| 1. |
- Jernfors, Toni, et al.
(author)
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Association between gut health and gut microbiota in a polluted environment
- 2024
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In: Science of the Total Environment. - 0048-9697 .- 1879-1026. ; 914
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Journal article (peer-reviewed)abstract
- Animals host complex bacterial communities in their gastrointestinal tracts, with which they share a mutualistic interaction. The numerous effects these interactions grant to the host include regulation of the immune system, defense against pathogen invasion, digestion of otherwise undigestible foodstuffs, and impacts on host behaviour. Exposure to stressors, such as environmental pollution, parasites, and/or predators, can alter the composition of the gut microbiome, potentially affecting host-microbiome interactions that can be manifest in the host as, for example, metabolic dysfunction or inflammation. However, whether a change in gut microbiota in wild animals associates with a change in host condition is seldom examined. Thus, we quantified whether wild bank voles inhabiting a polluted environment, areas where there are environmental radionuclides, exhibited a change in gut microbiota (using 16S amplicon sequencing) and concomitant change in host health using a combined approach of transcriptomics, histological staining analyses of colon tissue, and quantification of short-chain fatty acids in faeces and blood. Concomitant with a change in gut microbiota in animals inhabiting contaminated areas, we found evidence of poor gut health in the host, such as hypotrophy of goblet cells and likely weakened mucus layer and related changes in Clca1 and Agr2 gene expression, but no visible inflammation in colon tissue. Through this case study we show that inhabiting a polluted environment can have wide reaching effects on the gut health of affected animals, and that gut health and other host health parameters should be examined together with gut microbiota in ecotoxicological studies.
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| 2. |
- Ronkainen, Justiina, et al.
(author)
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LongITools: Dynamic longitudinal exposome trajectories in cardiovascular and metabolic noncommunicable diseases
- 2022
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In: Environmental Epidemiology. - 2474-7882. ; 6:1
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Journal article (peer-reviewed)abstract
- The current epidemics of cardiovascular and metabolic noncommunicable diseases have emerged alongside dramatic modifications in lifestyle and living environments. These correspond to changes in our "modern" postwar societies globally characterized by rural-to-urban migration, modernization of agricultural practices, and transportation, climate change, and aging. Evidence suggests that these changes are related to each other, although the social and biological mechanisms as well as their interactions have yet to be uncovered. LongITools, as one of the 9 projects included in the European Human Exposome Network, will tackle this environmental health equation linking multidimensional environmental exposures to the occurrence of cardiovascular and metabolic noncommunicable diseases.
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| 3. |
- Anton, Rikard, et al.
(author)
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A fully discrete approximation of the one-dimensional stochastic heat equation
- 2020
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In: IMA Journal of Numerical Analysis. - : Oxford University Press. - 0272-4979 .- 1464-3642. ; 40:1, s. 247-284
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Journal article (peer-reviewed)abstract
- A fully discrete approximation of the one-dimensional stochastic heat equation driven by multiplicative space–time white noise is presented. The standard finite difference approximation is used in space and a stochastic exponential method is used for the temporal approximation. Observe that the proposed exponential scheme does not suffer from any kind of CFL-type step size restriction. When the drift term and the diffusion coefficient are assumed to be globally Lipschitz this explicit time integrator allows for error bounds in Lq(Ω), for all q ≥ 2, improving some existing results in the literature. On top of this we also prove almost sure convergence of the numerical scheme. In the case of nonglobally Lipschitz coefficients, under a strong assumption about pathwise uniqueness of the exact solution, convergence in probability of the numerical solution to the exact solution is proved. Numerical experiments are presented to illustrate the theoretical results.
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| 4. |
- Anton, Rikard, 1989-
(author)
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Convergence of an exponential method for the stochastic Schrödinger equation with power-law nonlinearity
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Other publication (other academic/artistic)abstract
- A temporal approximation of the stochastic Schrödinger equation with a power-law nonlinearity and driven by multiplicative Ito noise is considered. Observe that the nonlinearity is not globally Lipschitz continuous and, in general, the exact solution cannot be assumed to remain bounded for all times. The first of these issues is handled by considering a truncated version of the equation. The second issue is handled by working with stopping times and random time intervals, on which the solution is almost surely bounded. For the time integration we use a stochastic exponential method. This exponential method has the advantage of being explicit and it does not suffer any CFL-type step size restrictions in general. In this work we prove almost sure convergence and convergence in probability, accompanied by convergence orders of 1/2- and 1/2, respectively. We also find that the regularity assumptions required on the noise and initial value are less restrictive for the convergence of the exponential scheme, compared to the Crank-Nicolson scheme. In addition, we provide numerical experiments that illustrate our theoretical results.
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| 5. |
- Anton, Rikard, 1989-
(author)
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Exponential integrators for stochastic partial differential equations
- 2018
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Doctoral thesis (other academic/artistic)abstract
- Stochastic partial differential equations (SPDEs) have during the past decades become an important tool for modeling systems which are influenced by randomness. Because of the complex nature of SPDEs, knowledge of efficient numerical methods with good convergence and geometric properties is of considerable importance. Due to this, numerical analysis of SPDEs has become an important and active research field.The thesis consists of four papers, all dealing with time integration of different SPDEs using exponential integrators. We analyse exponential integrators for the stochastic wave equation, the stochastic heat equation, and the stochastic Schrödinger equation. Our primary focus is to study strong order of convergence of temporal approximations. However, occasionally, we also analyse space approximations such as finite element and finite difference approximations. In addition to this, for some SPDEs, we consider conservation properties of numerical discretizations.As seen in this thesis, exponential integrators for SPDEs have many benefits over more traditional integrators such as Euler-Maruyama schemes or the Crank-Nicolson-Maruyama scheme. They are explicit and therefore very easy to implement and use in practice. Also, they are excellent at handling stiff problems, which naturally arise from spatial discretizations of SPDEs. While many explicit integrators suffer step size restrictions due to stability issues, exponential integrators do not in general.In Paper 1 we consider a full discretization of the stochastic wave equation driven by multiplicative noise. We use a finite element method for the spatial discretization, and for the temporal discretization we use a stochastic trigonometric method. In the first part of the paper, we prove mean-square convergence of the full approximation. In the second part, we study the behavior of the total energy, or Hamiltonian, of the wave equation. It is well known that for deterministic (Hamiltonian) wave equations, the total energy remains constant in time. We prove that for stochastic wave equations with additive noise, the expected energy of the exact solution grows linearly with time. We also prove that the numerical approximation produces a small error in this linear drift.In the second paper, we study an exponential integrator applied to the time discretization of the stochastic Schrödinger equation with a multiplicative potential. We prove strong convergence order 1 and 1/2 for additive and multiplicative noise, respectively. The deterministic linear Schrödinger equation has several conserved quantities, including the energy, the mass, and the momentum. We first show that for Schrödinger equations driven by additive noise, the expected values of these quantities grow linearly with time. The exponential integrator is shown to preserve these linear drifts for all time in the case of a stochastic Schrödinger equation without potential. For the equation with a multiplicative potential, we obtain a small error in these linear drifts.The third paper is devoted to studying a full approximation of the one-dimensional stochastic heat equation. For the spatial discretization we use a finite difference method and an exponential integrator is used for the temporal approximation. We prove mean-square convergence and almost sure convergence of the approximation when the coefficients of the problem are assumed to be Lipschitz continuous. For non-Lipschitz coefficients, we prove convergence in probability.In Paper 4 we revisit the stochastic Schrödinger equation. We consider this SPDE with a power-law nonlinearity. This nonlinearity is not globally Lipschitz continuous and the exact solution is not assumed to remain bounded for all times. These difficulties are handled by considering a truncated version of the equation and by working with stopping times and random time intervals. We prove almost sure convergence and convergence in probability for the exponential integrator as well as convergence orders of ½ − ?, for all ? > 0, and 1/2, respectively.
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| 6. |
- Anton, Rikard, et al.
(author)
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Exponential integrators for stochastic Schrödinger equations driven by Itô noise
- 2018
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In: Journal of Computational Mathematics. - : Global Science Press. - 0254-9409 .- 1991-7139. ; 36:2, s. 276-309
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Journal article (peer-reviewed)abstract
- We study an explicit exponential scheme for the time discretisation of stochastic Schr¨odinger Equations Driven by additive or Multiplicative Itô Noise. The numerical scheme is shown to converge with strong order 1 if the noise is additive and with strong order 1/2 for multiplicative noise. In addition, if the noise is additive, we show that the exact solutions of the linear stochastic Schr¨odinger equations satisfy trace formulas for the expected mass, energy, and momentum (i. e., linear drifts in these quantities). Furthermore, we inspect the behaviour of the numerical solutions with respect to these trace formulas. Several numerical simulations are presented and confirm our theoretical results.
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| 7. |
- Anton, Rikard, et al.
(author)
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Full discretisation of semi-linear stochastic wave equations driven by multiplicative noise
- 2015
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Other publication (other academic/artistic)abstract
- A fully discrete approximation of the semi-linear stochastic wave equation driven by multiplicative noise is presented. A standard linear finite element approximation is used in space and a stochastic trigonometric method for the temporal approximation. This explicit time integrator allows for mean-square error bounds indepen- dent of the space discretisation and thus do not suffer from a step size restriction as in the often used Störmer-Verlet- leap-frog scheme. Furthermore, it satisfies an almost trace formula (i. e., a linear drift of the expected value of the energy of the problem). Numerical experiments are presented and confirm the theoretical results.
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| 8. |
- Anton, Rikard, et al.
(author)
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Full discretization of semilinear stochastic wave equations driven by multiplicative noise
- 2016
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In: SIAM Journal on Numerical Analysis. - 0036-1429 .- 1095-7170. ; 54:2, s. 1093-1119
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Journal article (peer-reviewed)abstract
- A fully discrete approximation of the semilinear stochastic wave equation driven by multiplicative noise is presented. A standard linear finite element approximation is used in space, and a stochastic trigonometric method is used for the temporal approximation. This explicit time integrator allows for mean-square error bounds independent of the space discretization and thus does not suffer from a step size restriction as in the often used Stormer-Verlet leapfrog scheme. Furthermore, it satisfies an almost trace formula (i.e., a linear drift of the expected value of the energy of the problem). Numerical experiments are presented and confirm the theoretical results.
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| 9. |
- Bodén, Stina, et al.
(author)
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Dietary patterns, untargeted metabolite profiles and their association with colorectal cancer risk
- 2024
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In: Scientific Reports. - : Springer Nature. - 2045-2322 .- 2045-2322. ; 14:1
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Journal article (peer-reviewed)abstract
- We investigated data-driven and hypothesis-driven dietary patterns and their association to plasma metabolite profiles and subsequent colorectal cancer (CRC) risk in 680 CRC cases and individually matched controls. Dietary patterns were identified from combined exploratory/confirmatory factor analysis. We assessed association to LC–MS metabolic profiles by random forest regression and to CRC risk by multivariable conditional logistic regression. Principal component analysis was used on metabolite features selected to reflect dietary exposures. Component scores were associated to CRC risk and dietary exposures using partial Spearman correlation. We identified 12 data-driven dietary patterns, of which a breakfast food pattern showed an inverse association with CRC risk (OR per standard deviation increase 0.89, 95% CI 0.80–1.00, p = 0.04). This pattern was also inversely associated with risk of distal colon cancer (0.75, 0.61–0.96, p = 0.01) and was more pronounced in women (0.69, 0.49–0.96, p = 0.03). Associations between meat, fast-food, fruit soup/rice patterns and CRC risk were modified by tumor location in women. Alcohol as well as fruit and vegetables associated with metabolite profiles (Q2 0.22 and 0.26, respectively). One metabolite reflecting alcohol intake associated with increased CRC risk, whereas three metabolites reflecting fiber, wholegrain, and fruit and vegetables associated with decreased CRC risk.
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| 10. |
- Duchkov, Anton, et al.
(author)
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Prestack shot-gather depth migration by a `rigid' flow of Gaussian wave packets
- 2012
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In: Studia Geophysica et Geodaetica. - : Springer Science and Business Media LLC. - 0039-3169 .- 1573-1626. ; 56:1, s. 83-106
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Journal article (peer-reviewed)abstract
- Abstract in UndeterminedWe introduce a new method for prestack depth migration of seismic common-shot gathers.The computational procedure follows standard steps of the reverse-time migration, i.e.,downward continuation of the `source' and the `receiver' waveelds, followed by applicationof an imaging condition (e.g. zero-lag cross-correlation of these elds). In our method werst nd a sparse data representation with a small number of Gaussian wave packets. Wethen approximate the downward waveeld propagation (for the `source' and the `receiver'elds) by a `rigid'ow of these wave packets along seismic rays. In this case, the wavepackets are simply translated and rotated according to the ray geometry. One advantagewith using Gaussian wave packets is that analytic formulas can be used for translation, rotation, and the application of the cross-correlation imaging condition. Moreover, theyallow more sparse representations than competing methods. In combination, this yields acomputationally and memory ecient migration procedure, as only few rays have to betraced, and since it is cheap to compute the cross-correlation for the intersecting rays.
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