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: Rock permeability is an important parameter for the formation evaluation. In this paper, a new method with streaming current is proposed to determine the sample permeability based on the electrokinetic effects, and is proved by the experimental measurements. Corresponding to this method, we have designed an experimental setup and a test system, then performed the streaming current (potential) and electro-osmosis pressure experiments with 23 sandstone samples at 0.05 mol l –1 NaCl solution. The streaming current (potential) coefficient and electro-osmosis pressure coefficient are obtained, respectively, with the experimental data at low frequencies with AC lock-in technique. The electrokinetic permeabilities are further calculated with these coefficients. The results are consistent well with the gas permeability measured with Darcy's law, which verifies the current method for estimating rock permeability. Our measurements are also analysed and compared with previous measurements. The results indicate that our method can reflect the essence of electrokinetic effects better and simplify the electrokinetic measurements as well. In addition, we discuss the influences of experimental artefacts (core holder and confining pressure installation) on the electrokinetic data. The results show that the trough phenomenon, appeared in frequency curves of streaming current (potential) coefficients, is induced by the resonance of the core-holder/vibrator system. This is important for the design of electrokinetic setup and the analysis of low-frequency response of the electrokinetic coupling coefficients.

Description: Multiparameter full waveform inversion (FWI) applied to an elastic orthorhombic model description of the subsurface requires in theory a nine-parameter representation of each pixel of the model. Even with optimal acquisition on the Earth surface that includes large offsets, full azimuth, and multicomponent sensors, the potential for trade-off between the elastic orthorhombic parameters are large. The first step to understanding such trade-off is analysing the scattering potential of each parameter, and specifically, its scattering radiation patterns. We investigate such radiation patterns for diffraction and for scattering from a horizontal reflector considering a background isotropic model. The radiation patterns show considerable potential for trade-off between the parameters and the potentially limited resolution in their recovery. The radiation patterns of C 11 , C 22 , and C 33 are well separated so that we expect to recover these parameters with limited trade-offs. However, the resolution of their recovery represented by recovered range of model wavenumbers varies between these parameters. We can only invert for the short wavelength components (reflection) of C 33 while we can mainly invert for the long wavelength components (transmission) of the elastic coefficients C 11 and C 22 if we have large enough offsets. The elastic coefficients C 13 , C 23 , and C 12 suffer from strong trade-offs with C 55 , C 44 , and C 66 , respectively. The trade-offs between C 13 and C 55 , as well as C 23 and C 44 , can be partially mitigated if we acquire P – SV and SV – SV waves. However, to reduce the trade-offs between C 12 and C 66 , we require credible SH – SH waves. The analytical radiation patterns of the elastic constants are supported by numerical gradients of these parameters.

Description: Typically, seismic data are sparsely and irregularly sampled due to limitations in the survey environment and these cause problems for key seismic processing steps such as surface-related multiple elimination or wave-equation-based migration. Various interpolation techniques have been developed to alleviate the problems caused by sparse and irregular sampling. Among many interpolation techniques, matching pursuit interpolation is a robust tool to interpolate the regularly sampled data with large receiver separation such as crossline data in marine seismic acquisition when both pressure and particle velocity data are used. Multicomponent matching pursuit methods generally used the sinusoidal basis function, which have shown to be effective for interpolating multicomponent marine seismic data in the crossline direction. In this paper, we report the use of wavelet basis functions which further enhances the performance of matching pursuit methods for de-aliasing than sinusoidal basis functions. We also found that the range of the peak wavenumber of the wavelet is critical to the stability of the interpolation results and the de-aliasing performance and that the range should be determined based on Nyquist criteria. In addition, we reduced the computational cost by adopting the inner product of the wavelet and the input data to find the parameters of the wavelet basis function instead of using L-2 norm minimization. Using synthetic data, we illustrate that for aliased data, wavelet-based matching pursuit interpolation yields more stable results than sinusoidal function-based one when we use not only pressure data only but also both pressure and particle velocity together.

Description: Deep sea pockmarks underlain by chimney-like or pipe structures that contain methane hydrate are abundant along the Norwegian continental margin. In such hydrate provinces the interaction between hydrate formation and fluid flow has significance for benthic ecosystems and possibly climate change. The Nyegga region, situated on the western Norwegian continental slope, is characterized by an extensive pockmark field known to accommodate substantial methane gas hydrate deposits. The aim of this study is to detect and delineate both the gas hydrate and free gas reservoirs at one of Nyegga's pockmarks. In 2012, a marine controlled-source electromagnetic (CSEM) survey was performed at a pockmark in this region, where high-resolution 3-D seismic data were previously collected in 2006. 2-D CSEM inversions were computed using the data acquired by ocean bottom electrical field receivers. Our results, derived from unconstrained and seismically constrained CSEM inversions, suggest the presence of two distinctive resistivity anomalies beneath the pockmark: a shallow vertical anomaly at the underlying pipe structure, likely due to gas hydrate accumulation, and a laterally extensive anomaly attributed to a free gas zone below the base of the gas hydrate stability zone. This work contributes to a robust characterization of gas hydrate deposits within subseafloor fluid flow pipe structures.

Description: One of the main applications of magnetic field measurements in boreholes is the detection of unexploded ordnance or buried utility structures like pipes or tiebacks. Even though the advantage of fully oriented magnetic vector measurements have long been recognized and could significantly reduce costs and risks, the tools used for those purposes typically measure only the total magnetic field, the vertical and horizontal components or gradients thereof. The Göttingen Bohrloch Magnetometer uses three fibre optic gyros to record its orientation and thus enables us to compute high-quality three-component magnetic vector data regardless of borehole orientation. The measurements described in this paper were run in the scientific borehole Cuxhaven Lüdingworth 1/1A, which was drilled as a part of the ‘Coastal Aquifer Test field’ project to study the dynamics of the saltwater/freshwater interface. As the drill string got stuck during drilling of the first borehole, a second hole was drilled in the immediate vicinity. The drill string lies at a depth between 80 and 114 m at a distance of only 2.5 m southeast of the borehole used for the measurements, making it an ideal target to demonstrate the benefits of vector magnetic surveys. Although the theories to calculate magnetic fields of objects with different shapes is well established and do not need to be tested, they almost exclusively include approximations of the geometry. It is not obvious whether these approximations are suited to describe real data, or whether additional effects or refinements have to be considered. We use both a simplified monopole model and a cylinder model to fit the data and are able to determine the position of the drill string within a statistical error of approximately 10 cm. Additionally, we show that the location of the drill string could not have been determined by measurements of the total field or its horizontal and vertical component alone and that those methods would require the drilling of additional boreholes to obtain an unambiguous result.

Description: In this study, we isolated 15 endophytic fungi from five Sudanese medicinal plants. Each fungal endophytic strain was identified by sequencing of internal transcribed spacer (ITS) regions of rDNA. Ethyl acetate extracts were prepared from each endophyte cultivated in vitro and tested for their respective antibacterial activities and antiproliferative activities against human cancer cells. Antibacterial screening was carried out against two bacterial strains: Gram-negative Escherichia coli and Gram-positive methicillin-resistant Staphylococcus aureus , by the broth dilution method. Cell viability was evaluated by the MTT procedure after exposure of MCF7 breast cancer cells and HT29 or HCT116 human colon adenocarcinoma cells to each endophytic extract. Of interest, Byssochlamys spectabilis isolated from Euphorbia prostata showed cytotoxicity (IC 50 = 1.51 ± 0.2 μg mL –1 ) against MCF7 cells, but had a low effect against HT29 or HCT116 cells (IC 50 〉 20 μg mL –1 ). Cladosporium cladosporioides 2, isolated from Vernonia amygdalina leaves, showed antiproliferative activities against MCF7 cells (IC 50 = 10.5 ± 1.5 μg mL –1 ) only. On the other hand, B. spectabilis and Alternaria sp. extract had antibacterial activities against the S. aureus strain. The findings of this work revealed that endophytic fungi associated with medicinal plants from Sudan could be considered as an attractive source of new therapeutic compounds.

Description: Chromosome-long haplotyping of human genomes is important to identify genetic variants with differing gene expression, in human evolution studies, clinical diagnosis, and other biological and medical fields. Although several methods have realized haplotyping based on sequencing technologies or population statistics, accuracy and cost are factors that prohibit their wide use. Borrowing ideas from group testing theories, we proposed a clone-based haplotyping method by overlapping pool sequencing. The clones from a single individual were pooled combinatorially and then sequenced. According to the distinct pooling pattern for each clone in the overlapping pool sequencing, alleles for the recovered variants could be assigned to their original clones precisely. Subsequently, the clone sequences could be reconstructed by linking these alleles accordingly and assembling them into haplotypes with high accuracy. To verify the utility of our method, we constructed 130 110 clones in silico for the individual NA12878 and simulated the pooling and sequencing process. Ultimately, 99.9% of variants on chromosome 1 that were covered by clones from both parental chromosomes were recovered correctly, and 112 haplotype contigs were assembled with an N50 length of 3.4 Mb and no switch errors. A comparison with current clone-based haplotyping methods indicated our method was more accurate.

Description: Sexual differentiation of malaria parasites into gametocytes in the vertebrate host and subsequent gamete fertilization in mosquitoes is essential for the spreading of the disease. The molecular processes orchestrating these transitions are far from fully understood. Here, we report the first transcriptome analysis of male and female Plasmodium falciparum gametocytes coupled with a comprehensive proteome analysis. In male gametocytes there is an enrichment of proteins involved in the formation of flagellated gametes; proteins involved in DNA replication, chromatin organization and axoneme formation. On the other hand, female gametocytes are enriched in proteins required for zygote formation and functions after fertilization; protein-, lipid- and energy-metabolism. Integration of transcriptome and proteome data revealed 512 highly expressed maternal transcripts without corresponding protein expression indicating large scale translational repression in P. falciparum female gametocytes for the first time. Despite a high degree of conservation between Plasmodium species, 260 of these ‘repressed transcripts’ have not been previously described. Moreover, for some of these genes, protein expression is only reported in oocysts and sporozoites indicating that repressed transcripts can be partitioned into short- and long-term storage. Finally, these data sets provide an essential resource for identification of vaccine/drug targets and for further mechanistic studies.

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: Identifying large-scale structural variation in cancer genomes continues to be a challenge to researchers. Current methods rely on genome alignments based on a reference that can be a poor fit to highly variant and complex tumor genomes. To address this challenge we developed a method that uses available breakpoint information to generate models of structural variations. We use these models as references to align previously unmapped and discordant reads from a genome. By using these models to align unmapped reads, we show that our method can help to identify large-scale variations that have been previously missed.

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: Although seismic attenuation measurements have great potential to enhance our knowledge of physical conditions and rock properties, their application is limited because robust methods for improving both the resolution and accuracy of attenuation estimates have not yet been established. We propose attenuation estimation methods for zero-offset vertical seismic profile (VSP) data by combining seismic interferometry (SI) and the modified median frequency shift (MMFS) method developed for attenuation estimation using sonic waveform data. The configuration of zero-offset VSP data is redatumed to that of the sonic logging measurement by adopting two types of SI: deconvolution interferometry and crosscorrelation interferometry (CCI). Then, we can apply the MMFS method to the redatumed VSP data. Although the amplitude information estimated from CCI is biased, we propose a correction method for this bias to correctly estimate attenuation. First, to investigate the performance both in resolution and accuracy, we apply different trace separations to synthetic data with random noise at different signal-to-noise ratio levels. Second, we estimate the influence of residual reflection events after wavefield separation on attenuation estimation. The proposed methods provide more stable attenuation estimates in comparison with the spectral ratio method because the mean-median procedure suppresses random events and characteristic features caused by residual reflection events in spectral domain. Our numerical experiments also imply that the proposed methods can estimate scattering attenuation values even if frequency components are not changed between the two receiver depths. Finally, by preliminarily applying the proposed methods to field VSP data, we demonstrate the advantages of the proposed method in the resolution and stability of attenuation estimates and these observations correlate with those of numerical tests.

Description: Resveratrol is a well-known triphenolic natural product present in red wine. For its contribution to human health, the demand for resveratrol as a food and nutrition supplement has increased significantly. In recent years, the rapid development of synthetic biology has promoted extensive work to increase the production of resveratrol in microbes. However, supplementation of expensive phenylpropanoic precursors was required in current engineered strains. Here, we first utilized the site-specific integration strategy to produce resveratrol in Escherichia coli . The genes tal , 4cl and sts were site-specific integrated into the loci of genes tyrR and trpED in the chromosome of E. coli BW25113 (DE3). The final strain was capable of producing 4.612 mg L –1 of resveratrol from glucose.

Description: While extensively studied in several model organisms, the role of small, non-coding RNAs in the stress response remains largely unexplored in Clostridium organisms. About 100 years after the first industrial Acetone–Butanol–Ethanol fermentation process, based on the Weizmann Clostridium acetobutylicum strain, strain tolerance to butanol remains a crucial factor limiting the economics of the process. Several studies have examined the response of this organism to metabolite stress, and several genes have been engaged to impart enhanced tolerance, but no sRNAs have yet been directly engaged in this task. We show that the two stress-responsive sRNAs, 6S and tmRNA, upon overexpression impart tolerance to butanol as assessed by viability assays under process-relevant conditions. 6S overexpression enhances cell densities as well as butanol titres. We discuss the likely mechanisms that these two sRNAs might engage in this tolerance phenotype. Our data support the continued exploration of sRNAs as a basis for engineering enhanced tolerance and enhanced solvent production, especially because sRNA-based strategies impose a minimal metabolic burden on the cells.

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: Ten indole alkaloids were obtained from the marine sponge-associated fungus Neosartorya siamensis KUFA 0017. We studied the antimicrobial properties of these and of three other compounds previously isolated from the soil fungus N. siamensis KUFC 6349. Only neofiscalin A showed antimicrobial activity against Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus faecalis (VRE); with a minimum inhibitory concentration (MIC) of 8 μg mL –1 against both strains. Another compound, fiscalin C, presented synergistic activity against MRSA when combined with oxacillin, although alone showed no antibacterial effect. Moreover, neofiscalin A, when present at sub-MICs, hampered the ability of both MRSA and VRE strains to form a biofilm. Additionally, the biofilm inhibitory concentration values of neofiscalin A against the MRSA and VRE isolates were 96 and 80 μg mL –1 , respectively. At a concentration of 200 μg mL –1 , neofiscalin A was able to reduce the metabolic activity of the biofilms by ~50%. One important fact is that our results also showed that neofiscalin A had no cytotoxicity against a human brain capillary endothelial cell line.

Description: During unconventional protein secretion (UPS), proteins do not pass through the classical endoplasmic reticulum (ER)–Golgi-dependent pathway, but are transported to the cell membrane via alternative routes. One type of UPS is dependent on several autophagy-related (Atg) proteins in yeast and mammalian cells, but mechanisms for unconventional secretion are largely unknown for filamentous fungi. In this study, we investigated whether the autophagy machinery is used for UPS in the filamentous fungus Aspergillus niger . An aspartic protease, which we called PepN, was identified as being likely to be secreted unconventionally, as this protein is highly abundant in culture filtrates during carbon starvation while it lacks a conventional N-terminal secretion sequence. We analysed the presence of PepN in the culture filtrates of carbon starved wild-type, atg1 and atg8 deletion mutant strains by Western blot analysis and by secretome analysis using nanoLC-ESI-MS/MS (wild-type and atg8 deletion mutant). Besides the presence of carbohydrate-active enzymes and other types of proteases, PepN was abundantly found in culture filtrates of both wild-type and atg deletion strains, indicating that the secretion of PepN is independent of the autophagy machinery in A. niger and hence most likely occurs via a different mechanism.

Description: Capacitively Coupled Resistivity (CCR) is conventionally used to emulate DC resistivity measurements and may provide important information about the ice content of material in periglacial areas. The application of CCR theoretically enables the determination of both electrical parameters, that is, the resistivity and the electrical permittivity, by analysing magnitude and phase shift spectra. The electrical permittivity may dominate the impedance, especially in periglacial areas or regions of hydrogeological interest. However, previous theoretical work suggested that the phase shift may strongly depend on electrode height above ground, implying that electrode height must be known with great accuracy to determine electrical permittivity. Here, we demonstrate with laboratory test measurements, theoretical modelling and by analysing the Jacobian matrix of the inversion that the sensitivity towards electrode height is drastically reduced if the electrical permittivity is frequency dependent in a way that is typical for ice. For the first time, we used a novel broad-band CCR device ‘Chameleon’ for a field test located in one of the ridge galleries beneath the crest of Mount Zugspitze. A permanently ice covered bottom of a tunnel was examined. For the inversion of the measured spectra, the frequency dependence of the electrical parameters was parametrized in three different ways: A Debye Model for pure ices, a Cole–Cole Model for pure ices and a dual Cole–Cole Model including interfacial water additionally. The frequency-dependent resistivity and permittivity spectra obtained from the inversion, including low- and high-frequency limits, agree reasonably well with laboratory and field measurements reported in the literature.

Description: We evaluate the applicability and the effectiveness of GPR attribute analysis for high-resolution glacier imaging and characterization, testing this approach on 4-D GPR multifrequency data collected in a small glacier in the Eastern Alps, by repeating the acquisition along the same profiles in four different periods of the year 2013. The main objectives are to image and characterize the glacier's inner structure and to quantitatively monitor the seasonal thawing of near-surface frozen materials (snow/firn). A multiattribute approach is used to characterize the subsurface through different attribute categories, including instantaneous and textural attributes considering not only amplitude-, phase- and frequency-related attributes, but also other more complex and integrated parameters. We combine information from more than one attribute into a single image with composite displays, using overlays or mixed displays. The results demonstrate that the developed GPR attribute analysis can provide significant improvements in the discrimination of GPR signals, and obtain enhanced and more constrained data interpretations.

Description: Migration velocity analysis aims at automatically updating the large-scale components of the velocity model, called macromodel. Extended Common Image Gathers are panels used to evaluate focusing after imaging and are constructed as a function of a spatial shift introduced in the imaging condition. We investigate how transmitted waves can also be used in migration velocity analysis: instead of back-propagating the residuals associated with reflected waves, we propose to back-propagate the full wavefield. The image function, equivalent to the migrated section for reflected data, does not exhibit localized events in space along horizons but is still sensitive to the choice of the background velocity model and can thus be coupled to the same objective function defined in the image domain. In order to enhance the benefits of direct waves, we consider a cross-well configuration. Direct waves provide a large illumination between two vertical wells. Associated Common Image Gathers present different characteristics than the ones associated with reflected waves in surface acquisition. In particular, energy is spread over up to the maximum penetration depth. We invert cross-well seismic data along two lines. In the first case, the input data contain the full wavefield dominated by transmitted waves. It demonstrates the possibility to handle transmitted waves to determine the velocity model. It appears that the misfit in the data domain is largely reduced after inversion. In the second case, we use the same algorithm, but with reflected observed data only, as in a classical approach. Most of velocity updates are localized around the reflectivity, leading to an incorrect final model. This demonstrates the benefit of transmitted waves for migration velocity analysis in a cross-well configuration.

Description: An integrated approach to interpret Self-Potential (SP) anomalies based on spectral analysis and tomographic methods is presented. The Maximum Entropy Method (MEM) is used for providing accurate estimates of the depth of the anomaly source. The 2-D tomographic inversion technique, based on the underground charge occurrence probability (COP) function, is, then, used to fully characterize the anomalous body, as the MEM is not helpful in delineating the shape of the anomaly source. The proposed integrated approach is applied for the inversion of synthetic SP data generated by geometrically simple anomalous bodies, such as cylinders and inclined sheets. This numerical study has allowed the determination of mathematical relationships between zero lines of the COP distributions, the polarization angles and the positions along the profile of the causative sources, which have been of great help for interpreting the related SP anomalies. Finally, the analysis of field examples shows the high potential applicability of the proposed integrated approach for SP data inversion.

Description: Volcanic and tectonic events are the main processes involved in the generation of the oceanic crust and responsible for the seismicity associated with seafloor spreading. To monitor this activity, usually not or poorly detected by land-based seismological stations, we deployed from February 2012 to February 2013 a network of autonomous hydrophones to compare the behaviour of the ultraslow-spreading Southwest Indian ridge (SWIR) with that of the intermediate-spreading Southeast Indian ridge (SEIR). The rate of seismicity is similar for both ridges, suggesting that there is no systematic relationship between seismicity and spreading rates. The along-axis distribution of the seismic events, however, does differ, reflecting the rate dependence of accretion modes. Earthquakes are sparse and regularly spaced and scattered along the SWIR, reflecting prevailing tectonic processes. By contrast, along the SEIR, events are irregularly distributed and focus at ridge-segment ends and transforms faults, reflecting the ridge segmentation; only two swarms occurred at a segment centre and are probably caused by a magmatic event. This seismicity distribution thus looks controlled by segment-scale crustal heterogeneities along the SEIR and by regional-scale contrasting accretion processes along the SWIR, probably driven by different lithospheric and asthenospheric dynamics on either side of the Melville fracture zone. The comparison of hydroacoustic and teleseismic catalogues shows that, along these spreading ridges, the background seismicity observed in 1 yr by a hydroacoustic network is representative of the seismicity observed over two decades by land-based networks.

Description: Advanced sequencing technologies have generated a plethora of data for many chromatin marks in multiple tissues and cell types, yet there is lack of a generalized tool for optimal utility of those data. A major challenge is to quantitatively model the epigenetic dynamics across both the genome and many cell types for understanding their impacts on differential gene regulation and disease. We introduce IDEAS, an i ntegrative and d iscriminative e pigenome a nnotation s ystem, for jointly characterizing epigenetic landscapes in many cell types and detecting differential regulatory regions. A key distinction between our method and existing state-of-the-art algorithms is that IDEAS integrates epigenomes of many cell types simultaneously in a way that preserves the position-dependent and cell type-specific information at fine scales, thereby greatly improving segmentation accuracy and producing comparable annotations across cell types.

Description: Actin-like MreB paralogs play important roles in cell shape maintenance, cell wall synthesis and the regulation of the D,L-endopeptidases, CwlO and LytE. The gram-positive bacteria, Bacillus amyloliquefaciens LL3, is a poly--glutamic acid (-PGA) producing strain that contains three MreB paralogs: MreB, Mbl and MreBH. In B. amyloliquefaciens , CwlO and LytE can degrade -PGA. In this study, we aimed to test the hypothesis that modulating transcript levels of MreB paralogs would alter the synthesis and degradation of -PGA. The results showed that overexpression or inhibition of MreB, Mbl or MreBH had distinct effects on cell morphology and the molecular weight of the -PGA products. In fermentation medium, cells of mreB inhibition mutant were 50.2% longer than LL3, and the -PGA titer increased by 55.7%. However, changing the expression level of mbl showed only slight effects on the morphology, -PGA molecular weight and titer. In the mreBH inhibition mutant, -PGA production and its molecular weight increased by 56.7% and 19.4%, respectively. These results confirmed our hypothesis that suppressing the expression of MreB paralogs might reduce -PGA degradation, and that improving the cell size could strengthen -PGA synthesis. This is the first report of enhanced -PGA production via suppression of actin-like MreB paralogs.

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: Microbial production of acetone and butanol was one of the first large-scale industrial fermentation processes of global importance. During the first part of the 20th century, it was indeed the second largest fermentation process, superseded in importance only by the ethanol fermentation. After a rapid decline after the 1950s, acetone-butanol-ethanol (ABE) fermentation has recently gained renewed interest in the context of biorefinery approaches for the production of fuels and chemicals from renewable resources. The availability of new methods and knowledge opens many new doors for industrial microbiology, and a comprehensive view on this process is worthwhile due to the new interest. This thematic issue of FEMS Microbiology Letters, dedicated to the 100th anniversary of the first industrial exploitation of Chaim Weizmann's ABE fermentation process, covers the main aspects of old and new developments, thereby outlining a model development in biotechnology. All major aspects of industrial microbiology are exemplified by this single process. This includes new technologies, such as the latest developments in metabolic engineering, the exploitation of biodiversity and discoveries of new regulatory systems such as for microbial stress tolerance, as well as technological aspects, such as bio- and down-stream processing.

Description: Food-grade lactic acid bacteria, such as lactobacilli, represent good candidates for the development of mucosal vectors. Indeed, they are generally recognized as safe microorganisms and some strains display beneficial effects (probiotics). In this study, we described a new lactobacilli in vivo expression (LIVE) system for the production and delivery of therapeutic molecules at mucosal surfaces. The versatility and functionality of this system was successfully validated in several lactobacilli species; furthermore, we assessed in vivo LIVE system in two different mouse models of human pathologies: (i) a model of therapy against intestinal inflammation (inflammatory bowel diseases) and (ii) a model of vaccination against dental caries. We demonstrated that Lactobacillus gasseri expressing the anti-inflammatory cytokine IL-10 under LIVE system efficiently delivered the recombinant protein at mucosal surfaces and display anti-inflammatory effects. In the vaccination model against caries, LIVE system allowed the heterologous expression of Streptococcus mutans antigen GbpB by L. gasseri , leading to a stimulation of the host immune response.

Description: The microbial fermentation process is one of the sustainable and environment-friendly ways to produce 1-butanol and other bio-based chemicals. The success of the fermentation process greatly relies on the choice of bioreactors and the separation methods. In this review, the history and the performance of bioreactors for the acetone–butanol–ethanol (ABE) fermentation is discussed. The subject is then focused on in situ product recovery (ISPR) techniques, particularly for the integrated extraction-gas stripping. The usefulness of this promising hybrid ISPR device is acknowledged by its incorporation with batch, fed-batch and continuous processes to improve the performance of ABE fermentation.

Description: Geothermal well GRT-1 (Rittershoffen, Alsace) was drilled in 2012. Its open-hole section (extending down to a depth of 2.6 km) penetrated fractured sandstones and granite. In 2013, the well was subjected to Thermal, Chemical and Hydraulic (TCH) stimulation, which improved the injectivity index fivefold. The goal of the study was to assess the impact of the stimulation by comparing pre- and post-stimulation well-logging (acoustic and temperature [ T ] logs) and mud-logging data. This comparison revealed modifications of almost all the natural fractures. However, not all of these fractures are associated with permeability enhancement, and the post-stimulation T logs are important for characterizing this enhancement. Chemical alteration due to mechanical erosion at the tops and bottoms of the fractures was observed in the sandstones. These zones display indications of very small new permeability after the TCH stimulation. Because a major fault zone caved extensively where it crosses the borehole, it was not imaged in the acoustic logs. However, this originally permeable zone was enhanced as demonstrated by the T logs. Based on the natural injectivity of this fault zone, hydraulic erosion and thermal microcracking of its internal quartz veins are associated with this permeability enhancement. Although local changes in the borehole wall observed in the acoustic images cannot be directly linked to the improved injectivity index, the comparison of the acoustic image logs allows for identification of fracture zones impacted by the TCH stimulation.

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

Description: Recent tectonic reconstructions of the South Atlantic have partitioned the ocean basin into several segments based upon one or more proposed intraplate South American deformation zones. In several of these reconstructions, opening of the southern segment(s) by seafloor spreading prior to Aptian-Albian time is accompanied by contemporaneous strike-slip motion along an intraplate boundary extending southeastward from the Andean Cochabamba—Santa Cruz bend to the Rio Grande Fracture Zone (RGFZ). We have examined new magnetic data over the Pelotas, Santos and Campos Basins, offshore Argentina and Brazil, acquired by ION-GXT in tandem with long-offset, long record seismic reflection data, and identified seafloor spreading anomalies M4, M3, M2 and M0 (~131, ~129, ~128 and ~125 Ma). Integrating these results with our earlier work, we have been able to correlate magnetochrons M4, M3, M2 and M0 north and south of the RGFZ on the South American margin, and north and south of the Walvis Ridge on the African side. Our results are therefore inconsistent with diachronous opening models that involve substantial continental strike-slip motion north of RGFZ during M4 to M0 time. Although the ocean basin may have opened from south to north, our results indicate that seafloor spreading began north of the RGFZ earlier than previously proposed.

Description: A majority of large-scale bacterial genome rearrangements involve mobile genetic elements such as insertion sequence (IS) elements. Here we report novel insertions and excisions of IS elements and recombination between homologous IS elements identified in a large collection of Escherichia coli mutation accumulation lines by analysis of whole genome shotgun sequencing data. Based on 857 identified events (758 IS insertions, 98 recombinations and 1 excision), we estimate that the rate of IS insertion is 3.5 x 10 –4 insertions per genome per generation and the rate of IS homologous recombination is 4.5 x 10 –5 recombinations per genome per generation. These events are mostly contributed by the IS elements IS 1 , IS 2 , IS 5 and IS 186 . Spatial analysis of new insertions suggest that transposition is biased to proximal insertions, and the length spectrum of IS-caused deletions is largely explained by local hopping. For any of the ISs studied there is no region of the circular genome that is favored or disfavored for new insertions but there are notable hotspots for deletions. Some elements have preferences for non-coding sequence or for the beginning and end of coding regions, largely explained by target site motifs. Interestingly, transposition and deletion rates remain constant across the wild-type and 12 mutant E. coli lines, each deficient in a distinct DNA repair pathway. Finally, we characterized the target sites of four IS families, confirming previous results and characterizing a highly specific pattern at IS 186 target-sites, 5'-GGGG(N6/N7)CCCC-3'. We also detected 48 long deletions not involving IS elements.

Description: Determining thin layer thickness is very important for reservoir characterization and CO 2 quantification. Given its high time–frequency resolution and robustness, the complex spectral decomposition method was applied on time-lapse 3-D seismic data from the Ketzin pilot site for CO 2 storage to evaluate the frequency-dependent characteristics of thin layers at the injection level. Higher temporal resolution and more stratigraphic details are seen in the all-frequency and monochromatic reflectivity amplitude sections obtained by complex spectral decomposition compared to the stacked sections. The mapped geologic discontinuities within the reservoir are consistent with the preferred orientation of CO 2 propagation. Tuning frequency mapping shows the thicknesses of the reservoir sandstone and gaseous CO 2 is consistent with the measured thickness of the sandstone unit from well logging. An attempt to discriminate between pressure effects and CO 2 saturation using the extracted tuning frequency indicates that CO 2 saturation is the main contributor to the amplitude anomaly at the Ketzin site. On the basis of determined thickness of gaseous CO 2 in the reservoir, quantitative analysis of the amount of CO 2 was performed and shows a discrepancy between the injected and calculated CO 2 mass. This may be explained by several uncertainties, like structural reservoir heterogeneity, a limited understanding of the complex subsurface conditions, error of determined tuning frequency, the presence of ambient noise and ongoing CO 2 dissolution.

Description: Comprehensive analytical solutions to 3-D axisymmetric problems for static response of multilayered thermoelastic media subjected to surface loads and containing sources are presented in this study. The solution strategy employs Laplace and Hankel transforms to the field variables. The problem is formulated in cylindrical coordinate system and in this coordinate system vector surface harmonics and generalized propagator matrix are introduced to find the solution for the problem for the behaviour of thermoelastic multilayered media subject to surface loads and containing heat sources. A high-order adaptive Gaussian quadrature method with continued fraction expansions is employed to approximate the integral solutions expressed in terms of semi-infinite Hankel-type integrals. It is the first time to apply the proposed solution method to investigate the behaviour of repository for heat-emitting high-level nuclear waste (HLW) in a geological formation where the HLW can be regarded as a decaying with time point heat source.

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: Anaerobic Clostridium spp. is an important bioproduction microbial genus that can produce solvents and utilize a broad spectrum of substrates including cellulose and syngas. Genome-scale metabolic (GSM) models are increasingly being put forth for various clostridial strains to explore their respective metabolic capabilities and suitability for various bioconversions. In this study, we have selected representative GSM models for six different clostridia ( Clostridium acetobutylicum , C. beijerinckii , C. butyricum , C. cellulolyticum , C. ljungdahlii and C. thermocellum ) and performed a detailed model comparison contrasting their metabolic repertoire. We also discuss various applications of these GSM models to guide metabolic engineering interventions as well as assessing cellular physiology.

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

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

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

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

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