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  • JOURNAL ARTICLE
    Arnaudon A, 2018,

    Structure preserving noise and dissipation in the Toda lattice

    , Journal of Physics A: Mathematical and Theoretical, Vol: 51, ISSN: 1751-8113

    In this paper, we use Flaschka's change of variables of the open Toda latticeand its interpretation in term of the group structure of the LU factorisationas a coadjoint motion on a certain dual of Lie algebra to implement a structurepreserving noise and dissipation. Both preserve the structure of coadjointorbit, that is the space of symmetric tri-diagonal matrices and arise as a newtype of multiplicative noise and nonlinear dissipation of the Toda lattice. Weinvestigate some of the properties of these deformations and in particular thecontinuum limit as a stochastic Burger equation with a nonlinear viscosity.This work is meant to be exploratory, and open more questions that we cananswer with simple mathematical tools and without numerical simulations.

  • JOURNAL ARTICLE
    Arnaudon A, Ganaba N, Holm DD, 2018,

    The stochastic energy-Casimir method

    , Comptes Rendus Mécanique, ISSN: 1631-0721
  • JOURNAL ARTICLE
    Biffi C, de Marvao A, Attard MI, Dawes TJW, Whiffin N, Bai W, Shi W, Francis C, Meyer H, Buchan R, Cook SA, Rueckert D, O'Regan DPet al., 2018,

    Three-dimensional cardiovascular imaging-genetics: a mass univariate framework

    , BIOINFORMATICS, Vol: 34, Pages: 97-103, ISSN: 1367-4803
  • JOURNAL ARTICLE
    Dawes TJW, Cai J, Quinlan M, de Marvao A, Ostrowski PJ, Tokarczuk PF, Watson GMJ, Wharton J, Howard LSGE, Gibbs JSR, Cook SA, Wilkins MR, O'Regan DPet al., 2018,

    Fractal Analysis of Right Ventricular Trabeculae in Pulmonary Hypertension.

    , Radiology

    Purpose To measure right ventricular (RV) trabecular complexity by its fractal dimension (FD) in healthy subjects and patients with pulmonary hypertension (PH) and to assess its relationship with hemodynamic and functional parameters and future cardiovascular events. Materials and Methods This retrospective study used data acquired from May 2004 to October 2013 in 256 patients with newly diagnosed PH who underwent cardiac MRI, right-sided heart catheterization, and 6-minute walk distance testing, with median follow-up of 4.0 years. A total of 256 healthy control subjects underwent cardiac MRI only. Biventricular FD, volumes, and function were assessed on short-axis cine images. Reproducibility was assessed with the intraclass correlation coefficient, correlation between variables was assessed with the Pearson correlation test, and mortality prediction was compared by using uni- and multivariable Cox regression analyses. Results RV FD reproducibility had an intraclass correlation coefficient of 0.97 (95% confidence interval [CI]: 0.96, 0.98). RV FD was higher in patients with PH (median, 1.310; interquartile range [IQR], 1.281-1.341) than in healthy subjects (median, 1.264; IQR, 1.242-1.295; P < .001), with the greatest difference near the apex. RV FD was associated with pulmonary vascular resistance (r = 0.30, P < .001). At univariable Cox regression analysis, RV FD was a significant predictor of death (hazard ratio [HR], 1.256; 95% CI: 1.011, 1.560; P = .04); however, at multivariable analysis, RV FD did not enable prediction of survival independently of conventional parameters of RV remodeling (HR, 1.179; 95% CI: 0.871, 1.596; P = .29). Conclusion Fractal analysis of RV trabecular complexity is a highly reproducible measure of remodeling in patients with PH that is associated with afterload, although the gain in survival prediction over traditional markers is not significant. Published under a CC BY 4.0 license. Online supplemental material is available for

  • JOURNAL ARTICLE
    Kendall ML, Ayabina P, Xu Y, Stimson J, Colijn Cet al., 2018,

    Estimating Transmission from Genetic and Epidemiological Data: A Metric to Compare Transmission Trees

    , Statistical Science, Vol: 33, Pages: 70-85, ISSN: 0883-4237

    Reconstructing who infected whom is a central challenge in analysing epidemiological data. Recently, advances in sequencing technology have led to increasing interest in Bayesian approaches to inferring who infected whom using genetic data from pathogens. The logic behind such approaches is that isolates that are nearly genetically identical are more likely to have been recently transmitted than those that are very different. A number of methods have been developed to perform this inference. However, testing their convergence, examining posterior sets of transmission trees and comparing methods’ performance are challenged by the fact that the object of inference—the transmission tree—is a complicated discrete structure. We introduce a metric on transmission trees to quantify distances between them. The metric can accommodate trees with unsampled individuals, and highlights differences in the source case and in the number of infections per infector. We illustrate its performance on simple simulated scenarios and on posterior transmission trees from a TB outbreak. We find that the metric reveals where the posterior is sensitive to the priors, and where collections of trees are composed of distinct clusters. We use the metric to define median trees summarising these clusters. Quantitative tools to compare transmission trees to each other will be required for assessing MCMC convergence, exploring posterior trees and benchmarking diverse methods as this field continues to mature.

  • JOURNAL ARTICLE
    Liu D, Mannan AA, Han Y, Oyarzún DA, Zhang Fet al., 2018,

    Dynamic metabolic control: towards precision engineering of metabolism.

    , J Ind Microbiol Biotechnol

    Advances in metabolic engineering have led to the synthesis of a wide variety of valuable chemicals in microorganisms. The key to commercializing these processes is the improvement of titer, productivity, yield, and robustness. Traditional approaches to enhancing production use the "push-pull-block" strategy that modulates enzyme expression under static control. However, strains are often optimized for specific laboratory set-up and are sensitive to environmental fluctuations. Exposure to sub-optimal growth conditions during large-scale fermentation often reduces their production capacity. Moreover, static control of engineered pathways may imbalance cofactors or cause the accumulation of toxic intermediates, which imposes burden on the host and results in decreased production. To overcome these problems, the last decade has witnessed the emergence of a new technology that uses synthetic regulation to control heterologous pathways dynamically, in ways akin to regulatory networks found in nature. Here, we review natural metabolic control strategies and recent developments in how they inspire the engineering of dynamically regulated pathways. We further discuss the challenges of designing and engineering dynamic control and highlight how model-based design can provide a powerful formalism to engineer dynamic control circuits, which together with the tools of synthetic biology, can work to enhance microbial production.

  • JOURNAL ARTICLE
    McGrath T, Murphy KG, Jones NS, 2018,

    Quantitative approaches to energy and glucose homeostasis: machine learning and modelling for precision understanding and prediction

    , JOURNAL OF THE ROYAL SOCIETY INTERFACE, Vol: 15, ISSN: 1742-5689
  • JOURNAL ARTICLE
    Tomazou M, Barahona M, Polizzi KM, Stan G-Bet al., 2018,

    Computational Re-design of Synthetic Genetic Oscillators for Independent Amplitude and Frequency Modulation

    , CELL SYSTEMS, Vol: 6, Pages: 508-+, ISSN: 2405-4712
  • JOURNAL ARTICLE
    de Lorenzo V, Prather KL, Chen G-Q, O'Day E, von Kameke C, Oyarzún DA, Hosta-Rigau L, Alsafar H, Cao C, Ji W, Okano H, Roberts RJ, Ronaghi M, Yeung K, Zhang F, Lee SYet al., 2018,

    The power of synthetic biology for bioproduction, remediation and pollution control

    , EMBO Reports, Vol: 19, ISSN: 1469-221X
  • JOURNAL ARTICLE
    Aryaman J, Hoitzing H, Burgstaller JP, Johnston IG, Jones NSet al., 2017,

    Mitochondrial heterogeneity, metabolic scaling and cell death

    , BIOESSAYS, Vol: 39, ISSN: 0265-9247

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