ALBERT

Description: We describe a multihomogeneity theory for source-parameter estimation of potential fields. Similar to what happens for random source models, where the monofractal scaling-law has been generalized into a multifractal law, we propose to generalize the homogeneity law into a multihomogeneity law. This allows a theoretically correct approach to study real-world potential fields, which are inhomogeneous and so do not show scale invariance, except in the asymptotic regions (very near to or very far from their sources). Since the scaling properties of inhomogeneous fields change with the scale of observation, we show that they may be better studied at a set of scales than at a single scale and that a multihomogeneous model is needed to explain its complex scaling behaviour. In order to perform this task, we first introduce fractional-degree homogeneous fields, to show that: (i) homogeneous potential fields may have fractional or integer degree; (ii) the source-distributions for a fractional-degree are not confined in a bounded region, similarly to some integer-degree models, such as the infinite line mass and (iii) differently from the integer-degree case, the fractional-degree source distributions are no longer uniform density functions. Using this enlarged set of homogeneous fields, real-world anomaly fields are studied at different scales, by a simple search, at any local window W , for the best homogeneous field of either integer or fractional-degree, this yielding a multiscale set of local homogeneity-degrees and depth estimations which we call multihomogeneous model. It is so defined a new technique of source parameter estimation (Multi-HOmogeneity Depth Estimation, MHODE), permitting retrieval of the source parameters of complex sources. We test the method with inhomogeneous fields of finite sources, such as faults or cylinders, and show its effectiveness also in a real-case example. These applications show the usefulness of the new concepts, multihomogeneity and fractional homogeneity-degree, to obtain valid estimates of the source parameters in a consistent theoretical framework, so overcoming the limitations imposed by global-homogeneity to widespread methods, such as Euler deconvolution.

Description: In this paper, two separate but related goals are tackled. The first one is to demonstrate that in some saturated rock textures the non-linear behaviour of induced polarization (IP) and the violation of Ohm's law not only are real phenomena, but they can also be satisfactorily predicted by a suitable physical-mathematical model, which is our second goal. This model is based on Fick's second law. As the model links the specific dependence of resistivity and chargeability of a laboratory sample to the injected current and this in turn to its pore size distribution, it is able to predict pore size distribution from laboratory measurements, in good agreement with mercury injection capillary pressure test results. This fact opens up the possibility for hydrogeophysical applications on a macro scale. Mathematical modelling shows that the chargeability acquired in the field under normal conditions, that is at low current, will always be very small and approximately proportional to the applied current. A suitable field test site for demonstrating the possible reliance of both resistivity and chargeability on current was selected and a specific measuring strategy was established. Two data sets were acquired using different injected current strengths, while keeping the charging time constant. Observed variations of resistivity and chargeability are in agreement with those predicted by the mathematical model. These field test data should however be considered preliminary. If confirmed by further evidence, these facts may lead to changing the procedure of acquiring field measurements in future, and perhaps may encourage the design and building of a new specific geo-resistivity meter. This paper also shows that the well-known Marshall and Madden's equations based on Fick's law cannot be solved without specific boundary conditions.

Description: We present a new 3-D traveltime tomography code (TOMO3D) for the modelling of active-source seismic data that uses the arrival times of both refracted and reflected seismic phases to derive the velocity distribution and the geometry of reflecting boundaries in the subsurface. This code is based on its popular 2-D version TOMO2D from which it inherited the methods to solve the forward and inverse problems. The traveltime calculations are done using a hybrid ray-tracing technique combining the graph and bending methods. The LSQR algorithm is used to perform the iterative regularized inversion to improve the initial velocity and depth models. In order to cope with an increased computational demand due to the incorporation of the third dimension, the forward problem solver, which takes most of the run time (~90 per cent in the test presented here), has been parallelized with a combination of multi-processing and message passing interface standards. This parallelization distributes the ray-tracing and traveltime calculations among available computational resources. The code's performance is illustrated with a realistic synthetic example, including a checkerboard anomaly and two reflectors, which simulates the geometry of a subduction zone. The code is designed to invert for a single reflector at a time. A data-driven layer-stripping strategy is proposed for cases involving multiple reflectors, and it is tested for the successive inversion of the two reflectors. Layers are bound by consecutive reflectors, and an initial velocity model for each inversion step incorporates the results from previous steps. This strategy poses simpler inversion problems at each step, allowing the recovery of strong velocity discontinuities that would otherwise be smoothened.

Description: Iterative substitution of the coupled Marchenko equations is a novel methodology to retrieve the Green's functions from a source or receiver array at an acquisition surface to an arbitrary location in an acoustic medium. The methodology requires as input the single-sided reflection response at the acquisition surface and an initial focusing function, being the time-reversed direct wavefield from the acquisition surface to a specified location in the subsurface. We express the iterative scheme that is applied by this methodology explicitly as the successive actions of various linear operators, acting on an initial focusing function. These operators involve multidimensional crosscorrelations with the reflection data and truncations in time. We offer physical interpretations of the multidimensional crosscorrelations by subtracting traveltimes along common ray paths at the stationary points of the underlying integrals. This provides a clear understanding of how individual events are retrieved by the scheme. Our interpretation also exposes some of the scheme's limitations in terms of what can be retrieved in case of a finite recording aperture. Green's function retrieval is only successful if the relevant stationary points are sampled. As a consequence, internal multiples can only be retrieved at a subsurface location with a particular ray parameter if this location is illuminated by the direct wavefield with this specific ray parameter. Several assumptions are required to solve the Marchenko equations. We show that these assumptions are not always satisfied in arbitrary heterogeneous media, which can result in incomplete Green's function retrieval and the emergence of artefacts. Despite these limitations, accurate Green's functions can often be retrieved by the iterative scheme, which is highly relevant for seismic imaging and inversion of internal multiple reflections.

Description: Employing dynamic reciprocity can be an effective tool to simplify the calculation of elastic wavefields for borehole problems and to check the results. We analytically obtain the reciprocity relations for the elastodynamic fields generated by multipole sources in a fluid–solid configuration: if the multipole sources are located in the fluid, the particle displacement due to a dipole source is reciprocal to the particle acceleration due to a single force; the fluid pressure due to a dipole source is reciprocal to the particle acceleration due to a monopole source; the particle displacement due to a quadrupole source is reciprocal to the spatial partial derivative of the particle acceleration due to a single force; the fluid pressure due to a quadrupole source is reciprocal to the spatial partial derivative of the particle acceleration due to a monopole source. These relations are tested by numerical experiments for different borehole problems, including acoustic logging, single-well imaging and vertical seismic profiling. A reciprocity test can be used as a quick check of a finite-difference algorithm and the implementation of the sources, although it cannot detect errors due to improper discretization of the interfaces.

Description: Clonal populations accumulate mutations over time, resulting in different haplotypes. Deep sequencing of such a population in principle provides information to reconstruct these haplotypes and the frequency at which the haplotypes occur. However, this reconstruction is technically not trivial, especially not in clonal systems with a relatively low mutation frequency. The low number of segregating sites in those systems adds ambiguity to the haplotype phasing and thus obviates the reconstruction of genome-wide haplotypes based on sequence overlap information. Therefore, we present EVORhA, a haplotype reconstruction method that complements phasing information in the non-empty read overlap with the frequency estimations of inferred local haplotypes. As was shown with simulated data, as soon as read lengths and/or mutation rates become restrictive for state-of-the-art methods, the use of this additional frequency information allows EVORhA to still reliably reconstruct genome-wide haplotypes. On real data, we show the applicability of the method in reconstructing the population composition of evolved bacterial populations and in decomposing mixed bacterial infections from clinical samples.

Description: The area of the 9.1-km-deep Continental Deep Drillhole (KTB) in Germany is used as a case study for a geothermal reservoir situated in folded and faulted metamorphic crystalline crust. The presented approach is based on the analysis of 3-D seismic reflection data combined with borehole data and hydrothermal numerical modelling. The KTB location exemplarily contains all elements that make seismic prospecting in crystalline environment often more difficult than in sedimentary units, basically complicated tectonics and fracturing and low-coherent strata. In a first step major rock units including two known nearly parallel fault zones are identified down to a depth of 12 km. These units form the basis of a gridded 3-D numerical model for investigating temperature and fluid flow. Conductive and advective heat transport takes place mainly in a metamorphic block composed of gneisses and metabasites that show considerable differences in thermal conductivity and heat production. Therefore, in a second step, the structure of this unit is investigated by seismic waveform modelling. The third step of interpretation consists of applying wavenumber filtering and log-Gabor-filtering for locating fractures. Since fracture networks are the major fluid pathways in the crystalline, we associate the fracture density distribution with distributions of relative porosity and permeability that can be calibrated by logging data and forward modelling of the temperature field. The resulting permeability distribution shows values between 10 –16 and 10 –19 m 2 and does not correlate with particular rock units. Once thermohydraulic rock properties are attributed to the numerical model, the differential equations for heat and fluid transport in porous media are solved numerically based on a finite difference approach. The hydraulic potential caused by topography and a heat flux of 54 mW m –2 were applied as boundary conditions at the top and bottom of the model. Fluid flow is generally slow and mainly occurring within the two fault zones. Thus, our model confirms the previous finding that diffusive heat transport is the dominant process at the KTB site. Fitting the observed temperature–depth profile requires a correction for palaeoclimate of about 4 K at 1 km depth. Modelled and observed temperature data fit well within 0.2 °C bounds. Whereas thermal conditions are suitable for geothermal energy production, hydraulic conditions are unfavourable without engineered stimulation.

Description: Data on biological mechanisms of aging are mostly obtained from cross-sectional study designs. An inherent disadvantage of this design is that inter-individual differences can mask small but biologically significant age-dependent changes. A serially sampled design (same individual at different time points) would overcome this problem but is often limited by the relatively small numbers of available paired samples and the statistics being used. To overcome these limitations, we have developed a new vector-based approach, termed three-component analysis, which incorporates temporal distance, signal intensity and variance into one single score for gene ranking and is combined with gene set enrichment analysis. We tested our method on a unique age-based sample set of human skin fibroblasts and combined genome-wide transcription, DNA methylation and histone methylation (H3K4me3 and H3K27me3) data. Importantly, our method can now for the first time demonstrate a clear age-dependent decrease in expression of genes coding for proteins involved in translation and ribosome function. Using analogies with data from lower organisms, we propose a model where age-dependent down-regulation of protein translation-related components contributes to extend human lifespan.

Description: A major challenge in the field of shotgun metagenomics is the accurate identification of organisms present within a microbial community, based on classification of short sequence reads. Though existing microbial community profiling methods have attempted to rapidly classify the millions of reads output from modern sequencers, the combination of incomplete databases, similarity among otherwise divergent genomes, errors and biases in sequencing technologies, and the large volumes of sequencing data required for metagenome sequencing has led to unacceptably high false discovery rates (FDR). Here, we present the application of a novel, gene-independent and signature-based metagenomic taxonomic profiling method with significantly and consistently smaller FDR than any other available method. Our algorithm circumvents false positives using a series of non-redundant signature databases and examines G enomic O rigins T hrough T axonomic CHA llenge (GOTTCHA). GOTTCHA was tested and validated on 20 synthetic and mock datasets ranging in community composition and complexity, was applied successfully to data generated from spiked environmental and clinical samples, and robustly demonstrates superior performance compared with other available tools.

Description: This paper presents the results from the Deflo-hydroacoustic experiment in the Southern Indian Ocean using three autonomous underwater hydrophones, complemented by two permanent hydroacoustic stations. The array monitored for 14 months, from November 2006 to December 2007, a 3000 x 3000 km wide area, encompassing large segments of the three Indian spreading ridges that meet at the Indian Triple Junction. A catalogue of 11 105 acoustic events is derived from the recorded data, of which 55 per cent are located from three hydrophones, 38 per cent from 4, 6 per cent from five and less than 1 per cent by six hydrophones. From a comparison with land-based seismic catalogues, the smallest detected earthquakes are m b 2.6 in size, the range of recorded magnitudes is about twice that of land-based networks and the number of detected events is 5–16 times larger. Seismicity patterns vary between the three spreading ridges, with activity mainly focused on transform faults along the fast spreading Southeast Indian Ridge and more evenly distributed along spreading segments and transforms on the slow spreading Central and ultra-slow spreading Southwest Indian ridges; the Central Indian Ridge is the most active of the three with an average of 1.9 events/100 km/month. Along the Sunda Trench, acoustic events mostly radiate from the inner wall of the trench and show a 200-km-long seismic gap between 2 °S and the Equator. The array also detected more than 3600 cryogenic events, with different seasonal trends observed for events from the Antarctic margin, compared to those from drifting icebergs at lower (up to 50°S) latitudes. Vocalizations of five species and subspecies of large baleen whales were also observed and exhibit clear seasonal variability. On the three autonomous hydrophones, whale vocalizations dominate sound levels in the 20–30 and 100 Hz frequency bands, whereas earthquakes and ice tremor are a dominant source of ambient sound at frequencies 〈20 Hz.

Description: Seismic reflections from the oceanic water column contain information about ocean temperature and salinity. Even though seismic waveform inversion is effective for studying oceanic structure, its application is limited in the absence of sufficient direct temperature/velocity measurements. Here, two methods are developed to invert pre-stack seismic waveform data for temperature and salinity when independent temperature/velocity data are sparse or unavailable, allowing estimation of water-column temperature/salinity from any marine seismic reflection data set. The first method combines a genetic algorithm (GA) with non-linear least squares inversion, and the second method is a parallel implementation of a GA. Both methods produce results to an accuracy between 0 and 0.1 °C in estimating temperature when applied to a field data set from the South China Sea. Although the second approach is superior, it is computationally demanding and requires large parallel computers. The first approach runs extremely fast on parallel computers and can even be run on much smaller machines to provide results in a reasonable runtime. While both methods are viable choices for estimating temperature and salinity, the choice of one over the other will largely depend upon the available computational resources and the time frame within which the inversion needs to be completed.

Description: A new approach of seismoelectric imaging has been recently proposed to detect saturation fronts in which seismic waves are focused in the subsurface to scan its heterogeneous nature and determine saturation fronts. Such type of imaging requires however a complete modelling of the seismoelectric properties of porous media saturated by two immiscible fluid phases, one being usually electrically insulating (for instance water and oil). We combine an extension of Biot dynamic theory, valid for porous media containing two immiscible Newtonian fluids, with an extension of the electrokinetic theory based on the notion of effective volumetric charge densities dragged by the flow of each fluid phase. These effective charge densities can be related directly to the permeability and saturation of each fluid phase. The coupled partial differential equations are solved with the finite element method. We also derive analytically the transfer function connecting the macroscopic electrical field to the acceleration of the fast P wave (coseismic electrical field) and we study the influence of the water content on this coupling. We observe that the amplitude of the co-seismic electrical disturbance is very sensitive to the water content with an increase in amplitude with water saturation. We also investigate the seismoelectric conversions (interface effect) occurring at the water table. We show that the conversion response at the water table can be identifiable only when the saturation contrasts between the vadose and saturated zones are sharp enough. A relatively dry vadose zone represents the best condition to identify the water table through seismoelectric measurements. Indeed, in this case, the coseismic electrical disturbances are vanishingly small compared to the seismoelectric interface response.

Description: We analysed four newly retrieved tide gauge records of the 1998 July 17 Papua New Guinea (PNG) tsunami to study statistical and spectral properties of this tsunami. The four tide gauge records were from Lombrum (PNG), Rabaul (PNG), Malakal Island (Palau) and Yap Island (State of Yap) stations located 600–1450 km from the source. The tsunami registered a maximum trough-to-crest wave height of 3–9 cm at these gauges. Spectral analysis showed two dominant peaks at period bands of 2–4 and 6–20 min with a clear separation at the period of ~5 min. We interpreted these peak periods as belonging to the landslide and earthquake sources of the PNG tsunami, respectively. Analysis of the tsunami waveforms revealed 12–17 min delay in landslide generation compared to the origin time of the main shock. Numerical simulations including this delay fairly reproduced the observed tide gauge records. This is the first direct evidence of the delayed landslide source of the 1998 PNG tsunami which was previously indirectly estimated from acoustic T-phase records.

Description: For extensional wave propagation along a cylindrical pipe, there exists a natural stopband in the frequency range between the first and second modes. This study explores the feasibility and practicality of building a drill collar acoustic extensional-wave isolator by combining the stopbands of pipes of different thicknesses. Numerical modelling shows that this is indeed possible and a stopband of designated width can be obtained using an optimization procedure. Laboratory measurement on an optimized design further verified this concept. The result provides a viable approach for the acoustic isolation design of a logging while drilling acoustic tool.

Description: The Murray Ridge/Dalrymple Trough system forms the boundary between the Indian and Arabian plates in the northern Arabian Sea. Geodetic constraints from the surrounding continents suggest that this plate boundary is undergoing oblique extension at a rate of a few millimetres per year. We present wide-angle seismic data that constrains the composition of the Ridge and of adjacent lithosphere beneath the Indus Fan. We infer that Murray Ridge, like the adjacent Dalrymple Trough, is underlain by continental crust, while a thin crustal section beneath the Indus Fan represents thinned continental crust or exhumed serpentinized mantle that forms part of a magma-poor rifted margin. Changes in crustal structure across the Murray Ridge and Dalrymple Trough can explain short-wavelength gravity anomalies, but a long-wavelength anomaly must be attributed to deeper density contrasts that may result from a large age contrast across the plate boundary. The origin of this fragment of continental crust remains enigmatic, but the presence of basement fabrics to the south that are roughly parallel to Murray Ridge suggests that it separated from the India/Seychelles/Madagascar block by extension during early breakup of Gondwana.

Description: With read lengths of currently up to 2 x 300 bp, high throughput and low sequencing costs Illumina's MiSeq is becoming one of the most utilized sequencing platforms worldwide. The platform is manageable and affordable even for smaller labs. This enables quick turnaround on a broad range of applications such as targeted gene sequencing, metagenomics, small genome sequencing and clinical molecular diagnostics. However, Illumina error profiles are still poorly understood and programs are therefore not designed for the idiosyncrasies of Illumina data. A better knowledge of the error patterns is essential for sequence analysis and vital if we are to draw valid conclusions. Studying true genetic variation in a population sample is fundamental for understanding diseases, evolution and origin. We conducted a large study on the error patterns for the MiSeq based on 16S rRNA amplicon sequencing data. We tested state-of-the-art library preparation methods for amplicon sequencing and showed that the library preparation method and the choice of primers are the most significant sources of bias and cause distinct error patterns. Furthermore we tested the efficiency of various error correction strategies and identified quality trimming (Sickle) combined with error correction (BayesHammer) followed by read overlapping (PANDAseq) as the most successful approach, reducing substitution error rates on average by 93%.

Description: RNA-seq is a sensitive and accurate technique to compare steady-state levels of RNA between different cellular states. However, as it does not provide an account of transcriptional activity per se , other technologies are needed to more precisely determine acute transcriptional responses. Here, we have developed an easy, sensitive and accurate novel computational method, iRNA-seq , for genome-wide assessment of transcriptional activity based on analysis of intron coverage from total RNA-seq data. Comparison of the results derived from iRNA-seq analyses with parallel results derived using current methods for genome-wide determination of transcriptional activity, i.e. global run-on (GRO)-seq and RNA polymerase II (RNAPII) ChIP-seq, demonstrate that iRNA-seq provides similar results in terms of number of regulated genes and their fold change. However, unlike the current methods that are all very labor-intensive and demanding in terms of sample material and technologies, iRNA-seq is cheap and easy and requires very little sample material. In conclusion, iRNA-seq offers an attractive novel alternative to current methods for determination of changes in transcriptional activity at a genome-wide level.

Description: In conventional marine seismic surveys, due to the time-delayed reflections from the sea surface on both source and receiver sides, ghosts present in recorded seismograms and lead to both phase and spectrum distortions (especially near certain frequency notches). To achieve a high-quality broad-band image/velocity model with conventional reverse time migration (RTM)/full waveform inversion (FWI) that adopts a synthetic zero-phase source wavelet and absorbing surface condition during wavefield modelling, marine seismic data have to be pre-processed to remove ghost effects. However, seismic deghosting is not a trivial task. Instead of employing an external deghosting process, we propose a strategy to compensate for ghost effects during FWI and RTM, which consists of two parts: first, to address phase distortions due to ghost effects by means of obtaining an accurate source wavelet estimation and adopting an appropriate surface boundary condition in both forward and backward wave propagation to appropriately generate ghosts; secondly, to build a compensation operator in the adjoint state computation to mitigate spectrum distortions caused by dominant ghost effects. To demonstrate the success and robustness of the proposed strategy, we present both synthetic experiments and field examples, which suggest that this strategy can lead to successful applications of FWI/RTM directly on marine seismic data without an extra deghosting process.

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

Description: Non-linear resonant coupling of edge waves can occur with tsunamis generated by large-magnitude subduction zone earthquakes. Earthquake rupture zones that straddle beneath the coastline of continental margins are particularly efficient at generating tsunami edge waves. Using a stochastic model for earthquake slip, it is shown that a wide range of edge-wave modes and wavenumbers can be excited, depending on the variability of slip. If two modes are present that satisfy resonance conditions, then a third mode can gradually increase in amplitude over time, even if the earthquake did not originally excite that edge-wave mode. These three edge waves form a resonant triad that can cause unexpected variations in tsunami amplitude long after the first arrival. An M ~ 9, 1100 km-long continental subduction zone earthquake is considered as a test case. For the least-variable slip examined involving a Gaussian random variable, the dominant resonant triad includes a high-amplitude fundamental mode wave with wavenumber associated with the along-strike dimension of rupture. The two other waves that make up this triad include subharmonic waves, one of fundamental mode and the other of mode 2 or 3. For the most variable slip examined involving a Cauchy-distributed random variable, the dominant triads involve higher wavenumbers and modes because subevents, rather than the overall rupture dimension, control the excitation of edge waves. Calculation of the resonant period for energy transfer determines which cases resonant coupling may be instrumentally observed. For low-mode triads, the maximum transfer of energy occurs approximately 20–30 wave periods after the first arrival and thus may be observed prior to the tsunami coda being completely attenuated. Therefore, under certain circumstances the necessary ingredients for resonant coupling of tsunami edge waves exist, indicating that resonant triads may be observable and implicated in late, large-amplitude tsunami arrivals.

Description: One interpretation of a seismic image is the instantaneous scattered wave response of a colocated pseudo-source and pseudo-receiver at each point in the subsurface model. If there is no model perturbation at a point then there will be no instantaneous scattered wave so nothing will be imaged; if something is imaged then there must be a perturbation at that location. By extension, so-called extended images (EIs) represent the full spatio-temporal response between offset subsurface pseudo-sources and pseudo-receivers which can be used to constrain elastic properties around each image point. However, one-sided illumination of the subsurface (from the Earth's surface), errors in the initial velocity model estimate, and the use of a linearized, single-scattering assumption (as is usual in seismic imaging) cause errors in EI gathers such as missing events, incorrect amplitudes, and spurious energy. By creating elastic (P-to-P and P-to-S) EIs in a synthetic example of subsalt imaging, we demonstrate the advantages of incorporating multiply scattered waves correctly by non-linear imaging, and of including transmitted waves by using two-sided receiver arrays, and discuss how the recently developed autofocussing methods could provide us with the various required subsurface wavefields. Pre- and post-imaging f–k filtering procedures are introduced to further improve the quality of the EIs by (explicitly or implicitly) limiting the directions of waves arriving at the subsurface pseudo-source and receiver survey line. These filters suppress strong linear events that arise from the erroneous interaction of near-horizontally propagating waves which are not naturally accounted for due to the lack of sources and receivers on either side of the imaging target. Finally, we analyse the sensitivity of elastic P-to-P EIs to errors in the migration velocity models and show that events in the EI are shifted in opposite directions when constructed using reflection or transmission data. In other words, velocity errors are mapped into the EIs differently in the case of one-sided from two-sided illumination. This leads to the potential for new methods of migration velocity analysis when surface and borehole seismic data are jointly acquired.

Description: Uncertainty estimation is a vital part of geophysical numerical modelling. There exist a variety of methods aimed at uncertainty estimation, which are often complicated and difficult to implement. We present an inversion technique that produces multiple solutions, based on bootstrap resampling, to create a qualitative uncertainty measure for 2-D magnetotelluric inversion models. The approach is easy to implement, can be used with almost any inversion code, and does not require access to the inversion software's source code. It is capable of detecting the effect of data uncertainties on the model result rather than just analysing the effect of model variations on the model response. To obtain uncertainty estimates for an inversion model, the original data set is resampled repeatedly and alternate data set realizations are created and inverted. This ensemble of solutions is then statistically analysed to determine the variability between the different solutions. The process yields interpretable uncertainty maps for the inversion model and we demonstrate its effectiveness to qualitatively quantify uncertainty in synthetic model tests and a case study.

Description: Any given human individual carries multiple genetic variants that disrupt protein-coding genes, through structural variation, as well as nucleotide variants and indels. Predicting the phenotypic consequences of a gene disruption remains a significant challenge. Current approaches employ information from a range of biological networks to predict which human genes are haploinsufficient (meaning two copies are required for normal function) or essential (meaning at least one copy is required for viability). Using recently available study gene sets, we show that these approaches are strongly biased towards providing accurate predictions for well-studied genes. By contrast, we derive a haploinsufficiency score from a combination of unbiased large-scale high-throughput datasets, including gene co-expression and genetic variation in over 6000 human exomes. Our approach provides a haploinsufficiency prediction for over twice as many genes currently unassociated with papers listed in Pubmed as three commonly-used approaches, and outperforms these approaches for predicting haploinsufficiency for less-studied genes. We also show that fine-tuning the predictor on a set of well-studied ‘gold standard’ haploinsufficient genes does not improve the prediction for less-studied genes. This new score can readily be used to prioritize gene disruptions resulting from any genetic variant, including copy number variants, indels and single-nucleotide variants.

Description: Electromagnetic (EM) imaging methods are useful tools for monitoring subsurface changes in pore-fluid content and the associated changes in electrical permittivity and conductivity. The most common method for georadar tomography uses a high frequency ray-theoretic approximation that is valid when material variations are sufficiently small relative to the wavelength of the propagating wave. Georadar methods, however, often utilize EM waves that propagate within heterogeneous media at frequencies where ray theory may not be applicable. In this paper we describe EM wave propagation 3-D Fréchet sensitivity kernels that capture the data sensitivity to material perturbations for a given source–receiver combination. Various data functional types are formulated that consider all three components of the electric wavefield and incorporate near-, intermediate- and far-field contributions. We show that EM waves exhibit substantial variations for different relative source–receiver component orientations. The 3-D sensitivities also illustrate out of plane effects that are not captured in 2-D sensitivity kernels and can influence results obtained using 2-D inversion methods to image structures that are in reality 3-D.

Description: This paper focuses on the modelling of fluid-filled poroelastic double porosity media under quasi-static and dynamic regimes. The double porosity model is derived from a two-scale homogenization procedure, by considering a medium locally characterized by blocks of poroelastic Biot microporous matrix and a surrounding system of fluid-filled macropores or fractures. The derived double porosity description is a two-pressure field poroelastic model with memory and viscoelastic effects. These effects result from the ‘time-dependent’ interaction between the pressure fields in the two pore networks. It is shown that this homogenized double porosity behaviour arises when the characteristic time of consolidation in the microporous domain is of the same order of magnitude as the macroscopic characteristic time of transient regime. Conversely, single porosity behaviours occur when both timescales are clearly distinct. Moreover, it is established that the phenomenological approaches that postulate the coexistence of two pressure fields in ‘instantaneous’ interaction only describe media with two pore networks separated by an interface flow barrier. Hence, they fail at predicting and reproducing the behaviour of usual double porosity media. Finally, the results are illustrated for the case of stratified media.

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: Meta-analysis of gene expression has enabled numerous insights into biological systems, but current methods have several limitations. We developed a method to perform a meta-analysis using the elastic net, a powerful and versatile approach for classification and regression. To demonstrate the utility of our method, we conducted a meta-analysis of lung cancer gene expression based on publicly available data. Using 629 samples from five data sets, we trained a multinomial classifier to distinguish between four lung cancer subtypes. Our meta-analysis-derived classifier included 58 genes and achieved 91% accuracy on leave-one-study-out cross-validation and on three independent data sets. Our method makes meta-analysis of gene expression more systematic and expands the range of questions that a meta-analysis can be used to address. As the amount of publicly available gene expression data continues to grow, our method will be an effective tool to help distill these data into knowledge.

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: Frequency-domain loop–loop electromagnetic (EM) methods are sensitive to the magnetic susceptibility of the Earth as well as its resistivity. Thus, inversion techniques have been used to simultaneously reconstruct both resistivity and susceptibility models from EM data. However, to take full advantage of inversion methods, calibration errors must be assessed and removed because ignoring them can result in misleading models. We present a multidimensional inversion method that jointly inverts EM and direct current (DC) resistivity data to derive offset errors as well as resistivity and susceptibility models, assuming that calibration errors can be represented by in-phase and quadrature offsets at each frequency. Addition of independent data such as DC data is effective for more accurately estimating the offsets, resulting in more reliable subsurface models. Synthetic examples involving small-loop EM data show that simultaneous inversion for resistivity and susceptibility is not stable, because of strong correlations between in-phase offset parameters and background susceptibility, but that the offsets are well determined when the data misfit is reduced rapidly in the early iteration step. Improvements achieved by joint inversion are mainly on the resistivity model. For airborne electromagnetic (AEM) data, the inversion process is stable, because AEM data are acquired using more loop–loop geometries and a wider range of frequencies. As a result, both the resistivity and susceptibility models are significantly improved by joint inversion.

Description: We have developed an efficient numerical scheme for 3-D electromagnetic (EM) simulations using an exponential finite-difference (FD) method with non-uniform grids. The method uses the set of exponential basis functions {1, exp [ ± ( x x + y y + z z )]}, where the exponents x , y and z must be chosen carefully depending on the simulation frequency and local node conductivity. The method achieves an approximation of the oscillatory and exponentially decaying EM fields that is better than that obtained via the low-degree polynomial fitting from standard FDs—and hence also leads to more accurate results. An important property of the exponential FD method is that it tends to the standard FD method when the exponents x , y and z tend to zero. We applied the standard and exponential FD methods to three marine controlled-source EM modelling scenarios: deep-water, shallow-water and intermediate water depth. For the deep-water scenario, we found that the proposed exponential FD method gave two to three times more accurate results as compared to the standard FD method on the same grid. For the shallow-water and intermediate water depth scenarios, the exponential FD method improved the accuracy of the upgoing fields; it gave 2–2.5 times more accurate results for the upgoing fields than the standard FD method on the same grid. Consequently, the method can achieve the same accuracy with a coarser grid and hence is faster than the standard FD method, as demonstrated using a frequency-domain iterative solver.

Description: Rocks in nature are multiphase composites of minerals and fluids with varying elastic properties. Predicting the effects that geochemical and geological processes, which lead to removal, alteration or substitution of one or more phases, have on seismic velocities is of considerable practical interest in geophysics. We present a new theory that quantifies the effect of replacing ‘one' or ‘more' phases (fluid or solid) on the elastic properties of multimineralic isotropic rocks. These new exact solutions relax the assumption of unchanging rock microstructure upon substitution of the pore-filling material. By developing equations that do not depend on this assumption, which is fundamental to conventional substitution theories, for example, Biot–Gassmann theory, we expand their range of applicability. Since the new exact solutions require usually unknown parameters, we also develop approximations that depend only on initial effective stiffness, elastic properties and volume fractions of constituents.

Description: We present 1D anisotropic inversion of magnetotelluric (MT) data as a potential tool for mapping structural permeability in sedimentary basins. Using 1D inversions of a 171 site, broadband MT data set from the Koroit region of the Otway Basin, Victoria, Australia, we have delineated an electrically anisotropic layer at approximately 2.5 to 3.5 km depth. The anisotropy strike is consistent between stations at approximately 160° east of north. The depth of anisotropy corresponds to the top depth of the Lower Cretaceous Crayfish Group, and the anisotropy factor increases from west to east. We interpret the anisotropy as resulting from north–northwest oriented, fluid-filled fractures resulting in enhanced electrical and hydraulic conductivity. This interpretation is consistent with permeability data from well formation tests. It is also consistent with the orientation of mapped faults in the area, which are optimally oriented for reactivation in the current stress field.

Description: Extensive and multi-dimensional data sets generated from recent cancer omics profiling projects have presented new challenges and opportunities for unraveling the complexity of cancer genome landscapes. In particular, distinguishing the unique complement of genes that drive tumorigenesis in each patient from a sea of passenger mutations is necessary for translating the full benefit of cancer genome sequencing into the clinic. We address this need by presenting a data integration framework (OncoIMPACT) to nominate patient-specific driver genes based on their phenotypic impact. Extensive in silico and in vitro validation helped establish OncoIMPACT's robustness, improved precision over competing approaches and verifiable patient and cell line specific predictions (2/2 and 6/7 true positives and negatives, respectively). In particular, we computationally predicted and experimentally validated the gene TRIM24 as a putative novel amplified driver in a melanoma patient. Applying OncoIMPACT to more than 1000 tumor samples, we generated patient-specific driver gene lists in five different cancer types to identify modes of synergistic action. We also provide the first demonstration that computationally derived driver mutation signatures can be overall superior to single gene and gene expression based signatures in enabling patient stratification and prognostication. Source code and executables for OncoIMPACT are freely available from http://sourceforge.net/projects/oncoimpact .

Description: A recent paper by Tarasov and Titov suggested that the Cole–Cole conductivity models should be preferred to the Pelton resistivity model in fitting induced polarization responses. Each model has four parameters: resistivity (or its inverse conductivity ), chargeability m , time parameter and frequency dependence c . Tarasov and Titov showed that in fitting experimental data, 3 of the parameters directly correspond across the two formulations, but that there is a difference between the Pelton and Cole–Cole model in that parameter is only the same at low frequency, but is an entangled function with m and c at high frequencies in the Pelton formulation. This claim of inconsistent was based on using the Pelton complex resistivity formulation and the Cole–Cole complex conductivity equation to analyse complex conductivity data as a function of frequency. However, if Pelton and Cole–Cole models are used to fit complex resistivity, rather than fitting conductivity, then it is the Cole–Cole model that has an entangled parameter at high chargeability m values. Simple testing shows that a Pelton model used to fit resistivity has all four model parameters directly corresponding with conductivity data fitted with a Cole–Cole model. The conclusion is that Cole–Cole and Pelton models in fact require identical independent parameters that can fit experimental or synthetic data, provided the Pelton resistivity formulation is restricted to fitting to resistivity data, and the Cole–Cole conductivity formulation is restricted to fitting conductivity results.

Description: Stratum quality factors ( P -wave and S -wave quality factors, Q p and Q s ) have gradually been utilized in the study of physical state of crust and uppermost mantle, tectonic evolution, hydrogeololgy, gas hydrates, petroleum exploration, etc. Different opinions of the seismic attenuation mechanism result in various approaches to estimate the P -wave and S -wave quality factors. Considering the viscoelasticity of the underground medium, the constitutive matrix of the Earth medium is written as the superposition of homogeneous background medium, elastic perturbation medium and viscoelastic perturbation medium. Under the hypothesis of Born integral and stationary phase approximation, the seismic reflectivity is initially raised in terms of P -wave and S -wave moduli, density, P -wave and S -wave quality factors. Furthermore, incorporating the complex seismic traces with the seismic wavelets at different offsets, a two-step inversion approach is proposed to estimate the P -wave and S -wave quality factors. The AVO/AVA Bayesian inversion approach is suggested to estimate the P -wave modulus and S -wave modulus with the real component of the pre-stack seismic data initially. Taking the estimated P -wave and S -wave moduli as prior information, the P -wave and S -wave quality factors are further estimated with the imaginary component of the complex pre-stack seismic data, which is the quadrature of the original data. Finally, synthetic examples demonstrate that the proposed approach is able to estimate P -wave and S -wave quality factors stably and properly, and two field data examples demonstrate that the proposed approach may work as an efficient approach to fluid identification.

Description: Analysis of rewired upstream subnetworks impacting downstream differential gene expression aids the delineation of evolving molecular mechanisms. Cumulative statistics based on conventional differential correlation are limited for subnetwork rewiring analysis since rewiring is not necessarily equivalent to change in correlation coefficients. Here we present a computational method ChiNet to quantify subnetwork rewiring by statistical heterogeneity that enables detection of potential genotype changes causing altered transcription regulation in evolving organisms. Given a differentially expressed downstream gene set, ChiNet backtracks a rewired upstream subnetwork from a super-network including gene interactions known to occur under various molecular contexts. We benchmarked ChiNet for its high accuracy in distinguishing rewired artificial subnetworks, in silico yeast transcription-metabolic subnetworks, and rewired transcription subnetworks for Candida albicans versus Saccharomyces cerevisiae , against two differential-correlation based subnetwork rewiring approaches. Then, using transcriptome data from tolerant S. cerevisiae strain NRRL Y-50049 and a wild-type intolerant strain, ChiNet identified 44 metabolic pathways affected by rewired transcription subnetworks anchored to major adaptively activated transcription factor genes YAP1 , RPN4 , SFP1 and ROX1 , in response to toxic chemical challenges involved in lignocellulose-to-biofuels conversion. These findings support the use of ChiNet in rewiring analysis of subnetworks where differential interaction patterns resulting from divergent nonlinear dynamics abound.

Description: In this paper, we modelled the electrical transport behaviour of bimodal carbonate rocks from a reservoir in China using dual-pore networks. One basic assumption, generally supported by experimental data and microstructure observations in the reservoir samples, was that the low porosity, monomodal rocks had the same properties and structure as the microporous matrix of the high porosity, bimodal samples. We assumed that the matrix was homogeneous and always interconnected but that the connectivity and the pore size distribution of macropore system was randomly variable. Both pore systems were supposed to act locally as ‘in parallel’ electrical conductors, an approach previously used by Bauer et al. Hence, the effect of matrix properties, macropore size distribution and connectivity on electrical properties of bimodal rocks could be modelled and investigated. We simulated electrical current through 3-D, simple cubic and body-centred cubic networks with different coordination numbers, different pipe radius distributions of macropore system and different matrix properties. The main result was that the formation factor of dual-pore network obeyed a ‘universal’ scaling relationship (i.e. independent of lattice type). Based on this result, we extended the power-law model derived by Bernabé et al. for monomodal porous media. We developed methods for evaluating the scale-invariant pore structure parameters in the model using conventional core analysis and satisfactorily tested the proposed model against experimental data from the Chinese reservoir as well as some other previously published data sets.

Description: Asymptotic expressions are derived for electromagnetic fields induced by arbitrarily oriented electric and magnetic dipoles in a laterally isotropic stratified medium. Considering that the leading terms, which describe the airwave, decay in accordance with the same geometric law whether the source is a horizontal electric or magnetic dipole, it is suggested to use a transmitter, which combines these sources. It is shown that the airwave greatly diminishes if the amplitudes and phases of the horizontal current and magnetic moments of this transmitter are chosen to minimize the far-zone vertical magnetic field. A properly tuned combined transmitter will induce the electromagnetic field with a relatively small transverse electric mode. Raw electromagnetic data acquired with the combined transmitter will be more sensitive to parameters of the resistive reservoir than data acquired using the traditional horizontal electric dipole type of the transmitter.

Description: A Bayesian inversion methodology for identification of large-scale subsurface structures (strata) from controlled source electromagnetic data is developed. The Bayesian inverse problem is solved by sampling from the posterior probability distribution, using the ensemble Kalman filter. Prior knowledge is incorporated in the methodology by utilizing structural prior information from, for example, interpreted seismic data. A model-based, composite parametrization of the electric conductivity distribution is applied to represent the subsurface structures. The model-based representation also allows for estimation of variation of electric conductivity within each stratum. To enhance stability and reduce model nonlinearity, a reduced representation of structure boundaries and conductivity variation within each stratum is applied. Numerical experiments on various test cases show that the methodology is able to identify fairly complex subsurface conductivity distributions reasonably well, with and without a hydrocarbon reservoir present. These experiments included strata with weak conductivity contrast and the application of various prior probability distributions. Furthermore, the methodology shows the ability to (almost completely) remove a reservoir present in the prior model that is not present in the true model (‘false positive’).

Description: Non-linear inversion algorithms traverse a data misfit space over multiple iterations of trial models in search of either a global minimum or some target misfit contour. The success of the algorithm in reaching that objective depends upon the smoothness and predictability of the misfit space. For any given observation, there is no absolute form a datum must take, and therefore no absolute definition for the misfit space; in fact, there are many alternatives. However, not all misfit spaces are equal in terms of promoting the success of inversion. In this work, we appraise three common forms that complex data take in electromagnetic geophysical methods: real and imaginary components, a power of amplitude and phase, and logarithmic amplitude and phase. We find that the optimal form is logarithmic amplitude and phase. Single-parameter misfit curves of log-amplitude and phase data for both magnetotelluric and controlled-source electromagnetic methods are the smoothest of the three data forms and do not exhibit flattening at low model resistivities. Synthetic, multiparameter, 2-D inversions illustrate that log-amplitude and phase is the most robust data form, converging to the target misfit contour in the fewest steps regardless of starting model and the amount of noise added to the data; inversions using the other two data forms run slower or fail under various starting models and proportions of noise. It is observed that inversion with log-amplitude and phase data is nearly two times faster in converging to a solution than with other data types. We also assess the statistical consequences of transforming data in the ways discussed in this paper. With the exception of real and imaginary components, which are assumed to be Gaussian, all other data types do not produce an expected mean-squared misfit value of 1.00 at the true model (a common assumption) as the errors in the complex data become large. We recommend that real and imaginary data with errors larger than 10 per cent of the complex amplitude be withheld from a log-amplitude and phase inversion rather than retaining them with large error-bars.

Description: Seismic interferometry comprises a suite of methods to redatum recorded wavefields to those that would have been recorded if different sources (so-called virtual sources) had been activated. Seismic interferometry by cross-correlation has been formulated using either two-way (for full wavefields) or one-way (for directionally decomposed wavefields) representation theorems. To obtain improved Green's function estimates, the cross-correlation result can be deconvolved by a quantity that identifies the smearing of the virtual source in space and time, the so-called point-spread function. This type of interferometry, known as interferometry by multidimensional deconvolution (MDD), has so far been applied only to one-way directionally decomposed fields, requiring accurate wavefield decomposition from dual (e.g. pressure and velocity) recordings. Here we propose a form of interferometry by multidimensional deconvolution that uses full wavefields with two-way representations, and simultaneously invert for pressure and (normal) velocity Green's functions, rather than only velocity responses as for its one-way counterpart. Tests on synthetic data show that two-way MDD improves on results of interferometry by cross-correlation, and generally produces estimates of similar quality to those obtained by one-way MDD, suggesting that the preliminary decomposition into up- and downgoing components of the pressure field is not required if pressure and velocity data are jointly used in the deconvolution. We also show that constraints on the directionality of the Green's functions sought can be added directly into the MDD inversion process to further improve two-way multidimensional deconvolution. Finally, as a by-product of having pressure and particle velocity measurements, we adapt one- and two-way representation theorems to convert any particle velocity receiver into its corresponding virtual dipole/gradient source by means of MDD. Thus data recorded from standard monopolar (e.g. marine) pressure sources can be converted into data from dipolar (derivative) sources at no extra acquisition cost.

Description: The primary objective of this study is to evaluate the applicability and the effectiveness of ground-penetrating radar (GPR) to identify a thin burnt soil layer, buried more than 2 m below the topographic surface at the Liangzhu Site, in Southeastern China. The site was chosen for its relatively challenging conditions of GPR techniques due to electrical conductivity and to the presence of peach tree roots that produced scattering. We completed the data acquisition by using 100 and 200 MHz antennas in TE and TM broadside and cross-polarized configurations. In the data processing and interpretation phase, we used GPR attribute analysis, including instantaneous phase and geometrical attributes. Validation analysis ground-truthing performed after the geophysical surveys, validated the GPR imaging, confirmed the electrical conductivity and relative dielectric permittivity (RDP) measurements performed at different depths, and allowed a reliable quantitative correlation between GPR results and subsurface physical properties. The research demonstrates that multiple antenna configurations in GPR data acquisition combined with attribute analysis can enhance the ability to characterize prehistoric archaeological remains even in complex subsurface conditions.

Description: We critically examine the performance of sequential geostatistical resampling (SGR) as a model proposal mechanism for Bayesian Markov-chain-Monte-Carlo (MCMC) solutions to near-surface geophysical inverse problems. Focusing on a series of simple yet realistic synthetic crosshole georadar tomographic examples characterized by different numbers of data, levels of data error and degrees of model parameter spatial correlation, we investigate the efficiency of three different resampling strategies with regard to their ability to generate statistically independent realizations from the Bayesian posterior distribution. Quite importantly, our results show that, no matter what resampling strategy is employed, many of the examined test cases require an unreasonably high number of forward model runs to produce independent posterior samples, meaning that the SGR approach as currently implemented will not be computationally feasible for a wide range of problems. Although use of a novel gradual-deformation-based proposal method can help to alleviate these issues, it does not offer a full solution. Further, we find that the nature of the SGR is found to strongly influence MCMC performance; however no clear rule exists as to what set of inversion parameters and/or overall proposal acceptance rate will allow for the most efficient implementation. We conclude that although the SGR methodology is highly attractive as it allows for the consideration of complex geostatistical priors as well as conditioning to hard and soft data, further developments are necessary in the context of novel or hybrid MCMC approaches for it to be considered generally suitable for near-surface geophysical inversions.

Description: Ribosome biogenesis, a central and essential cellular process, occurs through sequential association and mutual co-folding of protein–RNA constituents in a well-defined assembly pathway. Here, we construct a network of co-evolving nucleotide/amino acid residues within the ribosome and demonstrate that assembly constraints are strong predictors of co-evolutionary patterns. Predictors of co-evolution include a wide spectrum of structural reconstitution events, such as cooperativity phenomenon, protein-induced rRNA reconstitutions, molecular packing of different rRNA domains, protein–rRNA recognition, etc. A correlation between folding rate of small globular proteins and their topological features is known. We have introduced an analogous topological characteristic for co-evolutionary network of ribosome, which allows us to differentiate between rRNA regions subjected to rapid reconstitutions from those hindered by kinetic traps. Furthermore, co-evolutionary patterns provide a biological basis for deleterious mutation sites and further allow prediction of potential antibiotic targeting sites. Understanding assembly pathways of multicomponent macromolecules remains a key challenge in biophysics. Our study provides a ‘proof of concept’ that directly relates co-evolution to biophysical interactions during multicomponent assembly and suggests predictive power to identify candidates for critical functional interactions as well as for assembly-blocking antibiotic target sites.

Description: The seismic properties of rocks are known to be sensitive to partial liquid or gas saturation, and to aligned fractures. P -wave anisotropy is widely used for fracture characterization and is known to be sensitive to the saturating fluid. However, studies combining the effect of multiphase saturation and aligned fractures are limited even though such conditions are common in the subsurface. An understanding of the effects of partial liquid or gas saturation on P -wave anisotropy could help improve seismic characterization of fractured, gas bearing reservoirs. Using octagonal-shaped synthetic sandstone samples, one containing aligned penny-shaped fractures and the other without fractures, we examined the influence of water saturation on P -wave anisotropy in fractured rocks. In the fractured rock, the saturation related stiffening effect at higher water saturation values is larger in the direction across the fractures than along the fractures. Consequently, the anisotropy parameter ‘ ’ decreases as a result of this fluid stiffening effect. These effects are frequency dependent as a result of wave-induced fluid flow mechanisms. Our observations can be explained by combining a frequency-dependent fractured rock model and a frequency-dependent partial saturation model.

Description: Electrical resistivity tomography (ERT) has been widely used in environmental applications to study processes associated with subsurface contaminants and contaminant remediation. Anthropogenic alterations in subsurface electrical conductivity associated with contamination often originate from highly industrialized areas with significant amounts of buried metallic infrastructure. The deleterious influence of such infrastructure on imaging results generally limits the utility of ERT where it might otherwise prove useful for subsurface investigation and monitoring. In this manuscript we present a method of accurately modelling the effects of buried conductive infrastructure within the forward modelling algorithm, thereby removing them from the inversion results. The method is implemented in parallel using immersed interface boundary conditions, whereby the global solution is reconstructed from a series of well-conditioned partial solutions. Forward modelling accuracy is demonstrated by comparison with analytic solutions. Synthetic imaging examples are used to investigate imaging capabilities within a subsurface containing electrically conductive buried tanks, transfer piping, and well casing, using both well casings and vertical electrode arrays as current sources and potential measurement electrodes. Results show that, although accurate infrastructure modelling removes the dominating influence of buried metallic features, the presence of metallic infrastructure degrades imaging resolution compared to ERT imaging in the absence of infrastructure. However, it is possible to rectify this degradation in resolution through appropriate placement of electrodes.

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: The emergence of new sequencing technologies has facilitated the use of bacterial whole genome alignments for evolutionary studies and outbreak analyses. These datasets, of increasing size, often include examples of multiple different mechanisms of horizontal sequence transfer resulting in substantial alterations to prokaryotic chromosomes. The impact of these processes demands rapid and flexible approaches able to account for recombination when reconstructing isolates’ recent diversification. Gubbins is an iterative algorithm that uses spatial scanning statistics to identify loci containing elevated densities of base substitutions suggestive of horizontal sequence transfer while concurrently constructing a maximum likelihood phylogeny based on the putative point mutations outside these regions of high sequence diversity. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistically parameterized models of bacterial evolution, and achieves convergence in only a few hours on alignments of hundreds of bacterial genome sequences. Gubbins is appropriate for reconstructing the recent evolutionary history of a variety of haploid genotype alignments, as it makes no assumptions about the underlying mechanism of recombination. The software is freely available for download at github.com/sanger-pathogens/Gubbins , implemented in Python and C and supported on Linux and Mac OS X.

Description: Genomic structural variation (SV), a common hallmark of cancer, has important predictive and therapeutic implications. However, accurately detecting SV using high-throughput sequencing data remains challenging, especially for ‘targeted’ resequencing efforts. This is critically important in the clinical setting where targeted resequencing is frequently being applied to rapidly assess clinically actionable mutations in tumor biopsies in a cost-effective manner. We present BreaKmer, a novel approach that uses a ‘kmer’ strategy to assemble misaligned sequence reads for predicting insertions, deletions, inversions, tandem duplications and translocations at base-pair resolution in targeted resequencing data. Variants are predicted by realigning an assembled consensus sequence created from sequence reads that were abnormally aligned to the reference genome. Using targeted resequencing data from tumor specimens with orthogonally validated SV, non-tumor samples and whole-genome sequencing data, BreaKmer had a 97.4% overall sensitivity for known events and predicted 17 positively validated, novel variants. Relative to four publically available algorithms, BreaKmer detected SV with increased sensitivity and limited calls in non-tumor samples, key features for variant analysis of tumor specimens in both the clinical and research settings.

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: 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: 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: 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: 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: 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: Detecting allelic biases from high-throughput sequencing data requires an approach that maximises sensitivity while minimizing false positives. Here, we present Allelome.PRO, an automated user-friendly bioinformatics pipeline, which uses high-throughput sequencing data from reciprocal crosses of two genetically distinct mouse strains to detect allele-specific expression and chromatin modifications. Allelome.PRO extends approaches used in previous studies that exclusively analyzed imprinted expression to give a complete picture of the ‘allelome’ by automatically categorising the allelic expression of all genes in a given cell type into imprinted, strain-biased, biallelic or non-informative. Allelome.PRO offers increased sensitivity to analyze lowly expressed transcripts, together with a robust false discovery rate empirically calculated from variation in the sequencing data. We used RNA-seq data from mouse embryonic fibroblasts from F1 reciprocal crosses to determine a biologically relevant allelic ratio cutoff, and define for the first time an entire allelome. Furthermore, we show that Allelome.PRO detects differential enrichment of H3K4me3 over promoters from ChIP-seq data validating the RNA-seq results. This approach can be easily extended to analyze histone marks of active enhancers, or transcription factor binding sites and therefore provides a powerful tool to identify candidate cis regulatory elements genome wide.

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: 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: Methods to interpret personal genome sequences are increasingly required. Here, we report a novel framework (EvoTol) to identify disease-causing genes using patient sequence data from within protein coding-regions. EvoTol quantifies a gene's intolerance to mutation using evolutionary conservation of protein sequences and can incorporate tissue-specific gene expression data. We apply this framework to the analysis of whole-exome sequence data in epilepsy and congenital heart disease, and demonstrate EvoTol's ability to identify known disease-causing genes is unmatched by competing methods. Application of EvoTol to the human interactome revealed networks enriched for genes intolerant to protein sequence variation, informing novel polygenic contributions to human disease.

Description: Detecting in vivo transcription factor (TF) binding is important for understanding gene regulatory circuitries. ChIP-seq is a powerful technique to empirically define TF binding in vivo . However, the multitude of distinct TFs makes genome-wide profiling for them all labor-intensive and costly. Algorithms for in silico prediction of TF binding have been developed, based mostly on histone modification or DNase I hypersensitivity data in conjunction with DNA motif and other genomic features. However, technical limitations of these methods prevent them from being applied broadly, especially in clinical settings. We conducted a comprehensive survey involving multiple cell lines, TFs, and methylation types and found that there are intimate relationships between TF binding and methylation level changes around the binding sites. Exploiting the connection between DNA methylation and TF binding, we proposed a novel supervised learning approach to predict TF–DNA interaction using data from base-resolution whole-genome methylation sequencing experiments. We devised beta-binomial models to characterize methylation data around TF binding sites and the background. Along with other static genomic features, we adopted a random forest framework to predict TF–DNA interaction. After conducting comprehensive tests, we saw that the proposed method accurately predicts TF binding and performs favorably versus competing methods.

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: 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: It is well known that sedimentary rocks having same porosity can have very different pore size distribution. The pore distribution determines many characteristics of the rock, among which its transport properties are often the most useful. Multifractal analysis is a powerful tool that is increasingly used to characterize the pore space. In this study, we performed multifractal analysis of pore distribution on simulated sedimentary rocks using the relaxed bidisperse ballistic deposition model (RBBDM). The RBBDM can generate a 3-D structure of sedimentary rocks of variable porosity by tuning the fraction p of particles of two different sizes. We also performed multifractal analysis on two samples of real sedimentary rock to compare with the simulation studies. One sample, an oolitic limestone is of high porosity (40 per cent) while the other is a reefal carbonate of low porosity, around 7 per cent. 2-D sections of X-ray microtomographs of the real rocks were stacked sequentially to reconstruct the real rock specimens. Both samples show multifractal character. The results from analysis of real rock agree quite well with the simulated structure of low porosity. The simulated rock of high porosity showed a weak multifractal nature though the real rock sample of similar porosity was found to be strongly multifractal. We propose a ‘structure parameter’ which is a function of porosity and the generalized dimensions, and controls the transport properties of the rock.

Description: This paper applies nonlinear Bayesian inversion to marine controlled source electromagnetic (CSEM) data collected near two sites of the Integrated Ocean Drilling Program (IODP) Expedition 311 on the northern Cascadia Margin to investigate subseafloor resistivity structure related to gas hydrate deposits and cold vents. The Cascadia margin, off the west coast of Vancouver Island, Canada, has a large accretionary prism where sediments are under pressure due to convergent plate boundary tectonics. Gas hydrate deposits and cold vent structures have previously been investigated by various geophysical methods and seabed drilling. Here, we invert time-domain CSEM data collected at Sites U1328 and U1329 of IODP Expedition 311 using Bayesian methods to derive subsurface resistivity model parameters and uncertainties. The Bayesian information criterion is applied to determine the amount of structure (number of layers in a depth-dependent model) that can be resolved by the data. The parameter space is sampled with the Metropolis–Hastings algorithm in principal-component space, utilizing parallel tempering to ensure wider and efficient sampling and convergence. Nonlinear inversion allows analysis of uncertain acquisition parameters such as time delays between receiver and transmitter clocks as well as input electrical current amplitude. Marginalizing over these instrument parameters in the inversion accounts for their contribution to the geophysical model uncertainties. One-dimensional inversion of time-domain CSEM data collected at measurement sites along a survey line allows interpretation of the subsurface resistivity structure. The data sets can be generally explained by models with 1 to 3 layers. Inversion results at U1329, at the landward edge of the gas hydrate stability zone, indicate a sediment unconformity as well as potential cold vents which were previously unknown. The resistivities generally increase upslope due to sediment erosion along the slope. Inversion results at U1328 on the middle slope suggest several vent systems close to Bullseye vent in agreement with ongoing interdisciplinary observations.

Description: We examine along-axis variations in melt content of the axial magma lens (AML) beneath the fast-spreading East Pacific Rise (EPR) using an amplitude variation with angle of incidence (AVA) crossplotting method applied to multichannel seismic data acquired in 2008. The AVA crossplotting method, which has been developed for and, so far, applied for hydrocarbon prospection in sediments, is for the first time applied to a hardrock environment. We focus our analysis on 2-D data collected along the EPR axis from 9°29.8'N to 9°58.4'N, a region which encompasses the sites of two well-documented submarine volcanic eruptions (1991–1992 and 2005–2006). AVA crossplotting is performed for a ~53 km length of the EPR spanning nine individual AML segments (ranging in length from ~3.2 to 8.5 km) previously identified from the geometry of the AML and disruptions in continuity. Our detailed analyses conducted at 62.5 m interval show that within most of the analysed segments melt content varies at spatial scales much smaller (a few hundred of metres) than the length of the fine-scale AML segments, suggesting high heterogeneity in melt concentration. At the time of our survey, about 2 yr after the eruption, our results indicate that the three AML segments that directly underlie the 2005–2006 lava flow are on average mostly molten. However, detailed analysis at finer-scale intervals for these three segments reveals AML pockets (from 〉62.5 to 812.5 m long) with a low melt fraction. The longest such mushy section is centred beneath the main eruption site at ~9°50.4'N, possibly reflecting a region of primary melt drainage during the 2005–2006 event. The complex geometry of fluid flow pathways within the crust above the AML and the different response times of fluid flow and venting to eruption and magma reservoir replenishment may contribute to the poor spatial correlation between incidence of hydrothermal vents and presence of highly molten AML. The presented results are an important step forward in our ability to resolve small-scale characteristics of the AML and recommend the AVA crossplotting as a tool for examining mid-ocean ridge magma-systems elsewhere.

Description: The relative permittivity ( r ) and the electrical conductivity ( ) of porous media are known to be functions of water saturation ( S ). As such, their measurements can be useful in effective characterisations and monitoring of geological carbon sequestration using geoelectrical measurement techniques. In this work, the effects of pressure, temperature and salt concentration on bulk r – S and – S relationships were investigated for carbonate (limestone) and silicate porous media (both unconsolidated domains) under dynamic and quasi-static supercritical CO 2 (scCO 2 )-brine/water flow. In the silica sand sample, the bulk r ( b ) for scCO 2 –water decreases as the temperature increases. On the contrary, slight increase was seen in the b with temperature in the carbonate sample for the scCO 2 -water system. These trends are more conspicuous at high water saturation. The b – S curves for the scCO 2 –water flow in the silica sand also show clear dependency on the domain pressure, where b increases as the domain pressure increases. Furthermore, the bulk ( b ), at any particular saturation for the scCO 2 -brine system rises as the temperature increases with more significant increase found at very high water saturation. Both b and b values are found to be greater in the limestone than silica sand porous samples for similar porosity values. Based on different injection rates investigated, we do not find significant dynamic effects in the b – S and b – S relationships for the scCO 2 -brine/water system. As such, geoelectrical characteristics can be taken as reliable in the monitoring of two-phase flow system in the porous media. It can be inferred from the results that the geoelectrical techniques are highly dependent on water saturation. This dependence is more conspicuous at higher water saturation. Different mathematical models examined show their reliability at different water saturation ranges. The polynomial fit developed in this work takes into consideration the fluid pressure in the system as well as the initial bulk relative permittivity prior to the injection of CO 2 . The polynomial fit shows a good reliability in the prediction of the geo-electrical properties of the CO 2 –water–porous media system, especially at higher water saturation. In comparison, the mixing model from the literature shows more reliability in the prediction of similar property at lower water saturation.

Description: The Canada Basin and the southern Alpha-Mendeleev ridge complex underlie a significant proportion of the Arctic Ocean, but the geology of this undrilled and mostly ice-covered frontier is poorly known. New information is encoded in seismic wide-angle reflections and refractions recorded with expendable sonobuoys between 2007 and 2011. Velocity–depth samples within the sedimentary succession are extracted from published analyses for 142 of these records obtained at irregularly spaced stations across an area of 1.9E + 06 km 2 . The samples are modelled at regional, subregional and station-specific scales using an exponential function of inverse velocity versus depth with regionally representative parameters determined through numerical regression. With this approach, smooth, non-oscillatory velocity–depth profiles can be generated for any desired location in the study area, even where the measurement density is low. Practical application is demonstrated with a map of sedimentary thickness, derived from seismic reflection horizons interpreted in the time domain and depth converted using the velocity–depth profiles for each seismic trace. A thickness of 12–13 km is present beneath both the upper Mackenzie fan and the middle slope off of Alaska, but the sedimentary prism thins more gradually outboard of the latter region. Mapping of the observed-to-predicted velocities reveals coherent geospatial trends associated with five subregions: the Mackenzie fan; the continental slopes beyond the Mackenzie fan; the abyssal plain; the southwestern Canada Basin; and, the Alpha-Mendeleev magnetic domain. Comparison of the subregional velocity–depth models with published borehole data, and interpretation of the station-specific best-fitting model parameters, suggests that sandstone is not a predominant lithology in any of the five subregions. However, the bulk sand-to-shale ratio likely increases towards the Mackenzie fan, and the model for this subregion compares favourably with borehole data for Miocene turbidites in the eastern Gulf of Mexico. The station-specific results also indicate that Quaternary sediments coarsen towards the Beaufort-Mackenzie and Banks Island margins in a manner that is consistent with the variable history of Laurentide Ice Sheet advance documented for these margins. Lithological factors do not fully account for the elevated velocity–depth trends that are associated with the southwestern Canada Basin and the Alpha-Mendeleev magnetic domain. Accelerated porosity reduction due to elevated palaeo-heat flow is inferred for these regions, which may be related to the underlying crustal types or possibly volcanic intrusion of the sedimentary succession. Beyond exploring the variation of an important physical property in the Arctic Ocean basin, this study provides comparative reference for global studies of seismic velocity, burial history, sedimentary compaction, seismic inversion and overpressure prediction, particularly in mudrock-dominated successions.

Description: Ongoing works on full waveform inversion (FWI) are yielding an increasing number of objective functions as alternative to the traditional L2-waveform. These studies aim at designing more robust functions and inversion strategies to reduce the intrinsic dependence of the FWI results on (1) the initial model and (2) the lowest frequency present in field data. In this work, we perform a comparative study of five objective functions in time domain under a common 2-D-acoustic FWI scheme using the Marmousi model as benchmark. In particular, we compare results obtained with L2-based functions that consider the minimization of different wave attributes; the waveform-based, non-integration-method; instantaneous envelope; a modified version of the wrapped instantaneous phase and an improved version of the cross-correlation travel time (CCTT) method; and hybrid strategies combining some of them. We evaluate the robustness of these functionals as a function of their performance with and without low frequencies in the data and the presence of random white Gaussian noise. Our results reveal promising strategies to invert noisy data with limited low-frequency content (≥4 Hz), which is the single strategy using the instantaneous phase objective function followed by the hybrid strategies using the instantaneous phase or CCTT as initial models, in particular the combinations [I. Phase + Waveform], [CCTT + Waveform] and [CCTT + I. Phase].

Description: Copy-number variants (CNVs) are a major form of genetic variation and a risk factor for various human diseases, so it is crucial to accurately detect and characterize them. It is conceivable that allele-specific reads from high-throughput sequencing data could be leveraged to both enhance CNV detection and produce allele-specific copy number (ASCN) calls. Although statistical methods have been developed to detect CNVs using whole-genome sequence (WGS) and/or whole-exome sequence (WES) data, information from allele-specific read counts has not yet been adequately exploited. In this paper, we develop an integrated method, called AS-GENSENG, which incorporates allele-specific read counts in CNV detection and estimates ASCN using either WGS or WES data. To evaluate the performance of AS-GENSENG, we conducted extensive simulations, generated empirical data using existing WGS and WES data sets and validated predicted CNVs using an independent methodology. We conclude that AS-GENSENG not only predicts accurate ASCN calls but also improves the accuracy of total copy number calls, owing to its unique ability to exploit information from both total and allele-specific read counts while accounting for various experimental biases in sequence data. Our novel, user-friendly and computationally efficient method and a complete analytic protocol is freely available at https://sourceforge.net/projects/asgenseng/ .

Description: Increased sequencing of microbial genomes has revealed that prevailing prokaryotic species assignments can be inconsistent with whole genome information for a significant number of species. The long-standing need for a systematic and scalable species assignment technique can be met by the genome-wide Average Nucleotide Identity (gANI) metric, which is widely acknowledged as a robust measure of genomic relatedness. In this work, we demonstrate that the combination of gANI and the alignment fraction (AF) between two genomes accurately reflects their genomic relatedness. We introduce an efficient implementation of AF,gANI and discuss its successful application to 86.5M genome pairs between 13,151 prokaryotic genomes assigned to 3032 species. Subsequently, by comparing the genome clusters obtained from complete linkage clustering of these pairs to existing taxonomy, we observed that nearly 18% of all prokaryotic species suffer from anomalies in species definition. Our results can be used to explore central questions such as whether microorganisms form a continuum of genetic diversity or distinct species represented by distinct genetic signatures. We propose that this precise and objective AF,gANI-based species definition: the MiSI (Microbial Species Identifier) method, be used to address previous inconsistencies in species classification and as the primary guide for new taxonomic species assignment, supplemented by the traditional polyphasic approach, as required.

Description: Classically or alternatively activated macrophages (M1 and M2, respectively) play distinct and important roles for microbiocidal activity, regulation of inflammation and tissue homeostasis. Despite this, their transcriptional regulatory dynamics are poorly understood. Using promoter-level expression profiling by non-biased deepCAGE we have studied the transcriptional dynamics of classically and alternatively activated macrophages. Transcription factor (TF) binding motif activity analysis revealed four motifs, NFKB1_REL_RELA, IRF1,2, IRF7 and TBP that are commonly activated but have distinct activity dynamics in M1 and M2 activation. We observe matching changes in the expression profiles of the corresponding TFs and show that only a restricted set of TFs change expression. There is an overall drastic and transient up-regulation in M1 and a weaker and more sustainable up-regulation in M2. Novel TFs, such as Thap6, Maff , (M1) and Hivep1, Nfil3, Prdm1 , (M2) among others, were suggested to be involved in the activation processes. Additionally, 52 (M1) and 67 (M2) novel differentially expressed genes and, for the first time, several differentially expressed long non-coding RNA (lncRNA) transcriptome markers were identified. In conclusion, the finding of novel motifs, TFs and protein-coding and lncRNA genes is an important step forward to fully understand the transcriptional machinery of macrophage activation.

Description: We study the well log and seismic responses of intensively fractured portions of deep intrusive/metamorphic rocks in southern Tuscany (Italy), which constitute the main drilling targets of the geothermal exploration in the Larderello–Travale area. In particular, the target we consider is located near the contact between a deep Pliocene granitic intrusion and the overlying Palaeozoic metamorphic basement. Sonic, density and borehole image logs are analysed together with post-stack reflection attributes and reflection amplitude versus source to receiver azimuth (AVAZ) responses. It turns out that the intense fracturing in the contact zone causes significant decreases in the density and P -wave velocity, and that fracture planes exhibit very high dips and a common preferential direction. The fractured zone found by the well coincides with peculiar alignments of high-amplitude signals in the 3-D seismic stack volume, which are particularly visible on the reflection strength and instantaneous phase time slices. The normal incidence synthetic seismogram based on the log data matches the observed stack trace nearest to the well and confirms that the high-amplitude reflection occurs at the fractured zone. We then consider the pre-stack domain to study the same reflections on bin gathers that are close to the well and coincident with the anomalies in the 3-D volume. In particular, we perform AVAZ analysis to detect possible anisotropic features in the reflected amplitudes due to the preferential orientation of the fractures, and we study the effect of crack density on the seismic responses and on velocity and density values. To this end, we build simplified models where a level with vertical fractures is encased in tight isotropic rocks. Notwithstanding the suboptimal quality of the seismic data, we estimate the overall matching between the borehole information and the seismic response as fair. In particular, the azimuthal amplitude variation of the reflections from the studied fractured zone has a sinusoidal trend that is quite consistent with the fracture planes’ orientation as indicated by the image logs. Moreover, the comparison between the actual AVAZ response and the AVAZ responses of synthetic seismograms generated on models with different crack densities suggests that it may be feasible to estimate crack density values from the azimuthal amplitude variation of the observed reflections, within the resolution of the seismic data.

Description: Surface-based monitoring of mass transfer caused by injections and extractions in deep boreholes is crucial to maximize oil, gas and geothermal production. Inductive electromagnetic methods, such as magnetotellurics, are appealing for these applications due to their large penetration depths and sensitivity to changes in fluid conductivity and fracture connectivity. In this work, we propose a 3-D Markov chain Monte Carlo inversion of time-lapse magnetotelluric data to image mass transfer following a saline fluid injection. The inversion estimates the posterior probability density function of the resulting plume, and thereby quantifies model uncertainty. To decrease computation times, we base the parametrization on a reduced Legendre moment decomposition of the plume. A synthetic test shows that our methodology is effective when the electrical resistivity structure prior to the injection is well known. The centre of mass and spread of the plume are well retrieved. We then apply our inversion strategy to an injection experiment in an enhanced geothermal system at Paralana, South Australia, and compare it to a 3-D deterministic time-lapse inversion. The latter retrieves resistivity changes that are more shallow than the actual injection interval, whereas the probabilistic inversion retrieves plumes that are located at the correct depths and oriented in a preferential north–south direction. To explain the time-lapse data, the inversion requires unrealistically large resistivity changes with respect to the base model. We suggest that this is partly explained by unaccounted subsurface heterogeneities in the base model from which time-lapse changes are inferred.

Description: Adaptive optimal experimental design methods use previous data and results to guide the choice and design of future experiments. This paper describes the formulation of an adaptive survey design technique to produce optimal resistivity imaging surveys for time-lapse geoelectrical monitoring experiments. These survey designs are time-dependent and, compared to dipole–dipole or static optimized surveys that do not change over time, focus a greater degree of the image resolution on regions of the subsurface that are actively changing. The adaptive optimization method is validated using a controlled laboratory monitoring experiment comprising a well-defined cylindrical target moving along a trajectory that changes its depth and lateral position. The algorithm is implemented on a standard PC in conjunction with a modified automated multichannel resistivity imaging system. Data acquisition using the adaptive survey designs requires no more time or power than with comparable standard surveys, and the algorithm processing takes place while the system batteries recharge. The results show that adaptively designed optimal surveys yield a quantitative increase in image quality over and above that produced by using standard dipole–dipole or static (time–independent) optimized surveys.

Description: The presence of mesoscopic heterogeneities in fluid-saturated porous rocks can produce measurable seismoelectric signals due to wave-induced fluid flow between regions of differing compressibility. The dependence of these signals on the petrophysical and structural characteristics of the probed rock mass remains largely unexplored. In this work, we derive an analytical solution to describe the seismoelectric response of a rock sample, containing a horizontal layer at its centre, that is subjected to an oscillatory compressibility test. We then adapt this general solution to compute the seismoelectric signature of a particular case related to a sample that is permeated by a horizontal fracture located at its centre. Analyses of the general and particular solutions are performed to study the impact of different petrophysical and structural parameters on the seismoelectric response. We find that the amplitude of the seismoelectric signal is directly proportional to the applied stress, to the Skempton coefficient contrast between the host rock and the layer, and to a weighted average of the effective excess charge of the two materials. Our results also demonstrate that the frequency at which the maximum electrical potential amplitude prevails does not depend on the applied stress or the Skempton coefficient contrast. In presence of strong permeability variations, this frequency is rather controlled by the permeability and thickness of the less permeable material. The results of this study thus indicate that seismoelectric measurements can potentially be used to estimate key mechanical and hydraulic rock properties of mesoscopic heterogeneities, such as compressibility, permeability and fracture compliance.

Description: The early detection of the oil–water encroachment front is of prime interest during the water flooding of an oil reservoir to maximize the production of oil and to avoid the oil–water encroachment front to come too close to production wells. We propose a new 4-D inversion approach based on the Gauss–Newton approach to invert cross-well resistance data. The goal of this study is to image the position of the oil–water encroachment front in a heterogeneous clayey sand reservoir. This approach is based on explicitly connecting the change of resistivity to the petrophysical properties controlling the position of the front (porosity and permeability) and to the saturation of the water phase through a petrophysical resistivity model accounting for bulk and surface conductivity contributions and saturation. The distributions of the permeability and porosity are also inverted using the time-lapse resistivity data in order to better reconstruct the position of the oil water encroachment front. In our synthetic test case, we get a better position of the front with the by-products of porosity and permeability inferences near the flow trajectory and close to the wells. The numerical simulations show that the position of the front is recovered well but the distribution of the recovered porosity and permeability is only fair. A comparison with a commercial code based on a classical Gauss–Newton approach with no information provided by the two-phase flow model fails to recover the position of the front. The new approach could be used for the time-lapse monitoring of various processes in both geothermal fields and oil and gas reservoirs using a combination of geophysical methods.

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

Description: Submarine mud volcanos at the seafloor are surface expressions of fluid flow systems within the seafloor. Since the electrical resistivity of the seafloor is mainly determined by the amount and characteristics of fluids contained within the sediment's pore space, electromagnetic methods offer a promising approach to gain insight into a mud volcano's internal resistivity structure. To investigate this structure, we conducted a controlled source electromagnetic experiment, which was novel in the sense that the source was deployed and operated with a remotely operated vehicle, which allowed for a flexible placement of the transmitter dipole with two polarization directions at each transmitter location. For the interpretation of the experiment, we have adapted the concept of rotational invariants from land-based electromagnetics to the marine case by considering the source normalized tensor of horizontal electric field components. We analyse the sensitivity of these rotational invariants in terms of 1-D models and measurement geometries and associated measurement errors, which resemble the experiment at the mud volcano. The analysis shows that any combination of rotational invariants has an improved parameter resolution as compared to the sensitivity of the pure radial or azimuthal component alone. For the data set, which was acquired at the ‘North Alex’ mud volcano, we interpret rotational invariants in terms of 1-D inversions on a common midpoint grid. The resulting resistivity models show a general increase of resistivities with depth. The most prominent feature in the stitched 1-D sections is a lens-shaped interface, which can similarly be found in a section from seismic reflection data. Beneath this interface bulk resistivities frequently fall in a range between 2.0 and 2.5 m towards the maximum penetration depths. We interpret the lens-shaped interface as the surface of a collapse structure, which was formed at the end of a phase of activity of an older mud volcano generation and subsequently refilled with new mud volcano sediments during a later stage of activity. Increased resistivities at depth cannot be explained by compaction alone, but instead require a combination of compaction and increased cementation of the older sediments, possibly in connection to trapped, cooled down mud volcano fluids, which have a depleted chlorinity. At shallow depths (≤50 m) bulk resistivities generally decrease and for locations around the mud volcano's centre 1-D models show bulk resistivities in a range between 0.5 and 0.7 m, which we interpret in terms of gas saturation levels by means of Archie's Law. After a detailed analysis of the material parameters contained in Archie's Law we derive saturation levels between 0 and 25 per cent, which is in accordance with observations of active degassing and a reflector with negative polarity in the seismics section just beneath the seafloor, which is indicative of free gas.