| 1. |
- Nyberg, Lena, 1979, et al.
(författare)
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A single-step competitive binding assay for mapping of single DNA molecules
- 2012
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Ingår i: Biochemical and Biophysical Research Communications - BBRC. - : Elsevier BV. - 0006-291X .- 1090-2104. ; 417:1, s. 404-408
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Tidskriftsartikel (refereegranskat)abstract
- Optical mapping of genomic DNA is of relevance for a plethora of applications such as scaffolding for sequencing and detection of structural variations as well as identification cif pathogens like bacteria and viruses. For future clinical applications it is desirable to have a fast and robust mapping method based on as few steps as possible. We here demonstrate a single-step method to obtain a DNA barcode that is directly visualized using nanofluidic devices and fluorescence microscopy. Using a mixture of YOYO-1, a bright DNA dye, and netropsin, a natural antibiotic with very high AT specificity, we obtain a DNA map with a fluorescence intensity profile along the DNA that reflects the underlying sequence. The netropsin binds to AT-tetrads and blocks these binding sites from YOYO-1 binding which results in lower fluorescence intensity from AT-rich regions of the DNA. We thus obtain a DNA barcode that is dark in AT-rich regions and bright in GC-rich regions with kilobasepair resolution. We demonstrate the versatility of the method by obtaining a barcode on DNA from the phage T4 that captures its circular permutation and agrees well with its known sequence.
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| 2. |
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| 3. |
- Byström, Pär, et al.
(författare)
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Preference for cannibalism and ontogenetic constraints in competitive ability of piscivorous top predators
- 2013
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8:7, s. e70404-
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Tidskriftsartikel (refereegranskat)abstract
- We experimentally show that the piscivorous top predator Arctic char (Salvelinus alpinus) have higher attack rates on cannibal prey compared to the interspecific prey species ninespine stickleback (Pungitius pungitius), and that sticklebacks are more efficient competitiors for zooplankton resources compared to juvenile char. We also conducted a literature survey that together with our experiments showed that piscivorous top consumers selected cannibal prey over interspecific prey in 9 out of 10 cases. Our literature survey also showed that specialist prey species are competitively superior compared to juvenile piscivorous species within the zooplankton niche. We discuss our results in relation to omnivory in fish communities and we suggest that the observed general preference for cannibal prey over interspecific prey in piscivores and the competitive advantage of prey species over juvenile piscivores may be major mechanisms for coexistence in fish communities.
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| 4. |
- Flodén, Liselott, 1967-, et al.
(författare)
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A myriad shades of green
- 2009
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Ingår i: Proceedings of Bridges 2009, Banff, Alberta, Canada.
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Konferensbidrag (refereegranskat)abstract
- We discuss the possible application of techniques inspired by the theories of G-convergence and homogenization to understand mixtures of colors and how they appear as observed by the human eye. The ideas are illustrated by pictures describing the equivalent of a convergence process for different kinds of mixtures of colors.
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| 5. |
- Flodén, Liselott, 1967-, et al.
(författare)
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Detection of scales of heterogeneity and parabolic homogenization applying very weak multiscale convergence
- 2011
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Ingår i: Annals of Functional Analysis. - Mashdad, Iran : TSMG. - 2008-8752. ; 2:1, s. 84-99
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Tidskriftsartikel (refereegranskat)abstract
- We apply a new version of multiscale convergence named very weak multiscale convergence to find possible frequencies of oscillation in an unknown coefficient of a diffeential equation from its solution. We also use thís notion to study homogenization of a certain linear parabolic problem with multiple spatial and temporal scales
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| 6. |
- Flodén, Liselott, et al.
(författare)
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Homogenization of a Hyperbolic-Parabolic Problem with Three Spatial Scales
- 2017
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Ingår i: Progress in Industrial Mathematics at ECMI 2016. - Cham : Springer. - 9783319630816 ; , s. 617-623
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Konferensbidrag (refereegranskat)abstract
- We study the homogenization of a certain linear hyperbolic-parabolic problem exhibiting two rapid spatial scales {ε; ε2}. The homogenization is performed by means of evolution multiscale convergence, a generalization of the concept of two-scale convergence to include any number of scales in both space and time. In particular we apply a compactness result for gradients. The outcome of the homogenization procedure is that we obtain a homogenized problem of hyperbolic-parabolic type together with two elliptic local problems, one for each rapid scale, for the correctors.
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| 7. |
- Flodén, Liselott, 1967-, et al.
(författare)
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Homogenization of parabolic equations with an arbitrary number of scales in both space and time
- 2014
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Ingår i: Journal of Applied Mathematics. - Boston : Hindawi Publishing Corporation. - 1110-757X .- 1687-0042. ; , s. Art. no. 101685-
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Tidskriftsartikel (refereegranskat)abstract
- The main contribution of this paper is the homogenization of the linearparabolic equationtu (x, t) − ·axq1, ...,xqn,tr1, ...,trmu (x, t)= f(x, t)exhibiting an arbitrary finite number of both spatial and temporal scales.We briefly recall some fundamentals of multiscale convergence and providea characterization of multiscale limits for gradients in an evolution settingadapted to a quite general class of well-separated scales, which we nameby jointly well-separated scales (see Appendix for the proof). We proceedwith a weaker version of this concept called very weak multiscale convergence.We prove a compactness result with respect to this latter typefor jointly well-separated scales. This is a key result for performing thehomogenization of parabolic problems combining rapid spatial and temporaloscillations such as the problem above. Applying this compactnessresult together with a characterization of multiscale limits of sequences ofgradients we carry out the homogenization procedure, where we togetherwith the homogenized problem obtain n local problems, i.e. one for eachspatial microscale. To illustrate the use of the obtained result we apply itto a case with three spatial and three temporal scales with q1 = 1, q2 = 2and 0 < r1 < r2.MSC: 35B27; 35K10
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| 8. |
- Flodén, Liselott, 1967-, et al.
(författare)
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On the determination of effective properties of certain structures with non-periodic temporal oscillations
- 2009
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Ingår i: MATHMOD 2009 - 6th Vienna International Conference on Mathematical Modelling. - Wien : Vienna University Press (WUV). - 9783901608353 ; , s. 2627-2630
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Konferensbidrag (refereegranskat)abstract
- We investigate the homogenization of an evolution problem modelled by a parabolic equation, where the coefficient describing the structure is periodic in space but may vary in time in a non-periodic way. This is performed applying a generalization of two-scale convergence called λ-scale convergence. We give a result on the characterization of the λ-scale limit of gradients under certain boundedness assumptions. This is then applied to perform the homogenization procedure. It turns out that, under a certain condition on the rate of change of the temporal variations, the effective property of the given structure can be determined the same way as in periodic cases.
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| 9. |
- Flodén, Liselott, 1967-, et al.
(författare)
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Two-scale convergence: Some remarks and extensions
- 2013
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Ingår i: Pure and Applied Mathematics Quarterly. - : International press of Boston. - 1558-8599 .- 1558-8602. ; 9:3, s. 461-486
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Tidskriftsartikel (refereegranskat)abstract
- We first study the fundamental ideas behind two-scale conver-gence to enhance an intuitive understanding of this notion. The classicaldefinitions and ideas are motivated with geometrical arguments illustratedby illuminating figures. Then a version of this concept, very weak two-scaleconvergence, is discussed both independently and brie°y in the context ofhomogenization. The main features of this variant are that it works alsofor certain sequences of functions which are not bounded inL2 and atthe same time is suited to detect rapid oscillations in some sequences whichare strongly convergent inL2 . In particular, we show how very weaktwo-scale convergence explains in a more transparent way how the oscilla-tions of the governing coe±cient of the PDE to be homogenized causes thedeviation of theG-limit from the weak L2 NxN-limit for the sequence ofcoe±cients. Finally, we investigate very weak multiscale convergence andprove a compactness result for separated scales which extends a previousresult which required well-separated scales.
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| 10. |
- Forssén, Jens, 1968, et al.
(författare)
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Wind Turbine Noise Propagation over Flat Ground: Measurements and Predictions
- 2010
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Ingår i: Acta Acustica united with Acustica. - Stuttgart : S. Hirzel Verlag. - 1610-1928 .- 1861-9959. ; 96:4, s. 753-760(8)
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Tidskriftsartikel (refereegranskat)abstract
- Noise from wind turbines is of concern in the planning process of new wind farms, and accurate estimations of immission noise levels at residents nearby are required. Sound propagation from wind turbine to receiver could be modelled by a simplified standard model assuming constant meteorological conditions, by an engineering method taking atmospheric and ground propagation conditions into account, or by a more exact model. Epidemiological studies have found a higher frequency of annoyance due to wind turbine noise than to other community noise sources at equal noise levels, indicating that the often used simplified model is not sufficient. This paper evaluates the variation of immission sound levels under the influence of meteorological variation and explores if the prediction of levels could be improved by taking the effect of wind speed on sound propagation into account. Long-term sound recordings and measurements at a distance of 530 m from a wind turbine show that the simplified standard model predicts the average sound pressure levels satisfactorily under downwind conditions, and that a more complex propagation model might not be needed for wind turbine noise at a relatively short distance. Large variations of sound immission levels at the same wind speed were however present. Statistical analysis revealed that these variations were influenced by meteorological parameters, such as temperature, static pressure and deviation from ideal downwind direction. The overall results indicate that meteorological factors influence the noise generated by the wind turbine rather than the sound propagation.
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