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Stochastic modeling

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https://www.readbyqxmd.com/read/28644841/low-dimensional-spike-rate-models-derived-from-networks-of-adaptive-integrate-and-fire-neurons-comparison-and-implementation
#1
Moritz Augustin, Josef Ladenbauer, Fabian Baumann, Klaus Obermayer
The spiking activity of single neurons can be well described by a nonlinear integrate-and-fire model that includes somatic adaptation. When exposed to fluctuating inputs sparsely coupled populations of these model neurons exhibit stochastic collective dynamics that can be effectively characterized using the Fokker-Planck equation. This approach, however, leads to a model with an infinite-dimensional state space and non-standard boundary conditions. Here we derive from that description four simple models for the spike rate dynamics in terms of low-dimensional ordinary differential equations using two different reduction techniques: one uses the spectral decomposition of the Fokker-Planck operator, the other is based on a cascade of two linear filters and a nonlinearity, which are determined from the Fokker-Planck equation and semi-analytically approximated...
June 23, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28641269/a-model-based-tool-for-the-analysis-and-design-of-gene-regulatory-network
#2
Liliana Ironi, Ettore Lanzarone
Computational and mathematical models have significantly contributed to the rapid progress in the study of gene regulatory networks (GRN), but researchers still lack a reliable model-based framework for computer-aided analysis and design. Such tool should both reveal the relation between network structure and dynamics and find parameter values and/or constraints that enable the simulated dynamics to reproduce specific behaviors. This paper addresses these issues and proposes a computational framework that facilitates network analysis or design...
June 19, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28640895/the-interplay-of-climate-intervention-and-imported-cases-as-determinants-of-the-2014-dengue-outbreak-in-guangzhou
#3
Qu Cheng, Qinlong Jing, Robert C Spear, John M Marshall, Zhicong Yang, Peng Gong
Dengue is a fast spreading mosquito-borne disease that affects more than half of the population worldwide. An unprecedented outbreak happened in Guangzhou, China in 2014, which contributed 52 percent of all dengue cases that occurred in mainland China between 1990 and 2015. Our previous analysis, based on a deterministic model, concluded that the early timing of the first imported case that triggered local transmission and the excessive rainfall thereafter were the most important determinants of the large final epidemic size in 2014...
June 22, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28640883/an-artificial-emg-generation-model-based-on-signal-dependent-noise-and-related-application-to-motion-classification
#4
Akira Furui, Hideaki Hayashi, Go Nakamura, Takaaki Chin, Toshio Tsuji
This paper proposes an artificial electromyogram (EMG) signal generation model based on signal-dependent noise, which has been ignored in existing methods, by introducing the stochastic construction of the EMG signals. In the proposed model, an EMG signal variance value is first generated from a probability distribution with a shape determined by a commanded muscle force and signal-dependent noise. Artificial EMG signals are then generated from the associated Gaussian distribution with a zero mean and the generated variance...
2017: PloS One
https://www.readbyqxmd.com/read/28640391/selective-sweeps-of-mitochondrial-dna-can-drive-the-evolution-of-uniparental-inheritance
#5
Joshua R Christie, Madeleine Beekman
While the uniparental (or maternal) inheritance of mitochondrial DNA (mtDNA) is widespread, the reasons for its evolution remain unclear. Two main hypotheses have been proposed: selection against individuals containing different mtDNAs (heteroplasmy) and selection against "selfish" mtDNA mutations. Recently, uniparental inheritance was shown to promote adaptive evolution in mtDNA, potentially providing a third hypothesis for its evolution. Here we explore this hypothesis theoretically and ask if the accumulation of beneficial mutations provides a sufficient fitness advantage for uniparental inheritance to invade a population in which mtDNA is inherited biparentally...
June 22, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28639869/economic-burden-of-inpatient-admission-of-ankle-fractures
#6
Justin D Stull, Suneel B Bhat, Justin M Kane, Steven M Raikin
BACKGROUND: Ankle fractures are among the most prevalent traumatic orthopaedic injuries. A large proportion of patients sustaining operative ankle fractures are admitted directly from the emergency department prior to operative management. In the authors' experience, however, many closed ankle injuries may be safely and effectively managed on an outpatient basis. The aim of this study was to characterize the economic impact of routine inpatient admission of ankle fractures. METHODS: A retrospective review of all outpatient ankle fracture surgery performed by a single foot and ankle fellowship-trained surgeon at a tertiary level academic center in 2012 was conducted to identify any patients requiring postoperative inpatient admission...
June 1, 2017: Foot & Ankle International
https://www.readbyqxmd.com/read/28638377/a-novel-bromodomain-inhibitor-reverses-hiv-1-latency-through-specific-binding-with-brd4-to-promote-tat-and-p-tefb-association
#7
Huachao Huang, Shuai Liu, Maxime Jean, Sydney Simpson, He Huang, Mark Merkley, Tsuyoshi Hayashi, Weili Kong, Irene Rodríguez-Sánchez, Xiaofeng Zhang, Hailemichael O Yosief, Hongyu Miao, Jianwen Que, James J Kobie, James Bradner, Netty G Santoso, Wei Zhang, Jian Zhu
While combinatory antiretroviral therapy (cART) can effectively reduce HIV-1 viremia, it cannot eliminate HIV-1 infection. In the presence of cART, viral reservoirs remain latent, impeding the cure of HIV-1/AIDS. Recently, latency-reversing agents (LRAs) have been developed with the intent of purging latent HIV-1, providing an intriguing strategy for the eradication of the residual viral reservoirs. Our earlier studies show that the first-generation, methyl-triazolo bromodomain, and extra-terminal domain inhibitor (BETi), JQ1, facilitates the reversal of HIV-1 latency...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28638046/a-note-on-the-stationary-distribution-of-stochastic-seir-epidemic-model-with-saturated-incidence-rate
#8
Qixing Han, Liang Chen, Daqing Jiang
The stochastic SEIR infectious diseases model with saturated incidence rate is studied in this paper. By constructing appropriate Lyapunov functions, we show that there is a stationary distribution for the system and the ergodicity holds provided [Formula: see text] > 1. In particular, we improve the results obtained by previous studies greatly, condition in our Theorem is more concise and elegant.
June 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28637916/model-based-analysis-of-an-outbreak-of-bubonic-plague-in-cairo-in-1801
#9
Xavier Didelot, Lilith K Whittles, Ian Hall
Bubonic plague has caused three deadly pandemics in human history: from the mid-sixth to mid-eighth century, from the mid-fourteenth to the mid-eighteenth century and from the end of the nineteenth until the mid-twentieth century. Between the second and the third pandemics, plague was causing sporadic outbreaks in only a few countries in the Middle East, including Egypt. Little is known about this historical phase of plague, even though it represents the temporal, geographical and phylogenetic transition between the second and third pandemics...
June 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28637875/coupled-feedback-loops-control-the-stimulus-dependent-dynamics-of-the-yeast-transcription-factor-msn2
#10
Yanfei Jiang, Zohreh AkhavanAghdam, Lev S Tsimring, Nan Hao
Information about environmental stimuli often can be encoded by the dynamics of signaling molecules or transcription factors. In the yeast Saccharomyces cerevisiae, different types of stresses induce distinct nuclear translocation dynamics of the general stress-responsive transcription factor Msn2, but the underlying mechanisms remain unclear. Using deterministic and stochastic modeling, we reproduced in silico the different dynamic responses of Msn2 to glucose limitation and osmotic stress observed in vivo and found that a positive feedback loop on protein kinase A mediated by the AMP-activated protein kinase Snf1 is coupled with a negative feedback loop to generate the characteristic pulsatile dynamics of Msn2...
June 21, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28637532/estimating-the-economic-impact-of-subclinical-ketosis-in-dairy-cattle-using-a-dynamic-stochastic-simulation-model
#11
P F Mostert, E A M Bokkers, C E van Middelaar, H Hogeveen, I J M de Boer
The objective of this study was to estimate the economic impact of subclinical ketosis (SCK) in dairy cows. This metabolic disorder occurs in the period around calving and is associated with an increased risk of other diseases. Therefore, SCK affects farm productivity and profitability. Estimating the economic impact of SCK may make farmers more aware of this problem, and can improve their decision-making regarding interventions to reduce SCK. We developed a dynamic stochastic simulation model that enables estimating the economic impact of SCK and related diseases (i...
June 22, 2017: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/28637491/stable-centromere-positioning-in-diverse-sequence-contexts-of-complex-and-satellite-centromeres-of-maize-and-wild-relatives
#12
Jonathan I Gent, Na Wang, R Kelly Dawe
BACKGROUND: Paradoxically, centromeres are known both for their characteristic repeat sequences (satellite DNA) and for being epigenetically defined. Maize (Zea mays mays) is an attractive model for studying centromere positioning because many of its large (~2 Mb) centromeres are not dominated by satellite DNA. These centromeres, which we call complex centromeres, allow for both assembly into reference genomes and for mapping short reads from ChIP-seq with antibodies to centromeric histone H3 (cenH3)...
June 21, 2017: Genome Biology
https://www.readbyqxmd.com/read/28637378/surveillance-to-inform-control-of-emerging-plant-diseases-an-epidemiological-perspective
#13
Stephen Parnell, Frank van den Bosch, Tim Gottwald, Christopher A Gilligan
The rise in emerging pathogens and strains has led to increased calls for more effective surveillance in plant health. We show how epidemiological insights about the dynamics of disease spread can improve the targeting of when and where to sample. We outline some relatively simple but powerful statistical approaches to inform surveillance and describe how they can be adapted to include epidemiological information. This enables us to address questions such as: Following the first report of an invading pathogen, what is the likely incidence of disease? If no cases of disease have been found, how certain can we be that the disease was not simply missed by chance? We illustrate the use of spatially explicit stochastic models to optimize targeting of surveillance and control resources...
June 21, 2017: Annual Review of Phytopathology
https://www.readbyqxmd.com/read/28636920/nanog-fluctuations-in-embryonic-stem-cells-highlight-the-problem-of-measurement-in-cell-biology
#14
Rosanna C G Smith, Patrick S Stumpf, Sonya J Ridden, Aaron Sim, Sarah Filippi, Heather A Harrington, Ben D MacArthur
A number of important pluripotency regulators, including the transcription factor Nanog, are observed to fluctuate stochastically in individual embryonic stem cells. By transiently priming cells for commitment to different lineages, these fluctuations are thought to be important to the maintenance of, and exit from, pluripotency. However, because temporal changes in intracellular protein abundances cannot be measured directly in live cells, fluctuations are typically assessed using genetically engineered reporter cell lines that produce a fluorescent signal as a proxy for protein expression...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636232/a-genetic-stochastic-process-model-for-genome-wide-joint-analysis-of-biomarker-dynamics-and-disease-susceptibility-with-longitudinal-data
#15
Liang He, Ilya Zhbannikov, Konstantin G Arbeev, Anatoliy I Yashin, Alexander M Kulminski
Unraveling the underlying biological mechanisms or pathways behind the effects of genetic variations on complex diseases remains one of the major challenges in the post-GWAS (where GWAS is genome-wide association study) era. To further explore the relationship between genetic variations, biomarkers, and diseases for elucidating underlying pathological mechanism, a huge effort has been placed on examining pleiotropic and gene-environmental interaction effects. We propose a novel genetic stochastic process model (GSPM) that can be applied to GWAS and jointly investigate the genetic effects on longitudinally measured biomarkers and risks of diseases...
June 21, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28634857/computational-modelling-of-cancer-development-and-growth-modelling-at-multiple-scales-and-multiscale-modelling
#16
Zuzanna Szymańska, Maciej Cytowski, Elaine Mitchell, Cicely K Macnamara, Mark A J Chaplain
In this paper, we present two mathematical models related to different aspects and scales of cancer growth. The first model is a stochastic spatiotemporal model of both a synthetic gene regulatory network (the example of a three-gene repressilator is given) and an actual gene regulatory network, the NF-[Formula: see text]B pathway. The second model is a force-based individual-based model of the development of a solid avascular tumour with specific application to tumour cords, i.e. a mass of cancer cells growing around a central blood vessel...
June 20, 2017: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/28634747/evaluation-of-vaccination-strategies-for-sir-epidemics-on-random-networks-incorporating-household-structure
#17
Frank Ball, David Sirl
This paper is concerned with the analysis of vaccination strategies in a stochastic susceptible [Formula: see text] infected [Formula: see text] removed model for the spread of an epidemic amongst a population of individuals with a random network of social contacts that is also partitioned into households. Under various vaccine action models, we consider both household-based vaccination schemes, in which the way in which individuals are chosen for vaccination depends on the size of the households in which they reside, and acquaintance vaccination, which targets individuals of high degree in the social network...
June 20, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28634366/quantifying-non-ergodicity-of-anomalous-diffusion-with-higher-order-moments
#18
Maria Schwarzl, Aljaž Godec, Ralf Metzler
Anomalous diffusion is being discovered in a fast growing number of systems. The exact nature of this anomalous diffusion provides important information on the physical laws governing the studied system. One of the central properties analysed for finite particle motion time series is the intrinsic variability of the apparent diffusivity, typically quantified by the ergodicity breaking parameter EB. Here we demonstrate that frequently EB is insufficient to provide a meaningful measure for the observed variability of the data...
June 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28634351/a-dynamical-model-for-activating-and-silencing-the-mitotic-checkpoint
#19
Richard Henze, Peter Dittrich, Bashar Ibrahim
The spindle assembly checkpoint (SAC) is an evolutionarily conserved mechanism, exclusively sensitive to the states of kinetochores attached to microtubules. During metaphase, the anaphase-promoting complex/cyclosome (APC/C) is inhibited by the SAC but it rapidly switches to its active form following proper attachment of the final spindle. It had been thought that APC/C activity is an all-or-nothing response, but recent findings have demonstrated that it switches steadily. In this study, we develop a detailed mathematical model that considers all 92 human kinetochores and all major proteins involved in SAC activation and silencing...
June 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28633937/our-teacher-likes-you-so-i-like-you-a-social-network-approach-to-social-referencing
#20
Marloes M H G Hendrickx, Tim Mainhard, Henrike J Boor-Klip, Mieke Brekelmans
A teacher is a social referent for peer liking and disliking when students adjust their evaluations of a peer based on their perceptions of teacher liking and disliking for this peer. The present study investigated social referencing as an intra-individual process that occurs over time, using stochastic actor-oriented modeling with RSiena. The co-evolution of peer-perceived teacher liking and disliking networks with peer liking and disliking networks was analyzed in 52 fifth-grade classes in the Netherlands, with 1370 students (Mage=10...
August 2017: Journal of School Psychology
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