ALBERT

Description: Repeatability of study setups and reproducibility of research results by underlying data are major requirements in science. Until now, abstract models for describing the structural logic of studies in environmental sciences are lacking and tools for data management are insufficient. Mandatory for repeatability and reproducibility is the use of sophisticated data management solutions going beyond data file sharing. Particularly, it implies maintenance of coherent data along workflows. Design data concern elements from elementary domains of operations being transformation, measurement and transaction. Operation design elements and method information are specified for each consecutive workflow segment from field to laboratory campaigns. The strict linkage of operation design element values, operation values and objects is essential. For enabling coherence of corresponding objects along consecutive workflow segments, the assignment of unique identifiers and the specification of their relations are mandatory. The abstract model presented here addresses these aspects, and the software DiversityDescriptions (DWB-DD) facilitates the management of thusly connected digital data objects and structures. DWB-DD allows for an individual specification of operation design elements and their linking to objects. Two workflow design use cases, one for DNA barcoding and another for cultivation of fungal isolates, are given. To publish those structured data, standard schema mapping and XML-provision of digital objects are essential. Schemas useful for this mapping include the Ecological Markup Language, the Schema for Meta-omics Data of Collection Objects and the Standard for Structured Descriptive Data. Data pipelines with DWB-DD include the mapping and conversion between schemas and functions for data publishing and archiving according to the Open Archival Information System standard. The setting allows for repeatability of study setups, reproducibility of study results and for supporting work groups to structure and maintain their data from the beginning of a study. The theory of ‘FAIR++’ digital objects is introduced.

Description: SUMMARY Seismic full waveform inversion (FWI) is a state-of-the-art technique for estimating subsurface physical models from recorded seismic waveform, but its application requires care because of high non-linearity and non-uniqueness. The final outcome of global convergence from conventional FWI using local gradient information relies on an informative starting model. Bayesian inference using Markov chain Monte Carlo (MCMC) sampling is able to remove such dependence, by a direct extensive search of the model space. We use a Bayesian trans-dimensional MCMC seismic FWI method with a parsimonious dipping layer parametrization, to invert for subsurface velocity models from pre-stack seismic shot gathers that contain mainly reflections. For the synthetic study, we use a simple four-layer model and a modified Marmousi model. A recently collected multichannel off-shore seismic reflection data set, from the Lord Howe Rise (LHR) in the east of Australia, is used for the field data test. The trans-dimensional FWI method is able to provide model ensembles for describing posterior distribution, when the dipping-layer model assumption satisfies the observed data. The model assumption requires narrow models, thus only near-offset data to be used. We use model stitching with lateral and depth constraints to create larger 2-D models from many adjacent overlapping submodel inversions. The inverted 2-D velocity model from the Bayesian inference can then be used as a starting model for the gradient-based FWI, from which we are able to obtain high-resolution subsurface velocity models, as demonstrated using the synthetic data. However, lacking far-offset data limits the constraints for the low-wavenumber part of the velocity model, making the inversion highly non-unique. We found it challenging to apply the dipping-layer based Bayesian FWI to the field data. The approximations in the source wavelet and forward modelling physics increase the multimodality of the posterior distribution; the sampled velocity models clearly show the trade-off between interface depth and velocity. Numerical examples using the synthetic and field data indicate that trans-dimensional FWI has the potential for inverting earth models from reflection waveform. However, a sparse model parametrization and far offset constraints are required, especially for field application.

Description: We present simulations of bar-unstable stellar discs in which the bars thicken into box/peanut shapes. Detailed analysis of the evolution of each model revealed three different mechanisms for thickening the bars. The first mechanism is the well-known buckling instability, the second is the vertical excitation of bar orbits by passage through the 2:1 vertical resonance, and the third is a gradually increasing fraction of bar orbits trapped into this resonance. Since bars in many galaxies may have formed and thickened long ago, we have examined the models for fossil evidence in the velocity distribution of stars in the bar, finding a diagnostic to discriminate between a bar that had buckled from the other two mechanisms.

Description: SUMMARY Bayesian inversion of magnetotelluric (MT) data is a powerful but computationally expensive approach to estimate the subsurface electrical conductivity distribution and associated uncertainty. Approximating the Earth subsurface with 1-D physics considerably speeds-up calculation of the forward problem, making the Bayesian approach tractable, but can lead to biased results when the assumption is violated. We propose a methodology to quantitatively compensate for the bias caused by the 1-D Earth assumption within a 1-D trans-dimensional Markov chain Monte Carlo sampler. Our approach determines site-specific likelihood functions which are calculated using a dimensionality discrepancy error model derived by a machine learning algorithm trained on a set of synthetic 3-D conductivity training images. This is achieved by exploiting known geometrical dimensional properties of the MT phase tensor. A complex synthetic model which mimics a sedimentary basin environment is used to illustrate the ability of our workflow to reliably estimate uncertainty in the inversion results, even in presence of strong 2-D and 3-D effects. Using this dimensionality discrepancy error model we demonstrate that on this synthetic data set the use of our workflow performs better in 80 per cent of the cases compared to the existing practice of using constant errors. Finally, our workflow is benchmarked against real data acquired in Queensland, Australia, and shows its ability to detect the depth to basement accurately.

Description: Nickel is a strongly compatible element in olivine, and thus fractional crystallization of olivine typically results in a concave-up trend on a Fo-Ni diagram. "Ni-enriched" olivine compositions are considered those that fall above such a crystallization trend. To explain Ni-enriched olivine crystals, we develop a set of theoretical and computational models to describe how primitive olivine phenocrysts from a parent (high-Mg, high-Ni) basalt re-equilibrate with an evolved (low-Mg, low-Ni) melt through diffusion. These models describe the progressive loss of Fo and Ni in olivine cores during protracted diffusion for various crystal shapes and different relative diffusivities for Ni and Fe-Mg. In the case when the diffusivity of Ni is lower than that for Fe-Mg interdiffusion, then olivine phenocrysts affected by protracted diffusion form a concave-down trend that contrasts with the concave-up crystallization trend. Models for different simple geometries show that the concavity of the diffusion trend does not depend on the size of the crystals and only weakly depends on their shape. We also find that the effect of diffusion anisotropy on trend concavity is in the same magnitude as the effect of crystal shape. Thus, both diffusion anisotropy and crystal shape do not significantly change the concave-down diffusion trend. Three-dimensional numerical diffusion models using a range of more complex, realistic olivine morphologies with anisotropy corroborate this conclusion. Thus, the curvature of the concave-down diffusion trend is mainly determined by the ratio of Ni and Fe-Mg diffusion coefficients. The initial and final points of the diffusion trend are in turn determined by the compositional contrast between mafic and more evolved melts that have mixed to cause disequilibrium between olivine cores and surrounding melt. We present several examples of measurements on olivine from arc basalts from Kamchatka, and several published olivine datasets from mafic magmas from non-subduction settings (lamproites and kimberlites) that are consistent with diffusion-controlled Fo-Ni behaviour. In each case the ratio of Ni and Fe-Mg diffusion coefficients is indicated to be 

Description: Despite significant advances in invertebrate phylogenomics over the past decade, the higher-level phylogeny of Pycnogonida (sea spiders) remains elusive. Due to the inaccessibility of some small-bodied lineages, few phylogenetic studies have sampled all sea spider families. Previous efforts based on a handful of genes have yielded unstable tree topologies. Here, we inferred the relationships of 89 sea spider species using targeted capture of the mitochondrial genome, 56 conserved exons, 101 ultraconserved elements, and three nuclear ribosomal genes. We inferred molecular divergence times by integrating morphological data for fossil species to calibrate 15 nodes in the arthropod tree of life. This integration of data classes resolved the basal topology of sea spiders with high support. The enigmatic family Austrodecidae was resolved as the sister group to the remaining Pycnogonida and the small-bodied family Rhynchothoracidae as the sister group of the robust-bodied family Pycnogonidae. Molecular divergence time estimation recovered a basal divergence of crown group sea spiders in the Ordovician. Comparison of diversification dynamics with other marine invertebrate taxa that originated in the Paleozoic suggests that sea spiders and some crustacean groups exhibit resilience to mass extinction episodes, relative to mollusk and echinoderm lineages.

Description: The genus Lodderena Iredale, 1924 has been classified in the Skeneidae by most recent authors. However, this family, originally characterized by their minute size, lack of nacre in the teleoconch and a rhipidoglossate radula, is currently considered to be polyphyletic assemblage, and preliminary molecular systematic data suggest exclusion of Lodderena from Skeneidae. In order to shed light on the systematic position of this genus, we provide a detailed description of the anatomy and histology of the type species, Lodderena minima (Tenison-Woods, 1878), and of L. ornata (Olsson & McGinty, 1958). The anatomical data confirm the vetigastropod-trochoid nature of Lodderena but exclude the genus from Skeneidae. Skeneidae are mainly characterized by a propodial penis, a hermaphroditic condition with separated testis and ovary, and a large receptaculum in the mantle roof. In contrast, Lodderena species lack both a copulatory organ and receptaculum, and have a true ovotestis. We also provide a critical review of nominal species in the genus. Based on molecular and morphological evidence, we exclude Lodderena from Skeneidae, instead treating it as a genus incertae sedis within Trochoidea. We discuss the implications of small size for functional morphology and reproduction.

Description: Translation of most cellular mRNAs in eukaryotes proceeds through a cap-dependent pathway, whereby the cap-binding complex, eIF4F, anchors the preinitiation complex at the 5′ end of mRNAs and regulates translation initiation. The requirement of Leishmania to survive in changing environments can explain why they encode multiple eIF4E (LeishIF4Es) and eIF4G (LeishIF4Gs) paralogs, as each could be assigned a discrete role during their life cycle. Here we show that the expression and activity of different LeishIF4Es change during the growth of cultured promastigotes, urging a search for regulatory proteins. We describe a novel LeishIF4E-interacting protein, Leish4E-IP2, which contains a conserved Y(X)4LΦ IF4E-binding-motif. Despite its capacity to bind several LeishIF4Es, Leish4E-IP2 was not detected in m7GTP-eluted cap-binding complexes, suggesting that it could inhibit the cap-binding activity of LeishIF4Es. Using a functional assay, we show that a recombinant form of Leish4E-IP2 inhibits the cap-binding activity of LeishIF4E-1 and LeishIF4E-3. Furthermore, we show that transgenic parasites expressing a tagged version of Leish4E-IP2 also display reduced cap-binding activities of tested LeishIF4Es, and decreased global translation. Given its ability to bind more than a single LeishIF4E, we suggest that Leish4E-IP2 could serve as a broad-range repressor of Leishmania protein synthesis.

Description: The mass-to-light ratio (M/L) is a key parameter in decomposing galactic rotation curves into contributions from the baryonic components and the dark halo of a galaxy. One direct observational method to determine the disc M/L is by calculating the surface mass density of the disc from the stellar vertical velocity dispersion and the scale height of the disc. Usually, the scale height is obtained from near-IR studies of edge-on galaxies and pertains to the older, kinematically hotter stars in the disc, while the vertical velocity dispersion of stars is measured in the optical band and refers to stars of all ages (up to ∼ 10 Gyr) and velocity dispersions. This mismatch between the scale height and the velocity dispersion can lead to underestimates of the disc surface density and a misleading conclusion of the sub-maximality of galaxy discs. In this paper we present the study of the stellar velocity dispersion of the disc galaxy NGC 6946 using integrated star light and individual planetary nebulae as dynamical tracers. We demonstrate the presence of two kinematically distinct populations of tracers which contribute to the total stellar velocity dispersion. Thus, we are able to use the dispersion and the scale height of the same dynamical population to derive the surface mass density of the disc over a radial extent. We find the disc of NGC 6946 to be closer to maximal with the baryonic component contributing most of the radial gravitational field in the inner parts of the galaxy ($ m V_{max}(bar)=0.76(pm 0.14)V_{max}$).

Description: Summary Seismic full waveform inversion (FWI) is a powerful method for estimating quantitative subsurface physical parameters from seismic data. As the full waveform inversion is a non-linear problem, the linearized approach updates model iteratively from an initial model, which can get trapped in local minima. In the presence of a high velocity contrast, such as at Moho, the reflection coefficient and recorded waveforms from wide-aperture seismic acquisition are extremely non-linear around critical angles. The problem at the Moho is further complicated by the interference of lower crustal (Pg) and upper mantle (Pn) turning ray arrivals with the critically reflected Moho arrivals (PmP). In order to determine velocity structure near Moho, a non-linear method should be used. We propose to solve this strong non-linear FWI problem at Moho using a trans-dimensional Markov chain Monte Carlo (MCMC) method, where the earth model between lower crust and upper mantle is idealy parameterized with a 1-D assumption using a variable number of velocity interfaces. Different from common MCMC methods that require determining the number of unknown as a fixed prior before inversion, trans-dimensional MCMC allows the flexibility for an automatic estimation of both the model complexity (e.g. the number of velocity interfaces) and the velocity-depth structure from the data. We first test the algorithm on synthetic data using four representative Moho models and then apply to an ocean bottom seismometer (OBS) data from the Mid-Atlantic Ocean. A 2-D finite-difference solution of an acoustic wave equation is used for data simulation at each iteration of MCMC search, for taking into account the lateral heterogeneities in the upper crust, which is constrained from travel time tomography and is kept unchanged during inversion; the 1-D model parameterization near Moho enables an efficient search of the trans-dimensional model space. Inversion results indicate that, with very little prior and the wide-aperture seismograms, the trans-dimensional FWI method is able to infer the posterior distribution of both the number of velocity interfaces and the velocity-depth model for a strong nonlinear problem, making the inversion a complete data-driven process. The distribution of interface matches the velocity discontinuities. We find that the Moho in the study area is a transition zone of 0.7 km, or a sharp boundary with velocities from around 7 km/s in the lower crust to 8 km/s of the upper mantle; both provide nearly identical waveform match for the field data. The ambiguity comes from the resolution limit of the band-limited seismic data and limited offset range for PmP arrivals.