ALBERT

Description: Seismic full waveform inversion (FWI) has been applied to simple elastic problems with certain symmetries, such as isotropic, transverse isotropic or vertical transversely isotropic media. In this study, the FWI concept is extended to the most general anisotropic case with 21 independent elastic material parameters and no symmetry plane (triclinic). Beside a short description of the 3-D finite-difference scheme to solve the forward problem and the FWI optimization algorithm, we present a sensitivity study for a simple anisotropic medium. This test problem consists of a homogenous triclinic anisotropic full space, which contains 21 spatially separated spheres. In each sphere one component of the elastic tensor deviates by 5 per cent from the background medium. The resolution of the different spheres, ambiguities between the different elastic parameters, as well as the effect of the acquisition geometry can be systematically investigated. Due to the high computational costs of the triclinic forward problem a few compromises have to be made regarding the acquisition geometries. Point sources are replaced by plane wave sources which lead to a limitation of incidence angles and therefore a strong decrease in resolution of the nondiagonal elastic tensor components. It is shown that, despite these limitations, a tomographic acquisition geometry would be able to resolve to some extent a monoclinic symmetry via FWI. Restricting the acquisition geometries (e.g. VSP combined with reflection seismic or reflection seismic only) significantly reduces the number of resolvable tensor elements in strict dependence of the covered incidence angles.

Description: The Okavango Delta of northern Botswana is one of the world's largest inland deltas or megafans. To obtain information on the character of sediments and basement depths, audiomagnetotelluric (AMT), controlled-source audiomagnetotelluric (CSAMT) and central-loop transient electromagnetic (TEM) data were collected on the largest island within the delta. The data were inverted individually and jointly for 1-D models of electric resistivity. Distortion effects in the AMT and CSAMT data were accounted for by including galvanic distortion tensors as free parameters in the inversions. By employing Marquardt–Levenberg inversion, we found that a 3-layer model comprising a resistive layer overlying sequentially a conductive layer and a deeper resistive layer was sufficient to explain all of the electromagnetic data. However, the top of the basal resistive layer from electromagnetic-only inversions was much shallower than the well-determined basement depth observed in high-quality seismic reflection images and seismic refraction velocity tomograms. To resolve this discrepancy, we jointly inverted the electromagnetic data for 4-layer models by including seismic depths to an interface between sedimentary units and to basement as explicit a priori constraints. We have also estimated the interconnected porosities, clay contents and pore-fluid resistivities of the sedimentary units from their electrical resistivities and seismic P -wave velocities using appropriate petrophysical models. In the interpretation of our preferred model, a shallow ~40 m thick freshwater sandy aquifer with 85–100 m resistivity, 10–32 per cent interconnected porosity and 〈13 per cent clay content overlies a 105–115 m thick conductive sequence of clay and intercalated salt-water-saturated sands with 15–20 m total resistivity, 1–27 per cent interconnected porosity and 15–60 per cent clay content. A third ~60 m thick sandy layer with 40–50 m resistivity, 10–33 per cent interconnected porosity and 〈15 per cent clay content is underlain by the basement with 3200–4000 m total resistivity. According to an interpretation of helicopter TEM data that cover the entire Okavango Delta and borehole logs, the second and third layers may represent lacustrine sediments from Paleo Lake Makgadikgadi and a moderately resistive freshwater aquifer comprising sediments of the recently proposed Paleo Okavango Megafan, respectively.

Description: We investigate the spatial coherence of underwater ambient noise using a yearlong time-series measured off Ascension Island. Qualitative agreement with observed cross-correlations is achieved using a simple range-dependent model, constrained by earlier, active tomographic studies in the area. In particular, the model correctly predicts the existence of two weakly dispersive normal modes in the microseism frequency range, with the group speed of one of the normal modes being smaller than the sound speed in water. The agreement justifies our interpretation of the peaks of the measured cross-correlation function of ambient noise as modal arrivals, with dispersion that is sensitive to crustal velocity structure. Our observations are consistent with Scholte to Moho head wave coupled propagation, with double mode conversion occurring due to the bathymetric variations between receivers. We thus demonstrate the feasibility of interrogating crustal properties using noise interferometry of moored hydrophone data at ranges in excess of 120 km.

Description: The Okavango Delta of northern Botswana is one of the world's largest inland deltas or megafans. To obtain information on the character of sediments and basement depths, audiomagnetotelluric (AMT), controlled-source audiomagnetotelluric (CSAMT) and central-loop transient electromagnetic (TEM) data were collected on the largest island within the delta. The data were inverted individually and jointly for 1-D models of electric resistivity. Distortion effects in the AMT and CSAMT data were accounted for by including galvanic distortion tensors as free parameters in the inversions. By employing Marquardt–Levenberg inversion, we found that a 3-layer model comprising a resistive layer overlying sequentially a conductive layer and a deeper resistive layer was sufficient to explain all of the electromagnetic data. However, the top of the basal resistive layer from electromagnetic-only inversions was much shallower than the well-determined basement depth observed in high-quality seismic reflection images and seismic refraction velocity tomograms. To resolve this discrepancy, we jointly inverted the electromagnetic data for 4-layer models by including seismic depths to an interface between sedimentary units and to basement as explicit a priori constraints. We have also estimated the interconnected porosities, clay contents and pore-fluid resistivities of the sedimentary units from their electrical resistivities and seismic P -wave velocities using appropriate petrophysical models. In the interpretation of our preferred model, a shallow ~40 m thick freshwater sandy aquifer with 85–100 m resistivity, 10–32 per cent interconnected porosity and 〈13 per cent clay content overlies a 105–115 m thick conductive sequence of clay and intercalated salt-water-saturated sands with 15–20 m total resistivity, 1–27 per cent interconnected porosity and 15–60 per cent clay content. A third ~60 m thick sandy layer with 40–50 m resistivity, 10–33 per cent interconnected porosity and 〈15 per cent clay content is underlain by the basement with 3200–4000 m total resistivity. According to an interpretation of helicopter TEM data that cover the entire Okavango Delta and borehole logs, the second and third layers may represent lacustrine sediments from Paleo Lake Makgadikgadi and a moderately resistive freshwater aquifer comprising sediments of the recently proposed Paleo Okavango Megafan, respectively.

Description: ChIP-seq is increasingly used to characterize transcription factor binding and chromatin marks at a genomic scale. Various tools are now available to extract binding motifs from peak data sets. However, most approaches are only available as command-line programs, or via a website but with size restrictions. We present peak-motifs , a computational pipeline that discovers motifs in peak sequences, compares them with databases, exports putative binding sites for visualization in the UCSC genome browser and generates an extensive report suited for both naive and expert users. It relies on time- and memory-efficient algorithms enabling the treatment of several thousand peaks within minutes. Regarding time efficiency, peak-motifs outperforms all comparable tools by several orders of magnitude. We demonstrate its accuracy by analyzing data sets ranging from 4000 to 1 28 000 peaks for 12 embryonic stem cell-specific transcription factors. In all cases, the program finds the expected motifs and returns additional motifs potentially bound by cofactors. We further apply peak-motifs to discover tissue-specific motifs in peak collections for the p300 transcriptional co-activator. To our knowledge, peak-motifs is the only tool that performs a complete motif analysis and offers a user-friendly web interface without any restriction on sequence size or number of peaks.

Description: The Quaternary Añavieja-Dévanos tufa system is located in the northern sector of the Iberian Chain. It has been previously tackled by means sedimentological studies focused on the available outcrops and some boreholes. They have permitted the proposal of a sedimentary scenario that fits with a pool-barrage fluvial tufa model. However a better knowledge of the characteristics and internal distribution of the usually non-outcropping pool deposits as well as of its relationship with barrage deposits has not been evaluated in detail yet. Palaeoenvironmental studies on tufas are usually biased because tufas are commonly delicate facies exposed to intense erosion during water level fall stages; for this reason outcrops are usually scarce and very often coincide with the most cemented barrage deposits. In order to analyse the internal characteristics of the tufa deposits under study, but also the lateral correlation among different facies, ground penetrating radar (GPR) has been employed both for the evaluation of its applicability in such kind of environments and to improve, if possible, the sedimentary model using geophysical data in sectors without outcrops. A GPR survey including different antennas ranging from 50 to 500 MHz along different sectors and its comparison with natural outcrops has been carried out. GPR results have permitted to deduce clear differences between pool and barrage deposits and to recognise its internal structure and geometrical relationships. The survey also permitted an approach to different scales of heterogeneities in the radarfacies evaluation by using distinct antennas and therefore, reaching different resolutions and penetrations. The resulting integration from different antennas allows three different attenuant and eight reflective radarfacies to be defined permitting a better approach to the real extension of the pool areas. These results have permitted to decipher the horizontal and vertical facies changes and the identification of a scarcer development of pool deposits than expected in the studied system.

Description: Noise interferometry is the process by which approximations to acoustic Green's functions, which describe sound propagation between two locations, are estimated by cross-correlating time series of ambient noise measured at those locations. Noise-interferometry-based approximations to Green's functions can be used as the basis for a variety of inversion algorithms, thereby providing a purely passive alternative to active-source ocean acoustic remote sensing. In this paper we give an overview of results from noise interferometry experiments conducted in the Florida Straits at 100 m depth in December 2012, and at 600 m depth in September/October 2013. Under good conditions for noise interferometry, estimates of cross-correlation functions are shown to allow one to perform advanced phase-coherent signal processing techniques to perform waveform inversions, estimate currents by exploiting non-reciprocity, perform time-reversal/back-propagation calculations and investigate modal dispersion using time-warping techniques. Conditions which are favourable for noise interferometry are identified and discussed.

Description: Deep transcriptome sequencing (RNA-Seq) has become a vital tool for studying the state of cells in the context of varying environments, genotypes and other factors. RNA-Seq profiling data enable identification of novel isoforms, quantification of known isoforms and detection of changes in transcriptional or RNA-processing activity. Existing approaches to detect differential isoform abundance between samples either require a complete isoform annotation or fall short in providing statistically robust and calibrated significance estimates. Here, we propose a suite of statistical tests to address these open needs: a parametric test that uses known isoform annotations to detect changes in relative isoform abundance and a non-parametric test that detects differential read coverages and can be applied when isoform annotations are not available. Both methods account for the discrete nature of read counts and the inherent biological variability. We demonstrate that these tests compare favorably to previous methods, both in terms of accuracy and statistical calibrations. We use these techniques to analyze RNA-Seq libraries from Arabidopsis thaliana and Drosophila melanogaster. The identified differential RNA processing events were consistent with RT–qPCR measurements and previous studies. The proposed toolkit is available from http://bioweb.me/rdiff and enables in-depth analyses of transcriptomes, with or without available isoform annotation.

Description: This paper describes computational studies of tangential ground motions generated by spherical explosions in a heavily jointed granite formation. Various factors affecting the shear wave generation are considered, including joint spacing, orientation and frictional properties. Simulations are performed both in 2-D for a single joint set to elucidate the basic response mechanisms, and in 3-D for multiple joint sets to realistically represent in situ conditions in a realistic geological setting. The joints are modelled explicitly using both contact elements and weakness planes in the material. Simulations are performed both deterministically and stochastically to quantify the effects of geological uncertainties on near field ground motions. The mechanical properties of the rock and the joints as well as the joint spacing and orientation are taken from experimental test data and geophysical logs corresponding to the Climax Stock granitic outcrop, which is the geological setting of the source physics experiment (SPE). Agreement between simulation results and near field wave motion data from SPE enables newfound understanding of the origin and extent of non-spherical motions associated with underground explosions in fractured geological media.