Recent Submissions

  • HyperTraPS: Inferring probabilistic patterns of trait acquisition in evolutionary and disease progression pathways 

    Greenbury, Sam; Barahona, Mauricio; Johnston, Iain (Cell Press, 2020)
    The explosion of data throughout the biomedical sciences provides unprecedented opportunities to learn about the dynamics of evolution and disease progression, but harnessing these large and diverse datasets remains ...
    Journal article
  • Consistent MPFA Discretization for Flow in the Presence of Gravity 

    Starnoni, Michele; Berre, Inga; Keilegavlen, Eirik; Nordbotten, Jan Martin (AGU, 2019)
    A standard practice used in the industry to discretizing the gravity term in the two‐phase Darcy flow equations is to apply an upwind strategy. In this paper, we show that this can give a persistent unphysical flux field ...
    Journal article
  • Iterative Linearisation Schemes for Doubly Degenerate Parabolic Equations 

    Both, Jakub; Kumar, Kundan; Nordbotten, Jan Martin; Pop, Iuliu Sorin; Radu, Florin Adrian (Springer, 2019)
    Mathematical models for flow and reactive transport in porous media often involve non-linear, degenerate parabolic equations. Their solutions have low regularity, and therefore lower order schemes are used for the numerical ...
    Conference object
  • Mitochondrial network state scales mtDNA genetic dynamics 

    Aryaman, Juvid; Bowles, Charlotte; Jones, Nick; Johnston, Iain George (Genetics Society of America, 2019)
    Mitochondrial DNA (mtDNA) mutations cause severe congenital diseases but may also be associated with healthy aging. mtDNA is stochastically replicated and degraded, and exists within organelles which undergo dynamic fusion ...
    Journal article
  • Model selection and parameter estimation for root architecture models using likelihood-free inference 

    Ziegler, Clare; Dyson, Rosemary; Johnston, Iain George (The Royal Society Publishing, 2019)
    Plant root systems play vital roles in the biosphere, environment and agriculture, but the quantitative principles governing their growth and architecture remain poorly understood. The ‘forward problem’ of what root forms ...
    Journal article
  • Impact of temporomandibular joint complaints on tinnitus-related distress 

    Edvall, Niklas K; Gunan, Edis; Genitsaridi, Eleni; Lazar, Andra; Mehraei, Golbarg; Billing, Mattias; Tullberg, Marie; Bulla, Jan; Whitton, Jonathon; Canlon, Barbara; Hall, Deborah A; Cederroth, Christopher R (Frontiers, 2019-08-22)
    There is increasing evidence of associations between the presence of temporomandibular joint (TMJ) disorders and tinnitus. It has been recently proposed that tinnitus patients with TMJ complaints could constitute a subtype, ...
    Journal article
  • Precision identification of high-risk phenotypes and progression pathways in severe malaria without requiring longitudinal data 

    Johnston, Iain George; Hoffmann, Till; Greenbury, Sam; Cominetti, Ornella; Jallow, Muminatou; Kwiatkowski, Dominic; Barahona, Mauricio; Jones, Nick; Casals-Pascual, Climent (Nature, 2019)
    More than 400,000 deaths from severe malaria (SM) are reported every year, mainly in African children. The diversity of clinical presentations associated with SM indicates important differences in disease pathogenesis that ...
    Journal article
  • Reactivation of fractures in subsurface reservoirs - A numerical approach using a static-dynamic friction model 

    Berge, Runar Lie; Berre, Inga; Keilegavlen, Eirik (Springer, 2019)
    Fluid-induced slip of fractures is characterized by strong multiphysics couplings. Three physical processes are considered: Flow, rock deformation and fracture deformation. The fractures are represented as lower-dimensional ...
  • Energetic costs of cellular and therapeutic control of stochastic mitochondrial DNA populations 

    Hoitzing, Hanne; Gammage, Payam; van Haute, Lindsey; Minczuk, Michal; Johnston, Iain; Jones, Nick (PLoS, 2019-06-26)
    The dynamics of the cellular proportion of mutant mtDNA molecules is crucial for mitochondrial diseases. Cellular populations of mitochondria are under homeostatic control, but the details of the control mechanisms involved ...
    Journal article
  • Does diabetes influence the probability of experiencing chronic low back pain? A population-based cohort study: the Nord-Trøndelag Health Study 

    Heuch, Ingrid; Heuch, Ivar; Hagen, Knut; Sørgjerd, Elin Pettersen; Åsvold, Bjørn Olav; Zwart, John-Anker (BMJ, 2019)
    Objective: Low back pain (LBP) is a major problem in modern society and it is important to study possible risk factors for this disorder. People with diabetes are often affected by LBP, but whether diabetes represents a ...
    Journal article
  • Implementation of mixed-dimensional models for flow in fractured porous media 

    Keilegavlen, Eirik; Fumagalli, Alessio; Berge, Runar Lie; Stefansson, Ivar (Springer, 2019)
    Models that involve coupled dynamics in a mixed-dimensional geometry are of increasing interest in several applications. Here, we describe the development of a simulation model for flow in fractured porous media, where the ...
    Journal article
  • Evolving mtDNA populations within cells 

    Johnston, Iain George; Burgstaller, Joerg (Portland Press, 2019)
    Mitochondrial DNA (mtDNA) encodes vital respiratory machinery. Populations of mtDNA molecules exist in most eukaryotic cells, subject to replication, degradation, mutation, and other population processes. These processes ...
    Journal article
  • Dual virtual element methods for discrete fracture matrix models 

    Fumagalli, Alessio; Keilegavlen, Eirik (EDP Open, 2019)
    The accurate description of fluid flow and transport in fractured porous media is of paramount importance to capture the macroscopic behavior of an oil reservoir, a geothermal system, or a CO2 sequestration site, to name ...
    Journal article
  • Conforming, non-conforming and non-matching discretization couplings in discrete fracture network simulations 

    Fumagalli, Alessio; Keilegavlen, Eirik; Scialo, Stefano (Elsevier, 2019)
    Simulations of fluid flow in naturally fractured rocks have implications for several subsurface applications, including energy storage and extraction, and waste disposal. We are interested in flow in discrete fracture ...
    Journal article
  • Sparse Dowker nerves 

    Brun, Morten; Blaser, Nello (Springer, 2019-06-29)
    We propose sparse versions of filtered simplicial complexes used to compute persistent homology of point clouds and of networks. In particular, we extend the Sparse Čech Complex of Cavanna et al. (A geometric perspective ...
    Journal article
  • Higher order space-time elements for a non-linear Biot model 

    Borregales Reveron, Manuel Antonio; Radu, Florin Adrian (Springer, 2019)
    In this work, we consider a non-linear extension of the linear, quasi-static Biot’s model. Precisely, we assume that the volumetric strain and the fluid compressibility are non-linear functions. We propose a fully discrete ...
    Conference object
  • An Upscaled Model for Permeable Biofilm in a Thin Channel and Tube 

    Marban, David Landa; Bødtker, Gunhild; Kumar, Kundan; Pop, Iuliu Sorin; Radu, Adrian Florin (Springer, 2020-01-21)
    In this paper, we derive upscaled equations for modeling biofilm growth in porous media. The resulting macroscale mathematical models consider permeable multi-species biofilm including water flow, transport, detachment and ...
    Journal article
  • Sur la distance à l'instabilité de polynômes matriciels quadratiques / On the distance to instability of quadratic matrix polynomials 

    Malyshev, Alexander; Sadkane, Miloud (Elsevier, 2019-06-27)
    A bisection method is developed for computing the distance to instability of quadratic matrix polynomials. The computation takes rounding errors into account.
    Journal article
  • Mathematics and Medicine: How mathematics, modelling and simulations can lead to better diagnosis and treatments 

    Hanson, Erik Andreas; Hodneland, Erlend; Lorentzen, Rolf Johan; Nævdal, Geir; Nordbotten, Jan Martin; Sævareid, Ove; Zanna, Antonella (Springer, 2019)
    Starting with the discovery of X-rays by Röntgen in 1895, the progress in medical imaging has been extraordinary and immensely beneficial to diagnosis and therapy. Parallel to the increase of imaging accuracy, there is the ...
  • The genetic vulnerability to cisplatin ototoxicity: a systematic review 

    Tserga, Evangelia; Nandwani, Tara; Edvall, Niklas K; Bulla, Jan; Patel, Poulam; Canlon, Barbara; Cederroth, Christopher R; Baguley, David M (Springer, 2019-03-05)
    Ototoxicity is one of the major side-effects of platinum-based chemotherapy, in particular cisplatin (cis-diammine dichloroplatinum II). To our knowledge, no systematic review has previously provided a quantitative summary ...
    Journal article

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