| 1. |
- Birney, Ewan, et al.
(författare)
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
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Tidskriftsartikel (refereegranskat)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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| 2. |
- Jones, Benedict C, et al.
(författare)
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To which world regions does the valence-dominance model of social perception apply?
- 2021
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Ingår i: Nature Human Behaviour. - : Springer Science and Business Media LLC. - 2397-3374. ; 5:1, s. 159-169
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Tidskriftsartikel (refereegranskat)abstract
- Over the past 10 years, Oosterhof and Todorov's valence-dominance model has emerged as the most prominent account of how people evaluate faces on social dimensions. In this model, two dimensions (valence and dominance) underpin social judgements of faces. Because this model has primarily been developed and tested in Western regions, it is unclear whether these findings apply to other regions. We addressed this question by replicating Oosterhof and Todorov's methodology across 11 world regions, 41 countries and 11,570 participants. When we used Oosterhof and Todorov's original analysis strategy, the valence-dominance model generalized across regions. When we used an alternative methodology to allow for correlated dimensions, we observed much less generalization. Collectively, these results suggest that, while the valence-dominance model generalizes very well across regions when dimensions are forced to be orthogonal, regional differences are revealed when we use different extraction methods and correlate and rotate the dimension reduction solution. PROTOCOL REGISTRATION: The stage 1 protocol for this Registered Report was accepted in principle on 5 November 2018. The protocol, as accepted by the journal, can be found at https://doi.org/10.6084/m9.figshare.7611443.v1 .
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| 3. |
- Gaulton, Kyle J, et al.
(författare)
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Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci.
- 2015
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 47:12, s. 1415-1415
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Tidskriftsartikel (refereegranskat)abstract
- We performed fine mapping of 39 established type 2 diabetes (T2D) loci in 27,206 cases and 57,574 controls of European ancestry. We identified 49 distinct association signals at these loci, including five mapping in or near KCNQ1. 'Credible sets' of the variants most likely to drive each distinct signal mapped predominantly to noncoding sequence, implying that association with T2D is mediated through gene regulation. Credible set variants were enriched for overlap with FOXA2 chromatin immunoprecipitation binding sites in human islet and liver cells, including at MTNR1B, where fine mapping implicated rs10830963 as driving T2D association. We confirmed that the T2D risk allele for this SNP increases FOXA2-bound enhancer activity in islet- and liver-derived cells. We observed allele-specific differences in NEUROD1 binding in islet-derived cells, consistent with evidence that the T2D risk allele increases islet MTNR1B expression. Our study demonstrates how integration of genetic and genomic information can define molecular mechanisms through which variants underlying association signals exert their effects on disease.
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| 4. |
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| 5. |
- Almquist, Martin, et al.
(författare)
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Elastic wave propagation in anisotropic solids using energy-stable finite differences with weakly enforced boundary and interface conditions
- 2021
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Ingår i: Journal of Computational Physics. - : Elsevier. - 0021-9991 .- 1090-2716. ; 424
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Tidskriftsartikel (refereegranskat)abstract
- Summation-by-parts (SBP) finite difference methods have several desirable properties for second-order wave equations. They combine the computational efficiency of narrow-stencil finite difference operators with provable stability on curvilinear multiblock grids. While several techniques for boundary and interface conditions exist, weak imposition via simultaneous approximation terms (SATs) is perhaps the most flexible one. Although SBP methods have been applied to elastic wave equations many times, an SBP-SAT method for general anisotropic elastic wave equations has not yet been presented in the literature. We fill this gap by deriving energy-stable self-adjoint SBP-SAT methods for general anisotropic materials on curvilinear multiblock grids. The methods are based on fully compatible SBP operators. Although this paper focuses on classical SBP finite difference operators, the presented boundary and interface treatments are general and apply to a range of methods that satisfy an SBP property. We demonstrate the stability and accuracy properties of a particular set of fully compatible SBP-SAT schemes using the method of manufactured solutions. We also demonstrate the utility of the new method in elastodynamic cloaking and seismic imaging in mountainous regions.
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| 6. |
- Almquist, Martin, et al.
(författare)
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Non-stiff boundary and interface penalties for narrow-stencil finite difference approximations of the Laplacian on curvilinear multiblock grids
- 2020
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Ingår i: Journal of Computational Physics. - : Elsevier BV. - 0021-9991 .- 1090-2716. ; 408
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Tidskriftsartikel (refereegranskat)abstract
- The Laplacian appears in several partial differential equations used to model wave propagation. Summation-by-parts simultaneous approximation term (SBP-SAT) finite difference methods are often used for such equations, as they combine computational efficiency with provable stability on curvilinear multiblock grids. However, the existing SBP-SAT discretization of the Laplacian quickly becomes prohibitively stiff as grid skewness increases. The stiffness stems from the SATs that impose inter-block couplings and Dirichlet boundary conditions. We resolve this issue by deriving stable SATs whose stiffness is almost insensitive to grid skewness. The new discretization thus allows for large time steps in explicit time integrators, even on very skewed grids. It also applies to the variable-coefficient generalization of the Laplacian. We demonstrate the efficacy and versatility of the new SATs by applying them to acoustic wave propagation problems inspired by marine seismic exploration and infrasound monitoring of volcanoes.
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| 7. |
- Bader, Milad, et al.
(författare)
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Modeling and inversion in acoustic-elastic coupled media using energy-stable summation-by-parts operators
- 2023
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Ingår i: Geophysics. - : SOC EXPLORATION GEOPHYSICISTS - SEG. - 0016-8033 .- 1942-2156. ; 88:3
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Tidskriftsartikel (refereegranskat)abstract
- Seismic data acquired at the seafloor are valuable in charac-terizing the subsurface and monitoring producing hydrocarbon fields. To fully use such data, a stable, accurate, and efficient numerical scheme is needed that accounts for acoustic and elas-tic wave propagation, their interaction at the seafloor interface, and for sources and receivers placed on either side of that inter-face. Existing methods either make incorrect assumptions or have high implementation and computational costs. We have developed a high-order finite-difference summation-by-parts framework for the acoustic-elastic wave equations in second -or-der form (in terms of displacements in the solid and an extension of velocity potential in the fluid). Our modified discretization of the elastic operator overcomes the dispersion errors known to plague displacement-based schemes in the high VP/VS limit. We weakly impose boundary and interface conditions using simulta-neous approximation terms, leading to an energy-stable numeri-cal scheme that rigorously handles point injection and extraction. The fully discrete system is self-adjoint after a time reversal and a sign flip and is furthermore a high-order accurate discretization of the continuous problem. The self-adjointness ensures that for-ward and adjoint wavefields are computed with similar accuracy and simplifies gradient computation for inversion purposes. We find that our numerical scheme achieves accuracy comparable to a more computationally expensive spectral-element method and demonstrate its application to full-waveform inversion using the Marmousi2 model.
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| 8. |
- Coppess, Katherine R., et al.
(författare)
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Ultra and Very Long Period Seismic Signatures of Unsteady Eruptions Predicted From Conduit Flow Models
- 2022
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Ingår i: Journal of Geophysical Research - Solid Earth. - : American Geophysical Union (AGU). - 2169-9313 .- 2169-9356. ; 127:6
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Tidskriftsartikel (refereegranskat)abstract
- Explosive volcanic eruptions radiate seismic waves as a consequence of pressure and shear traction changes within the conduit/chamber system. Kinematic source inversions utilize these waves to determine equivalent seismic force and moment tensor sources, but relation to eruptive processes is often ambiguous and nonunique. In this work, we provide an alternative, forward modeling approach to calculate moment tensor and force equivalents of a model of eruptive conduit flow and chamber depressurization. We explain the equivalence of two seismic force descriptions, the first in terms of traction changes on conduit/chamber walls, and the second in terms of changes in magma momentum, weight, and momentum transfer to the atmosphere. Eruption onset is marked by a downward seismic force, associated with loss of restraining shear tractions from fragmentation. This is followed by a much larger upward seismic force from upward drag of ascending magma and reduction of magma weight remaining in the conduit/chamber system. The static force is upward, arising from weight reduction. We calculate synthetic seismograms to examine the expression of eruptive processes at different receiver distances. Filtering these synthetics to the frequency band typically resolved by broadband seismometers produces waveforms similar to very long period seismic events observed in strombolian and vulcanian eruptions. However, filtering heavily distorts waveforms, accentuating processes in early, unsteady parts of eruptions and eliminating information about longer (ultra long period time scale depressurization and weight changes that dominate unfiltered seismograms. Our workflow can be utilized to directly and quantitatively connect eruption models with seismic observations.Plain Language SummaryVolcanic eruptions radiate seismic waves that can be recorded by seismometers placed on and around a volcano. Analysis of seismic data enables one to study eruptions, in particular the processes occurring in the magma-filled conduit and chamber that feeds the eruption. One process of particular interest is fragmentation, in which magma containing a mixture of liquid melt and gas bubbles breaks apart in the conduit and erupts explosively from the vent. We perform computer simulations of explosive eruptions and then use the output of those simulations to predict seismic radiation. We examine the seismograms produced by this workflow to identify features that are diagnostic of process, such as fragmentation, that occur at different times in the eruption. These predictions will guide interpretation of seismic data from real eruptions.
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| 9. |
- Erickson, Brittany A., et al.
(författare)
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Incorporating Full Elastodynamic Effects and Dipping Fault Geometries in Community Code Verification Exercises for Simulations of Earthquake Sequences and Aseismic Slip (SEAS)
- 2023
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Ingår i: Bulletin of The Seismological Society of America (BSSA). - : SEISMOLOGICAL SOC AMER. - 0037-1106 .- 1943-3573. ; 113:2, s. 499-523
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Tidskriftsartikel (refereegranskat)abstract
- Numerical modeling of earthquake dynamics and derived insight for seismic hazard relies on credible, reproducible model results. The sequences of earthquakes and aseismic slip (SEAS) initiative has set out to facilitate community code comparisons, and verify and advance the next generation of physics-based earthquake models that reproduce all phases of the seis-mic cycle. With the goal of advancing SEAS models to robustly incorporate physical and geo-metrical complexities, here we present code comparison results from two new benchmark problems: BP1-FD considers full elastodynamic effects, and BP3-QD considers dipping fault geometries. Seven and eight modeling groups participated in BP1-FD and BP3-QD, respectively, allowing us to explore these physical ingredients across multiple codes and better understand associated numerical considerations. With new comparison metrics, we find that numerical resolution and computational domain size are critical parameters to obtain matching results. Codes for BP1-FD implement different criteria for switching between quasi-static and dynamic solvers, which require tuning to obtain matching results. In BP3-QD, proper remote boundary conditions consistent with specified rigid body translation are required to obtain matching surface displacements. With these numerical and mathematical issues resolved, we obtain excellent quantitative agreements among codes in earthquake interevent times, event moments, and coseismic slip, with reasonable agreements made in peak slip rates and rupture arrival time. We find that including full inertial effects generates events with larger slip rates and rupture speeds compared to the quasi-dynamic counterpart. For BP3-QD, both dip angle and sense of motion (thrust versus normal faulting) alter ground motion on the hanging and foot walls, and influence event patterns, with some sequences exhibiting similar-size character-istic earthquakes, and others exhibiting different-size events. These findings underscore the importance of considering full elastodynamics and nonvertical dip angles in SEAS models, as both influence short-and long-term earthquake behavior and are relevant to seismic hazard.
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| 10. |
- Heimisson, Elias R., et al.
(författare)
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Poroelastic effects destabilize mildly rate-strengthening friction to generate stable slow slip pulses
- 2019
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Ingår i: Journal of the mechanics and physics of solids. - : Elsevier BV. - 0022-5096 .- 1873-4782. ; 130, s. 262-279
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Tidskriftsartikel (refereegranskat)abstract
- Slow slip events on tectonic faults, sliding instabilities that never accelerate to inertially limited ruptures or earthquakes, are one of the most enigmatic phenomena in frictional sliding. While observations of slow slip events continue to mount, a plausible mechanism that permits instability while simultaneously limiting slip speed remains elusive. Rate-and-state friction has been successful in describing most aspects of rock friction, faulting, and earthquakes; current explanations of slow slip events appeal to rate-weakening friction to induce instabilities, which are then stalled by additional stabilizing processes like dilatancy or a transition to rate-strengthening friction at high slip rates. However, the temperatures and/or clay-rich compositions at slow slip locations are almost ubiquitously associated with rate-strengthening friction. In this study, we propose a fundamentally different instability mechanism that may reconcile this contradiction, demonstrating how slow slip events can nucleate with mildly rate-strengthening friction. We identify two destabilizing mechanisms, both reducing frictional shear strength through reductions in effective normal stress, that counteract the stabilizing effects of rate-strengthening friction. The instability develops into slow slip pulses. We quantify parameter controls on pulse length, propagation speed, and other characteristics, and demonstrate broad consistency with observations of tectonic slow slip events as well as laboratory tribology experiments.
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