ALBERT

Description: Core-refracted phases such as SKS and SKKS are commonly used to probe seismic anisotropy in the upper and lowermost portions of the Earth’s mantle. Measurements of SK(K)S splitting are often interpreted in the context of ray theory, and their frequency dependent sensitivity to anisotropy remains imperfectly understood, particularly for anisotropy in the lowermost mantle. The goal of this work is to obtain constraints on the frequency dependent sensitivity of SK(K)S phases to mantle anisotropy, particularly at the base of the mantle, through global wavefield simulations. We present results from a new numerical approach to modelling the effects of seismic anisotropy of arbitrary geometry on seismic wave propagation in global 3-D earth models using the spectral element solver AxiSEM3D. While previous versions of AxiSEM3D were capable of handling radially anisotropic input models, here we take advantage of the ability of the solver to handle the full fourth-order elasticity tensor, with 21 independent coefficients. We take advantage of the computational efficiency of the method to compute wavefields at the relatively short periods (5 s) that are needed to simulate SK(K)S phases. We benchmark the code for simple, single-layer anisotropic models by measuring the splitting (via both the splitting intensity and the traditional splitting parameters ϕ and δt) of synthetic waveforms and comparing them to well-understood analytical solutions. We then carry out a series of numerical experiments for laterally homogeneous upper mantle anisotropic models with different symmetry classes, and compare the splitting of synthetic waveforms to predictions from ray theory. We next investigate the full wave sensitivity of SK(K)S phases to lowermost mantle anisotropy, using elasticity models based on crystallographic preferred orientation of bridgmanite and post-perovskite. We find that SK(K)S phases have significant sensitivity to anisotropy at the base of the mantle, and while ray theoretical approximations capture the first-order aspects of the splitting behaviour, full wavefield simulations will allow for more accurate modelling of SK(K)S splitting data, particularly in the presence of lateral heterogeneity. Lastly, we present a cross-verification test of AxiSEM3D against the SPECFEM3D_GLOBE spectral element solver for global seismic waves in an anisotropic earth model that includes both radial and azimuthal anisotropy. A nearly perfect agreement is achieved, with a significantly lower computational cost for AxiSEM3D. Our results highlight the capability of AxiSEM3D to handle arbitrary anisotropy geometries and its potential for future studies aimed at unraveling the details of anisotropy at the base of the mantle.

Description: Writing a 200-word abstract about the life of a 76-year-old scientist, in which luck played a significant role, is not an easy task. Even knowing this scientist well (for I am talking about myself) does not make it any easier. When you notice something is not right, do not fear changing your major (I changed twice before settling on Fisheries and Marine Science). For my PhD in neurobiology, I changed again. Grab opportunities when they arise. Join field trips and expeditions, attend conferences, and spread your interests widely. Spend time in different countries, learn new techniques and languages, and always stay curious. Remain humble. I carried out speleological research in Jamaica and France, participated in a 4-month South Atlantic Fisheries Research Trip and a 3-month Bioluminescence Expedition to the Moluccas, and pioneered comparative physiological and functional anatomical research in Antarctica and the Arctic. Be adventurous. My ethnobiological field work took me to Papua Niugini, NE-India, and Central Australia. Having lived in Australia, Finland, France, Germany, Jamaica, Japan, and New Zealand (I am a New Zealander currently living in Korea) and having spent sabbaticals in Brazil, India, New Caledonia, and North Korea, I consider myself a global scientist. You can become one too.

Description: SUMMARY We present a new approach to simulate high-frequency seismic wave propagation in and under the oceans. Based upon AxiSEM3D, this method supports a fluid ocean layer, with associated water-depth phases and seafloor topography (bathymetry). The computational efficiency and flexibility of this formulation means that high-frequency calculations may be carried out with relatively light computational loads. A validation of the fluid ocean implementation is shown, as is an evaluation of the oft-used ocean loading formulation, which we find breaks down at longer periods than was previously believed. An initial consideration of the effects of seafloor bathymetry on seismic wave propagation is also given, wherein we find that the surface waveforms are significantly modified in both amplitude and duration. When compared to observed data from isolated island stations in the Pacific, synthetics which include a global ocean and seafloor topography appear to more closely match the observed waveform features than synthetics generated from a model with topography on the solid surface alone. We envisage that such a method will be of use in understanding the new and exciting ocean-bottom and floating seismometer data sets now being regularly collected.

Description: SUMMARY Small-scale heterogeneities in the Earth’s mantle, the origin of which is likely compositional anomalies, can provide critical clues on the evolution of mantle convection. Seismological investigation of such small-scale heterogeneities can be facilitated by forward modelling of elastic wave scattering at high frequencies, but doing so with conventional 3-D numerical methods has been computationally prohibitive. We develop an efficient approach for computing high-frequency synthetic wavefields originating from small-scale mantle heterogeneities. Our approach delivers the exact elastodynamic wavefield and does not restrict the geometry or physical properties of the local heterogeneity and the background medium. It combines the technique of wavefield injection and a numerical method called AxiSEM3D. Wavefield injection can decompose the total wavefield into an incident and a scattered part. Both these two parts naturally have low azimuthal complexity and can thus be solved efficiently using AxiSEM3D under two different coordinate systems. With modern high-performance computing (on an order of magnitude of 105 CPU-hr), we have achieved a 1 Hz dominant frequency for global-scale problems with strong deep Earth scattering. Compared with previous global injection approaches, ours allows for a 3-D background medium and yields the exact solution without ignoring any higher-order scattering by the background medium. Technically, we develop a traction-free scheme for realizing wavefield injection in a spectral element method, which brings in several flexibilities and simplifies the implementation by avoiding stress or traction computation on the injection boundary. For a spherical heterogeneity in the mid-lower mantle, we compare the 3-D full-wave solution with two approximate ones obtained, respectively, by the perturbation theory and in-plane (axisymmetric) modelling. As a comprehensive application, we study S-wave scattering by a 3-D ultra-low velocity zone, incorporating 3-D crustal structures on the receiver side as part of the background model.

Description: Summary We develop a new approach for computing Fréchet sensitivity kernels in full waveform inversion by using the discrete adjoint approach in addition to the widely used continuous adjoint approach for seismic waveform inversion. This method is particularly well suited for the forward solver AxiSEM3D, a combination of the spectral-element method (SEM) and a Fourier pseudo-spectral method, which allows for a sparse azimuthal wavefield parametrization adaptive to wavefield complexity, leading to lower computational costs and better frequency scaling than conventional 3-D solvers. We implement the continuous adjoint method to serve as a benchmark, additionally allowing for simulating off-axis sources in axisymmetric or 3-D models. The kernels generated by both methods are compared to each other, and benchmarked against theoretical predictions based on linearized Born theory, providing an excellent fit to this independent reference solution. Our verification benchmarks show that the discrete adjoint method can produce exact kernels, largely identical to continuous kernels. While using the continuous adjoint method we lose the computational advantage and fall back on a full-3-D frequency scaling, using the discrete adjoint retains the speedup offered by AxiSEM3D. We also discuss the creation of a data-coverage based mesh to run the simulations on during the inversion process, which would allow to exploit the flexibility of the Fourier parametrization and thus the speedup offered by our method.

Description: Wolf–Rayet stars are advanced evolutionary stages of massive stars. Despite their large mass-loss rates and high wind velocities, none of them displays a bow shock, although a fraction of them are classified as runaway. Our 2.5-D numerical simulations of circumstellar matter around a $60mbox{-} m M_{odot }$ runaway star show that the fast Wolf–Rayet stellar wind is released into a wind-blown cavity filled with various shocks and discontinuities generated throughout the preceding evolutionary phases. The resulting fast-wind–slow-wind interaction leads to the formation of spherical shells of swept-up dusty material similar to those observed in the near-infrared at $24, m mu m m$ with Spitzer, which appear to be comoving with the runaway massive stars, regardless of their proper motion and/or the properties of the local ambient medium. We interpret bright infrared rings around runaway Wolf–Rayet stars in the Galactic plane as an indication of their very high initial masses and complex evolutionary history. Stellar-wind bow shocks become faint as stars run in diluted media, therefore our results explain the absence of bow shocks detected around Galactic Wolf–Rayet stars, such as the high-latitude, very fast-moving objects WR71, WR124 and WR148. Our results show that the absence of a bow shock is consistent with the runaway nature of some Wolf–Rayet stars. This questions the in situ star formation scenario of high-latitude Wolf–Rayet stars in favour of dynamical ejection from birth sites in the Galactic plane.

Description: Ceratonova shasta is an important myxozoan pathogen affecting the health of salmonid fishes in the Pacific Northwest of North America. Ceratonova shasta exists as a complex of host-specific genotypes, some with low to moderate virulence, and one that causes a profound, lethal infection in susceptible hosts. High throughput sequencing methods are powerful tools for discovering the genetic basis of these host/virulence differences, but deep sequencing of myxozoans has been challenging due to extremely fast molecular evolution of this group, yielding strongly divergent sequences that are difficult to identify, and unavoidable host contamination. We designed and optimized different bioinformatic pipelines to address these challenges. We obtained a unique set of comprehensive, host-free myxozoan RNA-seq data from C. shasta genotypes of varying virulence from different salmonid hosts. Analyses of transcriptome-wide genetic distances and maximum likelihood multigene phylogenies elucidated the evolutionary relationship between lineages and demonstrated the limited resolution of the established Internal Transcribed Spacer marker for C. shasta genotype identification, as this marker fails to differentiate between biologically distinct genotype II lineages from coho salmon and rainbow trout. We further analyzed the data sets based on polymorphisms in two gene groups related to virulence: cell migration and proteolytic enzymes including their inhibitors. The developed single-nucleotide polymorphism-calling pipeline identified polymorphisms between genotypes and demonstrated that variations in both motility and protease genes were associated with different levels of virulence of C. shasta in its salmonid hosts. The prospective use of proteolytic enzymes as promising candidates for targeted interventions against myxozoans in aquaculture is discussed. We developed host-free transcriptomes of a myxozoan model organism from strains that exhibited different degrees of virulence, as a unique source of data that will foster functional gene analyses and serve as a base for the development of potential therapeutics for efficient control of these parasites.

Description: We use the state-of-the-art semi-analytic galaxy formation model, shark, to investigate the physical processes involved in dictating the shape, scatter, and evolution of the Hi–halo mass (HIHM) relation at 0 ≤ z ≤ 2. We compare shark with Hi clustering and spectral stacking of the HIHM relation derived from observations finding excellent agreement with the former and a deficiency of Hi in shark at Mvir ≈ 1012–13 M⊙ in the latter. In shark, we find that the Hi mass increases with the halo mass up to a critical mass of ≈1011.8 M⊙; between ≈1011 and 1013 M⊙, the scatter in the relation increases by 0.7 dex and the Hi mass decreases with the halo mass on average (till $M_{ m vir}sim 10^{12.5}, m M_{odot }$, after which it starts increasing); at $M_{ m vir}gtrsim 10^{13}, m M_{odot }$, the Hi content continues to increase with increasing halo mass, as a result of the increasing Hi contribution from satellite galaxies. We find that the critical halo mass of ≈1012 M⊙ is set by feedback from active galactic nuclei (AGNs) which affects both the shape and scatter of the HIHM relation, with other physical processes playing a less significant role. We also determine the main secondary parameters responsible for the scatter of the HIHM relation, namely the halo spin parameter at ${M}_{ m vir}, lt $ 1011.8 M⊙, and the fractional contribution from substructure to the total halo mass ($M_{ m h}^{ m sat}/M_{ m vir}$) for ${M}_{ m vir}, gt $ 1013 M⊙. The scatter at 1011.8 M⊙$lt , {M}_{ m vir}, lt $ 1013 M⊙ is best described by the black hole-to-stellar mass ratio of the central galaxy, reflecting the relevance of AGN feedback. We present a numerical model to populate dark matter-only simulations with Hi at 0 ≤ z ≤ 2 based solely on halo parameters that are measurable in such simulations.

Description: Summary Transcription and DNA supercoiling are involved in a complex, dynamical and non-linear coupling that results from the basal interaction between DNA and RNA polymerase. We present the first software to simulate this coupling, applicable to a wide range of bacterial organisms. TwisTranscripT allows quantifying its contribution in global transcriptional regulation, and provides a mechanistic basis for the widely observed, evolutionarily conserved and currently unexplained co-regulation of adjacent operons that might play an important role in genome evolution. Availability and implementation TwisTranscripT is freely available at https://github.com/sammeyer2017/TwisTranscripT. It is implemented in Python3 and supported on MacOS X, Linux and Windows.

Description: Mucopolysaccharidosis type VI (MPS-VI), caused by mutational inactivation of the glycosaminoglycan-degrading enzyme arylsulfatase B (Arsb), is a lysosomal storage disorder primarily affecting the skeleton. We have previously reported that Arsb-deficient mice display high trabecular bone mass and impaired skeletal growth. In the present study, we treated them by weekly injection of recombinant human ARSB (rhARSB) to analyze the impact of enzyme replacement therapy (ERT) on skeletal growth and bone remodeling. We found that all bone-remodeling abnormalities of Arsb-deficient mice were prevented by ERT, whereas chondrocyte defects were not. Likewise, histologic analysis of the surgically removed femoral head from an ERT-treated MPS-VI patient revealed that only chondrocytes were pathologically affected. Remarkably, a side-by-side comparison with other cell types demonstrated that chondrocytes have substantially reduced capacity to endocytose rhARSB, together with low expression of the mannose receptor. We finally took advantage of Arsb-deficient mice to establish quantification of chondroitin sulfation for treatment monitoring. Our data demonstrate that bone-remodeling cell types are accessible to systemically delivered rhARSB, whereas the uptake into chondrocytes is inefficient.