| 1. |
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- 2017
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Ingår i: Physical Review D. - 2470-0010 .- 2470-0029. ; 96:2
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Tidskriftsartikel (refereegranskat)
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| 2. |
- Adrian-Martinez, S., et al.
(författare)
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A first search for coincident gravitational waves and high energy neutrinos using LIGO, Virgo and ANTARES data from 2007
- 2013
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Ingår i: Journal of Cosmology and Astroparticle Physics. - : IOP Publishing. - 1475-7516. ; :6
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Tidskriftsartikel (refereegranskat)abstract
- We present the results of the first search for gravitational wave bursts associated with high energy neutrinos. Together, these messengers could reveal new, hidden sources that are not observed by conventional photon astronomy, particularly at high energy. Our search uses neutrinos detected by the underwater neutrino telescope ANTARES in its 5 line configuration during the period January - September 2007, which coincided with the fifth and first science runs of LIGO and Virgo, respectively. The LIGO-Virgo data were analysed for candidate gravitational-wave signals coincident in time and direction with the neutrino events. No significant coincident events were observed. We place limits on the density of joint high energy neutrino - gravitational wave emission events in the local universe, and compare them with densities of merger and core-collapse events.
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| 3. |
- Pattaro, Cristian, et al.
(författare)
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Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function
- 2016
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Reduced glomerular filtration rate defines chronic kidney disease and is associated with cardiovascular and all-cause mortality. We conducted a meta-analysis of genome-wide association studies for estimated glomerular filtration rate (eGFR), combining data across 133,413 individuals with replication in up to 42,166 individuals. We identify 24 new and confirm 29 previously identified loci. Of these 53 loci, 19 associate with eGFR among individuals with diabetes. Using bioinformatics, we show that identified genes at eGFR loci are enriched for expression in kidney tissues and in pathways relevant for kidney development and transmembrane transporter activity, kidney structure, and regulation of glucose metabolism. Chromatin state mapping and DNase I hypersensitivity analyses across adult tissues demonstrate preferential mapping of associated variants to regulatory regions in kidney but not extra-renal tissues. These findings suggest that genetic determinants of eGFR are mediated largely through direct effects within the kidney and highlight important cell types and biological pathways.
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| 4. |
- Chasman, Daniel I., et al.
(författare)
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Integration of genome-wide association studies with biological knowledge identifies six novel genes related to kidney function
- 2012
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Ingår i: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 21:24, s. 5329-5343
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Tidskriftsartikel (refereegranskat)abstract
- In conducting genome-wide association studies (GWAS), analytical approaches leveraging biological information may further understanding of the pathophysiology of clinical traits. To discover novel associations with estimated glomerular filtration rate (eGFR), a measure of kidney function, we developed a strategy for integrating prior biological knowledge into the existing GWAS data for eGFR from the CKDGen Consortium. Our strategy focuses on single nucleotide polymorphism (SNPs) in genes that are connected by functional evidence, determined by literature mining and gene ontology (GO) hierarchies, to genes near previously validated eGFR associations. It then requires association thresholds consistent with multiple testing, and finally evaluates novel candidates by independent replication. Among the samples of European ancestry, we identified a genome-wide significant SNP in FBXL20 (P 5.6 10(9)) in meta-analysis of all available data, and additional SNPs at the INHBC, LRP2, PLEKHA1, SLC3A2 and SLC7A6 genes meeting multiple-testing corrected significance for replication and overall P-values of 4.5 10(4)2.2 10(7). Neither the novel PLEKHA1 nor FBXL20 associations, both further supported by association with eGFR among African Americans and with transcript abundance, would have been implicated by eGFR candidate gene approaches. LRP2, encoding the megalin receptor, was identified through connection with the previously known eGFR gene DAB2 and extends understanding of the megalin system in kidney function. These findings highlight integration of existing genome-wide association data with independent biological knowledge to uncover novel candidate eGFR associations, including candidates lacking known connections to kidney-specific pathways. The strategy may also be applicable to other clinical phenotypes, although more testing will be needed to assess its potential for discovery in general.
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| 5. |
- Köttgen, Anna, et al.
(författare)
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New loci associated with kidney function and chronic kidney disease
- 2010
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 42:5, s. 376-384
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Tidskriftsartikel (refereegranskat)abstract
- Chronic kidney disease (CKD) is a significant public health problem, and recent genetic studies have identified common CKD susceptibility variants. The CKDGen consortium performed a meta-analysis of genome-wide association data in 67,093 individuals of European ancestry from 20 predominantly population-based studies in order to identify new susceptibility loci for reduced renal function as estimated by serum creatinine (eGFRcrea), serum cystatin c (eGFRcys) and CKD (eGFRcrea < 60 ml/min/1.73 m2; n = 5,807 individuals with CKD (cases)). Follow-up of the 23 new genome-wide–significant loci (P < 5 × 10−8) in 22,982 replication samples identified 13 new loci affecting renal function and CKD (in or near LASS2, GCKR, ALMS1, TFDP2, DAB2, SLC34A1, VEGFA, PRKAG2, PIP5K1B, ATXN2, DACH1, UBE2Q2 and SLC7A9) and 7 loci suspected to affect creatinine production and secretion (CPS1, SLC22A2, TMEM60, WDR37, SLC6A13, WDR72 and BCAS3). These results further our understanding of the biologic mechanisms of kidney function by identifying loci that potentially influence nephrogenesis, podocyte function, angiogenesis, solute transport and metabolic functions of the kidney.
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| 6. |
- Pattaro, Cristian, et al.
(författare)
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Genome-Wide Association and Functional Follow-Up Reveals New Loci for Kidney Function
- 2012
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Ingår i: PLoS Genetics. - : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 8:3, s. e1002584-
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Tidskriftsartikel (refereegranskat)abstract
- Chronic kidney disease (CKD) is an important public health problem with a genetic component. We performed genomewide association studies in up to 130,600 European ancestry participants overall, and stratified for key CKD risk factors. We uncovered 6 new loci in association with estimated glomerular filtration rate (eGFR), the primary clinical measure of CKD, in or near MPPED2, DDX1, SLC47A1, CDK12, CASP9, and INO80. Morpholino knockdown of mpped2 and casp9 in zebrafish embryos revealed podocyte and tubular abnormalities with altered dextran clearance, suggesting a role for these genes in renal function. By providing new insights into genes that regulate renal function, these results could further our understanding of the pathogenesis of CKD.
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| 7. |
- Abreu, Leandra, I, et al.
(författare)
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Resolvent modelling of near-wall coherent structures in turbulent channel flow
- 2020
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Ingår i: International Journal of Heat and Fluid Flow. - : ELSEVIER SCIENCE INC. - 0142-727X .- 1879-2278. ; 85
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Tidskriftsartikel (refereegranskat)abstract
- Turbulent channel flow was analysed using direct numerical simulations at friction Reynolds numbers Re-tau = 180 and 550. The databases were studied using spectral proper orthogonal decomposition (SPOD) to identify dominant near-wall coherent structures, most of which turn out to be streaks and streamwise vortices. Resolvent analysis was used as a theoretical approach to model such structures, as it allows the identification of the optimal forcing and most amplified flow response; the latter may be related to the observed relevant structures obtained by SPOD, especially if the gain between forcing and response is much larger than what is found for suboptimal forcings or if the non-linear forcing is white noise. Results from SPOD and resolvent analysis were compared for several combinations of frequencies and wavenumbers. For both Reynolds numbers, the best agreement between SPOD and resolvent modes was observed for the cases where the lift-up mechanism from resolvent analysis is present, which are also the cases where the optimal resolvent gain is dominant. These results confirm the outcomes in our previous studies (Abreu et al., 2019; Abreu et al., 2020), where we used a DNS database of a pipe flow for the same Reynolds numbers.
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| 8. |
- Abreu, Leandra, I, et al.
(författare)
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Spanwise-coherent hydrodynamic waves around flat plates and airfoils
- 2021
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Ingår i: Journal of Fluid Mechanics. - : Cambridge University Press (CUP). - 0022-1120 .- 1469-7645. ; 927
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Tidskriftsartikel (refereegranskat)abstract
- We investigate spanwise-coherent structures in the turbulent flow around airfoils, motivated by their connection with trailing-edge noise. We analyse well-resolved large-eddy simulations (LES) of the flow around NACA 0012 and NACA 4412 airfoils, both at a Reynolds number of 400 000 based on the chord length. Spectral proper orthogonal decomposition performed on the data reveals that the most energetic coherent structures are hydrodynamic waves, extending over the turbulent boundary layers around the airfoils with significant amplitudes near the trailing edge. Resolvent analysis was used to model such structures, using the mean field as a base flow. We then focus on evaluating the dependence of such structures on the domain size, to ensure that they are not an artefact of periodic boundary conditions in small computational boxes. To this end, we performed incompressible LES of a zero-pressure-gradient turbulent boundary layer, for three different spanwise sizes, with the momentum-thickness Reynolds number matching those near the airfoils trailing edge. The same coherent hydrodynamic waves were observed for the three domains. Such waves are accurately modelled as the most amplified flow response from resolvent analysis. The signature of such wide structures is seen in non-premultiplied spanwise wavenumber spectra, which collapse for the three computational domains. These results suggest that the spanwise-elongated structures are not domain-size dependent for the studied simulations, indicating thus the presence of very wide structures in wall-bounded turbulent flows.
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| 9. |
- Abreu, Leandra, I, et al.
(författare)
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Spectral proper orthogonal decomposition and resolvent analysis of near-wall coherent structures in turbulent pipe flows
- 2020
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Ingår i: Journal of Fluid Mechanics. - : Cambridge University Press (CUP). - 0022-1120 .- 1469-7645. ; 900
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Tidskriftsartikel (refereegranskat)abstract
- Direct numerical simulations, performed with a high-order spectral-element method, are used to study coherent structures in turbulent pipe flow at friction Reynolds numbers Re-tau = 180 and 550. The database was analysed using spectral proper orthogonal decomposition (SPOD) to identify energetically dominant coherent structures, most of which turn out to be streaks and quasi-streamwise vortices. To understand how such structures can be modelled, the linear flow responses to harmonic forcing were computed using the singular value decomposition of the resolvent operator, using the mean field as a base flow. The SPOD and resolvent analysis were calculated for several combinations of frequencies and wavenumbers, allowing the mapping out of similarities between SPOD modes and optimal responses for a wide range of relevant scales in turbulent pipe flows. In order to explore physical reasons behind the agreement between both methods, an indicator of lift-up mechanism in the resolvent analysis was introduced, activated when optimal forcing is dominated by the wall-normal and azimuthal components, and associated response corresponds to streaks of streamwise velocity. Good agreement between leading SPOD and resolvent modes is observed in a large region of parameter space. In this region, a significant gain separation is found in resolvent analysis, which may be attributed to the strong amplification associated with the lift-up mechanism, here understood as nonlinear forcing terms leading to the appearance of streamwise vortices, which in turn form high-amplitude streaks. For both Reynolds numbers, the observed concordances were generally for structures with large energy in the buffer layer. The results highlight resolvent analysis as a pertinent reduced-order model for coherent structures in wall-bounded turbulence, particularly for streamwise elongated structures corresponding to near-wall streamwise vortices and streaks.
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| 10. |
- Abreu, Leandra I., et al.
(författare)
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Wavepackets in turbulent flows around airfoils
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Motivated by the recent analysis by Sano et al. 2019, Phys. Rev. Fluids, vol. 4, p. 094602, of spanwise-coherent structures in the turbulent flow around airfoils and their connection to trailing-edge noise, we carry out a thorough characterisation of such structures in three simulation databases. We analyse two different numerical simulations of incompressible flow in turbulent regime, both at chord Reynolds number of 400,000: a large-eddy simulation for a NACA 0012 profile at zero angle of attack, and a direct numerical simulation for a NACA 4412 airfoil with an angle of attack of 5 degrees. Snapshots of the flow field were analysed using Spectral Proper Orthogonal Decomposition (SPOD), in order to extract the dominant coherent structures of the flow. Focus is given to the aforementioned spanwise-coherent fluctuations, which two-dimensional disturbances in the computational domain due to the use of periodic boundary conditions. The leading SPOD modes show that the most energetic coherent structures are wavepackets, extending over the whole turbulent boundary layers around the airfoils with significant amplitudes near the trailing-edge. Higher amplitudes are observed in the region of stronger adverse pressure gradient at the suction side of the NACA 4412 airfoil. To understand how such structures in the turbulent field can be modelled, the linear response of the flow using the singular value decomposition of the linearised resolvent operator was performed, using the mean field as a base flow and considering a locally parallel approximation. Such analysis shows that the leading SPOD modes can be associated to optimal, linearised flow responses, particularly for stations far from the trailing edge; the latter introduces a discontinuity in boundary conditions, and the locally parallel approximation becomes questionable. We then focus on evaluating the dependence of such wavepackets on the domain size, to ensure that these structures are not an artifact of the use of periodic boundary conditions in small computational boxes. To do so, we performed an incompressible LES of a zero-pressure gradient turbulent boundary layer (ZPGTBL), for three different spanwise sizes: Lz=32 δ*, Lz=64 δ* and Lz=128 δ*, where δ* is a reference displacement thickness in a region of developed turbulent flow, with Reynolds number matching the values in the airfoil simulations. The signature of such wavepackets is seen in non-premultiplied spanwise wavenumber spectra, which reaches, for the three domain sizes, a plateau for spanwise wavelengths going to infinity (or wavenumbers going to zero); this plateau is representative of the spanwise-coherent structures seen in the airfoil simulations. Similar SPOD and resolvent analyses were carried out for the zero spanwise wavenumber of the ZPGTBL, and the same coherent wavepackets were observed for the three domains, with very similar amplitudes. Such wavepackets were also accurately modelled using the optimal resolvent response. These results confirm that the spanwise-elongated structures are not domain-size dependent for the studied simulations, and are thus a feature of turbulent boundary layers.
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