spins discretized from a continuous spectral density and (2) a bath of localized nuclear or electron spins...
January 7, 2018: Journal of Chemical Physics
Enrico Ne, Robert-Jan Palstra, Tokameh Mahmoudi
In this review, we cover transcription regulation of human immunodeficiency virus type 1 (HIV-1) gene expression, focusing on the invaluable contributions, made by HIV research over the years, toward the field of transcription. In this context, the HIV promoter can be considered to be a well-studied model promoter, which although a viral promoter, is subject to the same cellular regulatory mechanisms that modulate the transcriptional control of endogenous host cellular genes. The molecular control of HIV-1 transcription has been well studied and considerable knowledge toward development of alternative strategies for therapies aimed at eradicating both active but also latent HIV-1 has been obtained...
2018: International Review of Cell and Molecular Biology
Chrysantus Mbi Tanga, Fathiya Mbarak Khamis, Henri E Z Tonnang, Ivan Rwomushana, Gladys Mosomtai, Samira A Mohamed, Sunday Ekesi
Integrative taxonomy has resolved the species status of the potentially invasive Ceratitis rosa Karsch into two separate species with distinct ecological requirements: C. rosa "lowland type" and the newly described species Ceratitis quilicii De Meyer, Mwatawala & Virgilio sp. nov. "highland type". Both species are tephritid pests threatening the production of horticultural crops in Africa and beyond. Studies were carried out by constructing thermal reaction norms for each life stage of both species at constant and fluctuating temperatures...
2018: PloS One
Łukasz Kuśmierz, Taro Toyoizumi
In natural foraging, many organisms seem to perform two different types of motile search: directed search (taxis) and random search. The former is observed when the environment provides cues to guide motion towards a target. The latter involves no apparent memory or information processing and can be mathematically modeled by random walks. We show that both types of search can be generated by a common mechanism in which Lévy flights or Lévy walks emerge from a second-order gradient-based search with noisy observations...
December 22, 2017: Physical Review Letters
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