ALBERT

Description: This paper describes an alternative acceleration approach for determining GRACE monthly gravity field models. The main differences compared to the traditional acceleration approach can be summarized as: (1) The position errors of GRACE orbits in the functional model are taken into account; (2) The range ambiguity is eliminated via the difference of the range measurements and (3) The mean acceleration equation is formed based on Cowell integration. Using this developed approach, a new time-series of GRACE monthly solution spanning the period January 2003 to December 2010, called Tongji_Acc RL01, has been derived. The annual signals from the Tongji_Acc RL01 time-series agree well with those from the GLDAS model. The performance of Tongji_Acc RL01 shows that this new model is comparable with the RL05 models released by CSR and JPL as well as with the RL05a model released by GFZ.

Description: Wells and boreholes are routinely steel-cased in oil and gas fields and geological storage sites. There have been a number of studies on the effects of a steel-cased well on various electrical and electromagnetic (EM) geophysical methods. In this paper, we examine the use of a steel-cased well as a virtual vertical electric source for sensing deep localized resistive (e.g. CO 2 , oil and gas) and conductive (e.g. conductive-proppant-filled fractures) targets when concentric electric sources are grounded around the collar of the well. To simulate the casing effects, we present a 3-D finite-element time-domain (FETD) algorithm with tetrahedral elements. The FETD algorithm is designed to reduce memory usage in adaptive time stepping by utilizing parallel direct and iterative solvers appropriately together. To avoid a larger number of tiny elements required for discretizing a thin wall of the casing, the hollow casing is approximated with a rectangular prism. By not discretizing the thin wall of and the curvature of the round casing, the approximation not only reduces the number of unknowns by an order of magnitude but also improves overall mesh qualities. We show that surface EM responses over the hollow casing and the prism are practically the same. Through FETD modelling of a rectangular prism as an approximation of a steel casing, we demonstrate that a steel casing can serve as a conduit through which a high concentration of electrical currents can flow downward from the surface, interact with deep localized reservoirs/fractures and produce a measurable perturbation in the surface EM fields. Concentric electric sources can further improve both the sensitivity to the deep targets and the overall magnitude of surface EM fields.

Description: Protein sequences predicted from metagenomic datasets are annotated by identifying their homologs via sequence comparisons with reference or curated proteins. However, a majority of metagenomic protein sequences are partial-length, arising as a result of identifying genes on sequencing reads or on assembled nucleotide contigs, which themselves are often very fragmented. The fragmented nature of metagenomic protein predictions adversely impacts homology detection and, therefore, the quality of the overall annotation of the dataset. Here we present a novel algorithm called GRASP that accurately identifies the homologs of a given reference protein sequence from a database consisting of partial-length metagenomic proteins. Our homology detection strategy is guided by the reference sequence, and involves the simultaneous search and assembly of overlapping database sequences. GRASP was compared to three commonly used protein sequence search programs (BLASTP, PSI-BLAST and FASTM). Our evaluations using several simulated and real datasets show that GRASP has a significantly higher sensitivity than these programs while maintaining a very high specificity. GRASP can be a very useful program for detecting and quantifying taxonomic and protein family abundances in metagenomic datasets. GRASP is implemented in GNU C++, and is freely available at http://sourceforge.net/projects/grasp-release .

Description: Genetic screens of an unprecedented scale have recently been made possible by the availability of high-complexity libraries of synthetic oligonucleotides designed to mediate either gene knockdown or gene knockout, coupled with next-generation sequencing. However, several sources of random noise and statistical biases complicate the interpretation of the resulting high-throughput data. We developed HiTSelect, a comprehensive analysis pipeline for rigorously selecting screen hits and identifying functionally relevant genes and pathways by addressing off-target effects, controlling for variance in both gene silencing efficiency and sequencing depth of coverage and integrating relevant metadata. We document the superior performance of HiTSelect using data from both genome-wide RNAi and CRISPR/Cas9 screens. HiTSelect is implemented as an open-source package, with a user-friendly interface for data visualization and pathway exploration. Binary executables are available at http://sourceforge.net/projects/hitselect/ , and the source code is available at https://github.com/diazlab/HiTSelect .

Description: In this paper, we present a method for incorporating prior geological information into potential field data inversion problem. As opposed to the traditional inverse algorithm, our proposed method takes full advantage of prior geological information as a constraint and thus obtains a new objective function for inversion by adding Lagrangian multipliers and slack variables to the traditional inversion method. These additional parameters can be easily solved during iterations. We used both synthetic and observed data sets to test the stability and validity of the proposed method. Our results using synthetic gravity data show that our new method predicts depth and density anomalies more efficiently and accurately than the traditional inversion method that does not include prior geological constraints. Then using observed gravity data in the Three Gorges area and geological constraint information, we obtained the density distribution of the upper and middle crust in this area thus revealing its geological structure. These results confirm the proposed method's validity and indicate its potential application for magnetism data inversion and exploration of geological structures.

Description: Integrative analyses of epigenetic data promise a deeper understanding of the epigenome. Epidaurus is a bioinformatics tool used to effectively reveal inter-dataset relevance and differences through data aggregation, integration and visualization. In this study, we demonstrated the utility of Epidaurus in validating hypotheses and generating novel biological insights. In particular, we described the use of Epidaurus to (i) integrate epigenetic data from prostate cancer cell lines to validate the activation function of EZH2 in castration-resistant prostate cancer and to (ii) study the mechanism of androgen receptor ( AR ) binding deregulation induced by the knockdown of FOXA1 . We found that EZH2 's noncanonical activation function was reaffirmed by its association with active histone markers and the lack of association with repressive markers. More importantly, we revealed that the binding of AR was selectively reprogramed to promoter regions, leading to the up-regulation of hundreds of cancer-associated genes including EGFR . The prebuilt epigenetic dataset from commonly used cell lines (LNCaP, VCaP, LNCaP-Abl, MCF7, GM12878, K562, HeLa-S3, A549, HePG2) makes Epidaurus a useful online resource for epigenetic research. As standalone software, Epidaurus is specifically designed to process user customized datasets with both efficiency and convenience.

Description: RNA-protein complexes are essential in mediating important fundamental cellular processes, such as transport and localization. In particular, ncRNA-protein interactions play an important role in post-transcriptional gene regulation like mRNA localization, mRNA stabilization, poly-adenylation, splicing and translation. The experimental methods to solve RNA-protein interaction prediction problem remain expensive and time-consuming. Here, we present the RPI-Pred (RNA-protein interaction predictor), a new support-vector machine-based method, to predict protein-RNA interaction pairs, based on both the sequences and structures. The results show that RPI-Pred can correctly predict RNA-protein interaction pairs with ~94% prediction accuracy when using sequence and experimentally determined protein and RNA structures, and with ~83% when using sequences and predicted protein and RNA structures. Further, our proposed method RPI-Pred was superior to other existing ones by predicting more experimentally validated ncRNA-protein interaction pairs from different organisms. Motivated by the improved performance of RPI-Pred, we further applied our method for reliable construction of ncRNA-protein interaction networks. The RPI-Pred is publicly available at: http://ctsb.is.wfubmc.edu/projects/rpi-pred .

Description: A strategy is presented to incorporate prior information from conceptual geological models in probabilistic inversion of geophysical data. The conceptual geological models are represented by multiple-point statistics training images (TIs) featuring the expected lithological units and structural patterns. Information from an ensemble of TI realizations is used in two different ways. First, dominant modes are identified by analysis of the frequency content in the realizations, which drastically reduces the model parameter space in the frequency-amplitude domain. Second, the distributions of global, summary metrics (e.g. model roughness) are used to formulate a prior probability density function. The inverse problem is formulated in a Bayesian framework and the posterior pdf is sampled using Markov chain Monte Carlo simulation. The usefulness and applicability of this method is demonstrated on two case studies in which synthetic crosshole ground-penetrating radar traveltime data are inverted to recover 2-D porosity fields. The use of prior information from TIs significantly enhances the reliability of the posterior models by removing inversion artefacts and improving individual parameter estimates. The proposed methodology reduces the ambiguity inherent in the inversion of high-dimensional parameter spaces, accommodates a wide range of summary statistics and geophysical forward problems.

Description: Identifying conserved and divergent response patterns in gene networks is becoming increasingly important. A common approach is integrating expression information with gene association networks in order to find groups of connected genes that are activated or repressed. In many cases, researchers are also interested in comparisons across species (or conditions). Finding an active sub-network is a hard problem and applying it across species requires further considerations (e.g. orthology information, expression data and networks from different sources). To address these challenges we devised ModuleBlast, which uses both expression and network topology to search for highly relevant sub-networks. We have applied ModuleBlast to expression and interaction data from mouse, macaque and human to study immune response and aging. The immune response analysis identified several relevant modules, consistent with recent findings on apoptosis and NFB activation following infection. Temporal analysis of these data revealed cascades of modules that are dynamically activated within and across species. We have experimentally validated some of the novel hypotheses resulting from the analysis of the ModuleBlast results leading to new insights into the mechanisms used by a key mammalian aging protein.

Description: Here we used discriminative training methods to uncover the chromatin, transcription factor (TF) binding and sequence features of enhancers underlying gene expression in individual cardiac cells. We used machine learning with TF motifs and ChIP data for a core set of cardiogenic TFs and histone modifications to classify Drosophila cell-type-specific cardiac enhancer activity. We show that the classifier models can be used to predict cardiac cell subtype cis -regulatory activities. Associating the predicted enhancers with an expression atlas of cardiac genes further uncovered clusters of genes with transcription and function limited to individual cardiac cell subtypes. Further, the cell-specific enhancer models revealed chromatin, TF binding and sequence features that distinguish enhancer activities in distinct subsets of heart cells. Collectively, our results show that computational modeling combined with empirical testing provides a powerful platform to uncover the enhancers, TF motifs and gene expression profiles which characterize individual cardiac cell fates.

Description: Many rocks and layered/fractured sequences have a clearly expressed electrical anisotropy although it is rare in practice to incorporate anisotropy into resistivity inversion. In this contribution, we present a series of 2.5-D synthetic inversion experiments for various electrode configurations and 2-D anisotropic models. We examine and compare the image reconstructions obtained using the correct anisotropic inversion code with those obtained using the false but widely used isotropic assumption. Superior reconstruction in terms of reduced data misfit, true anomaly shape and position, and anisotropic background parameters were obtained when the correct anisotropic assumption was employed for medium to high coefficients of anisotropy. However, for low coefficient values the isotropic assumption produced better-quality results. When an erroneous isotropic inversion is performed on medium to high level anisotropic data, the images are dominated by patterns of banded artefacts and high data misfits. Various pole–pole, pole–dipole and dipole–dipole data sets were investigated and evaluated for the accuracy of the inversion result. The eigenvalue spectra of the pseudo-Hessian matrix and the formal resolution matrix were also computed to determine the information content and goodness of the results. We also present a data selection strategy based on high sensitivity measurements which drastically reduces the number of data to be inverted but still produces comparable results to that of the comprehensive data set. Inversion was carried out using transversely isotropic model parameters described in two different co-ordinate frames for the conductivity tensor, namely Cartesian versus natural or eigenframe. The Cartesian frame provided a more stable inversion product. This can be simply explained from inspection of the eigenspectra of the pseudo-Hessian matrix for the two model descriptions.

Description: We studied artificial ore models that contained galena, pyrite, magnetite, graphite and cryptomelane with the time domain induced polarization technique. The models were mixtures of sand and metallic-type, electronically conductive mineral particles. We varied the volumetric content of the particles, their mineral composition and average grain size, as well as the pore water salinity. Based on the Debye decomposition approach, we obtained relaxation time distributions, which contained peaks. From these distributions, we obtained the total chargeability and the peak relaxation time. We correlated these parameters with the particle mineral composition, grain size, particle content and the pore solution resistivity. We also compared the experimental data with the Wong model prediction, which was unable to explain the entire data set. The above-mentioned correlations, in conjunction with some previously published data, allowed us to formulate a new, semi-empirical model that links (1) the total chargeability with the volumetric content of the particles and the total chargeability of the host matrix and (2) the time constant with the particle mineralogy, the particle radius and the pore solution resistivity.

Description: Electrodes installed on active landslides and vulnerable earthworks to monitor changes in resistivity associated with moisture dynamics can be subject to movement. This affects the geoelectrical data and leads to errors in the resulting electrical resistivity tomography (ERT) images. This paper demonstrates the selection of appropriate ERT measurements to provide sensitivity to electrode displacements in both directions on a surface grid. Combinations of linear and equatorial dipole–dipole measurements are considered, which permit use on rectangular grids of any aspect ratio. A Gauss–Newton inversion scheme, initially based on simple homogeneous resistivity model calculations, is developed that allows for the incorporation of constraints based on the magnitude and direction of movement. The effects of the constraints are demonstrated with synthetic data, which are also used to show that displacement inversion can track electrodes positions during movement as a function of time. The conclusions of these simulations are subsequently confirmed by analogous experiments in a laboratory tank. The results show that tracking the positions of the electrodes is possible with sufficient accuracy, even in the presence of realistic subsurface resistivity structures, to correct the majority of distortions and resistivity anomalies caused by using the wrong electrode locations in ERT inversion. By incorporating estimates of the resistivity structure into the forward response modelling, the accuracy of the recovered displacements is improved. This also enables an iterative displacement and resistivity inversion to be developed that, for the first time, demonstrates the principle of using 3-D ERT data to monitor both subsurface geoelectrical properties and surface movements simultaneously.

Description: Seismic waves propagating in a porous medium, under favourable conditions, generate measurable electromagnetic fields due to electrokinetic effects. It has been proposed, following experimental and numerical studies, that these so-called ‘seismoelectromagnetic’ couplings depend on pore fluid properties. The theoretical frame describing these phenomena are based on the original Biot's theory, assuming that pores are fluid-filled. We study here the impact of a partially saturated medium on amplitudes of those seismoelectric couplings by comparing experimental data to an effective fluid model. We have built a 1-m-length-scale experiment designed for imbibition and drainage of an homogeneous silica sand; the experimental set-up includes a seismic source, accelerometers, electric dipoles and capacitance probes in order to monitor seismic and seismoelectric fields during water saturation. Apparent velocities and frequency spectra (in the kiloHertz range) are derived from seismic and electrical measurements during experiments in varying saturation conditions. Amplitudes of seismic and seismoelectric waves and their ratios (i.e. transfer functions) are discussed using a spectral analysis performed by continuous wavelet transform. The experiments reveal that amplitude ratios of seismic to coseismic electric signals remain rather constant as a function of the water saturation in the S w  = [0.2–0.9] range, consistently with theoretically predicted transfer functions.

Description: New marine geophysical data recorded across the Tonga-Kermadec subduction zone are used to image deformation and seismic velocity structures of the forearc and Pacific Plate where the Louisville Ridge seamount chain subducts. Due to the obliquity of the Louisville Ridge to the trench and the fast 128 mm yr –1 south–southwest migration of the ridge-trench collision zone, post-, current and pre-seamount subduction deformation can be investigated between 23°S and 28°S. We combine our interpretations from the collision zone with previous results from the post- and pre-collision zones to define the along-arc variation in deformation due to seamount subduction. In the pre-collision zone the lower-trench slope is steep, the mid-trench slope has ~3-km-thick stratified sediments and gravitational collapse of the trench slope is associated with basal erosion by subducting horst and graben structures on the Pacific Plate. This collapse indicates that tectonic erosion is a normal process affecting this generally sediment starved subduction system. In the collision zone the trench-slope decreases compared to the north and south, and rotation of the forearc is manifest as a steep plate boundary fault and arcward dipping sediment in a 12-km-wide, ~2-km-deep mid-slope basin. A ~3 km step increase in depth of the middle and lower crustal isovelocity contours below the basin indicates the extent of crustal deformation on the trench slope. At the leading edge of the overriding plate, upper crustal P -wave velocities are ~4.0 km s –1 and indicate the trench fill material is of seamount origin. Osbourn Seamount on the outer rise has extensional faulting on its western slope and mass wasting of the seamount provides the low V p material to the trench. In the post-collision zone to the north, the trench slope is smooth, the trench is deep, and the crystalline crust thins at the leading edge of the overriding plate where V p is low, ~5.5 km s –1 . These characteristics are attributed to a greater degree of extensional collapse of the forearc in the wake of seamount subduction. The northern end of a seismic gap lies at the transition from the smooth lower-trench slope of the post-collision zone, to the block faulted and elevated lower-trench slope in the collision zone, suggesting a causative link between the collapse of the forearc and seismogenesis. Along the forearc, the transient effects of a north-to-south progression of ridge subduction are preserved in the geomorphology, whereas longer-term effects may be recorded in the ~80 km offset in trench strike at the collision zone itself.

Description: Satellite radar altimetry observations are used to derive short wavelength gravity anomaly fields over the Persian Gulf and the Caspian Sea, where in situ and ship-borne gravity measurements have limited spatial coverage. In this study the retracking algorithm ‘Extrema Retracking’ (ExtR) was employed to improve sea surface height (SSH) measurements that are highly biased in the study regions due to land contaminations in the footprints of the satellite altimetry observations. ExtR was applied to the waveforms sampled by the five satellite radar altimetry missions: TOPEX/POSEIDON, JASON-1, JASON-2, GFO and ERS-1. Along-track slopes have been estimated from the improved SSH measurements and used in an iterative process to estimate deflections of the vertical, and subsequently, the desired gravity anomalies. The main steps of the gravity anomaly computations involve estimating improved SSH using the ExtR technique, computing deflections of the vertical from interpolated SSHs on a regular grid using a biharmonic spline interpolation and finally estimating gridded gravity anomalies. A remove–compute–restore algorithm, based on the fast Fourier transform, has been applied to convert deflections of the vertical into gravity anomalies. Finally, spline interpolation has been used to estimate regular gravity anomaly grids over the two study regions. Results were evaluated by comparing the estimated altimetry-derived gravity anomalies (with and without implementing the ExtR algorithm) with ship-borne free air gravity anomaly observations, and free air gravity anomalies from the Earth Gravitational Model 2008 (EGM2008). The comparison indicates a range of 3–5 mGal in the residuals, which were computed by taking the differences between the retracked altimetry-derived gravity anomaly and the ship-borne data. The comparison of retracked data with ship-borne data indicates a range in the root-mean-square-error (RMSE) between approximately 1.8 and 4.4 mGal and a bias between 0.4062 and 2.1413 mGal over different areas. Also a maximum RMSE of 4.4069 mGal, with a mean value of 0.7615 mGal was obtained in the residuals. An average improvement of 5.2746 mGal in the RMSE of the altimetry-derived gravity anomalies corresponding to 89.9 per cent was obtained after applying the ExtR post-processing.

Description: A LArge Reservoir Simulator (LARS) was equipped with an electrical resistivity tomography (ERT) array to monitor hydrate formation and dissociation experiments. During two hydrate formation experiments reaching 90 per cent bulk hydrate saturation, frequent measurements of the electrical properties within the sediment sample were performed. Subsequently, several common mixing rules, including two different interpretations of Archie's law, were tested to convert the obtained distribution of the electrical resistivity into the spatial distribution of local hydrate saturation. It turned out that the best results estimating values of local hydrate saturation were obtained using the Archie var – phi approach where the increasing hydrate phase is interpreted as part of the sediment grain framework reducing the sample's porosity. These values of local hydrate saturation were used to determine local permeabilities by applying the Carman-Kozeny relation. The formed hydrates were dissociated via depressurization. The decomposition onset as well as areas featuring hydrates and free gas were inferred from the ERT results. Supplemental consideration of temperature and pressure data granted information on discrete areas of hydrate dissociation.

Description: It remains enigmatic how slow slip events (SSEs) interact with other slow seismic events and large distant earthquakes at many subduction zones. Here we model the spatiotemporal slip evolution of the most recent long-term SSE in 2009–2011 in the Bungo Channel region, southwest Japan using GEONET GPS position time-series and a Kalman filter-based, time-dependent slip inversion method. We examine the space-time relationship between the geodetically determined slow slip transient and seismically observed low frequency earthquakes (LFEs) and very-low frequency earthquakes (V-LFEs) near the Nankai trough. We find a strong but distinct temporal correlation between transient slip and LFEs and V-LFEs, suggesting a different relationship to the SSE. We also find the great Tohoku-Oki earthquake appears to disrupt the normal source process of the SSE, probably reflecting large-scale stress redistribution caused by the earthquake. Comparison of the 2009–2011 SSE with others in the same region shows much similarity in slip and moment release, confirming its recurrent nature. Comparison of transient slip with plate coupling shows that slip transients mainly concentrate on the transition zone from strong coupling region to downdip LFEs with transient slip relieving elastic strain accumulation at transitional depth. The less consistent spatial correlation between the long-term SSE and seismic slow earthquakes, and susceptibility of these slow earthquakes to various triggering sources including long-term slow slip, suggests caution in using the seismically determined slow earthquakes as a proxy for slow slip.

Description: Normal mode treatments of the Earth's body tide response were developed in the 1980s to account for the effects of Earth rotation, ellipticity, anelasticity and resonant excitation within the diurnal band. Recent space-geodetic measurements of the Earth's crustal displacement in response to luni-solar tidal forcings have revealed geographical variations that are indicative of aspherical deep mantle structure, thus providing a novel data set for constraining deep mantle elastic and density structure. In light of this, we make use of advances in seismic free oscillation literature to develop a new, generalized normal mode theory for the tidal response within the semi-diurnal and long-period tidal band. Our theory involves a perturbation method that permits an efficient calculation of the impact of aspherical structure on the tidal response. In addition, we introduce a normal mode treatment of anelasticity that is distinct from both earlier work in body tides and the approach adopted in free oscillation seismology. We present several simple numerical applications of the new theory. First, we compute the tidal response of a spherically symmetric, non-rotating, elastic and isotropic Earth model and demonstrate that our predictions match those based on standard Love number theory. Second, we compute perturbations to this response associated with mantle anelasticity and demonstrate that the usual set of seismic modes adopted for this purpose must be augmented by a family of relaxation modes to accurately capture the full effect of anelasticity on the body tide response. Finally, we explore aspherical effects including rotation and we benchmark results from several illustrative case studies of aspherical Earth structure against independent finite-volume numerical calculations of the semi-diurnal body tide response. These tests confirm the accuracy of the normal mode methodology to at least the level of numerical error in the finite-volume predictions. They also demonstrate that full coupling of normal modes, rather than group coupling, is necessary for accurate predictions of the body tide response.

Description: Modelling of pressure transients recorded in wells allows for characterization of reservoirs surrounding the well. Simulation of pressure transients furthermore permits sensitivity studies for individual model parameters. We numerically simulated pumping tests in a vertical well intersecting a single horizontal fracture to evaluate the diagnostic potential of periodic pumping procedures for subsurface characterization. The pressure responses in the pumping and monitoring wells were analysed with respect to their sensitivity to geometrical and hydraulic properties of the fracture and of the surrounding rock material. We focused on interference analysis that for periodic pumping tests reduces to a consideration of amplitude ratio and phase shift between pressure transients recorded at an injection well and monitoring points. Fluid flow in the deformable fracture was modelled employing (1) a hybrid-dimensional hydro-mechanically coupled approach and (2) an uncoupled-diffusion equation. Results of both approaches were compared to quantify the effects of hydro-mechanical coupling. While in the uncoupled-diffusion approach a bulk storage capacity value is prescribed for the fracture, storage capacity is implicitly accounted for by the coupling in the hybrid-dimensional approach. Results reveal that hydro-mechanical coupling strongly affects the pressure transient at the pumping well and the monitoring points. Asymmetry of the pressure profiles between injection and production phases at the injection point is a peculiar characteristic of the hydro-mechanical results and is related to changes in fracture permeability with fluid pressure caused by fracture deformation. Further hydro-mechanical effects, such as reverse-pressure response, occur at monitoring points along the fracture domain, in particular at positions in the conduit where the contribution of diffusive pressure propagation remains small, that is, at monitoring distances large compared to classic scaling for penetration depth using hydraulic diffusivity. During periodic pumping tests the reverse response is potentially triggered various times within one period and thus chances to unequivocally recognize this effect are largely enhanced in comparison to conventional pulse or step testing procedures. The standard scaling relation for diffusion processes, often employed in the analysis of induced seismicity, has limited applicability to deformable fractures.

Description: Satellite radar altimetry observations are used to derive short wavelength gravity anomaly fields over the Persian Gulf and the Caspian Sea, where in situ and ship-borne gravity measurements have limited spatial coverage. In this study the retracking algorithm ‘Extrema Retracking’ (ExtR) was employed to improve sea surface height (SSH) measurements that are highly biased in the study regions due to land contaminations in the footprints of the satellite altimetry observations. ExtR was applied to the waveforms sampled by the five satellite radar altimetry missions: TOPEX/POSEIDON, JASON-1, JASON-2, GFO and ERS-1. Along-track slopes have been estimated from the improved SSH measurements and used in an iterative process to estimate deflections of the vertical, and subsequently, the desired gravity anomalies. The main steps of the gravity anomaly computations involve estimating improved SSH using the ExtR technique, computing deflections of the vertical from interpolated SSHs on a regular grid using a biharmonic spline interpolation and finally estimating gridded gravity anomalies. A remove–compute–restore algorithm, based on the fast Fourier transform, has been applied to convert deflections of the vertical into gravity anomalies. Finally, spline interpolation has been used to estimate regular gravity anomaly grids over the two study regions. Results were evaluated by comparing the estimated altimetry-derived gravity anomalies (with and without implementing the ExtR algorithm) with ship-borne free air gravity anomaly observations, and free air gravity anomalies from the Earth Gravitational Model 2008 (EGM2008). The comparison indicates a range of 3–5 mGal in the residuals, which were computed by taking the differences between the retracked altimetry-derived gravity anomaly and the ship-borne data. The comparison of retracked data with ship-borne data indicates a range in the root-mean-square-error (RMSE) between approximately 1.8 and 4.4 mGal and a bias between 0.4062 and 2.1413 mGal over different areas. Also a maximum RMSE of 4.4069 mGal, with a mean value of 0.7615 mGal was obtained in the residuals. An average improvement of 5.2746 mGal in the RMSE of the altimetry-derived gravity anomalies corresponding to 89.9 per cent was obtained after applying the ExtR post-processing.

Description: Subduction zones exhibit variable degrees of interseismic coupling as resolved by inversions of geodetic data and analyses of seismic energy release. The degree to which a plate boundary fault is coupled can have profound effects on its seismogenic behaviour. Here we use GPS measurements to estimate co- and post-seismic deformation from the 2012 August 27, M w 7.3 megathrust earthquake offshore El Salvador, which was a tsunami earthquake. Inversions of estimated coseismic displacements are in agreement with published seismically derived source models, which indicate shallow (〈20 km depth) rupture of the plate interface. Measured post-seismic deformation in the first year following the earthquake exceeds the coseismic deformation. Our analysis indicates that the post-seismic deformation is dominated by afterslip, as opposed to viscous relaxation, and we estimate a post-seismic moment release one to eight times greater than the coseismic moment during the first 500 d, depending on the relative location of coseismic versus post-seismic slip on the plate interface. We suggest that the excessive post-seismic motion is characteristic for the El Salvador–Nicaragua segment of the Central American margin and may be a characteristic of margins hosting tsunami earthquakes.

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 discuss an inverse source formulation aimed at focusing wave energy produced by ground surface sources to target subsurface poroelastic formations. The intent of the focusing is to facilitate or enhance the mobility of oil entrapped within the target formation. The underlying forward wave propagation problem is cast in two spatial dimensions for a heterogeneous poroelastic target embedded within a heterogeneous elastic semi-infinite host. The semi-infiniteness of the elastic host is simulated by augmenting the (finite) computational domain with a buffer of perfectly matched layers. The inverse source algorithm is based on a systematic framework of partial-differential-equation-constrained optimization. It is demonstrated, via numerical experiments, that the algorithm is capable of converging to the spatial and temporal characteristics of surface loads that maximize energy delivery to the target formation. Consequently, the methodology is well-suited for designing field implementations that could meet a desired oil mobility threshold. Even though the methodology, and the results presented herein are in two dimensions, extensions to three dimensions are straightforward.

Description: Attenuating random noise is of great significance in seismic data processing. In recent years, time–frequency peak filtering (TFPF) has been successfully applied to seismic random noise attenuation field. However, a fixed window length (WL) is used in the conventional TFPF. Since a short WL in the TFPF is used to preserve signals while a long WL can eliminate random noise effectively, signal preserving and noise attenuation cannot be balanced by a fixed WL especially when the signal-to-noise ratio of the noisy seismic record is low. Thus, we need to divide a noisy signal into signal and noise segments before the filtering. Then a short WL is used to the signal segments to preserve signals and a long WL is chosen for noise segments to eliminate random noise. In this paper, we test the smoothness of signals and random noise in time using the Hurst exponent which is a statistic for representing smoothness characteristics of signals. The time-series of signals with higher smoothness which lead to larger Hurst exponent values, however random noise is a random series in time without fixed waveforms and thus its smoothness is low, so the signal and noise segments can be divided by the Hurst exponent values. After the segmentation, we can adopt different filtering WLs in the TFPF for different segments to make a trade-off between signal preserving and random noise attenuation. Synthetic and real data experiments demonstrate that the proposed method can remove random noise from seismic record and preserve reflection events effectively.

Description: A key aspect of RNA secondary structure prediction is the identification of novel functional elements. This is a challenging task because these elements typically are embedded in longer transcripts where the borders between the element and flanking regions have to be defined. The flanking sequences impact the folding of the functional elements both at the level of computational analyses and when the element is extracted as a transcript for experimental analysis. Here, we analyze how different flanking region lengths impact folding into a constrained structure by computing probabilities of folding for different sizes of flanking regions. Our method, RNAcop (RNA context optimization by probability), is tested on known and de novo predicted structures. In vitro experiments support the computational analysis and suggest that for a number of structures, choosing proper lengths of flanking regions is critical. RNAcop is available as web server and stand-alone software via http://rth.dk/resources/rnacop .

Description: Often in geophysical monitoring experiments time-lapse inversion models vary too smoothly with time, owing to the strong imprint of regularization. Several methods have been proposed for focusing the spatiotemporal changes of the model parameters. In this study, we present two generalizations of the minimum support norm, which favour compact time-lapse changes and can be adapted to the specific problem requirements. Inversion results from synthetic direct current resistivity models that mimic developing plumes show that the focusing scheme significantly improves size, shape and magnitude estimates of the time-lapse changes. Inversions of the synthetic data also illustrate that the focused inversion gives robust results and that the focusing settings are easily chosen. Inversions of full-decay time-domain induced polarization (IP) field data from a CO 2 monitoring injection experiment show that the focusing scheme performs well for field data and inversions for all four Cole–Cole polarization parameters. Our tests show that the generalized minimum support norms react in an intuitive and predictable way to the norm settings, implying that they can be used in time-lapse experiments for obtaining reliable and robust results.

Description: We present a series of processes for understanding and analysing controlled-source electromagnetic (CSEM) responses for a conductive and permeable earth. To realize the CSEM response, a new 3-D CSEM forward modelling algorithm based on an edge finite element method for both electrically conductive and magnetically permeable heterogeneities is developed. The algorithm shows highly accurate results in validation tests against a semi-analytic solution for stratified earth and an integral form of the scattered field. We describe the vector behaviour of an anomalous magnetic field originating from a conductive and permeable anomaly when the loop sources are deployed over a conductive half-space. The CSEM response of the conductive and permeable anomaly is classified into three effects originating from: conductivity perturbations, permeability perturbations and the coupling of these two effects. The separated individual results and the corresponding integral equation form of the anomalous field help to better understand the physical behaviour. We confirm the characteristic features of the CSEM response from the conductive and permeable anomaly, for example, (1) the general dominance of the induction effect in the out-of-phase response accompanied by a non-negligible magnetization effect from the magnetic anomaly in a conductive half-space and (2) the dominance of near frequency-independent magnetization effects in the in-phase response at relatively low frequencies and change in ruling part of the in-phase response into the induction effect as the frequency increases. We also demonstrate the effect of coupling mode and show that its maximum contribution is limited to a few per cent level of other two modes, induction and magnetization mode, even when the heterogeneity of our model is strong. In our synthetic survey, using examples of land-based profiling surveys of low induction number and intermediate regime, we find that the effect of magnetization can be used as an indicator of the existence of magnetic material. One important point to note from this study is the importance of accurate cancelling-out or estimation of free-space responses, which can mask the magnetic responses to imaging the varying magnetic property.

Description: Extraction of fluids from subsurface reservoirs induces changes in pore pressure, leading not only to geomechanical changes, but also perturbations in seismic velocities and hence observable seismic attributes. Time-lapse seismic analysis can be used to estimate changes in subsurface hydromechanical properties and thus act as a monitoring tool for geological reservoirs. The ability to observe and quantify changes in fluid, stress and strain using seismic techniques has important implications for monitoring risk not only for petroleum applications but also for geological storage of CO 2 and nuclear waste scenarios. In this paper, we integrate hydromechanical simulation results with rock physics models and full-waveform seismic modelling to assess time-lapse seismic attribute resolution for dynamic reservoir characterization and hydromechanical model calibration. The time-lapse seismic simulations use a dynamic elastic reservoir model based on a North Sea deep reservoir undergoing large pressure changes. The time-lapse seismic traveltime shifts and time strains calculated from the modelled and processed synthetic data sets (i.e. pre-stack and post-stack data) are in a reasonable agreement with the true earth models, indicating the feasibility of using 1-D strain rock physics transform and time-lapse seismic processing methodology. Estimated vertical traveltime shifts for the overburden and the majority of the reservoir are within ±1 ms of the true earth model values, indicating that the time-lapse technique is sufficiently accurate for predicting overburden velocity changes and hence geomechanical effects. Characterization of deeper structure below the overburden becomes less accurate, where more advanced time-lapse seismic processing and migration is needed to handle the complex geometry and strong lateral induced velocity changes. Nevertheless, both migrated full-offset pre-stack and near-offset post-stack data image the general features of both the overburden and reservoir units. More importantly, the results from this study indicate that integrated seismic and hydromechanical modelling can help constrain time-lapse uncertainty and hence reduce risk due to fluid extraction and injection.

Description: A new plate motions model for the northwest Africa–North America Plate pair during the Oligocene and early Miocene is presented. The model is accompanied by a high-resolution isochron map for the central Atlantic region, resulting from a re-examination of 423 ship tracks from the NGDC data base for the area between the 15°20' FZ and the Azores triple junction. A new digital model of fracture zones for this region and a set of 309 magnetic profiles crossing the Oligocene to recent oceanic crust within the study area allowed to determine accurate finite reconstruction poles for the North America–northwest Africa conjugate plate pair between the early Miocene (Chron 6) and the early Oligocene (Chron 13). For times older than Chron 7 (~25 Ma), the finite reconstruction poles were calculated using a reliable data set coming exclusively from the region south of the Canary Islands FZ (~32°N), which allowed to test the rigidity of the northwest African oceanic lithosphere during the Oligocene–early Miocene phase of Atlas orogeny. A comparison of theoretical magnetic isochrons with observed magnetic lineations systematically shows that anomalously high spreading rates occurred in the area north of the Canary Islands FZ before Chron 7, thereby suggesting that the formation of the Atlas mountain, rather than being a localized intracontinental process, was logically linked to the central Atlantic spreading history. Thus, an independent Moroccan Plate could have existed during the Oligocene–early Miocene time interval, which included both the oceanic lithosphere north of the Canary Islands FZ and the northern Maghrebian areas of Morocco, Algeria and Tunisia. In this eventuality, the Atlas mountain belt should be reinterpreted as a giant flower structure associated with dextral transpression.

Description: Spectral induced polarization measurements are affected by temperature variations due to a variety of temperature-dependent parameters that control the complex electrical conductivity. Most important is the influence of the ion mobility, which increases with increasing temperature. It is responsible for the increase of the conductivity of the fluid in the pores with temperature and influences the electrical double layer on the mineral surface. This work is based on laboratory measurements of 13 sandstone samples from different sources with different geological and petrophysical characteristics. We measured the complex impedance in a frequency range from 0.01 to 100 Hz and a temperature range from 0 to 40 °C. The main observation is a decrease of the characteristic time (defined by the inverse of the frequency, at which the phase shift is maximum) with increasing temperature. The strength of this decrease differs from one sample to another. The temperature dependence of the phase shift magnitude cannot easily be generalized, as it depends on the particular sample. The experimental findings suggest that neglecting the influence of temperature on complex conductivity may lead to significant errors when estimating hydraulic conductivity from relaxation time. We also simulate the temperature dependence with a theoretical model of membrane polarization and review some of the model properties, with an emphasis on the temperature dependence of the parameters. The model reproduces several features characterizing the measured data, including the temperature dependence of the characteristic times. Computed tomography and microscope images of the pore structure of three samples also allow us to associate differences in the geometrical parameters used in the modelling with pore scale parameters of the actual samples.

Description: A sequence of large earthquakes occurred along the North Anatolian fault in the 20th century. These earthquakes, including the 1999 Izmit/Düzce earthquakes, generally propagated westward towards the Marmara Sea, defining the Main Marmara fault as a potential seismic gap. It is important to conduct a detailed assessment of the seismic hazards along the main Marmara fault because the megacity Istanbul lies only approximately 10 km north of the eastern segment of the Main Marmara fault, which is referred to as the Princes’ Islands Fault segment (PIF). Here, we study the locking status of this fault segment to evaluate the seismic hazard potential. For the first time, combined ascending and descending Interferometric Synthetic Aperture Radar and Global Positioning System observations were used to investigate the crustal deformation associated with the PIF. After careful corrections of the estimated ground velocity, a deformation pattern relating to fault locking near the Princes’ Islands was identified. The modeling results revealed that the slip rate and locking depth of the fault segment show a clear trade-off, which were estimated as 18.9 ± 7.2 mm yr –1 and 12.1 ± 7.0 km, respectively. With a moment accumulation rate of 1.7 ± 0.4  x  10 17 Nm yr –1 (proportional to the product of slip rate and locking depth), our results imply a build-up of a geodetic moment on the PIF and therefore a potential for earthquake hazards in the vicinity of the Istanbul megacity.

Description: Knowledge about the pressure dependency of elastic and electrical properties is important for a variety of geophysical applications. We present a technique to invert for the stiff and compliant porosity from velocity measurements made as a function of differential pressure on saturated sandstones. A dual porosity concept is used for dry rock compressibility and a squirt model is employed for the pressure and frequency dependent elastic properties of the rocks when saturated. The total porosity obtained from inversion shows satisfactory agreement with experimental results. The electrical cementation factor was determined using the inverted porosity in combination with measured electrical conductivity. It was found that cementation factor increased exponentially with increasing differential pressure during isostatic loading. Elastic compressibility, electrical cementation factor and electrical conductivity of the saturated rocks correlate linearly with compliant porosity, and electrical cementation factor and electrical conductivity exhibit linear correlations with elastic compressibility of the saturated rocks under loading. The results show that the dual porosity concept is sufficient to explain the pressure dependency of elastic, electrical and joint elastic-electrical properties of saturated porous sandstones.

Description: A new plate motions model for the northwest Africa–North America Plate pair during the Oligocene and early Miocene is presented. The model is accompanied by a high-resolution isochron map for the central Atlantic region, resulting from a re-examination of 423 ship tracks from the NGDC data base for the area between the 15°20' FZ and the Azores triple junction. A new digital model of fracture zones for this region and a set of 309 magnetic profiles crossing the Oligocene to recent oceanic crust within the study area allowed to determine accurate finite reconstruction poles for the North America–northwest Africa conjugate plate pair between the early Miocene (Chron 6) and the early Oligocene (Chron 13). For times older than Chron 7 (~25 Ma), the finite reconstruction poles were calculated using a reliable data set coming exclusively from the region south of the Canary Islands FZ (~32°N), which allowed to test the rigidity of the northwest African oceanic lithosphere during the Oligocene–early Miocene phase of Atlas orogeny. A comparison of theoretical magnetic isochrons with observed magnetic lineations systematically shows that anomalously high spreading rates occurred in the area north of the Canary Islands FZ before Chron 7, thereby suggesting that the formation of the Atlas mountain, rather than being a localized intracontinental process, was logically linked to the central Atlantic spreading history. Thus, an independent Moroccan Plate could have existed during the Oligocene–early Miocene time interval, which included both the oceanic lithosphere north of the Canary Islands FZ and the northern Maghrebian areas of Morocco, Algeria and Tunisia. In this eventuality, the Atlas mountain belt should be reinterpreted as a giant flower structure associated with dextral transpression.

Description: We present a distributed slip model for the 1999 M w 6.3 Chamoli earthquake of north India using interferometric synthetic aperture radar (InSAR) data from both ascending and descending orbits and Bayesian estimation of confidence levels and trade-offs of the model geometry parameters. The results of fault-slip inversion in an elastic half-space show that the earthquake ruptured a $9 _{ - 2.2}^{\circ + 3.4}$ northeast-dipping plane with a maximum slip of ~1 m. The fault plane is located at a depth of ~ $15.9_{ - 3.0}^{ + 1.1}$ km and is ~120 km north of the Main Frontal Thrust, implying that the rupture plane was on the northernmost detachment near the mid-crustal ramp of the Main Himalayan Thrust. The InSAR-determined moment is 3.35 x 10 18 Nm with a shear modulus of 30 GPa, equivalent to M w 6.3, which is smaller than the seismic moment estimates of M w 6.4–6.6. Possible reasons for this discrepancy include the trade-off between moment and depth, uncertainties in seismic moment tensor components for shallow dip-slip earthquakes and the role of earth structure models in the inversions. The released seismic energy from recent earthquakes in the Garhwal region is far less than the accumulated strain energy since the 1803 M s 7.5 earthquake, implying substantial hazard of future great earthquakes.

Description: Maximizing vertical resolution is a key objective in seismic data processing. Early deconvolution and spectral balancing algorithms assumed that the seismic source wavelet was temporally invariant, or stationary. In practice, seismic scattering and attenuation give rise to non-stationary seismic source wavelets. To address this issue, most conventional time-varying deconvolution wavelet shaping and spectral modelling techniques using the stationary polynomial fitting assume the wavelet to be locally stationary within a small number of overlapping analysis windows while the fitting coefficients are invariant with all the frequencies. In this paper, we show an improvement obtained by modelling smoothly varying spectra of the seismic wavelet using non-stationary polynomial fitting in the time–frequency domain. We first decompose each seismic trace using a generalized S-transform that provides a good time–frequency distribution for the estimation of the time-varying wavelet spectra. We then model the slowly varying source wavelet spectrum at each time sample by a smooth low-order polynomial. Finally, we spectrally balance the modelled wavelet to flatten the seismic response, thereby increasing vertical resolution. We calibrate the algorithm on a simple synthetic and then apply it to a 3-D land survey acquired in western China, showing the value on both vertical slices through seismic amplitude and attribute time slices. Our new algorithm significantly improves the vertical resolution of the seismic signal, while not increasing the noise.

Description: Knowledge about the pressure dependency of elastic and electrical properties is important for a variety of geophysical applications. We present a technique to invert for the stiff and compliant porosity from velocity measurements made as a function of differential pressure on saturated sandstones. A dual porosity concept is used for dry rock compressibility and a squirt model is employed for the pressure and frequency dependent elastic properties of the rocks when saturated. The total porosity obtained from inversion shows satisfactory agreement with experimental results. The electrical cementation factor was determined using the inverted porosity in combination with measured electrical conductivity. It was found that cementation factor increased exponentially with increasing differential pressure during isostatic loading. Elastic compressibility, electrical cementation factor and electrical conductivity of the saturated rocks correlate linearly with compliant porosity, and electrical cementation factor and electrical conductivity exhibit linear correlations with elastic compressibility of the saturated rocks under loading. The results show that the dual porosity concept is sufficient to explain the pressure dependency of elastic, electrical and joint elastic-electrical properties of saturated porous sandstones.

Description: It is being increasingly realized that nucleosome organization on DNA crucially regulates DNA–protein interactions and the resulting gene expression. While the spatial character of the nucleosome positioning on DNA has been experimentally and theoretically studied extensively, the temporal character is poorly understood. Accounting for ATPase activity and DNA-sequence effects on nucleosome kinetics, we develop a theoretical method to estimate the time of continuous exposure of binding sites of non-histone proteins (e.g. transcription factors and TATA binding proteins) along any genome. Applying the method to Saccharomyces cerevisiae , we show that the exposure timescales are determined by cooperative dynamics of multiple nucleosomes, and their behavior is often different from expectations based on static nucleosome occupancy. Examining exposure times in the promoters of GAL1 and PHO5, we show that our theoretical predictions are consistent with known experiments. We apply our method genome-wide and discover huge gene-to-gene variability of mean exposure times of TATA boxes and patches adjacent to TSS (+1 nucleosome region); the resulting timescale distributions have non-exponential tails.

Description: We use a Bayesian formalism combined with a grid node discretization for the linear inversion of gravimetric data in terms of 3-D density distribution. The forward modelling and the inversion method are derived from seismological inversion techniques in order to facilitate joint inversion or interpretation of density and seismic velocity models. The Bayesian formulation introduces covariance matrices on model parameters to regularize the ill-posed problem and reduce the non-uniqueness of the solution. This formalism favours smooth solutions and allows us to specify a spatial correlation length and to perform inversions at multiple scales. We also extract resolution parameters from the resolution matrix to discuss how well our density models are resolved. This method is applied to the inversion of data from the volcanic island of Basse-Terre in Guadeloupe, Lesser Antilles. A series of synthetic tests are performed to investigate advantages and limitations of the methodology in this context. This study results in the first 3-D density models of the island of Basse-Terre for which we identify: (i) a southward decrease of densities parallel to the migration of volcanic activity within the island, (ii) three dense anomalies beneath Petite Plaine Valley, Beaugendre Valley and the Grande-Découverte-Carmichaël-Soufrière Complex that may reflect the trace of former major volcanic feeding systems, (iii) shallow low-density anomalies in the southern part of Basse-Terre, especially around La Soufrière active volcano, Piton de Bouillante edifice and along the western coast, reflecting the presence of hydrothermal systems and fractured and altered rocks.

Description: In order to perform gas exploration and determine the distribution pattern of gas in the Yanchang Oil Field in the eastern part of the North Shaanxi Slope, Ordos Basin, China, gravity and magnetic survey data were systemically collated, processed and interpreted in combination with the drilling data and recent seismic data. The genesis of gravity and magnetic anomalies and the relationship between the characteristics of the gravity and magnetic fields and known gas distribution were explored in order to predict the favourable exploration targets for gas. Gravity anomalies resulted both from the lateral variation in density of the basement rock and lateral lithologic transformation in the sedimentary cover. The regional magnetic anomalies were mainly caused by the basement metamorphic rocks and the residual magnetic anomalies may reflect the amount and general location of the volcanic materials in the overlying strata. The residual gravity and magnetic anomalies generated by high-density sandstone and high content of volcanics in the gas reservoir of the upper Paleozoic distorted and deformed the anomaly curves when they were stacked onto the primary background anomaly. The gas wells were generally found to be located in the anomaly gradient zones, or the distorted part of contour lines, and the flanks of high and low anomalies, or the transitional zones between anomaly highs and lows. The characteristics of gravity and magnetic fields provide significant information that can be used for guidance when exploring the distribution of gas. Based on these characteristics, five favourable areas for gas exploration were identified; these are quasi-equally spaced like a strip extending from the southeast to the northwest.

Description: We compute the gravimetric factor at the Chandler wobble (CW) frequency using time-series from superconducting gravimeters (SG) longer than a decade. We first individually process the polar motion and data at each individual gravity station to estimate the gravimetric factor amplitude and phase, then we make a global analysis by applying a stacking method to different subsets of up to seven SG stations. The stacking is an efficient way of getting rid of local effects and improving the signal-to-noise ratio of the combined data sets. Using the stacking method, we find a gravimetric factor amplitude and phase of 1.118 ± 0.016 and –0.45 ± 0.66 deg, respectively, which is smaller in amplitude than expected. The sources of error are then carefully considered. For both local and global analyses, the uncertainties on our results are reliably constrained by computing the standard deviation of the estimates of the gravimetric factor amplitude and phase for increasing length of the time-series. Constraints on the CW anelastic dissipation can be set since any departure of the gravimetric factor from its elastic value may provide some insights into the dissipative processes that occur at the CW period. In particular, assuming given rheological models for the Earth's mantle enables us to make the link between the gravimetric factor phase and the CW quality factor.

Description: Spectral induced polarization measurements are affected by temperature variations due to a variety of temperature-dependent parameters that control the complex electrical conductivity. Most important is the influence of the ion mobility, which increases with increasing temperature. It is responsible for the increase of the conductivity of the fluid in the pores with temperature and influences the electrical double layer on the mineral surface. This work is based on laboratory measurements of 13 sandstone samples from different sources with different geological and petrophysical characteristics. We measured the complex impedance in a frequency range from 0.01 to 100 Hz and a temperature range from 0 to 40 °C. The main observation is a decrease of the characteristic time (defined by the inverse of the frequency, at which the phase shift is maximum) with increasing temperature. The strength of this decrease differs from one sample to another. The temperature dependence of the phase shift magnitude cannot easily be generalized, as it depends on the particular sample. The experimental findings suggest that neglecting the influence of temperature on complex conductivity may lead to significant errors when estimating hydraulic conductivity from relaxation time. We also simulate the temperature dependence with a theoretical model of membrane polarization and review some of the model properties, with an emphasis on the temperature dependence of the parameters. The model reproduces several features characterizing the measured data, including the temperature dependence of the characteristic times. Computed tomography and microscope images of the pore structure of three samples also allow us to associate differences in the geometrical parameters used in the modelling with pore scale parameters of the actual samples.

Description: The streaming potential phenomenon is produced by the flow of an electrolyte in a porous medium and is used for geophysical prospecting. It is quantified through an electrokinetic (EK) coefficient. The dependence of the EK coefficient on the conductivity of the electrolyte is described by the Helmholtz–Smoluchowski (HS) equation. This equation provides successful forecasts of the EK coefficient in the standard range of concentration. However, experimental measurements show deviations to this equation at extreme low and extreme high salinities. The aim of this study is to model the EK coefficient using Lattice Boltzmann simulations in a 2-D capillary channel, with a view to understanding these deviations. The effect of the constitutive parameters of the HS equation such as the permittivity and the viscosity is discussed. The validity of the HS equation using strong potentials is assessed. Finally, a model of bulk fluid conductivity is derived. This model allows to take into account the change of local ionic distribution in the vicinity of the mineral. It appears to have a significant impact on the derivation of potentials at low salinities and in the presence of polyvalent counterions.

Description: Analysing independent 1-yr data sets of 10 European superconducting gravimeters (SG) reveals statistically significant temporal variations of M2 tidal parameters. Both common short-term (〈2 yr) and long-term (〉2 yr) features are identified in all SG time-series but one. The averaged variations of the amplitude factor are about 0.2. The path of load vector variations equivalent to the temporal changes of tidal parameters suggests the presence of an 8.85 yr modulation (lunar perigee). The tidal waves having the potential to modulate M2 with this period belong to the 3rd degree constituents. Their amplitude factors turn out to be much closer to body tide model predictions than that of the main 2nd degree M2, which indicates ocean loading for 3rd degree waves to be less prominent than for 2nd degree waves within the M2 group. These two different responses to the loading suggest that the observed modulation is more due to insufficient frequency resolution of limited time-series rather than to time variable loading. Presently, SG gravity time-series are still too short to prove if time variable loading processes are involved too as in case of the annual M2 modulation known to appear for analysis intervals of less than 1 yr. Whatever the variations are caused by, they provide the upper accuracy limit for earth model validation and permit estimating the temporal stability of SG scale factors and assessing the quality of gravity time-series.

Description: Extraction of fluids from subsurface reservoirs induces changes in pore pressure, leading not only to geomechanical changes, but also perturbations in seismic velocities and hence observable seismic attributes. Time-lapse seismic analysis can be used to estimate changes in subsurface hydromechanical properties and thus act as a monitoring tool for geological reservoirs. The ability to observe and quantify changes in fluid, stress and strain using seismic techniques has important implications for monitoring risk not only for petroleum applications but also for geological storage of CO 2 and nuclear waste scenarios. In this paper, we integrate hydromechanical simulation results with rock physics models and full-waveform seismic modelling to assess time-lapse seismic attribute resolution for dynamic reservoir characterization and hydromechanical model calibration. The time-lapse seismic simulations use a dynamic elastic reservoir model based on a North Sea deep reservoir undergoing large pressure changes. The time-lapse seismic traveltime shifts and time strains calculated from the modelled and processed synthetic data sets (i.e. pre-stack and post-stack data) are in a reasonable agreement with the true earth models, indicating the feasibility of using 1-D strain rock physics transform and time-lapse seismic processing methodology. Estimated vertical traveltime shifts for the overburden and the majority of the reservoir are within ±1 ms of the true earth model values, indicating that the time-lapse technique is sufficiently accurate for predicting overburden velocity changes and hence geomechanical effects. Characterization of deeper structure below the overburden becomes less accurate, where more advanced time-lapse seismic processing and migration is needed to handle the complex geometry and strong lateral induced velocity changes. Nevertheless, both migrated full-offset pre-stack and near-offset post-stack data image the general features of both the overburden and reservoir units. More importantly, the results from this study indicate that integrated seismic and hydromechanical modelling can help constrain time-lapse uncertainty and hence reduce risk due to fluid extraction and injection.

Description: A sequence of large earthquakes occurred along the North Anatolian fault in the 20th century. These earthquakes, including the 1999 Izmit/Düzce earthquakes, generally propagated westward towards the Marmara Sea, defining the Main Marmara fault as a potential seismic gap. It is important to conduct a detailed assessment of the seismic hazards along the main Marmara fault because the megacity Istanbul lies only approximately 10 km north of the eastern segment of the Main Marmara fault, which is referred to as the Princes’ Islands Fault segment (PIF). Here, we study the locking status of this fault segment to evaluate the seismic hazard potential. For the first time, combined ascending and descending Interferometric Synthetic Aperture Radar and Global Positioning System observations were used to investigate the crustal deformation associated with the PIF. After careful corrections of the estimated ground velocity, a deformation pattern relating to fault locking near the Princes’ Islands was identified. The modeling results revealed that the slip rate and locking depth of the fault segment show a clear trade-off, which were estimated as 18.9 ± 7.2 mm yr –1 and 12.1 ± 7.0 km, respectively. With a moment accumulation rate of 1.7 ± 0.4  x  10 17 Nm yr –1 (proportional to the product of slip rate and locking depth), our results imply a build-up of a geodetic moment on the PIF and therefore a potential for earthquake hazards in the vicinity of the Istanbul megacity.

Description: Deformation analysis in general and strain analysis in particular using permanent GPS networks require proper analysis of time-series in which all functional effects are taken into consideration and all stochastic effects are captured using an appropriate noise model. This contribution addresses both issues when considering the strain parameters of a GPS network. Estimates of spatial correlation, time correlated noise, and multivariate power spectrum for daily position time-series of the Southern California Integrated GPS Network (SCIGN) stations collected between 1996 and 2011 are obtained. Significant signals with periods of 13.63 d and those related to the GPS draconitic year are identified in these time-series. We aim to assess the effect of a realistic noise model of the series on the uncertainties of the strain parameters including displacements, normal and shear strains, and rotations. For the SCIGN network considered, the following results are highlighted. Contrary to the common belief, the uncertainties of the displacements parameters become smaller when taking a realistic noise model into account. This however was not the case when assessing the noise characteristics of the normal and shear strain, and rotation parameters. The uncertainties increase nearly by a factor of two, in agreement to what is expected. Some of the significant deformation parameters of the white noise model become less significant in case of the realistic noise model.

Description: An experimental system is built for the electrokinetic measurements with a small scaled seismoelectric detector and a high resolution digitizer (1 MS s –1 , 22 bits). The acoustic and seismoelectric experiments are carried out in different borehole models at the high frequency of 90 kHz in the laboratory. All the localized seismoelectric signals that accompany compressional wave, shear wave and Stoneley wave are first clearly observed with a monopole source in sandstone boreholes that are saturated by tap water. The amplitudes of these signals are measured in the range of 1–120 μV, which is useful for designing the seismoelectric logging instruments. Then the amplitude ratio of electric signal to acoustic pressure (REP) for each of the three waves is calculated and compared with the theoretical simulations. Based on the experimental data, we find that seismoelectric logging signals as well as REP become stronger at the more permeable borehole model. We also find that seismoelectric logging signals are more sensitive to permeability and porosity compared with acoustic logging signals. Therefore, this study verifies the feasibility of seismoelectric well logging, and further indicates that the seismoelectric logging technique might be a preferable method to estimate formation parameters in the field measurements.

Description: Systems biologists aim to decipher the structure and dynamics of signaling and regulatory networks underpinning cellular responses; synthetic biologists can use this insight to alter existing networks or engineer de novo ones. Both tasks will benefit from an understanding of which structural and dynamic features of networks can emerge from evolutionary processes, through which intermediary steps these arise, and whether they embody general design principles. As natural evolution at the level of network dynamics is difficult to study, in silico evolution of network models can provide important insights. However, current tools used for in silico evolution of network dynamics are limited to ad hoc computer simulations and models. Here we introduce BioJazz, an extendable, user-friendly tool for simulating the evolution of dynamic biochemical networks. Unlike previous tools for in silico evolution, BioJazz allows for the evolution of cellular networks with unbounded complexity by combining rule-based modeling with an encoding of networks that is akin to a genome. We show that BioJazz can be used to implement biologically realistic selective pressures and allows exploration of the space of network architectures and dynamics that implement prescribed physiological functions. BioJazz is provided as an open-source tool to facilitate its further development and use. Source code and user manuals are available at: http://oss-lab.github.io/biojazz and http://osslab.lifesci.warwick.ac.uk/BioJazz.aspx .

Description: Overpressure and buoyant effect of underlying sediments are generally used to account for the upward motion or formation of submarine mud volcanoes and mud diapirs. In this study, we process and interpret the gravity anomalies associated with the active mud diapirs off SW Taiwan. Geologically, the mud diapirs are just formed and are still very active, thus we can better understand the initial process of the mud diapirs formation through the gravity analysis. Our results show that the density contrasts of the submarine mud diapirs with respect to the surroundings are generally positive. Because the study area is in a tectonically compressive regime and the gas plume venting from the submarine mud volcanoes is very active, we thus infer that mechanically the mud diapirs off SW Taiwan have been formed mainly due to the tectonic compression on the underlying sediments of high pore-fluid pressure, instead of the buoyancy of the buried sediments. The overpressured sediments and fluid are compressed and pushed upwards to pierce the overlying sediments and form the more compacted mud diapirs. The relatively denser material of the mud diapirs probably constrains the flowing courses of the submarine canyons off SW Taiwan, especially for the upper reaches of the Kaoping and Fangliao submarine canyons.

Description: Despite the biological importance of non-coding RNA, their structural characterization remains challenging. Making use of the rapidly growing sequence databases, we analyze nucleotide coevolution across homologous sequences via Direct-Coupling Analysis to detect nucleotide-nucleotide contacts. For a representative set of riboswitches, we show that the results of Direct-Coupling Analysis in combination with a generalized Nussinov algorithm systematically improve the results of RNA secondary structure prediction beyond traditional covariance approaches based on mutual information. Even more importantly, we show that the results of Direct-Coupling Analysis are enriched in tertiary structure contacts. By integrating these predictions into molecular modeling tools, systematically improved tertiary structure predictions can be obtained, as compared to using secondary structure information alone.

Description: Crustal vertical deformation (CVD) observed by continuous GPS height time-series can be explained largely by surface loading effects recovered from both Gravity Recover and Climate Experiment (GRACE) and General Circulation Models (GCMs) data. We first show that lower degree CVD spatial spectrum due to the Earth's elastic response to a uniform surface loading plays more important roles than that of high-degree case. We then demonstrate that GRACE data with 300–400 km spatial resolution have the ability to detect 99 per cent power of global and regional CVD in spatial spectrum domain using a global frequency–wavenumber spectrum method. We can just use either GRACE or GCMs 36 degree/order (d/o) spherical harmonic coefficients (SHCs) which correspond to 500 km spatial resolution to acquire more than 90 per cent variance of total CVD modeled by up to 180 d/o SHCs at 98 per cent global gridpoints. Globally, CVD modeled by GRACE loading can explain 72 per cent annual amplitude and 69 per cent variance of GPS observed height time-series, which is better than the GCMs results of 64 per cent for annual amplitude and 41 per cent for variance. Using a three cornered hat method, we also show that the noise level of monthly averaged CVD is about 3 mm for both GPS height time-series and GRACE loading result, while that of GCMs result is only 1.3 mm.

Description: We present a new method to derive 3-D surface deformation from an integration of interferometric synthetic aperture radar (InSAR) images and Global Navigation Satellite System (GNSS) observations based on Akaike's Bayesian Information Criterion (ABIC), considering relationship between deformations of neighbouring locations. This method avoids interpolated errors by excluding the interpolation of GNSS into the same spatial resolution as InSAR images and harnesses the data sets and the prior smooth constraints of surface deformation objectively and simultaneously by using ABIC, which were inherently unresolved in previous studies. In particular, we define surface roughness measuring smoothing degree to evaluate the performance of the prior constraints and deduce the formula of the covariance for the estimation errors to estimate the uncertainty of modelled solution. We validate this method using synthetic tests and the 2008 M w 7.9 Wenchuan earthquake. We find that the optimal weights associated with ABIC minimum are generally at trade-off locations that balance contributions from InSAR, GNSS data sets and the prior constraints. We use this method to evaluate the influence of the interpolated errors from the Ordinary Kriging algorithm on the derivation of surface deformation. Tests show that the interpolated errors may contribute to biasing very large weights imposed on Kriged GNSS data, suggesting that fixing the relative weights is required in this case. We also make a comparison with SISTEM method, indicating that our method allows obtaining better estimations even with sparse GNSS observations. In addition, this method can be generalized to provide a solution for situations where some types of data sets are lacking and can be exploited further to account for data sets such as the integration of displacements along radar lines and offsets along satellite tracks.

Description: This paper presents the gravimetric analysis together with seismic data as an integral application in order to identify the continental–oceanic crust boundary (COB) of the Argentine continental margin from 36°S to 50°S in a continuous way. The gravimetric and seismic data are made up of large grids of data obtained from satellite altimetry and marine research. The methodology consists of three distinct methods: (i) the application of enhancement techniques to gravimetric anomalies, (ii) the calculation of crustal thinning from 3-D gravity inversion modelling of the crust–mantle discontinuity and (iii) 2-D gravimetric modelling supported by multichannel reflection and refraction seismic profiles. In the first method, the analytic signal, Theta map, and tilt angle and its horizontal derivative were applied. In the second method, crustal thickness was obtained as the difference in the depths of the crystalline basement and the crust–mantle discontinuity; the latter was obtained via gravimetric inversion. Finally, 2-D modelling was performed from free-air anomalies in two representative sections by considering as restriction surfaces those coming from the interpretation of seismic data. The results of the joint application of enhancement techniques and 2-D and 3-D modelling have enabled continuous interpretation of the COB. In this study, the COB was determined continuously from the integration of 2-D profiles of the enhancement techniques, taking account of crustal thickness and performing 2-D gravimetric modelling. The modelling technique was complemented by regional studies integrated with multichannel seismic reflection and seismic refraction lines, resulting in consistent enhancement techniques.

Description: While it has been known for some time that offsets in the time-series of Global Navigation Satellite System (GNSS) position estimates degrade station velocity determinations, the magnitude of the effect has not been clear. Using products of the International GNSS Service (IGS), we assess the impact empirically by injecting progressively larger numbers of artificial offsets and solving for a series of long-term secular GNSS frames. Our results show that the stability of the IGS global frame datum is fairly robust, with significant effects at the formal error level only for the R x (and Y-pole) and R z rotational orientations. On the other hand, station velocity estimates are more seriously affected, especially the vertical component. For the typical IGS station, the mean vertical rate uncertainty is already limited to 0.34 mm yr –1 for the current set of position discontinuities. If the number of breaks doubles, which might occur using newer detection schemes, then that uncertainty will worsen by ~40 per cent to 0.48 mm yr –1 . This error source is generally a more important component of realistic velocity uncertainties than any other, including accounting for temporal correlations in the GNSS data. The only way to improve future GNSS velocity estimates is to severely limit manmade displacements at the tracking stations.

Description: This work is concerned with the Biot/squirt (BISQ) models for wave propagation in saturated porous media. We show that the models allow exponentially exploding solutions, as time goes to infinity, when the characteristic squirt-flow coefficient is negative or has a non-zero imaginary part. We also show that the squirt-flow coefficient does have non-zero imaginary parts for some experimental parameters or for low angular frequencies. Because the models are linear, the existence of such exploding solutions indicates instability of the BISQ models. This result, for the first time, provides a theoretical explanation of the well-known empirical observation that BISQ model is not reliable (not consistent with Gassmann's formula) at low frequencies. It calls on a reconsideration of the widely used BISQ theory. On the other hand, we demonstrate that the 3-D isotropic BISQ model is stable when the squirt-flow coefficient is positive. In particular, the original Biot model is unconditionally stable where the squirt-flow coefficient is 1.

Description: Sequence variations in regulatory DNA regions are known to cause functionally important consequences for gene expression. DNA sequence variations may have an essential role in determining phenotypes and may be linked to disease; however, their identification through analysis of massive genome-wide sequencing data is a great challenge. In this work, a new computational pipeline, a Bayesian method for protein–DNA interaction with binding affinity ranking (BayesPI-BAR), is proposed for quantifying the effect of sequence variations on protein binding. BayesPI-BAR uses biophysical modeling of protein–DNA interactions to predict single nucleotide polymorphisms (SNPs) that cause significant changes in the binding affinity of a regulatory region for transcription factors (TFs). The method includes two new parameters (TF chemical potentials or protein concentrations and direct TF binding targets) that are neglected by previous methods. The new method is verified on 67 known human regulatory SNPs, of which 47 (70%) have predicted true TFs ranked in the top 10. Importantly, the performance of BayesPI-BAR, which uses principal component analysis to integrate multiple predictions from various TF chemical potentials, is found to be better than that of existing programs, such as sTRAP and is-rSNP, when evaluated on the same SNPs. BayesPI-BAR is a publicly available tool and is able to carry out parallelized computation, which helps to investigate a large number of TFs or SNPs and to detect disease-associated regulatory sequence variations in the sea of genome-wide noncoding regions.

Description: We have extended backwards from 2001 to 1979 the current release 05 (RL05) of the Gravity Recovery and Climate Experiment (GRACE) Atmospheric and Oceanic De-aliasing Level-1B (AOD1B) product and studied the impact of this and a previous release 04 (RL04) of the AOD1B product on precise orbits of five altimetry satellites (ERS-1, ERS-2, TOPEX/Poseidon, Envisat and Jason-1) for the time span 1991–2012, as compared to the case when no AOD1B product is used. We have found that using AOD1B RL05 product reduces root mean square (RMS) fits of satellite laser ranging (SLR) observations by about 1.0–6.4 per cent, 2-d arc overlaps in radial, cross-track and along-track directions by about 1.3–12.0, 0.3–10.0 and 2.0–10.0 per cent, respectively, for various satellites tested, as compared to the case without AOD1B product. Using AOD1B RL05 product instead of RL04 one reduces SLR RMS fits by 0.1–0.7 per cent, 2-d arc overlaps in radial, cross-track and along-track directions by 0.1–0.6, 0.1–1.3 and 0.2–1.2 per cent, respectively, for the satellite orbits tested. The multi-mission crossover analysis shows that the application of an AOD1B product reduces the scatter of radial errors by 0.4–2.8 per cent for the satellite missions studied. At the regions with the most pronounced changes the use of the AOD1B products improves the consistency between the sea level as measured by the TOPEX and ERS-2 missions and by the Jason-1 and Envisat missions by 5 to 10 per cent (globally by about 2 per cent). The results of our study show that extended AOD1B RL05 product performs better than the AOD1B RL04 and improves orbits of altimetry satellites and consistency of sea level products.

Description: Sequence elements, at all levels—DNA, RNA and protein, play a central role in mediating molecular recognition and thereby molecular regulation and signaling. Studies that focus on measuring and investigating sequence-based recognition make use of statistical and computational tools, including approaches to searching sequence motifs. State-of-the-art motif searching tools are limited in their coverage and ability to address large motif spaces. We develop and present statistical and algorithmic approaches that take as input ranked lists of sequences and return significant motifs. The efficiency of our approach, based on suffix trees, allows searches over motif spaces that are not covered by existing tools. This includes searching variable gap motifs—two half sites with a flexible length gap in between—and searching long motifs over large alphabets. We used our approach to analyze several high-throughput measurement data sets and report some validation results as well as novel suggested motifs and motif refinements. We suggest a refinement of the known estrogen receptor 1 motif in humans, where we observe gaps other than three nucleotides that also serve as significant recognition sites, as well as a variable length motif related to potential tyrosine phosphorylation.

Description: Cataloging the association of transcripts to genetic variants in recent years holds the promise for functional dissection of regulatory structure of human transcription. Here, we present a novel approach, which aims at elucidating the joint relationships between transcripts and single-nucleotide polymorphisms (SNPs). This entails detection and analysis of modules of transcripts, each weakly associated to a single genetic variant, together exposing a high-confidence association signal between the module and this ‘main’ SNP. To explore how transcripts in a module are related to causative loci for that module, we represent such dependencies by a graphical model. We applied our method to the existing data on genetics of gene expression in the liver. The modules are significantly more, larger and denser than found in permuted data. Quantification of the confidence in a module as a likelihood score, allows us to detect transcripts that do not reach genome-wide significance level. Topological analysis of each module identifies novel insights regarding the flow of causality between the main SNP and transcripts. We observe similar annotations of modules from two sources of information: the enrichment of a module in gene subsets and locus annotation of the genetic variants. This and further phenotypic analysis provide a validation for our methodology.

Description: Phase variation of surface structures occurs in diverse bacterial species due to stochastic, high frequency, reversible mutations. Multiple genes of Campylobacter jejuni are subject to phase variable gene expression due to mutations in polyC/G tracts. A modal length of nine repeats was detected for polyC/G tracts within C. jejuni genomes. Switching rates for these tracts were measured using chromosomally-located reporter constructs and high rates were observed for cj1139 (G8) and cj0031 (G9). Alteration of the cj1139 tract from G8 to G11 increased mutability 10-fold and changed the mutational pattern from predominantly insertions to mainly deletions. Using a multiplex PCR, major changes were detected in ‘on/off’ status for some phase variable genes during passage of C. jejuni in chickens. Utilization of observed switching rates in a stochastic, theoretical model of phase variation demonstrated links between mutability and genetic diversity but could not replicate observed population diversity. We propose that modal repeat numbers have evolved in C. jejuni genomes due to molecular drivers associated with the mutational patterns of these polyC/G repeats, rather than by selection for particular switching rates, and that factors other than mutational drift are responsible for generating genetic diversity during host colonization by this bacterial pathogen.

Description: Control of translation in eukaryotes is complex, depending on the binding of various factors to mRNAs. Available data for subsets of mRNAs that are translationally up- and down-regulated in yeast eIF4E-binding protein (4E-BP) deletion mutants are coupled with reported mRNA secondary structure measurements to investigate whether 5'-UTR secondary structure varies between the subsets. Genes with up-regulated translational efficiencies in the caf20 mutant have relatively high averaged 5'-UTR secondary structure. There is no apparent wide-scale correlation of RNA-binding protein preferences with the increased 5'-UTR secondary structure, leading us to speculate that the secondary structure itself may play a role in differential partitioning of mRNAs between eIF4E/4E-BP repression and eIF4E/eIF4G translation initiation. Both Caf20p and Eap1p contain stretches of positive charge in regions of predicted disorder. Such regions are also present in eIF4G and have been reported to associate with mRNA binding. The pattern of these segments, around the canonical eIF4E-binding motif, varies between each 4E-BP and eIF4G. Analysis of gene ontology shows that yeast proteins containing predicted disordered segments, with positive charge runs, are enriched for nucleic acid binding. We propose that the 4E-BPs act, in part, as differential, flexible, polyelectrostatic scaffolds for mRNAs.

Description: The activation of cryptic 5' splice sites (5' SSs) is often related to human hereditary diseases. The DNA-based mutation screening strategies are commonly used to recognize the cryptic 5' SSs, because features of the local DNA sequence can influence the choice of cryptic 5' SSs. To improve the identification of the cryptic 5' SSs, we developed a structure-based method, named SPO (structure profiles and odds measure), which combines two parameters, the structural feature derived from hydroxyl radical cleavage pattern and odds measure, to assess the likelihood of a cryptic 5' SS activation in competing with its paired authentic 5' SS. Compared to the current tools for identifying activated cryptic 5' SSs, the SPO algorithm achieves higher prediction accuracy than the other methods, including MaxEnt, MDD, Markov model, weight matrix model, Shapiro and Senapathy matrix, R i and G . In addition, the predicted SPO scores from the SPO algorithm exhibited a greater degree of correlation with the strength of cryptic 5' SS activation than that measured from the other seven methods. In conclusion, the SPO algorithm provides an optimal identification of cryptic 5' SSs, can be applied in designing mutagenesis experiments for various splicing events and may be helpful to investigate the relationship between structural variants and human hereditary diseases.

Description: Determining the taxonomic affiliation of sequences assembled from metagenomes remains a major bottleneck that affects research across the fields of environmental, clinical and evolutionary microbiology. Here, we introduce MyTaxa, a homology-based bioinformatics framework to classify metagenomic and genomic sequences with unprecedented accuracy. The distinguishing aspect of MyTaxa is that it employs all genes present in an unknown sequence as classifiers, weighting each gene based on its (predetermined) classifying power at a given taxonomic level and frequency of horizontal gene transfer. MyTaxa also implements a novel classification scheme based on the genome-aggregate average amino acid identity concept to determine the degree of novelty of sequences representing uncharacterized taxa, i.e. whether they represent novel species, genera or phyla. Application of MyTaxa on in silico generated (mock) and real metagenomes of varied read length (100–2000 bp) revealed that it correctly classified at least 5% more sequences than any other tool. The analysis also showed that ~10% of the assembled sequences from human gut metagenomes represent novel species with no sequenced representatives, several of which were highly abundant in situ such as members of the Prevotella genus. Thus, MyTaxa can find several important applications in microbial identification and diversity studies.

Description: Increasing numbers of protein structures are solved each year, but many of these structures belong to proteins whose sequences are homologous to sequences in the Protein Data Bank. Nevertheless, the structures of homologous proteins belonging to the same family contain useful information because functionally important residues are expected to preserve physico-chemical, structural and energetic features. This information forms the basis of our method, which detects RNA-binding residues of a given RNA-binding protein as those residues that preserve physico-chemical, structural and energetic features in its homologs. Tests on 81 RNA-bound and 35 RNA-free protein structures showed that our method yields a higher fraction of true RNA-binding residues (higher precision) than two structure-based and two sequence-based machine-learning methods. Because the method requires no training data set and has no parameters, its precision does not degrade when applied to ‘novel’ protein sequences unlike methods that are parameterized for a given training data set. It was used to predict the ‘unknown’ RNA-binding residues in the C-terminal RNA-binding domain of human CPEB3. The two predicted residues, F430 and F474, were experimentally verified to bind RNA, in particular F430, whose mutation to alanine or asparagine nearly abolished RNA binding. The method has been implemented in a webserver called DR_bind1, which is freely available with no login requirement at http://drbind.limlab.ibms.sinica.edu.tw .

Description: Nanotechnology and synthetic biology currently constitute one of the most innovative, interdisciplinary fields of research, poised to radically transform society in the 21st century. This paper concerns the synthetic design of ribonucleic acid molecules, using our recent algorithm, RNAiFold , which can determine all RNA sequences whose minimum free energy secondary structure is a user-specified target structure. Using RNAiFold , we design ten cis -cleaving hammerhead ribozymes, all of which are shown to be functional by a cleavage assay. We additionally use RNAiFold to design a functional cis -cleaving hammerhead as a modular unit of a synthetic larger RNA. Analysis of kinetics on this small set of hammerheads suggests that cleavage rate of computationally designed ribozymes may be correlated with positional entropy, ensemble defect, structural flexibility/rigidity and related measures. Artificial ribozymes have been designed in the past either manually or by SELEX (Systematic Evolution of Ligands by Exponential Enrichment); however, this appears to be the first purely computational design and experimental validation of novel functional ribozymes. RNAiFold is available at http://bioinformatics.bc.edu/clotelab/RNAiFold/ .

Description: The paper in question by Van Camp and co-authors [MVC] challenges previous work showing that ground gravity data arising from hydrology can provide a consistent signal for the comparison with satellite gravity data. The data sets used are similar to those used previously, that is, the gravity field as measured by the GRACE satellites versus ground-based data from superconducting gravimeters (SGs) over the same continental area, in this case Central Europe. One of the main impediments in this paper is the presentation that is frequently confusing and misleading as to what the data analysis really shows, for example, the irregular treatment of annual components that are first subtracted then reappear in the analysis. More importantly, we disagree on specific points. Two calculations are included in our comment to illustrate where we believe that the processing in [MVC] paper is deficient. The first deals with their erroneous treatment of the global hydrology using a truncated spherical harmonic approach which explains almost a factor 2 error in their computation of the loading. The second shows the effect of making the wrong assumption in the GRACE/hydrology/surface gravity comparison by inverting the whole of the hydrology loading for underground stations. We also challenge their claims that empirical orthogonal function techniques cannot be done in the presence of periodic components, and that SG data cannot be corrected for comparisons with GRACE data. The main conclusion of their paper, that there is little coherence between ground gravity stations and this invalidates GRACE comparisons, is therefore questionable. There is nothing in [MVC] that contradicts any of the previous papers that have shown clearly a strong relation between seasonal signals obtained from both ground gravity and GRACE satellite data.

Description: The influence of changes in surface ice-mass redistribution and associated viscoelastic response of the Earth, known as glacial isostatic adjustment (GIA), on the Earth's rotational dynamics has long been known. Equally important is the effect of the changes in the rotational dynamics on the viscoelastic deformation of the Earth. This signal, known as the rotational feedback, or more precisely, the rotational feedback on the sea level equation, has been mathematically described by the sea level equation extended for the term that is proportional to perturbation in the centrifugal potential and the second-degree tidal Love number. The perturbation in the centrifugal force due to changes in the Earth's rotational dynamics enters not only into the sea level equation, but also into the conservation law of linear momentum such that the internal viscoelastic force, the perturbation in the gravitational force and the perturbation in the centrifugal force are in balance. Adding the centrifugal-force perturbation to the linear-momentum balance creates an additional rotational feedback on the viscoelastic deformations of the Earth. We term this feedback mechanism, which is studied in this paper, as the rotational feedback on the linear-momentum balance. We extend both the time-domain method for modelling the GIA response of laterally heterogeneous earth models developed by Martinec and the traditional Laplace-domain method for modelling the GIA-induced rotational response to surface loading by considering the rotational feedback on linear-momentum balance. The correctness of the mathematical extensions of the methods is validated numerically by comparing the polar-motion response to the GIA process and the rotationally induced degree 2 and order 1 spherical harmonic component of the surface vertical displacement and gravity field. We present the difference between the case where the rotational feedback on linear-momentum balance is considered against that where it is not. Numerical simulations show that the resulting difference in radial displacement and sea level change between these situations since the Last Glacial Maximum reaches values of ±25 and ±1.8 m, respectively. Furthermore, the surface deformation pattern is modified by up to 10 per cent in areas of former or ongoing glaciation, but by up to 50 per cent at the bottom of the southern Indian ocean. This also results in the movement of coastlines during the last deglaciation to differ between the two cases due to the difference in the ocean loading, which is seen for instance in the area around Hudson Bay, Canada and along the Chinese, Australian or Argentinian coastlines.

Description: Passive interferometry technology is based on the relation between the reflection and the transmission responses of the subsurface. The transmission response can be received at surface in the presence of the ambient noise source in the subsurface with the cross-correlation (CC) or multidimensional deconvolution methods. We investigate the feasibility of electromagnetic (EM) wave passive interferometry with CC method. We design a 2-D finite-difference time domain (FDTD) algorithm to simulate the long-duration ground penetrating radar (GPR) measurements with random distribution of passive EM sources. The noise sources have random duration time, waveform and spatial distribution. We test the FDTD GPR passive interferometry code with above source characteristics and apply the method to light non-aqueous phase liquid (LNAPL) monitoring. Based on the model simulation data, by using common midpoint velocity analysis and normal move out correction to process the interferometry retrieve record, we can accurately obtain the dynamic changing characteristics of the target's permittivity. The LNAPL dynamic leakage model can be imaged as well. The synthetic results demonstrate that the GPR passive interferometry is feasible in subsurface LNAPL monitoring. Our work provides a foundation for a passive interferometry field application using GPR.

Description: 3-D electrical resistivity surveys and inversion models are required to accurately resolve structures in areas with very complex geology where 2-D models might suffer from artefacts. Many 3-D surveys use a grid where the number of electrodes along one direction ( x ) is much greater than in the perpendicular direction ( y ). Frequently, due to limitations in the number of independent electrodes in the multi-electrode system, the surveys use a roll-along system with a small number of parallel survey lines aligned along the x -direction. The ‘Compare R’ array optimization method previously used for 2-D surveys is adapted for such 3-D surveys. Offset versions of the inline arrays used in 2-D surveys are included in the number of possible arrays (the comprehensive data set) to improve the sensitivity to structures in between the lines. The array geometric factor and its relative error are used to filter out potentially unstable arrays in the construction of the comprehensive data set. Comparisons of the conventional (consisting of dipole-dipole and Wenner–Schlumberger arrays) and optimized arrays are made using a synthetic model and experimental measurements in a tank. The tests show that structures located between the lines are better resolved with the optimized arrays. The optimized arrays also have significantly better depth resolution compared to the conventional arrays.

Description: We apply a reversible-jump Markov chain Monte Carlo method to sample the Bayesian posterior model probability density function of 2-D seafloor resistivity as constrained by marine controlled source electromagnetic data. This density function of earth models conveys information on which parts of the model space are illuminated by the data. Whereas conventional gradient-based inversion approaches require subjective regularization choices to stabilize this highly non-linear and non-unique inverse problem and provide only a single solution with no model uncertainty information, the method we use entirely avoids model regularization. The result of our approach is an ensemble of models that can be visualized and queried to provide meaningful information about the sensitivity of the data to the subsurface, and the level of resolution of model parameters. We represent models in 2-D using a Voronoi cell parametrization. To make the 2-D problem practical, we use a source–receiver common midpoint approximation with 1-D forward modelling. Our algorithm is transdimensional and self-parametrizing where the number of resistivity cells within a 2-D depth section is variable, as are their positions and geometries. Two synthetic studies demonstrate the algorithm's use in the appraisal of a thin, segmented, resistive reservoir which makes for a challenging exploration target. As a demonstration example, we apply our method to survey data collected over the Scarborough gas field on the Northwest Australian shelf.

Description: Compressional and shear wave seismic measurements were performed in an old railway tunnel and in galleries excavated in a 250-m-thick Toarcian claystone formation in the Tournemire experimental station (France). Three component (3C) geophones and three orthogonal orientations of the vibroseismic force source were used. Additionally, vertical seismic profiling (VSP) measurements were recorded with a 3C borehole geophone, a hydrophone and a microphone in a 159 m deep borehole (ID180) in the tunnel. The seismic data show that Toarcian claystone has strong transverse isotropy (TI) with a vertical symmetry axis. The qP , SH and qSV wave propagation velocities in horizontal directions—the plane of isotropy of the TI medium—are measured as 3550, 1850 and 1290 m s –1 , respectively. The zero-offset VSP reveals that only one shear wave propagates in the vertical (depth) direction and the P - and S -wave velocities are 3100 and 1375 m s –1 , respectively. Four elastic moduli of the TI medium are determined from the seismic velocities and from the bulk density of 2.53 g cm –3 : c 11 = 31.9 GPa, c 33 = 24.3 GPa, c 44 = 4.5 GPa and c 66 = 8.7 GPa. A walkaway VSP with the borehole geophone at 50 m depth in borehole ID180 and shot points in the galleries leads to oblique seismic ray paths which allow us to determine the fifth elastic modulus of the TI medium to c 13 = 16 GPa. The tube wave recorded by a hydrophone in the water filled lower part of the borehole propagates with 1350 m s –1 , which confirms the estimate of the elastic constant c 66 . The analysis of body wave and surface wave data from a seismic experiment in Galerie Est shows reflections from several fracture zones in the gallery floor. The thickness of the excavation damaged zone (EDZ) in the floor of Galerie Est is estimated to 0.7 m.

Description: During megathrust earthquakes, great ruptures are accompanied by large scale mass redistribution inside the solid Earth and by ocean mass redistribution due to bathymetry changes. These large scale mass displacements can be detected using the monthly gravity maps of the GRACE satellite mission. In recent years it has become increasingly common to use the long wavelength changes in the Earth's gravity field observed by GRACE to infer seismic source properties for large megathrust earthquakes. An important advantage of space gravimetry is that it is independent from the availability of land for its measurements. This is relevant for observation of megathrust earthquakes, which occur mostly offshore, such as the $M_{\text{w}} \sim 9$ 2004 Sumatra–Andaman, 2010 Maule (Chile) and 2011 Tohoku-Oki (Japan) events. In Broerse et al. , we examined the effect of the presence of an ocean above the rupture on long wavelength gravity changes and showed it to be of the first order. Here we revisit the implementation of an ocean layer through the sea level equation and compare the results with approximated methods that have been used in the literature. One of the simplifications usually lies in the assumption of a globally uniform ocean layer. We show that especially in the case of the 2010 Maule earthquake, due to the closeness of the South American continent, the uniform ocean assumption is not valid and causes errors up to 57 per cent for modelled peak geoid height changes (expressed at a spherical harmonic truncation degree of 40). In addition, we show that when a large amount of slip occurs close to the trench, horizontal motions of the ocean floor play a mayor role in the ocean contribution to gravity changes. Using a slip model of the 2011 Tohoku-Oki earthquake that places the majority of slip close to the surface, the peak value in geoid height change increases by 50 per cent due to horizontal ocean floor motion. Furthermore, we test the influence of the maximum spherical harmonic degree at which the sea level equation is performed for sea level changes occurring along coastlines, which shows to be important for relative sea level changes occurring along the shore. Finally, we demonstrate that ocean floor loading, self-gravitation of water and conservation of water mass are of second order importance for coseismic gravity changes. When GRACE observations are used to determine earthquake parameters such as seismic moment or source depth, the uniform ocean layer method introduces large biases, depending on the location of the rupture with respect to the continent. The same holds for interpreting shallow slip when horizontal motions are not properly accounted for in the ocean contribution. In both cases the depth at which slip occurs will be underestimated.

Description: The Tonga-Kermadec forearc is deforming in response to on-going subduction of the Pacific Plate beneath the Indo-Australian Plate. Previous research has focussed on the structural development of the forearc where large bathymetric features such as the Hikurangi Plateau and Louisville Ridge seamount chain are being subducted. Consequently, knowledge of the ‘background’ forearc in regions of normal plate convergence is limited. We report on an ~250-km-long multichannel seismic reflection profile that was shot perpendicular to the Tonga-Kermadec trench at ~28°S to determine the lateral and temporal variations in the structure, stratigraphy and deformation of the Kermadec forearc resulting solely from Pacific Plate subduction. Interpretation of the seismic profile, in conjunction with regional swath bathymetry data, shows that the Pacific Plate exhibits horst and graben structures that accommodate bending-induced extensional stresses, generated as the trenchward dip of the crust increases. Trench infill is also much thicker than expected at 1 km which, we propose, results from increased sediment flux into and along the trench. Pervasive normal faulting of the mid-trench slope most likely accommodates the majority of the observed forearc extension in response to basal subduction erosion, and a structural high is located between the mid- and upper-trench slopes. We interpret this high as representing a dense and most likely structurally robust region of crust lying beneath this region. Sediment of the upper-trench slope documents depositional hiatuses and on-going uplift of the arc. Strong along-arc currents appear to erode the Kermadec volcanic arc and distribute this sediment to the surrounding basins, while currents over the forearc redistribute deposits as sediment waves. Minor uplift of the transitional Kermadec forearc, observed just to the north of the profile, appears to relate to an underlying structural trend as well as subduction of the Louisville Ridge seamount chain 250 km to the north. Relative uplift of the Kermadec arc is observed from changes in the tilt of upper-trench slope deposits and extensional faulting of the basement immediately surrounding the Louisville Ridge.

Description: While mRNA stability has been demonstrated to control rates of translation, generating both global and local synonymous codon biases in many unicellular organisms, this explanation cannot adequately explain why codon bias strongly tracks neighboring intergene GC content; suggesting that structural dynamics of DNA might also influence codon choice. Because minor groove width is highly governed by 3-base periodicity in GC, the existence of triplet-based codons might imply a functional role for the optimization of local DNA molecular dynamics via GC content at synonymous sites (GC3). We confirm a strong association between GC3-related intrinsic DNA flexibility and codon bias across 24 different prokaryotic multiple whole-genome alignments. We develop a novel test of natural selection targeting synonymous sites and demonstrate that GC3-related DNA backbone dynamics have been subject to moderate selective pressure, perhaps contributing to our observation that many genes possess extreme DNA backbone dynamics for their given protein space. This dual function of codons may impose universal functional constraints affecting the evolution of synonymous and non-synonymous sites. We propose that synonymous sites may have evolved as an ‘accessory’ during an early expansion of a primordial genetic code, allowing for multiplexed protein coding and structural dynamic information within the same molecular context.

Description: Long-term volcanic subsidence provides insight into intereruptive processes, which comprise the longest portion of the eruptive cycle. Ground-based geodetic surveys of Medicine Lake Volcano (MLV), northern CA, document subsidence at rates of ~–10 mm yr –1 between 1954 and 2004. The long observation period plus the duration and stable magnitude of this signal presents an ideal opportunity to study long-term volcanic deformation, but this first requires accurate knowledge of the geometry and magnitude of the source. Best-fitting analytical source models to past levelling and GPS data sets show conflicting source parameters—primarily the model depth. To overcome this, we combine multiple tracks of InSAR data, each with a different look angle, to improve upon the spatial resolution of ground-based measurements. We compare the results from InSAR to those of past geodetic studies, extending the geodetic record to 2011 and demonstrating that subsidence at MLV continues at ~–10 mm yr –1 . Using geophysical inversions, we obtain the best-fitting analytical source model—a sill located at 9–10 km depth beneath the caldera. This model geometry is similar to those of past studies, providing a good fit to the high spatial density of InSAR measurements, while accounting for the high ratio of vertical to horizontal deformation derived from InSAR and recorded by existing levelling and GPS data sets. We discuss possible causes of subsidence and show that this model supports the hypothesis that deformation at MLV is driven by tectonic extension, gravitational loading, plus a component of volume loss at depth, most likely due to cooling and crystallization within the intrusive complex that underlies the edifice. Past InSAR surveys at MLV, and throughout the Cascades, are of variable success due to dense vegetation, snow cover and atmospheric artefacts. In this study, we demonstrate how InSAR may be successfully used in this setting by applying a suite of multitemporal analysis methods that account for atmospheric and orbital noise sources. These methods include: a stacking strategy based upon the noise characteristics of each data set; pixelwise rate-map formation (-RATE) and persistent scatterer InSAR (StaMPS).

Description: In the literature, the inverted coseismic slip models from seismological and geodetic data for the 2011 Tohoku-Oki earthquake portray significant discrepancies, in particular regarding the intensity and the distribution of the rupture near the trench. For a megathrust earthquake, it is difficult to discern the slip along the shallow part of the fault from the geodetic data, which are often acquired on land. In this paper, we discuss the uncertainties in the slip distribution inversion using the geodetic data for the 2011 Tohoku earthquake and the Fully Bayesian Inversion method. These uncertainties are due to the prior information regarding the boundary conditions at the edges of the fault, the dip subduction angle and the smoothing operator. Using continuous GPS data from the Japan Island, the results for the rigid and free boundary conditions show that they produce remarkably different slip distributions at shallow depths, with the latter producing a large slip exceeding 30 m near the surface. These results indicate that the smoothing operator (gradient or Laplacian schemes) does not severely affect the slip pattern. To better invert the coseismic slip, we then introduce the ocean bottom GPS (OB-GPS) data, which improve the resolution of the shallow part of the fault. We obtain a near-trench slip greater than 40 m that reaches the Earth's surface, regardless of which boundary condition is used. Additionally, we show that using a mean dip angle for the fault as derived from subduction models is adequate if the goal is to invert for the general features of the slip pattern of this megathrust event.

Description: The thermophilic fungus Chaetomium thermophilum holds great promise for structural biology. To increase the efficiency of its biochemical and structural characterization and to explore its thermophilic properties beyond those of individual proteins, we obtained transcriptomics and proteomics data, and integrated them with computational annotation methods and a multitude of biochemical experiments conducted by the structural biology community. We considerably improved the genome annotation of Chaetomium thermophilum and characterized the transcripts and expression of thousands of genes. We furthermore show that the composition and structure of the expressed proteome of Chaetomium thermophilum is similar to its mesophilic relatives. Data were deposited in a publicly available repository and provide a rich source to the structural biology community.

Description: New methods are required to combine the information contained in the passive electrical and seismic signals to detect, localize and monitor hydromechanical disturbances in porous media. We propose a field experiment showing how passive seismic and electrical data can be combined together to detect a preferential flow path associated with internal erosion in a Earth dam. Continuous passive seismic and electrical (self-potential) monitoring data were recorded during a 7-d full-scale levee (earthen embankment) failure test, conducted in Booneschans, Netherlands in 2012. Spatially coherent acoustic emissions events and the development of a self-potential anomaly, associated with induced concentrated seepage and internal erosion phenomena, were identified and imaged near the downstream toe of the embankment, in an area that subsequently developed a series of concentrated water flows and sand boils, and where liquefaction of the embankment toe eventually developed. We present a new 4-D grid-search algorithm for acoustic emissions localization in both time and space, and the application of the localization results to add spatially varying constraints to time-lapse 3-D modelling of self-potential data in the terms of source current localization. Seismic signal localization results are utilized to build a set of time-invariant yet spatially varying model weights used for the inversion of the self-potential data. Results from the combination of these two passive techniques show results that are more consistent in terms of focused ground water flow with respect to visual observation on the embankment. This approach to geophysical monitoring of earthen embankments provides an improved approach for early detection and imaging of the development of embankment defects associated with concentrated seepage and internal erosion phenomena. The same approach can be used to detect various types of hydromechanical disturbances at larger scales.

Description: The rapid discovery of potential driver mutations through large-scale mutational analyses of human cancers generates a need to characterize their cellular phenotypes. Among the techniques for genome editing, recombinant adeno-associated virus (rAAV)-mediated gene targeting is suited for knock-in of single nucleotide substitutions and to a lesser degree for gene knock-outs. However, the generation of gene targeting constructs and the targeting process is time-consuming and labor-intense. To facilitate rAAV-mediated gene targeting, we developed the first software and complementary automation-friendly vector tools to generate optimized targeting constructs for editing human protein encoding genes. By computational approaches, rAAV constructs for editing ~71% of bases in protein-coding exons were designed. Similarly, ~81% of genes were predicted to be targetable by rAAV-mediated knock-out. A Gateway-based cloning system for facile generation of rAAV constructs suitable for robotic automation was developed and used in successful generation of targeting constructs. Together, these tools enable automated rAAV targeting construct design, generation as well as enrichment and expansion of targeted cells with desired integrations.

Description: Degenerate codon (DC) libraries efficiently address the experimental library-size limitations of directed evolution by focusing diversity toward the positions and toward the amino acids (AAs) that are most likely to generate hits; however, manually constructing DC libraries is challenging, error prone and time consuming. This paper provides a dynamic programming solution to the task of finding the best DCs while keeping the size of the library beneath some given limit, improving on the existing integer-linear programming formulation. It then extends the algorithm to consider multiple DCs at each position, a heretofore unsolved problem, while adhering to a constraint on the number of primers needed to synthesize the library. In the two library-design problems examined here, the use of multiple DCs produces libraries that very nearly cover the set of desired AAs while still staying within the experimental size limits. Surprisingly, the algorithm is able to find near-perfect libraries where the ratio of amino-acid sequences to nucleic-acid sequences approaches 1; it effectively side-steps the degeneracy of the genetic code. Our algorithm is freely available through our web server and solves most design problems in about a second.

Description: Full waveform inversion (FWI) is a powerful tool used to quantify the elastic properties of the subsurface from seismic data. Because of very high computational cost, the technique has so far been used for either 2-D full elastic or 3-D acoustic media while the extension to 3-D elastic media to a realistic model size is still a challenging task. However, the Earth being 3-D, elastic and highly heterogeneous, one would require a full 3-D elastic wave equation for accurate modelling of amplitudes and phases within the inversion process. The acoustic approximation could significantly impact the final waveform inversion results, mainly due to the amplitude variation with offset effect. This effect becomes extremely important in the presence of strong contrasts in S -wave velocity and density, specifically when long-offset reflection data are included for waveform inversion. Recent increase in computer power allows for more efficient parallel computing using thousands of processors simultaneously thus making 3-D elastic waveform inversion feasible today. In this paper we consider a synthetic study based on a 3-D elastic medium for inversion of both P - and S -wave velocities using multicomponent, ocean-bottom cable seismic data. Both the forward modelling part and the inversion part are carried out in the time domain. The inverse problem is parametrized in terms of P - and S -wave velocities, while the density, being difficult to reconstruct, is not inverted and is linked to the P -wave velocity. Among several synthetic examples, a successful experiment on a small part of a 3-D SEG/EAGE overthrust model is presented, demonstrating the feasibility of inverting and accurately quantifying both P - and S -wave velocities. The resolution analysis of the waveform inversion is tested using a checkerboard model. Our results show that 3-D elastic FWI of sparsely spaced sources can retrieve P - and S -wave velocities accurately.

Description: In general, observations are normally considered to refer to an epoch in time, however, observations take time. During this time span temporal variations of the observable alias the measurement. Similar phenomenon can be defined in the space domain as well: data treated to refer to a geographical location often contains integrated information of the surroundings. In each case the appropriate signal content can partially be recovered by desmoothing the averaged data. The present study delivers the theoretical foundation of a desmoothing method, and suggests its use on different applications in geodesy. The theoretical formulation of the desmoothing has been derived for 1-D and 2-D signals, the latter is interpreted on a plain and also on a sphere. The presented case studies are less elaborated, but intended to demonstrate the need and usefulness of the desmoothing tool.

Description: Interpolation and random noise removal is a pre-requisite for multichannel techniques because the irregularity and random noise in observed data can affect their performances. Projection Onto Convex Sets (POCS) method can better handle seismic data interpolation if the data's signal-to-noise ratio (SNR) is high, while it has difficulty in noisy situations because it inserts the noisy observed seismic data in each iteration. Weighted POCS method can weaken the noise effects, while the performance is affected by the choice of weight factors and is still unsatisfactory. Thus, a new weighted POCS method is derived through the Iterative Hard Threshold (IHT) view, and in order to eliminate random noise, a new adaptive method is proposed to achieve simultaneous seismic data interpolation and denoising based on dreamlet transform. Performances of the POCS method, the weighted POCS method and the proposed method are compared in simultaneous seismic data interpolation and denoising which demonstrate the validity of the proposed method. The recovered SNRs confirm that the proposed adaptive method is the most effective among the three methods. Numerical examples on synthetic and real data demonstrate the validity of the proposed adaptive method.

Description: In presence of large wavelength-scale shear-velocity variations in the Earth, acoustic waveform inversion may not be sufficient even when inverting long-offset data to retrieve the long-to-intermediate wavelengths of the compressional velocity. An acoustic modelling does not always correctly represent the compressional/primary waves when tuning effects and energy conversion between compressional and shear waves occur. Elastic waveform inversion with land data is challenging not only because of its computational cost but also due to the presence of the very energetic ground roll. To avoid inverting the ground roll and focus the inversion on the body waves recorded at long offsets, we propose to modify the surface boundary conditions in the elastic modelling. Zeroing the normal derivatives of the shear stress components parallel to the surface instead of the shear stress components themselves as with the free-surface boundary conditions leads to an elastic modelling that does not generate ground roll. These modified elastic surface conditions allow us to invert the seismic data that have been pre-processed to remove the ground roll as we do in acoustic waveform inversion. In this way, the inversion can focus on the retrieval of the long-to-intermediate wavelengths of the compressional velocity and we can apply the standard frequency continuation approach without having to process out the ground roll in the (elastic) synthetic data. An analysis of the modified surface conditions based on a plane wave decomposition shows that the reflection coefficients at the surface do not depend on incident angles and earth parameters. With a not too high shear-to-compressional ( S -to- P ) velocity ratio at the surface, the PP -reflection coefficients are close to the ones with the free-surface conditions, but with a high ratio they differ significantly. The approximation is then valid when the ( S -to- P ) velocity ratio is not too high at the surface in the actual Earth. Based on some synthetic examples, we discuss the limitations of the approach and the possible computational gain by playing with the shear velocity background value. This elastic modelling with the modified surface boundary conditions aims at inverting low-frequency wide-aperture active land seismic data that correspond to measurements of the vertical component of the particle displacement or velocity due to a vertical force source. It may be seen as an intermediate step between the acoustic waveform inversion and the elastic waveform inversion with the free-surface conditions.

Description: Electrical resistivity tomography (ERT) is a useful tool to detect and track water flow paths in the subsoil. However, measurements are strongly affected by subsurface heterogeneities such as fissures of different sizes and genesis (shrinking-swelling, macropores and deformation). In this work, we focus on surface fissures characterized by dimensions lower than the interelectrode spacing and correct their effect on apparent resistivity pseudo-sections by incorporating fissure geometry in the topography. We show that fissures with depths greater than 0.10 times the interelectrode spacing for a dipole–dipole array and equal to 0.16 for the gradient array and the Wenner–Schlumberger arrays create significant anomalies (greater than 5 per cent) in the pseudo-section. Surface fissure widths and dip angles have little effect with respect to the fissure depths which can increase the apparent resistivity up to 200 per cent. The clogging of the fissures with water or soil material decreases the anomaly effect linearly with the percentage of filling. The correction of apparent resistivity values is possible for relatively simple fissure geometries and only requires a manual survey of the surface fissures. It allows to improve the quality of the inverted resistivity section by mitigating the inversion artefacts and therefore a better interpretation.

Description: Extracting geophysical signals from Global Positioning System (GPS) coordinate time-series is a well-established practice that has led to great insights into how the Earth deforms. Often small discontinuities are found in such time-series and are traceable to either broad-scale deformation (i.e. earthquakes) or discontinuities due to equipment changes and/or failures. Estimating these offsets accurately enables the identification of coseismic deformation estimates in the former case, and the removal of unwanted signals in the latter case which then allows tectonic rates to be estimated more accurately. We develop a method to estimate accurately discontinuities in time series of GPS positions at specified epochs, based on a so-called ‘offset series’. The offset series are obtained by varying the amount of GPS data before and after an event while estimating the offset. Two methods, a mean and a weighted mean method, are then investigated to produce the estimated discontinuity from the offset series. The mean method estimates coseismic offsets without making assumptions about geophysical processes that may be present in the data (i.e. tectonic rate, seasonal variations), whereas the weighted mean method includes estimating coseismic offsets with a model of these processes. We investigate which approach is the most appropriate given certain lengths of available data and noise within the time-series themselves. For the Sumatra–Andaman event, with 4.5 yr of pre-event data, we show that between 2 and 3 yr of post-event data are required to produce accurate offset estimates with the weighted mean method. With less data, the mean method should be used, but the uncertainties of the estimated discontinuity are larger.

Description: Transcription regulation in multicellular eukaryotes is orchestrated by a number of DNA functional elements located at gene regulatory regions. Some regulatory regions (e.g. enhancers) are located far away from the gene they affect. Identification of distal regulatory elements is a challenge for the bioinformatics research. Although existing methodologies increased the number of computationally predicted enhancers, performance inconsistency of computational models across different cell-lines, class imbalance within the learning sets and ad hoc rules for selecting enhancer candidates for supervised learning, are some key questions that require further examination. In this study we developed DEEP, a novel ensemble prediction framework. DEEP integrates three components with diverse characteristics that streamline the analysis of enhancer's properties in a great variety of cellular conditions. In our method we train many individual classification models that we combine to classify DNA regions as enhancers or non-enhancers. DEEP uses features derived from histone modification marks or attributes coming from sequence characteristics. Experimental results indicate that DEEP performs better than four state-of-the-art methods on the ENCODE data. We report the first computational enhancer prediction results on FANTOM5 data where DEEP achieves 90.2% accuracy and 90% geometric mean (GM) of specificity and sensitivity across 36 different tissues. We further present results derived using in vivo -derived enhancer data from VISTA database. DEEP-VISTA, when tested on an independent test set, achieved GM of 80.1% and accuracy of 89.64%. DEEP framework is publicly available at http://cbrc.kaust.edu.sa/deep/ .

Description: We propose a two-phase damage theory in a viscoelastic medium to study the pressure and porosity diffusion in fractured near-surface porous rocks. The key ingredient in the viscoelastic theory is that the pressure difference between solid and fluid is divided into three parts, which contribute to reversible elastic potential energy, irreversible viscous entropy production and surface energy stored during deformation. The resulting continuum description of weakening and failure (distributed void generation and microcracking) in a linear Kelvin body accounts for surface energy being created by both viscous and elastic deformational work. The model shows that while non-linear permeability models leads to an enhanced diffusivity, damage makes the matrix more compressible if we assume the geometry/size of cracks remain unchanged. The net effect is that the porosity diffusivity is reduced causing fluid infiltration to accumulate closer to the injection source, leading to a slower fluid diffusion during hydraulic fracturing with a fixed porosity boundary condition. However if a constant overpressure boundary condition is applied, a weakened matrix with damage leads to greater pressure diffusivity than for porosity.

Description: Complications arise in the interpretation of gravity fields because of interference from systematic degradations, such as boundary blurring and distortion. The major sources of these degradations are the various systematic errors that inevitably occur during gravity field data acquisition, discretization and geophysical forward modelling. To address this problem, we evaluate deconvolution method that aim to detect the clear horizontal boundaries of anomalous sources by the suppression of systematic errors. A convolution-based multilayer projection model, based on the classical 3-D gravity field forward model, is innovatively derived to model the systematic error degradation. Our deconvolution algorithm is specifically designed based on this multilayer projection model, in which three types of systematic error are defined. The degradations of the different systematic errors are considered in the deconvolution algorithm. As the primary source of degradation, the convolution-based systematic error is the main object of the multilayer projection model. Both the random systematic error and the projection systematic error are shown to form an integral part of the multilayer projection model, and the mixed norm regularization method and the primal-dual optimization method are therefore employed to control these errors and stabilize the deconvolution solution. We herein analyse the parameter identification and convergence of the proposed algorithms, and synthetic and field data sets are both used to illustrate their effectiveness. Additional synthetic examples are specifically designed to analyse the effects of the projection systematic error, which is caused by the uncertainty associated with the estimation of the impulse response function.

Description: We define an algorithm in the time domain for computing the unwrapped instantaneous phase and its derivative, the instantaneous frequency, using only derivatives and integrals. It does not require user-defined parameters, like most algorithms proposed so far. We validate and compare its performance with respect to open-source and commercial software by synthetic and real data examples.

Description: Simulating electromagnetic fields in the quasi-static regime by solving Maxwell's equations is a central task in many geophysical applications. In most cases, geophysical targets of interest exhibit complex topography and bathymetry as well as layers and faults. Capturing these effects with a sufficient level of detail is a huge challenge for numerical simulations. Standard techniques require a very fine discretization that can result in an impracticably large linear system to be solved. A remedy is to use locally refined and adaptive meshes, however, the potential coarsening is limited in the presence of highly heterogeneous and anisotropic conductivities. In this paper, we discuss the application of multiscale finite volume (MSFV) methods to Maxwell's equations in frequency domain. Given a partition of the fine mesh into a coarse mesh the idea is to obtain coarse-to-fine interpolation by solving local versions of Maxwell's equations on each coarsened grid cell. By construction, the interpolation accounts for fine scale conductivity changes, yields a natural homogenization, and reduces the fine mesh problem dramatically in size. To improve the accuracy for singular sources, we use an irregular coarsening strategy. We show that using MSFV methods we can simulate electromagnetic fields with reasonable accuracy in a fraction of the time as compared to state-of-the-art solvers for the fine mesh problem, especially when considering parallel platforms.

Description: The Joint BioEnergy Institute Inventory of Composable Elements (JBEI-ICEs) is an open source registry platform for managing information about biological parts. It is capable of recording information about ‘legacy’ parts, such as plasmids, microbial host strains and Arabidopsis seeds, as well as DNA parts in various assembly standards. ICE is built on the idea of a web of registries and thus provides strong support for distributed interconnected use. The information deposited in an ICE installation instance is accessible both via a web browser and through the web application programming interfaces, which allows automated access to parts via third-party programs. JBEI-ICE includes several useful web browser-based graphical applications for sequence annotation, manipulation and analysis that are also open source. As with open source software, users are encouraged to install, use and customize JBEI-ICE and its components for their particular purposes. As a web application programming interface, ICE provides well-developed parts storage functionality for other synthetic biology software projects. A public instance is available at public-registry.jbei.org, where users can try out features, upload parts or simply use it for their projects. The ICE software suite is available via Google Code, a hosting site for community-driven open source projects.

Description: Wave-equation tomography (WT) and full waveform inversion (FWI) are combined through a hybrid misfit function to estimate high-resolution subsurface structures starting from a poorly constrained initial velocity model. Both methods share the same wavefield forward modelling and inversion schemes, while they differ only on the ways to calculate misfit functions and hence the ways to sample in the model space. Aiming at minimizing the cross-correlation phase delay between synthetic and real data, WT can be used to retrieve the long- and middle-wavelength model components, which are essential to FWI. Compared to ray-based traveltime tomography that is based on asymptotic high-frequency approximation, WT provides a better resolution by exploring the band-limited feature of seismic wavefield. On the other hand, FWI is capable of resolving the short-wavelength model component, complementing the WT. In this study, we apply WT to surface first-arrival refraction data, and apply FWI to both refraction and reflection data. We assign adaptive weights to the two different misfit measurements and build a progressive inversion strategy. To illustrate the advantage of our strategy over conventional ‘ray tomography + FWI’ approach, we show in a synthetic lens test that WT can provide extra subsurface information that is critical for a successful FWI application. To further show the efficiency, we test our strategy on the 2-D Marmousi model where satisfactory inversion results are achieved without much manual intervention. Finally, we apply the inversion strategy to a deep-water seismic data set acquired offshore Sumatra with a 12-km-long streamer. In order to alleviate several practical problems posed by the deep-water setting, we apply downward continuation (DC) to generate a virtual ocean bottom experiment data set prior to inversion. The new geometry after DC boosts up the shallow refractions, as well as avoiding cumbersome modelling through the thick water column, thus reducing the computation cost by 85 per cent. The inversion result from the new data set shows high-resolution shallow sediment structures and the migration images prove the superiority of the inverted model over a conventional tomography model.

Description: The activation of Late Quaternary faults in the Central Apennines (Italy) could generate earthquakes with magnitude of about 6.5, and the Monte Vettore fault system probably belongs to the same category of seismogenetic faults. Such structure has been defined ‘silent’, because of its geological and geomorphological evidences of past activation, but the absence of historical records in the seismic catalogues to be associated with its activation. The ‘Piano di Castelluccio’ intramountain basin, resulting from the Quaternary activity of normal faults, is characterized by a secondary fault strand highlighted by a NW–SE fault scarp: it has been already studied through palaeoseismological trenches, which highlighted evidences of Quaternary shallow faulting due to strong earthquakes, and through a 2-D ground penetrating radar (GPR) survey, showing the first geophysical signature of faulting for this site. Within the same place, a 3-D GPR volume over a 20 20 m area has been collected. The collection of radar echoes in three dimensions allows to map both the vertical and lateral continuity of shallow geometries of the fault zone (Fz), imaging features with high resolution, ranging from few metres to centimetres and therefore imaging also local variations at the microscale. Several geophysical markers of faulting, already highlighted on this site, have been taken as reference to plan the 3-D survey. In this paper, we provide the first 3-D subsurface imaging of an active shallow fault belonging to the Umbria-Marche Apennine highlighting the subsurface fault geometry and the stratigraphic sequence up to a depth of about 5 m. From our data, geophysical faulting signatures are clearly visible in three dimensions: diffraction hyperbolas, truncations of layers, local attenuated zones and varying dip of the layers have been detected within the Fz. The interpretation of the 3-D data set provided qualitative and quantitative geological information in addition to the fault location, like its geometry, boundaries and an estimation of the fault throw.

Description: Shotgun metagenome sequencing has become a fast, cheap and high-throughput technology for characterizing microbial communities in complex environments and human body sites. However, accurate identification of microorganisms at the strain/species level remains extremely challenging. We present a novel k -mer-based approach, termed GSMer, that identifies genome-specific markers (GSMs) from currently sequenced microbial genomes, which were then used for strain/species-level identification in metagenomes. Using 5390 sequenced microbial genomes, 8 770 321 50-mer strain-specific and 11 736 360 species-specific GSMs were identified for 4088 strains and 2005 species (4933 strains), respectively. The GSMs were first evaluated against mock community metagenomes, recently sequenced genomes and real metagenomes from different body sites, suggesting that the identified GSMs were specific to their targeting genomes. Sensitivity evaluation against synthetic metagenomes with different coverage suggested that 50 GSMs per strain were sufficient to identify most microbial strains with ≥0.25 x coverage, and 10% of selected GSMs in a database should be detected for confident positive callings. Application of GSMs identified 45 and 74 microbial strains/species significantly associated with type 2 diabetes patients and obese/lean individuals from corresponding gastrointestinal tract metagenomes, respectively. Our result agreed with previous studies but provided strain-level information. The approach can be directly applied to identify microbial strains/species from raw metagenomes, without the effort of complex data pre-processing.

Description: To estimate the seismic hazard, the geometry (dip, length and orientation) and the dynamics (type of displacements and amplitude) of the faults in the area of interest need to be understood. In this paper, in addition to geomorphologic observations, we present the results of two ground penetrating radar (GPR) campaigns conducted in 2010 and 2011 along the Emeelt fault in the vicinity of Ulaanbaatar, capital of Mongolia, located in an intracontinental region with low deformation rate that induces long recurrence time between large earthquakes. As the geomorphology induced by the fault activity has been highly smoothed by erosion processes since the last event, the fault location and geometry is difficult to determine precisely. However, by using GPR first, a non-destructive and fast investigation, the fault and the sedimentary deposits near the surface can be characterized and the results can be used for the choice of trench location. GPR was performed with a 50 MHz antenna over 2-D lines and with a 500 MHz antenna for pseudo-3-D surveys. The 500 MHz GPR profiles show a good consistency with the trench observations, dug next to the pseudo-3-D surveys. The 3-D 500 MHz GPR imaging of a palaeochannel crossed by the fault allowed us to estimate its lateral displacement to be about 2 m. This is consistent with a right lateral strike-slip displacement induced by an earthquake around magnitude 7 or several around magnitude 6. The 2-D 50 MHz profiles, recorded perpendicular to the fault, show a strong reflection dipping to the NE, which corresponds to the fault plane. Those profiles provided complementary information on the fault such as its location at shallow depth, its dip angle (from 23° to 35°) and define its lateral extension.

Description: We propose to test if gravimetry can prove useful in discriminating different models of long-term deep crustal processes in the case of the Taiwan mountain belt. We discuss two existing tectonic models that differ in the deep processes proposed to sustain the long-term growth of the orogen. One model assumes underplating of the uppermost Eurasian crust with subduction of the deeper part of the crust into the mantle. The other one suggests the accretion of the whole Eurasian crust above crustal-scale ramps, the lower crust being accreted into the collisional orogen. We compute the temporal gravity changes caused only by long-term rock mass transfers at depth for each of them. We show that the underplating model implies a rate of gravity change of –6 x 10 –2 μGal yr –1 , a value that increases to 2 x 10 –2 μGal yr –1 if crustal subduction is neglected. If the accretion of the whole Eurasian crust occurs, a rate of 7 x 10 –2 μGal yr –1 is obtained. The two models tested differ both in signal amplitude and spatial distribution. The yearly gravity changes expected by long-term deep crustal mass processes in Taiwan are two orders of magnitude below the present-day uncertainty of land-based gravity measurements. Assuming that these annually averaged long-term gravity changes will linearly accumulate with ongoing mountain building, multidecadal time-series are needed to identify comparable rates of gravity change. However, as gravity is sensitive to any mass redistribution, effects of short-term processes such as seismicity and surface mass transfers (erosion, sedimentation, ground-water) may prevent from detecting any long-term deep signal. This study indicates that temporal gravity is not appropriate for deciphering the long-term deep crustal processes involved in the Taiwan mountain belt.

Description: A new method to obtain the statistics of a geostatistical model is introduced. The method elicits the statistical information from a geological expert directly, by iteratively updating a population of vectors of statistics, based on the expert's subjective opinion of the corresponding geological simulations. Thus, it does not require the expert to have knowledge of the mathematical and statistical details of the model. The process uses a genetic algorithm to generate new vectors. We demonstrate the methodology for a particular geostatistical model used to model rock pore-space, which simulates the spatial distribution of matrix and pores over a 2-D grid, using multipoint statistics specified by conditional probabilities. Experts were asked to use the algorithm to estimate the statistics of a given target pore-space image with known statistics; thus, their numerical rates of convergence could be calculated. Convergence was measured for all experts, showing that the algorithm can be used to find appropriate probabilities given the expert's subjective input. However, considerable and apparently irreducible residual misfit was found between the true statistics and the estimates of statistics obtained by the experts, with the root-mean-square error on the conditional probabilities typically 〉0.1. This is interpreted as the limit of the experts’ abilities to distinguish between realizations of different spatial statistics using the algorithm. More accurate discrimination is therefore likely to require complementary elicitation techniques or sources of information independent of expert opinion.