ALBERT

Description: Measurements of ground deformation can be used to identify and interpret geophysical processes occurring at volcanoes. Most studies rely on a single geodetic technique, or fit a geophysical model to the results of multiple geodetic techniques. Here we present a methodology that combines GPS, Total Station measurements and InSAR into a single reference frame to produce an integrated 3-D geodetic velocity surface without any prior geophysical assumptions. The methodology consists of five steps: design of the network, acquisition and processing of the data, spatial integration of the measurements, time series computation and finally the integration of spatial and temporal measurements. The most significant improvements of this method are (1) the reduction of the required field time, (2) the unambiguous detection of outliers, (3) an increased measurement accuracy and (4) the construction of a 3-D geodetic velocity field. We apply this methodology to ongoing motion on Arenal's western flank. Integration of multiple measurement techniques at Arenal volcano revealed a deformation field that is more complex than that described by individual geodetic techniques, yet remains consistent with previous studies. This approach can be applied to volcano monitoring worldwide and has the potential to be extended to incorporate other geodetic techniques and to study transient deformation.

Description: Combinatorial transcription factor (TF) binding is essential for cell-type-specific gene regulation. However, much remains to be learned about the mechanisms of TF interactions, including to what extent constrained spacing and orientation of interacting TFs are critical for regulatory element activity. To examine the relative prevalence of the ‘enhanceosome’ versus the ‘TF collective’ model of combinatorial TF binding, a comprehensive analysis of TF binding site sequences in large scale datasets is necessary. We developed a motif-pair discovery pipeline to identify motif co-occurrences with preferential distance(s) between motifs in TF-bound regions. Utilizing a compendium of 289 mouse haematopoietic TF ChIP-seq datasets, we demonstrate that haematopoietic-related motif-pairs commonly occur with highly conserved constrained spacing and orientation between motifs. Furthermore, motif clustering revealed specific associations for both heterotypic and homotypic motif-pairs with particular haematopoietic cell types. We also showed that disrupting the spacing between motif-pairs significantly affects transcriptional activity in a well-known motif-pair—E-box and GATA, and in two previously unknown motif-pairs with constrained spacing—Ets and Homeobox as well as Ets and E-box. In this study, we provide evidence for widespread sequence-specific TF pair interaction with DNA that conforms to the ‘enhanceosome’ model, and furthermore identify associations between specific haematopoietic cell-types and motif-pairs.

Description: In autumn 2012, the new release 05 (RL05) of monthly geopotencial spherical harmonics Stokes coefficients (SC) from Gravity Recovery and Climate Experiment (GRACE) mission was published. This release reduces the noise in high degree and order SC, but they still need to be filtered. One of the most common filtering processing is the combination of decorrelation and Gaussian filters. Both of them are parameters dependent and must be tuned by the users. Previous studies have analyzed the parameters choice for the RL05 GRACE data for oceanic applications, and for RL04 data for global application. This study updates the latter for RL05 data extending the statistics analysis. The choice of the parameters of the decorrelation filter has been optimized to: (1) balance the noise reduction and the geophysical signal attenuation produced by the filtering process; (2) minimize the differences between GRACE and model-based data and (3) maximize the ratio of variability between continents and oceans. The Gaussian filter has been optimized following the latter criteria. Besides, an anisotropic filter, the fan filter, has been analyzed as an alternative to the Gauss filter, producing better statistics.

Description: We present high-resolution tomographic images in source areas of 26 large crustal earthquakes ( M 6.0–7.2) which occurred in Northeast Japan (Tohoku) during the past 120 yr from 1894 to 2014. Prominent low-velocity (low- V ) and high Poisson's ratio (high- ) anomalies are revealed in the crust and mantle wedge under the source areas. Beneath the volcanic front and backarc areas, the low- V and high- zones reflect arc-magma related high-temperature anomalies which are produced by joint effects of corner flow in the mantle wedge and fluids from dehydration of the subducting Pacific slab. The hot anomalies cause locally thinning and weakening of the brittle seismogenic layer above them. Low-frequency micro-earthquakes are observed in the lower crust and uppermost mantle in or around the low- V zones, which reflect ascending of arc magma and fluids from the mantle wedge to the crust. No volcano and magma exist in the forearc area due to low temperature there, hence the low- V zones in the forearc reflect fluids from the slab dehydration. The ascending fluids may have produced a ‘water wall’ in the mantle wedge and crust beneath the forearc area. When the water enters active faults in the crust, the fault-zone friction is reduced and so large earthquakes can be induced. These results indicate that the nucleation of a large earthquake is not entirely a mechanical process, but is closely associated with subduction dynamics and physical and chemical properties of rocks in the crust and upper mantle. In particular, arc magma and fluids play an important role in the seismogenesis.

Description: Homologous non-coding RNAs frequently exhibit domain insertions, where a branch of secondary structure is inserted in a sequence with respect to its homologs. Dynamic programming algorithms for common secondary structure prediction of multiple RNA homologs, however, do not account for these domain insertions. This paper introduces a novel dynamic programming algorithm methodology that explicitly accounts for the possibility of inserted domains when predicting common RNA secondary structures. The algorithm is implemented as Dynalign II, an update to the Dynalign software package for predicting the common secondary structure of two RNA homologs. This update is accomplished with negligible increase in computational cost. Benchmarks on ncRNA families with domain insertions validate the method. Over base pairs occurring in inserted domains, Dynalign II improves accuracy over Dynalign, attaining 80.8% sensitivity (compared with 14.4% for Dynalign) and 91.4% positive predictive value (PPV) for tRNA; 66.5% sensitivity (compared with 38.9% for Dynalign) and 57.0% PPV for RNase P RNA; and 50.1% sensitivity (compared with 24.3% for Dynalign) and 58.5% PPV for SRP RNA. Compared with Dynalign, Dynalign II also exhibits statistically significant improvements in overall sensitivity and PPV. Dynalign II is available as a component of RNAstructure, which can be downloaded from http://rna.urmc.rochester.edu/RNAstructure.html .

Description: Genome-wide assessment of protein–DNA interaction by chromatin immunoprecipitation followed by massive parallel sequencing (ChIP-seq) is a key technology for studying transcription factor (TF) localization and regulation of gene expression. Signal-to-noise-ratio and signal specificity in ChIP-seq studies depend on many variables, including antibody affinity and specificity. Thus far, efforts to improve antibody reagents for ChIP-seq experiments have focused mainly on generating higher quality antibodies. Here we introduce KOIN (knockout implemented normalization) as a novel strategy to increase signal specificity and reduce noise by using TF knockout mice as a critical control for ChIP-seq data experiments. Additionally, KOIN can identify ‘hyper ChIPable regions’ as another source of false-positive signals. As the use of the KOIN algorithm reduces false-positive results and thereby prevents misinterpretation of ChIP-seq data, it should be considered as the gold standard for future ChIP-seq analyses, particularly when developing ChIP-assays with novel antibody reagents.

Description: DNA methylation is an important epigenetic modification that has essential roles in cellular processes including gene regulation, development and disease and is widely dysregulated in most types of cancer. Recent advances in sequencing technology have enabled the measurement of DNA methylation at single nucleotide resolution through methods such as whole-genome bisulfite sequencing and reduced representation bisulfite sequencing. In DNA methylation studies, a key task is to identify differences under distinct biological contexts, for example, between tumor and normal tissue. A challenge in sequencing studies is that the number of biological replicates is often limited by the costs of sequencing. The small number of replicates leads to unstable variance estimation, which can reduce accuracy to detect differentially methylated loci (DML). Here we propose a novel statistical method to detect DML when comparing two treatment groups. The sequencing counts are described by a lognormal-beta-binomial hierarchical model, which provides a basis for information sharing across different CpG sites. A Wald test is developed for hypothesis testing at each CpG site. Simulation results show that the proposed method yields improved DML detection compared to existing methods, particularly when the number of replicates is low. The proposed method is implemented in the Bioconductor package DSS.

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

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

Description: Epigenetic regulation of gene expression involves, besides DNA and histone modifications, the relative positioning of DNA sequences within the nucleus. To trace specific DNA sequences in living cells, we used programmable sequence-specific DNA binding of designer transcription activator-like effectors (dTALEs). We designed a recombinant dTALE (msTALE) with variable repeat domains to specifically bind a 19-bp target sequence of major satellite DNA. The msTALE was fused with green fluorescent protein (GFP) and stably expressed in mouse embryonic stem cells. Hybridization with a major satellite probe (3D-fluorescent in situ hybridization) and co-staining for known cellular structures confirmed in vivo binding of the GFP-msTALE to major satellite DNA present at nuclear chromocenters. Dual tracing of major satellite DNA and the replication machinery throughout S-phase showed co-localization during mid to late S-phase, directly demonstrating the late replication timing of major satellite DNA. Fluorescence bleaching experiments indicated a relatively stable but still dynamic binding, with mean residence times in the range of minutes. Fluorescently labeled dTALEs open new perspectives to target and trace DNA sequences and to monitor dynamic changes in subnuclear positioning as well as interactions with functional nuclear structures during cell cycle progression and cellular differentiation.

Description: Coupling bisulfite conversion with next-generation sequencing (Bisulfite-seq) enables genome-wide measurement of DNA methylation, but poses unique challenges for mapping. However, despite a proliferation of Bisulfite-seq mapping tools, no systematic comparison of their genomic coverage and quantitative accuracy has been reported. We sequenced bisulfite-converted DNA from two tissues from each of two healthy human adults and systematically compared five widely used Bisulfite-seq mapping algorithms: Bismark, BSMAP, Pash, BatMeth and BS Seeker. We evaluated their computational speed and genomic coverage and verified their percentage methylation estimates. With the exception of BatMeth, all mappers covered 〉70% of CpG sites genome-wide and yielded highly concordant estimates of percentage methylation ( r 2 ≥ 0.95). Fourfold variation in mapping time was found between BSMAP (fastest) and Pash (slowest). In each library, 8–12% of genomic regions covered by Bismark and Pash were not covered by BSMAP. An experiment using simulated reads confirmed that Pash has an exceptional ability to uniquely map reads in genomic regions of structural variation. Independent verification by bisulfite pyrosequencing generally confirmed the percentage methylation estimates by the mappers. Of these algorithms, Bismark provides an attractive combination of processing speed, genomic coverage and quantitative accuracy, whereas Pash offers considerably higher genomic coverage.

Description: Three-dimensional organization of chromatin is fundamental for transcriptional regulation. Tissue-specific transcriptional programs are orchestrated by transcription factors and epigenetic regulators. The RUNX2 transcription factor is required for differentiation of precursor cells into mature osteoblasts. Although organization and control of the bone-specific Runx2-P1 promoter have been studied extensively, long-range regulation has not been explored. In this study, we investigated higher-order organization of the Runx2-P1 promoter during osteoblast differentiation. Mining the ENCODE database revealed interactions between Runx2-P1 and  Supt3h promoters in several non-mesenchymal human cell lines. Supt3h is a ubiquitously expressed gene located within the first intron of Runx2 . These two genes show shared synteny across species from humans to sponges. Chromosome conformation capture analysis in the murine pre-osteoblastic MC3T3-E1 cell line revealed increased contact frequency between Runx2-P1 and Supt3h promoters during differentiation. This increase was accompanied by enhanced DNaseI hypersensitivity along with RUNX2 and CTCF binding at the Supt3h promoter. Furthermore, interplasmid-3C and luciferase reporter assays showed that the Supt3h promoter can modulate Runx2-P1 activity via direct association. Taken together, our data demonstrate physical proximity between Runx2-P1 and Supt3h promoters, consistent with their syntenic nature. Importantly, we identify the Supt3h promoter as a potential regulator of the bone-specific Runx2-P1 promoter .

Description: For a period of about 1 yr between the summers of 2010 and 2011, 25 broad-band seismographs were deployed in a roughly linear array across the eastern end of the Qaidam basin and the Qilian Shan in the northeastern Tibetan plateau. This region is probably the most suitable place to study the ongoing convergence interaction between the high Tibetan plateau and the main Asian continental plate. Low-frequency P receiver function analysis of the data provides an image of the crust and mantle down to 700 km depth. In addition to the Moho at 45–65 km depth beneath the profile, the 410 and 660 km discontinuities bounding the mantle transition zone can be identified at 400–410 and 650–660 km depths, respectively. A possible increase in temperature in the upper mantle thought to exist beneath the northern part of the high Tibetan plateau is thus confined to this part of the plateau and lower upper-mantle temperatures similar to those beneath southern Tibet occur beneath the Qaidam basin and Qilian Shan. When higher frequencies are included in the P receiver function analysis, a positive Ps converter dipping down to the south from 70–75 km depth at 37.9°N to about 110 km depth at 36°N is imaged. As this feature is only seen in high-frequency images and not in the low-frequency image, it is modelled as the positive Ps conversion from the base of an approximately 5-km-thick anisotropic layer at the top of the Asian mantle lithosphere which is currently subducting. This south-dipping converter continues to the south on the INDEPTH IV profile. S receiver function analysis completes the image of the structure below the Qilian Shan profile with the identification of the lithosphere–asthenosphere boundary (LAB). The LAB of the Asian Plate is identified for a reference slowness of 6.4 s deg –1 at 12–14 s (105–125 km depth) between 38 and 41°N below the northern part of the S receiver function profile. To the south it increases in depth such that it is at about 19 s (170 km depth) between 34 and 35°N at the southern end of the profile. The LAB of the Asian Plate occurs at similar depths on the INDEPTH IV profile at the latitudes where the INDEPTH IV and Qilian Shan profiles overlap. As on the INDEPTH IV profile to the south, between 34 and 35°N at the southern end of the Qilian Shan profile there is evidence from the S receiver functions for the LAB of a separate Tibetan Plate.

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

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

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

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

Description: Lower and upper bounds for present deformation rates across faults in central California between the San Andreas Fault and Pacific coast are estimated from a new Global Positioning System (GPS) velocity field for central, western California in light of geodetic evidence presented in a companion paper for slow, but significant deformation within the Pacific Plate between young seafloor in the eastern Pacific and older seafloor elsewhere on the plate. Transects of the GPS velocity field across the San Andreas Fault between Parkfield and San Juan Buatista, where fault slip is dominated by creep and the velocity field thus reveals the off-fault deformation, show that GPS sites in westernmost California move approximately parallel to the fault at an average rate of 3.4 ± 0.4 mm yr –1 relative to the older interior of the Pacific Plate, but only 1.8 ± 0.6 mm yr –1 if the Pacific Plate frame of reference is corrected for deformation within the plate. Modelled interseismic elastic deformation from the weakly coupled creeping segment of the San Andreas Fault is an order-of-magnitude too small to explain the southeastward motions of coastal sites in western California. Similarly, models that maximize residual viscoelastic deformation from the 1857 Fort Tejon and 1906 San Francisco earthquakes mismatch both the rates and directions of GPS site motions in central California relative to the Pacific Plate. Neither thus explains the site motions southwest of the San Andreas fault, indicating that the site motions measure deformation across faults and folds outboard of the San Andreas Fault. The non-zero site velocities thus constitute strong evidence for active folding and faulting outboard from the creeping segment of the San Andreas Fault and suggest limits of 0–2 mm yr –1 for the Rinconada Fault slip rate and 1.8 ± 0.6 to 3.4 ± 0.4 mm yr –1 for the slip rates integrated across near-coastal faults such as the Hosgri, San Gregorio and San Simeon faults.

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

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

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

Description: We combine new, well-determined GPS velocities from Clarion, Guadalupe and Socorro islands on young seafloor in the eastern Pacific basin with newly estimated velocities for 26 GPS sites from older seafloor in the central, western and southern parts of the Pacific Plate to test for deformation within the interior of the Pacific Plate and estimate the viscosity of the asthenosphere below the plate. Relative to a Pacific Plate reference frame defined from the velocities of the 26 GPS sites in other areas of the Pacific Plate, GPS sites on Clarion and Guadalupe islands in the eastern Pacific move 1.2 ± 0.6 mm yr –1 (1) towards S09°W ± 38° and 1.9 ± 0.3 mm yr –1 towards S19°E ± 10°, respectively. The two velocities, which are consistent within their 95 per cent uncertainties, both differ significantly from Pacific Plate motion. Transient volcanic deformation related to a 1993–1996 eruption of the Socorro Island shield volcano renders our GPS velocity from that island unreliable for the tectonic analysis although its motion is also southward like those of Clarion and Guadalupe islands. We test but reject the possibilities that drift of Earth's origin in ITRF2008 or unmodelled elastic offsets due to large-magnitude earthquakes around the Pacific rim since 1993 can be invoked to explain the apparent slow southward motions of Clarion and Guadalupe islands. Similarly, corrections to the Pacific Plate GPS velocity field for possible viscoelastic deformation triggered by large-magnitude earthquakes since 1950 also fail to explain the southward motions of the two islands. Viscoelastic models with prescribed asthenospheric viscosities lower than 1  x 10 19 Pa s instead introduce statistically significant inconsistencies into the Pacific Plate velocity field, suggesting that the viscosity of the asthenosphere below the plate is higher than 1  x 10 19 Pa s. Elastic deformation from locked Pacific–North America Plate boundary faults is also too small to explain the southward motions of the two islands. Horizontal thermal contraction of the plate interior may explain the motion observed at Clarion and Guadalupe islands, as might long-term tectonic deformation of the plate interior.

Description: In this study, a new method for computing the sensitivity of the glacial isostatic adjustment (GIA) forward solution with respect to the Earth's mantle viscosity, the so-called the forward sensitivity method (FSM), and a method for computing the gradient of data misfit with respect to viscosity parameters, the so-called adjoint-state method (ASM), are presented. These advanced formal methods complement each other in the inverse modelling of GIA-related observations. When solving this inverse problem, the first step is to calculate the forward sensitivities by the FSM and use them to fix the model parameters that do not affect the forward model solution, as well as identifying and removing redundant parts of the inferred viscosity structure. Once the viscosity model is optimized in view of the forward sensitivities, the minimization of the data misfit with respect to the viscosity parameters can be carried out by a gradient technique which makes use of the ASM. The aim is this paper is to derive the FSM and ASM in the forms that are closely associated with the forward solver of GIA developed by Martinec. Since this method is based on a continuous form of the forward model equations, which are then discretized by spectral and finite elements, we first derive the continuous forms of the FSM and ASM and then discretize them by the spectral and finite elements used in the discretization of the forward model equations. The advantage of this approach is that all three methods (forward, FSM and ASM) have the same matrix of equations and use the same methodology for the implementation of the time evolution of stresses. The only difference between the forward method and the FSM and ASM is that the different numerical differencing schemes for the time evolution of the Maxwell and generalized Maxwell viscous stresses are applied in the respective methods. However, it requires only a little extra computational time for carrying out the FSM and ASM numerically. An straightforward approach to compute the gradient of the data misfit is the brute-force method, whereby the partial derivatives of the misfit with respect to model parameters are approximated by the centred difference of two forward model runs. Although the brute-force method is useful for computing the gradient of the data misfit with respect to a small number of model parameters, it becomes expensive for a viscosity model with a large number of parameters. The ASM offers an efficient alternative for computing the gradient of the misfit since the computational time of the ASM is independent of the number of viscosity parameters. The ASM is thus highly efficient for calculating the gradient of the misfit for models with large numbers of parameters. However, the forward-model solution for each time step must be stored, hence the memory demands scale linearly with the number of time steps. This is the main drawback of the ASM.

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

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

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

Description: Relative to the gravitational potential energy of the Earth's monopole, the multipole energy has received far less attention. In this paper, we recapitulate the basic physics from first principles and derive the formulas for multipole energies in analogy to classical electrostatic theory. We focus on the zonal quadrupole energy associated with the Earth's oblateness, the dominant term in Earth's gravity field apart from the monopole. We find the gravitational energy E oblateness 10 –6 | E monopole | = +2.5 x 10 26 J. We examine the implications of E oblateness and its changes associated with long-term ‘secular’ decreases in the oblateness parameter J 2 . We find the rate of loss of E oblateness due to the Earth rounding induced by the present-day GIA is about –200 GW, an amount quite significant in the kinetic energy budget of the mantle heat engine that drives the plate tectonics that has been estimated to be ~1 TW. We also assert that the tidal braking and the global earthquake dislocations, both resulting in Earth rounding on long-term geological timescales, are accompanied with a secular decrease of E oblateness at nearly the same rate of several GW.

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

Description: Large-scale chemical lateral heterogeneities are inferred in the Earth's lowermost mantle by seismological studies. We explore the model space of thermochemical convection that can maintain reservoirs of dense material for a long period of time, by using similar analysis in 3-D spherical geometry. In this study, we focus on the parameters thought to be important in controlling the stability and structure of primordial dense reservoirs in the lower mantle, including the chemical density contrast between the primordial dense material and the regular mantle material (buoyancy ratio), thermal and chemical viscosity contrasts, volume fraction of primordial dense material and the Clapeyron slope of the phase transition at 660 km depth. We find that most of the findings from the 3-D Cartesian study still apply to 3-D spherical cases after slight modifications. Varying buoyancy ratio leads to different flow patterns, from rapid upwelling to stable layering; and large thermal viscosity contrasts are required to generate long wavelength chemical structures in the lower mantle. Chemical viscosity contrasts in a reasonable range have a second-order role in modifying the stability of the dense anomalies. The volume fraction of the initial primordial dense material does not effect the results with large thermal viscosity contrasts, but has significant effects on calculations with intermediate and small thermal viscosity contrasts. The volume fraction of dense material at which the flow pattern changes from unstable to stable depends on buoyancy ratio and thermal viscosity contrast. An endothermic phase transition at 660 km depth acts as a ‘filter’ allowing cold slabs to penetrate while blocking most of the dense material from penetrating to the upper mantle.

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

Description: Relative sea level curves contain coupled information about absolute sea level change and vertical lithospheric movement. Such curves may be constructed based on, for example tide gauge data for the most recent times and different types of geological data for ancient times. Correct account for vertical lithospheric movement is essential for estimation of reliable values of absolute sea level change from relative sea level data and vise versa. For modern times, estimates of vertical lithospheric movement may be constrained by data (e.g. GPS-based measurements), which are independent from the relative sea level data. Similar independent data do not exist for ancient times. The purpose of this study is to test two simple inversion approaches for simultaneous estimation of lithospheric uplift rates and absolute sea level change rates for ancient times in areas where a dense coverage of relative sea level data exists and well-constrained average lithospheric movement values are known from, for example glacial isostatic adjustment (GIA) models. The inversion approaches are tested and used for simultaneous estimation of lithospheric uplift rates and absolute sea level change rates in southwest Scandinavia from modern relative sea level data series that cover the period from 1900 to 2000. In both approaches, a priori information is required to solve the inverse problem. A priori information about the average vertical lithospheric movement in the area of interest is critical for the quality of the obtained results. The two tested inversion schemes result in estimated absolute sea level rise of ~1.2/1.3 mm yr –1 and vertical uplift rates ranging from approximately –1.4/–1.2 mm yr –1 (subsidence) to about 5.0/5.2 mm yr –1 if an a priori value of 1 mm yr –1 is used for the vertical lithospheric movement throughout the study area. In case the studied time interval is broken into two time intervals (before and after 1970), absolute sea level rise values of ~0.8/1.2 mm yr –1 (before 1970) and ~2.0 mm yr –1 (after 1970) are found. The uplift patterns resulting from the different inversions suggest that the lithospheric post-GIA response changes near the border between the Danish Basin and the Fennoscandian Shield. The obtained patterns of vertical lithospheric movement rates are comparable to results from other studies based on different and similar data types. Main differences between the inversion results and the results from other studies are caused by factors such as the simplifications included in the inversion approach, such as neglecting local sea level variation caused by the dominant wind patterns, and the a priori values chosen for the vertical uplift rates. The tests of the inversion schemes reveal that realistic values of absolute sea level rise and lithospheric uplift may be simultaneously estimated provided that reliable prior knowledge regarding the overall lithospheric uplift in the study area is available beforehand. In the presented parametrizations, only one absolute sea level change rate value is estimated for each studied time interval while several vertical movement rates are found, and the inverse estimate of absolute sea level change rate is practically insensitive with respect to the choice of a priori value of absolute sea level change, as long as the uncertainty assigned to this a priori value is kept sufficiently high.

Description: In 1356, a magnitude 6–7 earthquake occurred near Basel, in Switzerland. But recent compilations of GPS measurements reveal that measured horizontal deformation rates in northwestern continental Europe are smaller than error bars on the measurements, proving present tectonic activity, if any, is very small in this area. We propose to reconcile these apparently antinomic observations with a mechanical model of the lithosphere that takes into account the geometry of the lithosphere–asthenosphere boundary, assuming that the only loading mechanism is gravity. The lithosphere is considered to be an elastoplastic material satisfying a Von Mises plasticity criterion. The model, which is 400 km long, 360 km wide and 230 km thick, is centred near Belfort in eastern France, with its width oriented parallel to the N145°E direction. It also takes into account the real topography of both the ground surface and that of the Moho discontinuity. Not only does the model reproduce observed principal stress directions orientations, it also identifies a plastic zone that fits roughly the most seismically active domain of the region. Interestingly, a somewhat similar stress map may be produced by considering an elastic lithosphere and an ad-hoc horizontal ‘tectonic’ stress field. However, for the latter model, examination of the plasticity criterion suggests that plastic deformation should have taken place. It is concluded that the present-day stress field in this region is likely controlled by gravity and rheology, rather than by active Alpine tectonics.

Description: We have investigated variations in transition zone thickness under the Borborema Province of NE Brazil by migrating and stacking teleseismic P -wave receiver functions at 32 seismic stations in the region. The Borborema Province represents the western portion of a larger Neoproterozoic mobile belt that occupied much of northern Gondwana, where extensional processes in the Mesozoic lead to the formation of a number of intracontinental basins and ultimately continental breakup. Episodes of intraplate volcanism and uplift marked the evolution of the Province during the Cenozoic, but it is unclear whether those episodes originated from shallow or deep-seated magmatic sources. On one hand, the elliptical shape of the uplifted area, the stress pattern of the Cenozoic deformation and the time overlap between uplift and volcanism suggest doming from thermal activation due to a deep-seated mantle plume. On the other hand, geochronological dates of volcanic bodies in the Province are better understood if resulting from lithospheric erosion by a shallow, small-scale convection cell. Large temperature anomalies are expected to be associated with mantle upwellings, and constraints on the depth extent of the upwellings can be obtained from transition zone thickness. Thinning of the transition zone with respect to its nominal 250 km value is considered diagnostic for positive temperature anomalies, while thickening is considered diagnostic for negative anomalies. Our results show that transition zone thickness is normal, around 250 km, throughout the Province and suggest that thermal perturbations—if present—are confined to the upper mantle. We argue that our results are consistent with a local, shallow magmatic source for the Cenozoic intraplate volcanism of the Borborema Province, although other proposed scenarios—such as channeling of upwelling plume material along lithospheric thin spots—cannot be ruled out with our analysis.

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

Description: Standard techniques for computed tomography imaging are not directly applicable to a carbonate rock because of the geometric complexity of its pore space. In this study, we first characterized the pore structure in Majella limestone with 30 per cent porosity. Microtomography data acquired on this rock was partitioned into three distinct domains: macropores, solid grains, and an intermediate domain made up of voxels of solid embedded with micropores below the resolution. A morphological analysis of the microtomography images shows that in Majella limestone both the solid and intermediate domains are interconnected in a manner similar to that reported previously in a less porous limestone. We however show that the macroporosity in Majella limestone is fundamentally different, in that it has a percolative backbone which may contribute significantly to its permeability. We then applied for the first time 3-D-volumetric digital image correlation (DIC) to characterize the mode of mechanical failure in this limestone. Samples were triaxially deformed over a wide range of confining pressures. Tomography imaging was performed on these samples before and after deformation. Inelastic compaction was observed at all tested pressures associated with both brittle and ductile behaviors. Our DIC analysis reveals the structure of compacting shear bands in Majella limestone deformed in the transitional regime. It also indicates an increase of geometric complexity with increasing confinement—from a planar shear band, to a curvilinear band, and ultimately to a diffuse multiplicity of bands, before shear localization is inhibited as the failure mode completes the transition to delocalized cataclastic flow.

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

Description: Wide-angle reflection/refraction seismic profiles were recorded across the Cyprus Arc, the plate boundary between the African Plate and the Aegean–Anatolian microplate, from the Eratosthenes Seamount to the Hecataeus Rise immediately south of Cyprus. The resultant models were able to resolve detail of significant lateral velocity variations, though the deepest crust and Moho are not well resolved from the seismic data alone. Conclusions from the modelling suggest that (i) Eratosthenes Seamount consists of continental crust but exhibits a laterally variable velocity structure with a thicker middle crust and thinner lower crust to the northeast; (ii) the Hecataeus Rise has a thick sedimentary rock cover on an indeterminate crust (likely continental) and the crust is significantly thinner than Eratosthenes Seamount based on gravity modelling; (iii) high velocity basement blocks, coincident with highs in the magnetic field, occur in the deep water between Eratosthenes and Hecataeus, and are separated and bounded by deep low-velocity troughs and (iv) one of the high velocity blocks runs parallel to the Cyprus Arc, while the other two appear linked based on the magnetic data and run NW–SE, parallel to the margin of the Hecataeus Rise. The high velocity block beneath the edge of Eratosthenes Seamount is interpreted as an older magmatic intrusion while the linked high velocity blocks along Hecataeus Rise are interpreted as deformed remnant Tethyan oceanic crust or mafic intrusives from the NNW–SSE oriented transform margin marking the northern boundary of Eratosthenes Seamount. Eratosthenes Seamount, the northwestern limit of rifted continental crust from the Levant Margin, is part of a jagged rifted margin transected by transform faults on the northern edge of the lower African Plate that is being obliquely subducted under the Aegean–Anatolian upper plate. The thicker crust of Eratosthenes Seamount may be acting as an asperity on the subducting slab, locally locking up subduction of the Cyprus Arc on its northern margin, while deformed Tethyan oceanic crust remains trapped between its northeastern margin and the Hecataeus Rise.

Description: We present an up-to-date high resolution picture of the ongoing crustal deformation field of Italy, based on an extensive combination of permanent and non-permanent GPS observations carried out since 1994. In addition, we present an updated map of contemporary S Hmax orientations computed by a multidisciplinary data set of well-constrained stress indicators, including both published results and novel analyses. The comparison of stress and geodetic strain-rates directions reveals that both patterns are near-parallel over a large part of the investigated area, highlighting that crustal stress and surface deformation are driven by the same mechanism. The comparison of the azimuthal patterns of surface strain and mantle deformation shows a modest correlation on the Alps and a low correlation along the Apennines chain and the Calabro-Peloritan Arc. Along the Apennines chain, this feature suggests the occurrence of significant strain partitioning and crust–mantle mechanical decoupling. Along the Calabro-Peloritan Arc, the apparent low correlation reflects a different mantle–crust mechanism of deformation to the ongoing subduction and rollback of the Ionian slab. In addition, the superposition of regional/local effects related to second-order sources (crustal lateral density changes, strength contrasts), which at regional/local scale modulate the crustal stress/strain-rate pattern, cannot be ruled out.

Description: A series of linear analysis was performed on the onset of thermal convection of highly compressible fluids, in order to deepen the fundamental insights into the mantle convection of massive super-Earths in the presence of strong adiabatic compression. We consider the temporal evolution (growth or decay) of an infinitesimal perturbation superimposed to a highly compressible fluid which is in a hydrostatic (motionless) and conductive state in a basally heated horizontal layer. As a model of pressure-dependence in material properties, we employed an exponential decrease in thermal expansivity α and exponential increase in (reference) density with depth. The linearized equations for conservation of mass, momentum and internal (thermal) energy are numerically solved for the critical Rayleigh number as well as the vertical profiles of eigenfunctions for infinitesimal perturbations. The above calculations are repeatedly carried out by systematically varying (i) the dissipation number (Di), (ii) the temperature at the top surface and (iii) the magnitude of pressure-dependence in α and . Our analysis demonstrated that the onset of thermal convection is strongly affected by the adiabatic compression, in response to the changes in the static stability of thermal stratification in the fluid layer. For sufficiently large Di where a thick sublayer of stable stratification develops in the layer, for example, the critical Rayleigh number explosively increases with Di, together with drastic decreases in the length scales of perturbations both in vertical and horizontal directions. In particular, for very large Di, a thick ‘stratosphere’ occurs in the fluid layer where the vertical motion is significantly suppressed, resulting in a shrink of the incipient convection in a thin sublayer of unstable thermal stratification. In addition, when Di exceeds a threshold value above which a thermal stratification becomes stable in the entire layer, no perturbation is allowed to grow with time regardless of the Rayleigh number and/or the horizontal wavelength. We also found that the effect of adiabatic compression becomes prominent for higher temperature at the top surface of the fluid layer. These findings may imply the crucial importance of adiabatic compression in understanding the dynamics and evolution of the mantles of massive super-Earths, particularly for those orbiting their parent stars very closely.

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

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

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

Description: In this paper, we propose an approach to compute the coseismic Earth's volume change based on a spherical-Earth elastic dislocation theory. We present a general expression of the Earth's volume change for three typical dislocations: the shear, tensile and explosion sources. We conduct a case study for the 2004 Sumatra earthquake ( M w 9.3), the 2010 Chile earthquake ( M w 8.8), the 2011 Tohoku-Oki earthquake ( M w 9.0) and the 2013 Okhotsk Sea earthquake ( M w 8.3). The results show that mega-thrust earthquakes make the Earth expand and earthquakes along a normal fault make the Earth contract. We compare the volume changes computed for finite fault models and a point source of the 2011 Tohoku-Oki earthquake ( M w 9.0). The big difference of the results indicates that the coseismic changes in the Earth's volume (or the mean radius) are strongly dependent on the earthquakes’ focal mechanism, especially the depth and the dip angle. Then we estimate the cumulative volume changes by historical earthquakes ( M w ≥ 7.0) since 1960, and obtain an Earth mean radius expanding rate about 0.011 mm yr –1 .

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

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

Description: We present the crustal resistivity structure of the Pamir and Southern Tian Shan orogenic belts at the northwestern promontory of the India–Asia collision zone. The magnetotelluric (MT) data were recorded along a roughly north–south trending, 350 km long corridor from the Pamir Plateau in southern Tajikistan across the Pamir frontal ranges, the Alai Valley and the southwestern Tian Shan to Osh in the Kyrgyz part of the Fergana Basin. In total, we measured at 178 sites, whereof 26 combine broad band and long period recordings. One of the most intriguing features of the 2-D and 3-D inversion results is a laterally extended zone of high electrical conductivity below the Pamir Plateau, with resistivities below 1 m, starting at a depth of ~10–15 km. The high conductivity can be explained with the presence of partially molten rocks at middle to lower crustal levels, possibly related to ongoing migmatization and/or middle/lower crustal flow underneath the Southern Pamir. This interpretation is consistent with a low velocity zone found from local earthquake tomography, relatively high v p / v s ratios, elevated surface heat flow, and thermomechanical modelling suggesting that melting temperatures are reached in the felsic middle crust. In the upper crust of the Pamir and Tian Shan, the Palaeozoic–Mesozoic suture zones appear as electrically conductive, whereas the compact metamorphic rocks of the Muskol-Shatput Dome of the Central Pamir are highly resistive. The intra-montane basin of the Alai Valley—sandwiched between the Pamir and Tian Shan—exhibits a generally conductive upper crust that bifurcates into two conductors at depth. One of them connects to the active Main Pamir Thrust, which is absorbing most of today's convergence between the Pamir and the Tian Shan. Several deeper zones of high conductivity in the middle and lower crust of Central and Northern Pamir likely record fluid release due to metamorphism associated with active continental subduction/delamination.

Description: A new model of the deglaciation history of Antarctica over the past 25 kyr has been developed, which we refer to herein as ICE-6G_C (VM5a). This revision of its predecessor ICE-5G (VM2) has been constrained to fit all available geological and geodetic observations, consisting of: (1) the present day uplift rates at 42 sites estimated from GPS measurements, (2) ice thickness change at 62 locations estimated from exposure-age dating, (3) Holocene relative sea level histories from 12 locations estimated on the basis of radiocarbon dating and (4) age of the onset of marine sedimentation at nine locations along the Antarctic shelf also estimated on the basis of 14 C dating. Our new model fits the totality of these data well. An additional nine GPS-determined site velocities are also estimated for locations known to be influenced by modern ice loss from the Pine Island Bay and Northern Antarctic Peninsula regions. At the 42 locations not influenced by modern ice loss, the quality of the fit of postglacial rebound model ICE-6G_C (VM5A) is characterized by a weighted root mean square residual of 0.9 mm yr –1 . The Southern Antarctic Peninsula is inferred to be rising at 2 mm yr –1 , requiring there to be less Holocene ice loss there than in the prior model ICE-5G (VM2). The East Antarctica coast is rising at approximately 1 mm yr –1 , requiring ice loss from this region to have been small since Last Glacial Maximum. The Ellsworth Mountains, at the base of the Antarctic Peninsula, are inferred to be rising at 5–8 mm yr –1 , indicating large ice loss from this area during deglaciation that is poorly sampled by geological data. Horizontal deformation of the Antarctic Plate is minor with two exceptions. First, O'Higgins, at the tip of the Antarctic Peninsula, is moving southeast at a significant 2 mm yr –1 relative to the Antarctic Plate. Secondly, the margins of the Ronne and Ross Ice Shelves are moving horizontally away from the shelf centres at an approximate rate of 0.8 mm yr –1 , in viscous response to the early Holocene unloading of ice from the current locations of the ice shelf centers. ICE-6G_C (VM5A) fits the horizontal observations well (wrms residual speed of 0.7 mm yr –1 ), there being no need to invoke any influence of lateral variation in mantle viscosity. ICE-6G_C (VM5A) differs in several respects from the recently published W12A model of Whitehouse et al. First, the upper-mantle viscosity in VM5a is 5 10 20 Pa s, half that in W12A. The VM5a profile, which is identical to that inferred on the basis of the Fennoscandian relaxation spectrum, North American relative sea level histories and Earth rotation constraints, when coupled with the revised ICE-6G_C deglaciation history, fits all of the available constraints. Secondly, the net contribution of Antarctica ice loss to global sea level rise is 13.6 m, 2/3 greater than the 8 m in W12A. Thirdly, ice loss occurs quickly from 12 to 5 ka, and the contribution to global sea level rise during Meltwater Pulse 1B (11.5 ka) is large (5 m), consistent with sedimentation constraints from cores from the Antarctica ice shelf. Fourthly, in ICE-6G_C there is no ice gain in the East Antarctica interior, as there is in W12A. Finally, the new model of Antarctic deglaciation reconciles the global constraint upon the global mass loss during deglaciation provided by the Barbados record of relative sea level history when coupled with the Northern Hemisphere counterpart of this new model.

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

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

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

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

Description: The Himalaya is the result of the on-going convergence and collision of India and Asia. The internal configuration and processes that govern the rise of the Himalayan Mountains and Tibetan Plateau are crucial to understand continental collision zones. However, knowledge of the prior configuration of the colliding plates is equally important, since inherited (pre-orogenic/basement) structures can undeniably influence the development of the orogenic architecture throughout the orogen's cycle of collision and eventual collapse. Three northeast-trending palaeotopographic ridges of faulted Precambrian Indian basement underlie the Ganga basin south of the Himalaya. Our paper illustrates a crustal-scale fault origin for these ridges and succeeds in determining how far north beneath the Himalayan system they extend and how they ultimately govern the location of upper crustal faults in southern Tibet. Spectrally filtered EGM2008 Bouguer gravity data and edges in its horizontal gradient at different source depths (‘gravity worms’) over northern Peninsular India, the Himalaya and southern Tibet reveal several continuous Himalayan cross-strike discontinuities interpreted to represent crustal faults. Gravity lineaments in Peninsular India coincide with edges of the Precambrian basement ridges and megakinks up to 100 km wide develop in foreland cover sequences between the interpreted basement faults. The interpreted basement faults project northward beneath the Himalayan system and southern Tibet. Our results suggest that several active Himalayan cross-strike faults, such as the ones related to many graben in southern Tibet, are rooted in the underplated Indian lower crust or step en échelon along interpreted basement faults. Our interpretation thus suggests that south Tibet graben are spatially related to deep-seated crustal-scale faults rooted in the underplated Indian crust. These major discontinuities partition the Himalayan range into distinct zones, and could ultimately contribute to lateral variability in tectonic evolution along the orogen's strike.

Description: We explore the impact of deep ductile shear zones on post-seismic deformation following a finite length strike-slip earthquake. We show that the pattern of post-seismic vertical surface deformation surrounding the fault is a discriminant for the existence of high viscosities immediately below the seismogenic layer, regardless of whether the model contains purely distributed creep or also includes a component of localized creep at subseismogenic depths. Post-seismic deformation characterized by initially fast relaxation followed by a slower relaxation is predicted by models that include both localized creep in a subseismogenic shear zone and distributed creep in the surrounding region, even if they only contain steady Maxwell viscoelasticity. This post-seismic deformation is similar to that in models that approximate the ductile lithosphere and/or asthenosphere with Burgers viscoelasticity. We find that the post-seismic deformation following the 1997 M w 7.6 Manyi, China, earthquake, is consistent with a post-seismic model composed of a lower Maxwell viscoelastic region with viscosity 10 19 Pa s and a 5 km wide, Maxwell viscoelastic shear zone with viscosity 10 18 Pa s beneath the fault.

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

Description: The Amundsen Sea Embayment of West Antarctica represents a key component in the tectonic history of Antarctic–New Zealand continental breakup. The region played a major role in the plate-kinematic development of the southern Pacific from the inferred collision of the Hikurangi Plateau with the Gondwana subduction margin at approximately 110–100 Ma to the evolution of the West Antarctic Rift System. However, little is known about the crustal architecture and the tectonic processes creating the embayment. During two ‘RV Polarstern’ expeditions in 2006 and 2010 a large geophysical data set was collected consisting of seismic-refraction and reflection data, ship-borne gravity and helicopter-borne magnetic measurements. Two P -wave velocity–depth models based on forward traveltime modelling of nine ocean bottom hydrophone recordings provide an insight into the lithospheric structure beneath the Amundsen Sea Embayment. Seismic-reflection data image the sedimentary architecture and the top-of-basement. The seismic data provide constraints for 2-D gravity modelling, which supports and complements P -wave modelling. Our final model shows 10–14-km-thick stretched continental crust at the continental rise that thickens to as much as 28 km beneath the inner shelf. The homogenous crustal architecture of the continental rise, including horst and graben structures are interpreted as indicating that wide-mode rifting affected the entire region. We observe a high-velocity layer of variable thickness beneath the margin and related it, contrary to other ‘normal volcanic type margins’, to a proposed magma flow along the base of the crust from beneath eastern Marie Byrd Land—West Antarctica to the Marie Byrd Seamount province. Furthermore, we discuss the possibility of upper mantle serpentinization by seawater penetration at the Marie Byrd Seamount province. Hints of seaward-dipping reflectors indicate some degree of volcanism in the area after break-up. A set of gravity anomaly data indicate several phases of fully developed and failed rift systems, including a possible branch of the West Antarctic Rift System in the Amundsen Sea Embayment.

Description: The computation of quasi-static deformation for axisymmetric viscoelastic structures on a gravitating spherical earth is addressed using the spectral element method (SEM). A 2-D spectral element domain is defined with respect to spherical coordinates of radius and angular distance from a pole of symmetry, and 3-D viscoelastic structure is assumed to be azimuthally symmetric with respect to this pole. A point dislocation source that is periodic in azimuth is implemented with a truncated sequence of azimuthal order numbers. Viscoelasticity is limited to linear rheologies and is implemented with the correspondence principle in the Laplace transform domain. This leads to a series of decoupled 2-D problems which are solved with the SEM. Inverse Laplace transform of the independent 2-D solutions leads to the time-domain solution of the 3-D equations of quasi-static equilibrium imposed on a 2-D structure. The numerical procedure is verified through comparison with analytic solutions for finite faults embedded in a laterally homogeneous viscoelastic structure. This methodology is applicable to situations where the predominant structure varies in one horizontal direction, such as a structural contrast across (or parallel to) a long strike-slip fault.

Description: Geophysical data are the main source of information about the subsurface. Geophysical techniques are, however, highly non-unique in determining specific physical parameters and boundaries of subsurface objects. To obtain actual physical information, an inversion process is often applied, in which measurements at or above the Earth surface are inverted into a 2- or 3-D subsurface spatial distribution of the physical property. Interpreting these models into structural objects, related to physical processes, requires a priori knowledge and expert analysis which is susceptible to subjective choices and is therefore often non-repeatable. In this research, we implemented a recently introduced object-based approach to interpret the 3-D inversion results of a single geophysical technique using the available a priori information and the physical and geometrical characteristics of the interpreted objects. The introduced methodology is semi-automatic and repeatable, and allows the extraction of subsurface structures using 3-D object-oriented image analysis (3-D OOA) in an objective knowledge–based classification scheme. The approach allows for a semi-objective setting of thresholds that can be tested and, if necessary, changed in a very fast and efficient way. These changes require only changing the thresholds used in a so-called ruleset, which is composed of algorithms that extract objects from a 3-D data cube. The approach is tested on a synthetic model, which is based on a priori knowledge on objects present in the study area (Tanzania). Object characteristics and thresholds were well defined in a 3-D histogram of velocity versus depth, and objects were fully retrieved. The real model results showed how 3-D OOA can deal with realistic 3-D subsurface conditions in which the boundaries become fuzzy, the object extensions become unclear and the model characteristics vary with depth due to the different physical conditions. As expected, the 3-D histogram of the real data was substantially more complex. Still, the 3-D OOA-derived objects were extracted based on their velocity and their depth location. Spatially defined boundaries, based on physical variations, can improve the modelling with spatially dependent parameter information. With 3-D OOA, the non-uniqueness on the location of objects and their physical properties can be potentially significantly reduced.

Description: The geodetic rates for the gravity variation and vertical uplift in polar regions subject to past and present-day ice-mass changes (PDIMCs) provide important insight into the rheological structure of the Earth. We provide an update of the rates observed at Ny-Ålesund, Svalbard. To do so, we extract and remove the significant seasonal content from the observations. The rate of gravity variations, derived from absolute and relative gravity measurements, is –1.39 ± 0.11 μGal yr –1 . The rate of vertical displacements is estimated using GPS and tide gauge measurements. We obtain 7.94 ± 0.21 and 8.29 ± 1.60 mm yr –1 , respectively. We compare the extracted signal with that predicted by GLDAS/Noah and ERA-interim hydrology models. We find that the seasonal gravity variations are well-represented by local hydrology changes contained in the ERA-interim model. The phase of seasonal vertical displacements are due to non-local continental hydrology and non-tidal ocean loading. However, a large part of the amplitude of the seasonal vertical displacements remains unexplained. The geodetic rates are used to investigate the asthenosphere viscosity and lithosphere/asthenosphere thicknesses. We first correct the updated geodetic rates for those induced by PDIMCs in Svalbard, using published results, and the sea level change due to the melting of the major ice reservoirs. We show that the latter are at the level of the geodetic rate uncertainties and are responsible for rates of gravity variations and vertical displacements of –0.29 ± 0.03 μGal yr –1 and 1.11 ± 0.10 mm yr –1 , respectively. To account for the late Pleistocene deglaciation, we use the global ice evolution model ICE-3G. The Little Ice Age (LIA) deglaciation in Svalbard is modelled using a disc load model with a simple linear temporal evolution. The geodetic rates at Ny-Ålesund induced by the past deglaciations depend on the viscosity structure of the Earth. We find that viscous relaxation time due to the LIA deglaciation in Svalbard is more than 60 times shorter than that due to the Pleistocene deglaciation. We also find that the response to past and PDIMCs of an Earth model with asthenosphere viscosities ranging between 1.0 and 5.5 x 10 18 Pa s and lithosphere (resp. asthenosphere) thicknesses ranging between 50 and 100 km (resp. 120 and 170 km) can explain the rates derived from geodetic observations.

Description: We estimate Eurasia-North America Plate motion rotations at ~1-Myr intervals for the past 20 Myr from more than 11 000 crossings of 21 magnetic reversals from Chron 1n (0.78 Ma) to C6no (19.72 Ma) and flow lines digitized from the Charlie Gibbs, Bight and Molloy fracture zones and transform faults. Adjusted for outward displacement, the 21 best-fitting rotations determined from a simultaneous inversion of the numerous kinematic data reconstruct the reversal crossings with weighted root mean square misfits of only 1–2 km and 0.2–7 km for the transform fault and fracture zone crossings. The new rotations clearly define a ~1000 km southward shift of the rotation pole and 20 per cent slowdown in seafloor spreading rates between 7 and 6 Ma, preceded by apparently steady plate motion from 19.7 to ~7 Ma. Data for times since C3An.2 (6.7 Ma) are well fit by a stationary pole of rotation and constant rate of angular opening, consistent with steady motion since 6.7 Ma. The southward shift of the rotation pole at 7–6 Ma implies that Eurasia-North America motion in northeastern Asia changed from slowly convergent before 7 Ma to slowly divergent afterward. Crossings of magnetic reversals C1n through C3An.1 (6.0 Ma) are well fit everywhere in the Arctic basin and south to the Azores triple junction, indicating that the Eurasia and North America plates have not deformed along their mutual boundary since at least 6.0 Ma. However, the new rotations systematically overrotate magnetic lineations older than C3An.1 (6.0 Ma) within 200 km of the Azores triple junction and also overrotate lineations older than C5n along the Gakkel Ridge in the Arctic Basin. Barring misidentifications of the magnetic anomalies in those areas, the pattern and magnitude of the systematic misfits imply that slow (~1 mm yr –1 ) distributed or microplate deformation occurred in one or both regions.

Description: We show analytically that a well-known transfer function previously derived for the scalar acoustic problem that converts measurements from a 3-D (real-world) setting to a 2-D equivalent is directly applicable to the vector electromagnetic borehole ground penetrating radar problem. We also show that the transfer function's precision is improved for the low-loss case through the use of complex velocity. The transfer function has a strong effect on amplitude, and is therefore a critical preprocessing step for 2-D full-wave inversion when finding conductivity is of concern. We demonstrate the effectiveness of the transfer function through various numerical experiments and a synthetic frequency-domain full-wave inversion. We also compare the effectiveness of this curved-ray transfer function to a quasi-straight-ray transfer function. The inversion demonstrates the positive effect the transfer functions have on recovering conductivity and also that they are effective even when there are sharp velocity contrasts.

Description: Here we inverted the GPS data to infer the coseismic slip of the Tohoku-Oki earthquake and the time-dependent afterslip distribution in the 4 months following the main shock. The Tohoku-Oki earthquake showed an unexpected magnitude and a characteristic depth-dependent differentiation of seismic energy radiation. In this context the estimation and comparison of the distribution of the fault portions that slip coseismically and post-seismically contribute to a better understanding of the variation of frictional characteristics of the plate interface. The inferred coseismic slip extends in a relatively compact region located updip from the hypocentre and reaches its highest value (about 60 m) near the trench. Afterslip occurs mostly outside the coseismic rupture and is distributed in two main modal centres. It reaches its largest values in an area located downdip of the coseismic slip and extends to a depth of 80 km. In the depth range between 30 and 50 km afterslip overlaps the portion of the fault that experienced historical moderate earthquakes, high-frequency seismic radiation and thrust-type aftershocks. The behaviour of this area can be explained by a rheologically heterogeneous region made of a ductile fault matrix interspersed with compact brittle asperities. On the contrary, the region beneath 50–60 km depth is probably characterized by a fully velocity strengthening behaviour. Southern afterslip, located off-Chiba Prefecture, is probably related to the M w 7.9 Ibaraki-Oki aftershock. The northward extension of the afterslip stops at a latitude of about 40°N, just south of the off-Aomori region. This may be related to three large events occurred in this area during the last century and the consequent strong coupling or complete depletion of the accumulated strain that characterize this region.

Description: Understanding the role of a given transcription factor (TF) in regulating gene expression requires precise mapping of its binding sites in the genome. Chromatin immunoprecipitation-exo, an emerging technique using exonuclease to digest TF unbound DNA after ChIP, is designed to reveal transcription factor binding site (TFBS) boundaries with near-single nucleotide resolution. Although ChIP-exo promises deeper insights into transcription regulation, no dedicated bioinformatics tool exists to leverage its advantages. Most ChIP-seq and ChIP-chip analytic methods are not tailored for ChIP-exo, and thus cannot take full advantage of high-resolution ChIP-exo data. Here we describe a novel analysis framework, termed MACE (model-based analysis of ChIP-exo) dedicated to ChIP-exo data analysis. The MACE workflow consists of four steps: (i) sequencing data normalization and bias correction; (ii) signal consolidation and noise reduction; (iii) single-nucleotide resolution border peak detection using the Chebyshev Inequality and (iv) border matching using the Gale-Shapley stable matching algorithm. When applied to published human CTCF, yeast Reb1 and our own mouse ONECUT1/HNF6 ChIP-exo data, MACE is able to define TFBSs with high sensitivity, specificity and spatial resolution, as evidenced by multiple criteria including motif enrichment, sequence conservation, direct sequence pileup, nucleosome positioning and open chromatin states. In addition, we show that the fundamental advance of MACE is the identification of two boundaries of a TFBS with high resolution, whereas other methods only report a single location of the same event. The two boundaries help elucidate the in vivo binding structure of a given TF, e.g. whether the TF may bind as dimers or in a complex with other co-factors.

Description: We present a revised interpretation of magnetic anomalies and fracture zones on the Southwest Indian Ridge (SWIR; Africa–Antarctica) and the Southeast Indian Ridge (SEIR; Capricorn–Antarctica) and use them to calculate 2-plate finite rotations for anomalies 34 to 20 (84 to 43 Ma). Central Indian Ridge (CIR; Capricorn–Africa) rotations are calculated by summing the SWIR and SEIR rotations. These rotations provide a high-resolution record of changes in the motion of India and Africa at the time of the onset of the Reunion plume head. An analysis of the relative velocities of India, Africa and Antarctica leads to a refinement of previous observations that the speedup of India relative to the mantle was accompanied by a slowdown of Africa. The most rapid slowdown of Africa occurs around Chron 32Ay (71 Ma), the time when India's motion relative to Africa notably starts to accelerate. Using the most recent Geomagnetic Polarity Timescale (GTS12) we show that India's velocity relative to Africa was characterized by an acceleration from roughly 60 to 180 mm yr –1 between 71 and 66 Ma, a short pulse of superfast motion (~180 mm yr –1 ) between 66 and 63 Ma, an abrupt slowdown to 120 mm yr –1 between 63 and 62 Ma, and then a long period (63 to 47 Ma) of gradual slowing, but still fast motion (~100 mm yr –1 ), which ends with a rapid slowdown after Chron 21o (47 Ma). Changes in the velocities of Africa and India with respect to the mantle follow a similar pattern. The fastest motion of India relative to the mantle, ~220 mm yr –1 , occurs during Chron 29R. The SWIR rotations constrain three significant changes in the migration path of the Africa–Antarctic stage poles: following Chron 33y (73 Ma), following Chron 31y (68 Ma), and following Chron 24o (54 Ma). The change in the migration path of the SWIR stage poles following Chron 33y is coincident with the most rapid slowdown in Africa's motion. The change in the migration path after Chron 31y, although coincident with the most rapid acceleration of India's northward motion, may be related to changes in ridge push forces on the SWIR associated with the onset of extension along the Bain transform fault zone. The initial slowdown in India's motion relative to Africa between 63 and 62 Ma is more abrupt than predictions based on published plume head force models, suggesting it might have been caused by a change in plate boundary forces. The abrupt change in the migration path of the SWIR stage poles after Chron 24o is not associated with major changes in the velocities of either Africa or India and may reflect Atlantic basin plate motion changes associated with the arrival at the Earth's surface of the Iceland plume head. The abruptness of India's slowdown after Chron 21o is consistent with a collision event.

Description: The 2 principle and the unbiased predictive risk estimator are used to determine optimal regularization parameters in the context of 3-D focusing gravity inversion with the minimum support stabilizer. At each iteration of the focusing inversion the minimum support stabilizer is determined and then the fidelity term is updated using the standard form transformation. Solution of the resulting Tikhonov functional is found efficiently using the singular value decomposition of the transformed model matrix, which also provides for efficient determination of the updated regularization parameter each step. Experimental 3-D simulations using synthetic data of a dipping dike and a cube anomaly demonstrate that both parameter estimation techniques outperform the Morozov discrepancy principle for determining the regularization parameter. Smaller relative errors of the reconstructed models are obtained with fewer iterations. Data acquired over the Gotvand dam site in the south-west of Iran are used to validate use of the methods for inversion of practical data and provide good estimates of anomalous structures within the subsurface.

Description: Global navigation satellite systems (GNSSs) have revealed that a mega-thrust earthquake that occurs in an island-arc trench system causes post-seismic crustal deformation. Such crustal deformation data have been interpreted by combining three mechanisms: afterslip, poroelastic rebound and viscoelastic relaxation. It is seismologically important to determine the contribution of each mechanism because it provides frictional properties between the plate boundaries and viscosity estimates in the asthenosphere which are necessary to evaluate the stress behaviour during earthquake cycles. However, the observation sites of GNSS are mostly deployed over land and can detect only a small part of the large-scale deformation, which precludes a clear separation of the mechanisms. To extend the spatial coverage of the deformation area, recent studies started to use satellite gravity data that can detect long-wavelength deformations over the ocean. To date, compared with theoretical models for calculating the post-seismic crustal deformation, a few models have been proposed to interpret the corresponding gravity variations. Previous approaches have adopted approximations for the effects of compressibility, sphericity and self-gravitation when computing gravity changes. In this study, a new spectral-finite element approach is presented to consider the effects of material compressibility for Burgers viscoelastic earth model with a laterally heterogeneous viscosity distribution. After the basic principles are explained, it is applied to the 2004 Sumatra–Andaman earthquake. For this event, post-seismic deformation mechanisms are still a controversial topic. Using the developed approach, it is shown that the spatial patterns of gravity change generated by the above three mechanisms clearly differ from one another. A comparison of the theoretical simulation results with the satellite gravity data obtained from the Gravity Recovery and Climate Experiment reveals that both afterslip and viscoelastic relaxation are occurring. Considering the spatial patterns in satellite gravity fields is an effective method for investigating post-seismic deformation mechanisms.

Description: Thin plate flexure theory provides an accurate model for the response of the lithosphere to vertical loads on horizontal length scales ranging from tens to hundreds of kilometres. Examples include flexure at seamounts, fracture zones, sedimentary basins and subduction zones. When applying this theory to real world situations, most studies assume a locally uniform plate thickness to enable simple Fourier transform solutions. However, in cases where the amplitude of the flexure is prominent, such as subduction zones, or there are rapid variations in seafloor age, such as fracture zones, these models are inadequate. Here we present a computationally efficient algorithm for solving the thin plate flexure equation for non-uniform plate thickness and arbitrary vertical load. The iterative scheme takes advantage of the 2-D fast Fourier transform to perform calculations in both the spatial and spectral domains, resulting in an accurate and computationally efficient solution. We illustrate the accuracy of the method through comparisons with known analytic solutions. Finally, we present results from three simple models demonstrating the differences in trench outer rise flexure when 2-D variations in plate rigidity and applied bending moment are taken into account. Although we focus our analysis on ocean trench flexure, the method is applicable to other 2-D flexure problems having spatial rigidity variations such as seamount loading of a thermally eroded lithosphere or flexure across the continental–oceanic crust boundary.

Description: Theory has been long established for computing the elastic response of a spherically symmetric terrestrial planetary body to both body tide and surface loading forces. However, for a planet with laterally heterogeneous mantle structure, the response is usually computed using a fully numerical approach. In this paper, we develop a semi-analytic method based on perturbation theory to solve for the elastic response of a planetary body with lateral heterogeneities in its mantle. We present a derivation of the governing equations for our second-order perturbation method and use them to study the high-order tidal effects caused by mode coupling between degree-2 body tide forcing and the laterally heterogeneous elastic structure of the mantle. We test our method by applying it to the Moon in which small long-wavelength lateral heterogeneities are assumed to exist in the elastic moduli of the lunar mantle. The tidal response of the Moon is determined mode by mode, for lateral heterogeneities with different depth ranges within the mantle and different horizontal scales. Our perturbation method solutions are compared with numerical results, showing remarkable agreement between the two methods. We conclude that our perturbation method provides accurate results and can be adapted to address a variety of forward and inverse response problems.

Description: Functional mechanisms of biomolecules often manifest themselves precisely in transient conformational substates. Researchers have long sought to structurally characterize dynamic processes in non-coding RNA, combining experimental data with computer algorithms. However, adequate exploration of conformational space for these highly dynamic molecules, starting from static crystal structures, remains challenging. Here, we report a new conformational sampling procedure, KGSrna, which can efficiently probe the native ensemble of RNA molecules in solution. We found that KGSrna ensembles accurately represent the conformational landscapes of 3D RNA encoded by NMR proton chemical shifts. KGSrna resolves motionally averaged NMR data into structural contributions; when coupled with residual dipolar coupling data, a KGSrna ensemble revealed a previously uncharacterized transient excited state of the HIV-1 trans-activation response element stem–loop. Ensemble-based interpretations of averaged data can aid in formulating and testing dynamic, motion-based hypotheses of functional mechanisms in RNAs with broad implications for RNA engineering and therapeutic intervention.

Description: Binding of transcription factors to their binding sites in promoter regions is the fundamental event in transcriptional gene regulation. When a transcription factor binding site is located within a nucleosome, the DNA has to partially unwrap from the nucleosome to allow transcription factor binding. This reduces the rate of transcription factor binding and is a known mechanism for regulation of gene expression via chromatin structure. Recently a second mechanism has been reported where transcription factor off-rates are dramatically increased when binding to target sites within the nucleosome. There are two possible explanations for such an increase in off-rate short of an active role of the nucleosome in pushing the transcription factor off the DNA: (i) for dimeric transcription factors the nucleosome can change the equilibrium between monomeric and dimeric binding or (ii) the nucleosome can change the equilibrium between specific and non-specific binding to the DNA. We explicitly model both scenarios and find that dimeric binding can explain a large increase in off-rate while the non-specific binding model cannot be reconciled with the large, experimentally observed increase. Our results suggest a general mechanism how nucleosomes increase transcription factor dissociation to promote exchange of transcription factors and regulate gene expression.

Description: Teleseismic data recorded at 13 broad-band seismological stations across northwest part of the Tethyan Himalaya and eastern Ladakh are analysed to determine the seismic characteristics of the crust and upper mantle beneath the northwest India–Asia collision zone. The receiver functions computed from teleseismic P- waveform for a wide range of backazimuth show strong azimuthal variation in the Indus suture zone (ISZ), the zone which marks the collision and subsequent subduction of both the Tethyan oceanic plate and Indian continental plate beneath Eurasia. The teleseismic waves piercing the ISZ do not show clear P -to- S ( Ps ) converted phase at the depth of Moho. In contrast, the waves piercing the Karakoram zone, Ladakh batholith and the Tethyan Himalayan region south of the ISZ clearly show the Moho converted Ps phase and corresponding inverted models reveal variation of crustal thickness from ~60 km beneath the Tethyan Himalaya to ~80 km beneath the Karakoram fault zone. A prominent intracrustal low velocity zone (IC-LVZ) is detected in the shear wave velocity models within the depth range ~15–40 km. The IC-LVZ identified at the stations both north and south of the ISZ can be interpreted as due to presence of fluid/partial melt. Our study provides compelling evidence that the mid-crustal low velocity zone does extend across the suture zone, in to the Tethyan Himalaya. The contact between this serpentinized ultramafic rocks and the eclogitized Indian continental crust in the suture zone is identified at ~47–50 km depth.

Description: We report and analyse the tsunami recorded in the northwestern Indian Ocean at the Makran region following the M w 7.7 Pakistan inland strike-slip earthquake on 2013 September 24. We analyse eleven tide gauge records as well as one DART record of this tsunami and perform numerical modelling of the tsunami that would be triggered by a range of possible sources. The tsunami registered a maximum wave height of 109 cm at the Qurayat tide gauge station (Oman). The dominant period of the tsunami was around 12 min, although wavelet analysis showed that parts of the tsunami energy were partitioned into a slightly wider period range of 7 and 16 min. Tsunami backward ray tracing showed that the tsunami source was possibly located offshore Jiwani (Pakistan) and that the tsunami was most likely triggered by the main shock. The aftershocks are distributed in the inland region and the coseismic vertical and horizontal displacements are also limited inland implying that the tsunami was generated by secondary sources triggered by the earthquake. Different possible tsunami sources including a mud volcano at the location of the newly generated island, and a mud volcano or diapir at offshore deep water were examined through numerical modelling and all failed to reproduce the observed waveforms. Numerical modelling showed that a submarine slump with a source dimension of about 10–15 km and a thickness of about 100 m located at 61.49°E and 24.62°N, that is, about 60–70 km off the Jiwani coast (Pakistan), seems capable of reasonably reproducing the wave amplitudes and periods of the observed tsunami waveforms. This event was the second instrumentally recorded tsunami in the region, after the Makran tsunami of 1945 November, and provides evidence for a hazard from landslide/slump-generated waves following seismic activity in the area.

Description: Joint inversion of different geophysical data sets is becoming a more popular and powerful tool, and it has been performed on data sensitive both to the same physical parameter and to different physical parameters. Joint inversion is undertaken to reduce acceptable model space and to increase sensitivity to model parameters that one method alone is unable to resolve adequately. We examine and implement a novel hybrid joint inversion approach. In our inversion scheme a model—the reference model—is fixed, and the information shared with the subsurface structure obtained from another method will be maximized; in our case conductivity structures from magnetotelluric (MT) inversion. During inversion, the joint probability distribution of the MT and the specified reference model is estimated and its entropy minimized in order to guide the inversion result towards a solution that is statistically compatible with the reference model. The powerful feature of this technique is that no explicit relationships between estimated model parameters and reference model ones are presumed: if a link exists in data then it is highlighted in the estimation of the joint probability distribution, if no link is required, then none is enforced. Tests performed verify the robustness of this method and the advantages of it in a 1-D anisotropic scenario are demonstrated. A case study was performed with data from Central Germany, effectively fitting an MT data set from a single station within as minimal an amount of anisotropy as required.

Description: Some of the major geothermal anomalies in central Europe are linked to tectonic structures within the top of crystalline basement, which modify strongly the top of this basement. Their assessment is a major challenge in exploration geophysics. Gravity has been proven to be suitable for the detection of mainly large scale lithological and structural inhomogeneities. Indeed, it is well known and proven by different wells that, for example, in northern Switzerland extended negative anomalies are linked to such structures. Due to depth limitation of wells, there vertical extension is often unknown. In this study, we have investigated the potential of gravity for the geometrical characterization of such basement structures. Our approach consists in the combination of the series of Butterworth filters, geological modelling and best-fitting between observed and computed residual anomalies. In this respect, filters of variable wavelength are applied to observed and computed gravity data. The geological model is discretized into a finite element mesh. Near-surface anomalies and the effect of the sedimentary cover were eliminated using cut-off wavelength of 10 km and geological and seismic information. We analysed the potential of preferential Butterworth filtering in a sensitivity study and applied the above mentioned approach to part of the Swiss molasses basin. Sensitivity analyses reveal that such sets of residual anomalies represents a pseudo-tomography revealing the distribution of different structures with depth. This finding allows for interpreting negative anomalies in terms of 3-D volumes. Best-fitting then permits determination of the most likely 3-D geometries of such basement structures. Our model fits both, geological observations and gravity: among 10 deep boreholes in the studied area, six reach the respective units and confirm our distribution of the negative (and positive) anomalies.

Description: Several slope failures are observed near the deformation front on the frontal ridges of the northern Cascadia accretionary margin off Vancouver Island. The cause for these events is not clear, although several lines of evidence indicate a possible connection between the occurrence of gas hydrate and submarine landslide features. The presence of gas hydrate is indicated by a prominent bottom-simulating reflector (BSR), at a depth of ~265–275 m beneath the seafloor (mbsf), as interpreted from vertical-incidence and wide-angle seismic data beneath the ridge crests of the frontal ridges. For one slide, informally called Slipstream Slide, the velocity structure inferred from tomography analyses shows anomalous high velocities values of about 2.0 km s –1 at shallow depths of 100 mbsf. The estimated depth of the glide plane (100 ± 10 m) closely matches the depth of these shallow high velocities. In contrast, at a frontal ridge slide just to the northwest (informally called Orca Slide), the glide plane occurs at the same depth as the current BSR. Our new results indicate that the glide plane of the Slipstream slope failure is associated with the contrast between sediments strengthened by gas hydrate and overlying sediments where little or no hydrate is present. In contrast, the glide plane of Orca Slide is between sediment strengthened by hydrate underlain by sediments beneath the gas hydrate stability zone, possibly containing free gas. Additionally, a set of margin perpendicular normal faults are imaged from seafloor down to BSR depth at both frontal ridges. As inferred from the multibeam bathymetry, the estimated volume of the material lost during the slope failure at Slipstream Slide is about 0.33 km 3 , and ~0.24 km 3 of this volume is present as debris material on the ocean basin floor. The 20 per cent difference is likely due to more widely distributed fine sediments not easily detectable as bathymetric anomalies. These volume estimates on the Cascadia margin are approaching the mass failure volume for other slides that have generated large tsunamis—for example 1–3 km 3 for a 1998 Papua New Guinea slide.

Description: The method presented here aims to assess the tsunami threat very rapidly after the occurrence of a large earthquake, using as input the parameters of the seismic source, and an approach based on Green's summation. We show that the main weakness of the approach (the need to consider only linear shallow water propagation) is largely compensated by the advantages in terms of computing performance and independence with respect to pre-computed scenarios. To test the approach and to illustrate its implementation in a real environment, we focus on the Sea of Oman, a tsunamigenic area characterized by Makran subduction zone which detailed structure is partially unknown and where secondary tsunami sources must also be taken into account, both for hazard studies and warning purposes. The potential source area is partitioned into a grid of unity water sources. A shallow water (SW) numerical model is used to pre-compute the corresponding empirical Green's functions on several points of interest located on the coasts of Iran, Pakistan and Oman. The comparison between Green's summation and the direct SW computation using the full resolution of the bathymetric grid shows that the accuracy is good enough for practical applications.

Description: Clay minerals as products of hydrothermal alteration significantly influence the hydraulic and mechanical properties of crystalline rock. Therefore, the localization and characterization of alteration zones by downhole measurements is a great challenge for the development of geothermal reservoirs. The magnetite bearing granite of the geothermal site in Soultz-sous-Forêts (France) experienced hydrothermal alteration during several tectonic events and clay mineral formation is especially observed in alteration halos around fracture zones. During the formation of clay minerals, magnetite was oxidized into hematite, which significantly reduces the magnetic susceptibility of the granite from ferrimagnetic to mostly paramagnetic values. The aim of this study was to find out if there exists a correlation between synthetic clay content logs (SCCLs) and measurements of magnetic susceptibility on cuttings in the granite in order to characterize their alteration mineralogy. Such a correlation has been proven for core samples of the EPS1 reference well. SCCLs were created from gamma ray and fracture density logs using a neural network. These logs can localize altered fracture zones in the GPK1-4 wells, where no core material is available. Mass susceptibility from 261 cutting samples of the wells GPK1–GPK4 was compared with the neural network derived synthetic logs. We applied a combination of temperature dependent magnetic susceptibility measurements with optical and electron microscopy, and energy dispersive X-ray spectroscopy to discriminate different stages of alteration. We found, that also in the granite cuttings an increasing alteration grade is characterized by an advancing oxidation of magnetite into hematite and a reduction of magnetic susceptibility. A challenge to face for the interpretation of magnetic susceptibility data from cuttings material is that extreme alteration grades can also display increased susceptibilities due to the formation of secondary magnetite. Low magnetic susceptibility can also be attributed to primary low magnetite content, if the granite facies changes. In order to interpret magnetic susceptibility from cuttings, contaminations with iron from wear debris of the drilling tools must be eliminated. Provided that the magnetic mineralogy of the granite is known in detail, this method in combination with petrographic investigations is suited to indicate and characterize hydrothermal alteration and the appearance of clay.

Description: The Tien Shan is the largest active intracontinental orogenic belt on Earth. To better understand the processes causing mountains to form at great distances from a plate boundary, we analyse passive source seismic data collected on 40 broad-band stations of the MANAS project (2005–2007) and 12 stations of the permanent KRNET seismic network to determine variations in crustal thickness and shear wave speed across the range. We jointly invert P - and S -wave receiver functions with surface wave observations from both earthquakes and ambient noise to reduce the ambiguity inherent in the images obtained from the techniques applied individually. Inclusion of ambient noise data improves constraints on the upper crust by allowing dispersion measurements to be made at shorter periods. Joint inversion can also reduce the ambiguity in interpretation by revealing the extent to which various features in the receiver functions are amplified or eliminated by interference from multiples. The resulting wave speed model shows a variation in crustal thickness across the range. We find that crustal velocities extend to ~75 km beneath the Kokshaal Range, which we attribute to underthrusting of the Tarim Basin beneath the southern Tien Shan. This result supports the plate model of intracontinental convergence. Crustal thickness elsewhere beneath the range is about 50 km, including beneath the Naryn Valley in the central Tien Shan where previous studies reported a shallow Moho. This difference apparently is the result of wave speed variations in the upper crust that were not previously taken into account. Finally, a high velocity lid appears in the upper mantle of the Central and Northern part of the Tien Shan, which we interpret as a remnant of material that may have delaminated elsewhere under the range.

Description: Errors in the satellite orbits are considered to be a limitation for Interferometric Synthetic Aperture Radar (InSAR) time-series techniques to accurately measure long-wavelength (〉50 km) ground displacements. Here we examine how orbital errors propagate into relative InSAR line-of-sight velocity fields and evaluate the contribution of orbital errors to the InSAR uncertainty. We express the InSAR uncertainty due to the orbital errors in terms of the standard deviations of the velocity gradients in range and azimuth directions (range and azimuth uncertainties). The range uncertainty depends on the magnitude of the orbital errors, the number and time span of acquisitions. Using reported orbital uncertainties we find range uncertainties of less than 1.5 mm yr –1  100 km –1 for ERS, less than 0.5 mm yr –1  100 km –1 for Envisat and ~0.2 mm yr –1  100 km –1 for TerraSAR-X and Sentinel-1. Under a conservative scenario, we find azimuth uncertainties of better than 1.5 mm yr –1  100 km –1 for older satellites (ERS and Envisat) and better than 0.5 mm yr –1  100 km –1 for modern satellites (TerraSAR-X and Sentinel-1). We validate the expected uncertainties using LOS velocity fields obtained from Envisat SAR imagery. We find residual gradients of 0.8 mm yr –1  100 km –1 or less in range and of 0.95 mm yr –1  100 km –1 or less in azimuth direction, which fall within the 1 to 2 uncertainties. The InSAR uncertainties due to the orbital errors are significantly smaller than generally expected. This shows the potential of InSAR systems to constrain long-wavelength geodynamic processes, such as continent-scale deformation across entire plate boundary zones.

Description: A method for subsurface recognition of blind geological bodies is presented using combined surface constraints and 3-D structural modelling that incorporates constraints from detailed mapping, and potential-field inversion modelling. This method is applied to the Mount Painter Province and demonstrates that addition of low density material is required to reconcile the gravity signature of the region. This method may be an effective way to construct 3-D models in regions of excellent structural control, and can be used to assess the validity of surface structures with 3-D architecture. Combined geological and potential-field constrained inversion modelling of the Mount Painter Province was conducted to assess the validity of the geological models of the region. Magnetic susceptibility constrained stochastic property inversions indicates that the northeast to southwest structural trend of the relatively magnetic meta-sedimentary rocks of the Radium Creek Group in the Mount Painter Inlier is reconcilable with the similar, northeast to southwest trending positive magnetic anomalies in the region. Radium Creek Group packages are the major contributor of the total magnetic response of the region. However field mapping and the results of initial density constrained stochastic property inversion modelling do not correlate with a large residual negative gravity anomaly central to the region. Further density constrained inversion modelling indicates that an additional large body of relatively low density material is needed within the model space to account for this negative density anomaly. Through sensitivity analysis of multiple geometrical and varied potential-field property inversions, the best-fitting model records a reduction in gravity rms misfit from 21.9 to 1.69 mGal, representing a reduction from 56 to 4.5 per cent in respect to the total dynamic range of 37.5 mGal of the residual anomaly. This best-fitting model incorporates a volumetrically significant source body of interpreted felsic, low density material (10 12 m 3 ) impinging on the central-west of the Mount Painter Inlier and overlying Neoproterozoic sequences, and the emplacement of more mafic affinities in the northeast and east. The spatial association and circular geometry of these granitoid bodies suggests an affinity with the Palaeozoic ~460–440 Ma British Empire Granite that outcrops in the Mount Painter Inlier. The intrusion of this additional material in the Palaeozoic could either be the product of; or contributed to, an increased local geotherm and heat flow in the region during the Palaeozoic.

Description: The Pacific and Australian plates in the South Island, New Zealand (NZ) converge at a rate of about 4 cm yr –1 . Accommodation of the continental part of this convergence in the lithospheric mantle is both poorly understood and currently controversial yet it is a problem of fundamental importance for understanding lithospheric thickening. End-member possibilities range from the classical model of asymmetric subduction to symmetric viscous thickening. Seismic tomography has the potential to image this process. However, tomographic images to date are poorly constrained due to the lack of appropriate earthquakes. Improved teleseismic tomography of the region has been achieved by increasing data coverage and applying a novel scheme of correcting for crustal structure by ray tracing through a newly created model of shallow shear wave velocity derived from the inversion of noise-based dispersion measurements. Our resulting models suggest the lithospheric mantle high velocities at the continental plate boundary extend no deeper than approximately 125 km, evidence against both previous models of viscous drip and typical asymmetric subduction zones. This high velocity core extends from north to south along the axis of South Island suggesting that mantle convergence is accommodated along the older, mid-Cenozoic, plate boundary. West of South Island, a high velocity west dipping zone may define the remnant Cretaceous subduction zone that has been distorted by Cenozoic transcurrent deformation. We present our new 3-D seismic velocity models together with a compatible tectonic model and discuss their implications for the nature of lithospheric evolution at this convergent boundary.

Description: We use continuous GPS measurements from 31 stations in southern Mexico to model coseismic slip and post-seismic deformation from the 2012 March 20 M w  = 7.5 Ometepec earthquake, the first large thrust earthquake to occur below central Mexico during the modern GPS era. Coseismic offsets ranging from ~280 mm near the epicentre to 5 mm or less at sites far from the epicentre are fit best by a rupture focused between ~15 and 35 km depth, consistent with an independent seismological estimate. The corresponding geodetic moment of 1.4 10 20 N·m is within 10 per cent of two independent seismic estimates. Transient post-seismic motion recorded by GPS sites as far as 300 km from the rupture has a different horizontal deformation gradient and opposite sense of vertical motion than do the coseismic offsets. A forward model of viscoelastic relaxation as a result of our new coseismic slip solution incorrectly predicts uplift in areas where post-seismic subsidence was recorded and indicates that viscoelastic deformation was no more than a few per cent of the measured post-seismic deformation. The deformation within 6 months of the earthquake was thus strongly dominated by fault afterslip. The post-seismic GPS time-series are well fit as logarithmically decaying fault afterslip on an area of the subduction interface up to 10 times larger than the earthquake rupture zone, extending as far as 220 km inland. Afterslip had a cumulative geodetic moment of 2.0 10 20 N·m, ~40 per cent larger than the Ometepec earthquake. Tests for the shallow and deep limits for the afterslip require that it included much of the earthquake rupture zone as well as regions of the subduction interface where slow slip events and non-volcanic tremor have been recorded and areas even farther downdip on the flat interface. Widespread afterslip below much of central Mexico suggests that most of the nearly flat subduction interface in this region is conditionally stable and thus contributes measurable transient deformation to large areas of Mexico south of and in the volcanic belt.

Description: We have derived a shallow subsurface 2-D tomographic P -wave velocity image of the Deccan Volcanic Province (DVP) of India using first-arrival traveltime data along a 90-km-long N–S trending seismic profile in the Deccan Syneclise region. The tomographic image depicts smooth velocity variations of Quaternary and Tertiary (2.0–3.0 km s –1 ) sediments, basalts/traps (5.0–5.5 km s –1 ), sub-trappean Mesozoic sediments (4.3–4.5 km s –1 ) as well as the basement (5.9–6.1 km s –1 ) geometry down to a maximum depth of 5.0 km. Due to Late Cretaceous volcanism and outpouring of basaltic lava flows, this region is affected by numerous dyke intrusions and thick basaltic trap (2–3 km) exposed on the surface and surrounded by graben structures due to deep basinal faults forming a large igneous province. Although sub-basalt imaging is a major challenge for the oil industry, with the help of tomographic imaging technique of first-arrival seismic refraction data, we were able to image sub-trappean Mesozoic sediments (〈0.75 km) deposited below the two sequences of thick basaltic flows above the basement. The imaged Mesozoic sediments are expected to contain hydrocarbon because of their wide extension in this sedimentary basin with suitable trapping mechanism due to basalts. The robustness of the velocity image is assessed through numerous tests like velocity perturbations, 2 estimates, rms residuals of traveltime fit, uncertainty estimates through computation of ray-density or hits and series of checkerboard resolution tests with velocity anomalies having different cell size. The thickness of the basalt and the sub-trappean Mesozoic sediments along with the basement geometry obtained from tomography are constrained through ray-trace modelling and pre-stack depth migration (PSDM) of the wide-angle reflection phases for different shot gathers along the profile.

Description: Elastic and mechanical weakening from water saturation are widely known to occur in sedimentary rocks, and particularly in carbonate rocks. To improve our understanding of the physics underlying this phenomenon, ultrasonic ( f  ~ 0.5 MHz) elastic properties are measured on a large suite of clean limestones and sandstones at very low saturations from relative humidity (RH) variations at ambient conditions. Measurements clearly highlight an elastic weakening (i.e. decrease in elastic wave velocity) from moisture adsorption. P - and S -wave velocities are similarly affected by adsorption, but in a different way for limestones and sandstone samples. While the elastic properties of limestone samples show almost no RH dependence, a large weakening is observed for samples of Fontainebleau sandstone that increases with the samples’ porosity. The main elastic weakening effect is likely to result from adsorption of fluid at grain contacts. It thus affects particularly granular rocks such as sandstones while well-cemented limestones are not affected. The granular model from Murphy et al. , accounting for surface energy effects, proves to be appropriate. Applying this model, it is shown that (i) P - and S -wave velocities have the same dependence on surface energy, which is consistent with the measurements and (ii) surface energy values obtained from the ultrasonic data using this model correlate with RH, and are consistent with the expected value for quartz crystals at vapour pressure. Yet, porosity, which relates to degree of cementation in the particular case of Fontainebleau sandstone, appears to be an additional parameter. A modified model is thus derived using the cementation model from Digby, accounting for a bonding radius at grain contact. It proves to apply well to the measured data. The fundamental difference between limestones’ and sandstones’ dependence to RH appears to be related to a microstructural difference. Saturation variations from RH increase depend on specific surface area, which is particularly low in Fontainebleau sandstones and large in microporous limestones. However elastic weakening from RH is more important in sandstones owing to their granular microstructure.

Description: High-throughput sequencing technologies, including RNA-seq, have made it possible to move beyond gene expression analysis to study transcriptional events including alternative splicing and gene fusions. Furthermore, recent studies in cancer have suggested the importance of identifying transcriptionally altered loci as biomarkers for improved prognosis and therapy. While many statistical methods have been proposed for identifying novel transcriptional events with RNA-seq, nearly all rely on contrasting known classes of samples, such as tumor and normal. Few tools exist for the unsupervised discovery of such events without class labels. In this paper, we present SigFuge for identifying genomic loci exhibiting differential transcription patterns across many RNA-seq samples. SigFuge combines clustering with hypothesis testing to identify genes exhibiting alternative splicing, or differences in isoform expression. We apply SigFuge to RNA-seq cohorts of 177 lung and 279 head and neck squamous cell carcinoma samples from the Cancer Genome Atlas, and identify several cases of differential isoform usage including CDKN2A , a tumor suppressor gene known to be inactivated in a majority of lung squamous cell tumors. By not restricting attention to known sample stratifications, SigFuge offers a novel approach to unsupervised screening of genetic loci across RNA-seq cohorts. SigFuge is available as an R package through Bioconductor.

Description: A novel experimental method is introduced to estimate the Thomsen's elastic anisotropy parameters and of a transversely isotropic shale under variable stress and saturation conditions. The method consists in recording P -wave velocities along numerous paths on a cylindrical specimen using miniature ultrasonic transducers. Such an overdetermined set of measurements is specifically designed to reduce the uncertainty associated with the determination of Thomsen's parameter compared to the classical method for which a single off-axis measurement is used (usually at 45° to the specimen's axis). This method is applied to a specimen of Opalinus Clay recovered from the Mont-Terri Underground Research Laboratory in Switzerland. The specimen is first saturated with brine at low effective pressure and then subjected to an effective pressure cycle up to 40 MPa, followed by a triaxial loading up to failure. During saturation and deformation, the evolution of P -wave velocities along a maximum of 240 ray paths is monitored and Thomsen's parameters α , and are computed by fitting Thomsen's weak anisotropy model to the data. The values of and obtained at the highest confining pressures reached during the experiment are comparable with those predicted from X-ray diffraction texture analysis and modelling for Opalinus Clay reported in the literature. These models neglect the effect of soft-porosity on elastic properties, but become relevant when soft porosity is closed at high effective pressure.

Description: Numerical experiments of convection with grain-damage are used to develop scaling laws for convective heat flow, mantle velocity and plate velocity across the stagnant lid and plate-tectonic regimes. Three main cases are presented in order of increasing complexity: a simple case wherein viscosity is only dependent on grain size, a case where viscosity depends on temperature and grain size, and finally a case where viscosity is temperature and grain size sensitive, and the grain-growth (or healing) is also temperature sensitive. In all cases, convection with grain-damage scales differently than Newtonian convection; whereas the Nusselt number (Nu), typically scales with the reference Rayleigh number, Ra 0 , to the 1/3 power, for grain-damage this exponent is larger because increasing Ra 0 also enhances damage. In addition, Nu, mantle velocity, and plate velocity are also functions of the damage to healing ratio, ( D / H ); increasing D / H increases Nu because more damage leads to more vigorous convection. For the fully realistic case, numerical results show stagnant lid convection, fully mobilized convection that resembles the temperature-independent viscosity case, and partially mobile or transitional convection, depending on D / H , Ra 0 , and the activation energies for viscosity and healing. Applying our scaling laws for the fully realistic case to Earth and Venus we demonstrate that increasing surface temperature dramatically decreases plate speed and heat flow, essentially shutting down plate tectonics, due to increased healing in lithospheric shear zones, as proposed previously. Contrary to many previous studies, the transitional regime between the stagnant lid and fully mobilized regimes is large, and the transition from stagnant lid to mobile convection is gradual and continuous. Thus planets could exhibit a full range of surface mobility, as opposed to the bimodal distribution of fully mobile lid planets and stagnant lid planets that is typically assumed.

Description: We present a novel accurate and efficient goal-oriented adaptive finite-element method solution for complex multi-electrodes resistivity system with arbitrary smooth surface topographies. A simple Green's function of a half-space model is adopted to eliminate the singularity. A unified boundary value problem for the regular potential is formulated for a multi-electrodes system so that it shares a common system matrix. In addition, a goal-oriented error estimation technique is developed to generate an optimal common grid so that highly accurate solutions are obtained with minimum computation cost. Synthetic models are used to verify our algorithm and excellent agreements are obtained by comparing with other methods.

Description: Three magnetotelluric (MT) profiles in northwestern Canada cross the central and western segments of Great Slave Lake shear zone (GSLsz), a continental scale strike-slip structure active during the Slave-Rae collision in the Proterozoic. Dimensionality analysis indicates that (i) the resistivity structure is approximately 2-D with a geoelectric strike direction close to the dominant geological strike of N45°E and that (ii) electrical anisotropy may be present in the crust beneath the two southernmost profiles. Isotropic and anisotropic 2-D inversion and isotropic 3-D inversions show different resistivity structures on different segments of the shear zone. The GSLsz is imaged as a high resistivity zone (〉5000  m) that is at least 20 km wide and extends to a depth of at least 50 km on the northern profile. On the southern two profiles, the resistive zone is confined to the upper crust and pierces an east-dipping crustal conductor. Inversions show that this dipping conductor may be anisotropic, likely caused by conductive materials filling a network of fractures with a preferred spatial orientation. These conductive regions would have been disrupted by strike-slip, ductile deformation on the GSLsz that formed granulite to greenschist facies mylonite belts. The pre-dominantly granulite facies mylonites are resistive and explain why the GSLsz appears as a resistive structure piercing the east-dipping anisotropic layer. The absence of a dipping anisotropic/conductive layer on the northern MT profile, located on the central segment of the GSLsz, is consistent with the lack of subduction at this location as predicted by geological and tectonic models.

Description: On 2008 October 5, a magnitude 6.6 earthquake struck the eastern termination of the intermontane Alai valley between the southern Tien Shan and the northern Pamir of Kyrgyzstan. The shallow thrust earthquake occurred in the footwall of the Main Pamir thrust, where the Pamir orogen is colliding with the southern Tien Shan mountains. We measure the coseismic surface displacements using SAR (Synthetic Aperture RADAR) data; the results show clear gradients in the vertical and horizontal directions along a complex pattern of surface ruptures and active faults. To integrate and to interpret these observations in the context of the regional tectonics, we complement the SAR data analysis with seismological data and geological field observations. While the main moment release of the Nura earthquake appears to be on the Pamir Frontal thrust, the main surface displacements and surface rupture occurred in the footwall along the NE–SW striking Irkeshtam fault. With InSAR data from ascending and descending tracks along with pixel offset measurements, we model the Nura earthquake source as a segmented rupture. One fault segment corresponds to high-angle brittle faulting at the Pamir Frontal thrust and two more fault segments show moderate-angle and low-friction thrusting at the Irkeshtam fault. Our integrated analysis of the coseismic deformation argues for rupture segmentation and strain partitioning associated to the earthquake. It possibly activated an orogenic wedge in the easternmost segment of the Pamir-Alai collision zone. Further, the style of the segmentation may be associated with the presence of Palaeogene evaporites.

Description: The Geological Survey of Sweden has been collecting airborne tensor very low frequency data (VLF) over several decades, covering large parts of the country. The data has been an invaluable source of information for identifying conductive structures that can among other things be related to water-filled fault zones, wet sediments that fill valleys or ore mineralizations. Because the method only uses two differently polarized plane waves of very similar frequency, vertical resolution is low and interpretation is in most cases limited to maps that are directly derived from the data. Occasionally, 2-D inversion is carried out along selected profiles. In this paper, we present for the first time a 3-D inversion for tensor VLF data in order to further increase the usefulness of the data set. The inversion is performed using a non-linear conjugate gradient scheme (Polak-Ribière) with an inexact line-search. The gradient is obtained by an algebraic adjoint method that requires one additional forward calculation involving the adjoint system matrix. The forward modelling is based on integral equations with an analytic formulation of the half-space Green's tensor. It avoids typically required Hankel transforms and is particularly amenable to singularity removal prior to the numerical integration over the volume elements. The system is solved iteratively, thus avoiding construction and storage of the dense system matrix. By using fast 3-D Fourier transforms on nested grids, subsequently farther away interactions are represented with less detail and therefore with less computational effort, enabling us to bridge the gap between the relatively short wavelengths of the fields (tens of metres) and the large model dimensions (several square kilometres). We find that the approximation of the fields can be off by several per cent, yet the transfer functions in the air are practically unaffected. We verify our code using synthetic calculations from well-established 2-D methods, and trade modelling accuracy off against computational effort in order to keep the inversion feasible in both respects. Our compromise is to limit the permissible resistivity to not fall below 100 m to maintain computational domains as large as 10 10 km 2 and computation times on the order of a few hours on standard PCs. We investigate the effect of possible local violations of these limits. Even though the conductivity magnitude can then not be recovered correctly, we do not observe any structural artefacts related to this in our tests. We invert a data set from northern Sweden, where we find an excellent agreement of known geological features, such as contacts or fault zones, with elongated conductive structures, while high resistivity is encountered in probably less disturbed geology, often related to topographic highs, which have survived predominantly glacial erosion processes. As expected from synthetic studies, the resolution is laterally high, but vertically limited down to the top of conductive structures.

Description: Induced polarization is a geophysical method looking to image and interpret low-frequency polarization mechanisms occurring in porous media. Below 10 kHz, the quadrature conductivity of metal-free sandy and clayey materials exhibits a distribution of relaxation times, which can be related to the pore size distribution of these porous materials. When the polarization spectra are fitted with a Cole–Cole model, we first observe that the main relaxation time is controlled by the main pore size of the material and that the Cole–Cole exponent c is never much above 0.5, a value corresponding to a Warburg function. The complex conductivity is then obtained through a convolution product between the pore size distribution and such Warburg function. We also provide a way to recover the pore size distribution by performing a deconvolution of measured spectra using the Warburg function. A new dataset of mercury porosimetry and induced polarization data of six siliciclastic materials supports the hypothesis that the Cole–Cole relaxation time is strongly controlled by the pore size, and especially the characteristic pore size corresponding to the peak of the pore size distribution from mercury porosimetry. The distribution of the pore throat sizes of these materials seems fairly well recovered using the Warburg decomposition of the spectral induced polarization spectra but additional data will be needed to confirm this finding.

Description: The 3-D shear velocity structure beneath South India's Dharwar Craton determined from fundamental mode Rayleigh waves phase velocities reveals the existence of anomalously high velocity materials in the depth range of 50–100 km. Tomographic analysis of seismograms recorded on a network of 35 broad-band seismographs shows the uppermost mantle shear wave speeds to be as high as 4.9 km s –1 in the northwestern Dharwar Craton, decreasing both towards the south and the east. Below ~100 km, the shear wave speed beneath the Dharwar Craton is close to the global average shear wave speed at these depths. Limitations of usable Rayleigh phase periods, however, have restricted the analysis to depths of 120 km, precluding the delineation of the lithosphere–asthenosphere boundary in this region. However, pressure–temperature analysis of xenoliths in the region suggests a lithospheric thickness of at least ~185 km during the mid-Proterozoic period. The investigations were motivated by a search for seismic indicators in the shallow mantle beneath the distinctly different parts of the Dharwar Craton otherwise distinguished by their lithologies, ages and crustal structure. Since the ages of cratonic crust and of the associated mantle lithosphere around the globe have been found to be broadly similar and their compositions bimodal in time, any distinguishing features of the various parts of the Dharwar shallow mantle could thus shed light on the craton formation process responsible for stabilizing the craton during the Meso- and Neo-Archean.

Description: We propose a new, simple and efficient method to image electrical resistivity between a set of wells. Our procedure consists of two steps: first, we map the interfaces between various subsurface formations using seismoelectric conversions; second, we derive the formation resistivity using image-guided cross-well electric tomography. In the first step, we focus seismic energy at a set of points located on a regular grid between wells, which enables us to map the geological formations in terms of heterogeneities in electrical, hydraulic and/or seismic properties. The density of the scanning points (i.e. the seismoelectric image resolution) is related to the wavelength of the seismic impulse used to scan the formations. Each time the seismic energy is focused at a point, the resulting electrical potential burst (equivalent to the one generated by a volumetric seismic source) is recorded remotely at a set of electrodes positioned in wells (the reference electrode can be located on the ground surface or far enough to be considered at infinity). We construct a high-resolution ‘seismoelectric’ image by assigning the electrical potential simulated at these fixed electrodes to the location of the seismic focus. In a follow-up step, the structure of this image is used in image-guided inversion to improve electrical resistivity tomography between the two wells. The structural information from the seismoelectric image is used to impose constraints on the model covariance matrix used in the inversion of the electrical resistivity data. This approach offers new perspectives in recovering fine structure of resistivity (high definition resistivity tomography) between the wells, which cannot be resolved through conventional cross-well resistivity or from seismic tomography alone.

Description: Frontier hydrocarbon development projects in the deepwater slopes of the Gulf of Mexico Basin, Santos Basin and Lower Congo Basin all require wells to cross ductile layers of autochthonous or allochthonous salt moving at peak rates of 100 mm yr –1 . The Couette–Poiseuille number is introduced here to help pinpoint the depth of shear stress reversal in such salt layers. For any well-planned through salt, the probable range of creep forces of moving salt needs to be taken into account when designing safety margins and load-factor tolerance of the well casing. Drag forces increase with wellbore diameter, but more significantly with effective viscosity and speed of the creeping salt layer. The potential drag forces on cased wellbores in moving salt sheets are estimated analytically using a range of salt viscosities (10 15 –10 19 Pa s) and creep rates (0–10 mm yr –1 ). Drag on perfectly rigid casing of infinite strength may reach up to 13 Giga Newton per meter wellbore length in salt having a viscosity of 10 19 Pa s. Well designers may delay stress accumulations due to salt drag when flexible casing accommodates some of the early displacement and strain. However, all creeping salt could displace, fracture and disconnect well casing, eventually. The shear strength of typical heavy duty well casing (about 1000 MPa) can be reached due to drag by moving salt. Internal flow of salt will then fracture the casing near salt entry and exit points, but the structural damage is likely to remain unnoticed early in the well-life when the horizontal shift of the wellbore is still negligibly small (at less than 1 cm yr –1 ). Disruption of casing and production flow lines within the anticipated service lifetime of a well remains a significant risk factor within distinct zones of low-viscosity salt which may reach ultrafast creep rates of 100 mm yr –1 .

Description: The terrestrial reference frame is a cornerstone for modern geodesy and its applications for a wide range of Earth sciences. The underlying assumption for establishing a terrestrial reference frame is that the motion of the solid Earth's figure centre relative to the mass centre of the Earth system on a multidecadal timescale is linear. However, past international terrestrial reference frames (ITRFs) showed unexpected accelerated motion in their translation parameters. Based on this underlying assumption, the inconsistency of relative origin motions of the ITRFs has been attributed to data reduction imperfection. We investigated the impact of surface mass loading from atmosphere, ocean, snow, soil moisture, ice sheet, glacier and sea level from 1983 to 2008 on the geocentre variations. The resultant geocentre time-series display notable trend acceleration from 1998 onward, in particular in the z -component. This effect is primarily driven by the hydrological mass redistribution in the continents (soil moisture, snow, ice sheet and glacier). The acceleration is statistically significant at the 99 per cent confidence level as determined using the Mann–Kendall test, and it is highly correlated with the satellite laser ranging determined translation series. Our study, based on independent geophysical and hydrological models, demonstrates that, in addition to systematic errors from analysis procedures, the observed non-linearity of the Earth-system behaviour at interannual timescales is physically driven and is able to explain 42 per cent of the disparity between the origins of ITRF2000 and ITRF2005, as well as the high level of consistency between the ITRF2005 and ITRF2008 origins.

Description: The Antarctic Peninsula (AP) consists of a long lived and uniquely well preserved magmatic arc system. The broad tectonic structure of the AP arc is well understood. However, magmatic processes occurring along the arc are only constrained by regional geophysical and relatively sparse geological data. Key questions remain about the timing, volume, and structural controls on magma emplacement. We present new high resolution aeromagnetic data across Adelaide Island, on the western margin of the AP revealing the complex structure of the AP arc/forearc boundary. Using digital enhancement, 2-D modelling and 3-D inversion we constrain the form of the magnetic sources at the arc/forearc boundary. Our interpretation of these magnetic data, guided by geological evidence and new zircon U-Pb dating, suggests significant Palaeogene to Neogene magmatism formed ~25 per cent of the upper crust in this region (~7500 km 3 ). Significant structural control on Neogene magma emplacement along the arc/forearc boundary is also revealed. We hypothesize that this Neogene magmatism reflects mantle return flow through a slab window generated by Late Palaeogene cessation of subduction south of Adelaide Island. This mantle process may have affected the final stages of arc magmatism along the AP margin.

Description: This paper presents a novel mathematical reformulation of the theory of the free wobble/nutation of an axisymmetric reference earth model in hydrostatic equilibrium, using the linear momentum description. The new features of this work consist in the use of (i) Clairaut coordinates (rather than spherical polars), (ii) standard spherical harmonics (rather than generalized spherical surface harmonics), (iii) linear operators (rather than J-square symbols) to represent the effects of rotational and ellipticity coupling between dependent variables of different harmonic degree and (iv) a set of dependent variables all of which are continuous across material boundaries. The resulting infinite system of coupled ordinary differential equations is given explicitly, for an elastic solid mantle and inner core, an inviscid outer core and no magnetic field. The formulation is done to second order in the Earth's ellipticity. To this order it is shown that for wobble modes (in which the lowest harmonic in the displacement field is degree 1 toroidal, with azimuthal order m  = ±1), it is sufficient to truncate the chain of coupled displacement fields at the toroidal harmonic of degree 5 in the solid parts of the earth model. In the liquid core, however, the harmonic expansion of displacement can in principle continue to indefinitely high degree at this order of accuracy. The full equations are shown to yield correct results in three simple cases amenable to analytic solution: a general earth model in rigid rotation, the tiltover mode in a homogeneous solid earth model and the tiltover and Chandler periods for an incompressible homogeneous solid earth model. Numerical results, from programmes based on this formulation, are presented in part II of this paper.

Description: Numerical solutions are presented for the formulation of the linear momentum description of Earth's dynamics using Clairaut coordinates. We have developed a number of methods to integrate the equations of motion, including starting at the Earth's centre of mass, starting at finite radius and separating the displacement associated with the primary rigid rotation. We include rotation and ellipticity to second order up to spherical harmonic T $_5^m$ , starting with the primary displacement T $_1^m$ with m  = ±1. We are able to confirm many of the previous results for models PREM (with no surface ocean) and 1066A, both in their original form and with neutrally stratified liquid cores. Our period search ranges from the near-seismic band [0.1 sidereal days (sd)] to 3500 sd, within which we have identified the four well-known wobble-nutation modes: the Free Core Nutation (retrograde) at –456 sd, the Free Inner Core Nutation (FICN, prograde) at 468 sd, the Chandler Wobble (prograde) at 402 sd, and the Inner Core Wobble (ICW, prograde) at about 2842 sd (7.8 yr) for neutral PREM. The latter value varies significantly with earth model and integration method. In addition we have verified to high accuracy the tilt-over mode at 1 sd within a factor 10 –6 . In an exhaustive search we found no additional near-diurnal wobble modes that could be identified as nutations. We show that the eigenfunctions for the as-yet-unidentified ICW are extremely sensitive to the details of the earth model, especially the core stability profile and there is no well-defined sense of its wobble relative to the mantle. Calculations are also done for a range of models derived from PREM with homogeneous layers, as well as with incompressible cores. For this kind of model the ICW ceases to have just a simple IC rigid motion when the fluid compressibility is either unchanged or multiplied by a factor 10; in this case the outer core exhibits oscillations that arise from an unstable fluid density stratification. For the FICN our results for the truncation at harmonic T 5 show less change from the T 3 truncation than a similar result reported elsewhere. Finally, we give a thorough discussion of the complete spectrum of the characteristic determinant including the location of poles and non-wobble gravity modes, and discuss in general the dynamics of the inviscid core at periods short compared to those involved in the geodynamo.

Description: Considering the drawback of existing global weighted mean temperature model, this paper uses 2006–2012 NCEP reanalysis data to establish global empirical model for mapping zenith wet delays onto precipitable water—GTm_N, takes the influence of half-year periodicity of Tm into account when modelling and estimate the initial phase of each cycle. In order to evaluate the precision of GTm_N, we use three different Tm data sets from the NCEP during 2013, 650 radiosonde stations and COSMIC occultation in 2011 to test this model. The results show that GTm_N has higher precision in both ocean and continental area in every moment of every day. The accuracy of GTm_N is higher than Bevis formulas and GTm_II models. In addition, the actual surface temperature is not required in GTm_N model, and it will have wide application in GPS meteorology.

Description: In subduction zones, shallow subsurface structures are the manifestation of the plate interactions at depth. However, significant water depths, rough bathymetry and presence of heavily deformed accretionary wedge materials hamper imaging of the near-surface features to a great extent using conventional imaging techniques. In this study, we show results using an integrated processing technique to a multichannel seismic data set acquired in 2006 from the northwestern offshore Sumatra. We start with first downward continuing the 12-km-long surface streamer data to the seafloor, followed by a high-resolution traveltime tomography of refracted phases to determine a detailed velocity–depth model of subsurface, which in turns, is used for pre-stack depth migration in order to delineate the shallow subsurface structures beneath the trench, subduction front and outer accretionary wedge. Our velocity–depth model and the depth migrated image depict variation of sediment properties across the front and structures of uppermost sedimentary sequence with an unprecedented high resolution providing the precise location of the frontal and conjugate thrusts, highly folded sedimentary sequences, which in turns describe their relationship with the top of the subducting plate and factors that control rupture propagation to the trench. Furthermore, we estimate the porosity distribution across the front, where we find a 12 and 18 per cent decrease in porosity beneath the deformation front and the inner accretionary plateau at 500 m below the seafloor, respectively, which we interpret to be due to the compaction. A significant decrease in porosity at the plate interface below 5–6-km thick sediments near the deformation front would increase the coupling, leading to the rupture propagation up to the trench, uplifting 4.5 km water and producing large tsunami.