ALBERT

Beschreibung: We develop an approach for simulating acousto-elastic wave phenomena, including scattering from fluid–solid boundaries, where the solid is allowed to be anisotropic, with the discontinuous Galerkin method. We use a coupled first-order elastic strain-velocity, acoustic velocity–pressure formulation, and append penalty terms based on interior boundary continuity conditions to the numerical (central) flux so that the consistency condition holds for the discretized discontinuous Galerkin weak formulation. We incorporate the fluid–solid boundaries through these penalty terms and obtain a stable algorithm. Our approach avoids the diagonalization into polarized wave constituents such as in the approach based on solving elementwise Riemann problems.

Beschreibung: Next generation sequencing of cellular RNA is making it possible to characterize genes and alternative splicing in unprecedented detail. However, designing bioinformatics tools to accurately capture splicing variation has proven difficult. Current programs can find major isoforms of a gene but miss lower abundance variants, or are sensitive but imprecise. CLASS2 is a novel open source tool for accurate genome-guided transcriptome assembly from RNA-seq reads based on the model of splice graph. An extension of our program CLASS, CLASS2 jointly optimizes read patterns and the number of supporting reads to score and prioritize transcripts, implemented in a novel, scalable and efficient dynamic programming algorithm. When compared against reference programs, CLASS2 had the best overall accuracy and could detect up to twice as many splicing events with precision similar to the best reference program. Notably, it was the only tool to produce consistently reliable transcript models for a wide range of applications and sequencing strategies, including ribosomal RNA-depleted samples. Lightweight and multi-threaded, CLASS2 requires 〈3GB RAM and can analyze a 350 million read set within hours, and can be widely applied to transcriptomics studies ranging from clinical RNA sequencing, to alternative splicing analyses, and to the annotation of new genomes.

Beschreibung: Next-generation sequencing (NGS) approaches rapidly produce millions to billions of short reads, which allow pathogen detection and discovery in human clinical, animal and environmental samples. A major limitation of sequence homology-based identification for highly divergent microorganisms is the short length of reads generated by most highly parallel sequencing technologies. Short reads require a high level of sequence similarities to annotated genes to confidently predict gene function or homology. Such recognition of highly divergent homologues can be improved by reference-free ( de novo ) assembly of short overlapping sequence reads into larger contigs. We describe an ensemble strategy that integrates the sequential use of various de Bruijn graph and overlap-layout-consensus assemblers with a novel partitioned sub-assembly approach. We also proposed new quality metrics that are suitable for evaluating metagenome de novo assembly. We demonstrate that this new ensemble strategy tested using in silico spike-in, clinical and environmental NGS datasets achieved significantly better contigs than current approaches.

Beschreibung: The relative seismic velocity variations possibly associated to large earthquakes can be readily monitored via cross-correlation of seismic noise. In a recently published study, more than 2 yr of continuous seismic records have been analysed from three stations surrounding the epicentre of the 2009 April 6, M w 6.1 L'Aquila earthquake, observing a clear decrease of seismic velocities likely corresponding to the co-seismic shaking. Here, we extend the analysis in space, including seismic stations within a radius of 60 km from the main shock epicentre, and in time, collecting 5 yr of data for the six stations within 40 km of it. Our aim is to investigate how far the crustal damage is visible through this technique, and to detect a potential post-seismic recovery of velocity variations. We find that the co-seismic drop in velocity variations extends up to 40 km from the epicentre, with spatial distribution (maximum around the fault and in the north–east direction from it) in agreement with the horizontal co-seismic displacement detected by global positioning system (GPS). In the first few months after L'Aquila earthquake, the crust's perturbation in terms of velocity variations displays a very unstable behaviour, followed by a slow linear recovery towards pre-earthquake conditions; by almost 4 yr after the event, the co-seismic drop of seismic velocity is not yet fully recovered. The strong oscillations of the velocity changes in the first months after the earthquake prevent to detect the fast exponential recovery seen by GPS data. A test of differently parametrized fitting curves demonstrate that the post-seismic recovery is best explained by a sum of a logarithmic and a linear term, suggesting that processes like viscoelastic relaxation, frictional afterlip and poroelastic rebound may be acting concurrently.

Beschreibung: Computationally efficient 3-D frequency-domain full waveform inversion (FWI) is applied to ocean-bottom cable data from the Valhall oil field in the visco-acoustic vertical transverse isotropic (VTI) approximation. Frequency-domain seismic modelling is performed with a parallel sparse direct solver on a limited number of computer nodes. A multiscale imaging is performed by successive inversions of single frequencies in the 3.5–10 Hz frequency band. The vertical wave speed is updated during FWI while density, quality factor Q P and anisotropic Thomsen's parameters and are kept fixed to their initial values. The final FWI model shows the resolution improvement that was achieved compared to the initial model that was built by reflection traveltime tomography. This FWI model shows a glacial channel system at 175 m depth, the footprint of drifting icebergs on the palaeo-seafloor at 500 m depth, a detailed view of a gas cloud at 1 km depth and the base cretaceous reflector at 3.5 km depth. The relevance of the FWI model is assessed by frequency-domain and time-domain seismic modelling and source wavelet estimation. The agreement between the modelled and recorded data in the frequency domain is excellent up to 10 Hz although amplitudes of modelled wavefields propagating across the gas cloud are overestimated. This might highlight the footprint of attenuation, whose absorption effects are underestimated by the homogeneous background Q P model ( Q P = 200). The match between recorded and modelled time-domain seismograms suggests that the inversion was not significantly hampered by cycle skipping. However, late arrivals in the synthetic seismograms, computed without attenuation and with a source wavelet estimated from short-offset early arrivals, arrive 40 ms earlier than the recorded seismograms. This might result from dispersion effects related to attenuation. The repeatability of the source wavelets inferred from data that are weighted by a linear gain with offset is dramatically improved when they are estimated in the FWI model rather than in the smooth initial model. The two source wavelets, estimated in the FWI model from data with and without offset gain, show a 40 ms time-shift, which is consistent with the previous analysis of the time-domain seismograms. The computational efficiency of our frequency-domain approach is assessed against a recent time-domain FWI case study performed in a similar geological environment. This analysis highlights the efficiency of the frequency-domain approach to process a large number of sources and receivers with limited computational resources, thanks to the efficiency of the substitution step performed by the direct solver. This efficiency can be further improved by using a block-low rank version of the multifrontal solver and by exploiting the sparsity of the source vectors during the substitution step. Future work will aim to update attenuation and density at the same time of the vertical wave speed.

Beschreibung: In this study we derive a spectral model describing the source, propagation and site characteristics of S waves recorded in central Italy. To this end, we compile and analyse a high-quality data set composed of more than 9000 acceleration and velocity waveforms in the local magnitude ( M l ) range 3.0–5.8 recorded at epicentral distances smaller than 120 km. The data set spans the time period from 2008 January 1 to 2013 May 31, and includes also the 2009 L'Aquila (moment magnitude M w 6.1, M l = 5.8) sequence. This data set is suitable for the application of data-driven approaches to derive the empirical functions for source, attenuation and site terms. Therefore, we apply a non-parametric inversion scheme to the acceleration Fourier spectra of the S waves of 261 earthquakes recorded at 129 stations. In a second step, with the aim of defining spectral models suitable for the implementation in numerical simulation codes, we represent the obtained non-parametric source and propagation terms by fitting standard parametric models. The frequency-dependent attenuation with distance r shows a complex trend that we parametrize in terms of geometrical spreading, anelastic attenuation and high-frequency decay parameter k. The geometrical spreading term is described by a piecewise linear model with crossover distances at 10 and 70 km: in the first segment, the spectral ordinates decay as 〈 tex – mathid = " IM 0001" 〉 r – 1.01 while in the second as 〈 tex – mathid = " IM 0002" 〉 r – 1.68 . Beyond 70 km, the attenuation decreases and the spectral amplitude attenuate as 〈 tex – mathid = " IM 0003" 〉 r – 0.64 . The quality factor Q ( f ) and the high-frequency attenuation parameter k , are 〈 tex – mathid = " IM 0004" 〉 Q ( f ) = 290 f 0.16 and k = 0.012 s, respectively, the latter being applied only for frequencies higher than 10 Hz. The source spectra are well described by 2 models, from which seismic moment and stress drops of 231 earthquakes are estimated. We calibrate a new regional relationship between seismic moment and local magnitude that improves the existing ones and extends the validity range to 3.0–5.8. We find a significant stress drop increase with seismic moment for events with M w larger than 3.75, with so-called scaling parameter  close to 1.5. We also observe that the overall offset of the stress-drop scaling is controlled by earthquake depth. We evaluate the performance of the proposed parametric models through the residual analysis of the Fourier spectra in the frequency range 0.5–25 Hz. The results show that the considered stress-drop scaling with magnitude and depth reduces, on average, the standard deviation by 18 per cent with respect to a constant stress-drop model. The overall quality of fit (standard deviation between 0.20 and 0.27, in the frequency range 1–20 Hz) indicates that the spectral model calibrated in this study can be used to predict ground motion in the L'Aquila region.

Beschreibung: During arc-continent collision, buoyant sections of sediments and rifted continental crust from a subducting plate will accrete to the forearc of the upper plate as long as this backstop remains intact. Deformation of the oceanic arc and forearc block may ultimately lead to accretion of these mafic rock units to the new orogen. The Taiwan mountain belt, which formed at ~6.5 Ma by oblique convergence between the Eurasian passive margin and the overriding Luzon arc in northern Taiwan, offers important insight in this process, since the collision is more advanced in the north than in the south. The incipient stage of arc-collision can be studied in southern Taiwan, while the northern portion of the orogen is presently undergoing collapse due to a flip in the subduction polarity between the Eurasian Plate and the Philippine Sea Plate. In this study, we seismically image the structure of the northern section of the mountain belt with a tomographic inversion. We present marine and land-based seismic refraction data, as well as local earthquake data, from transect T6 of the Taiwan Integrated Geodynamic Research (TAIGER) program across the Taiwan mountain belt and the adjacent Ryukyu arc. Our 2-D compressional seismic velocity model for this transect, which is based on a tomographic inversion of 10 213 P -wave arrival times, shows that the Eurasian crystalline continental crust thickens from ~24 km in the Taiwan Strait to ~40 km beneath the eastern Central Range of Taiwan. The detailed seismic velocity structure of the Taiwan mountain belt shows vertical continuity in the upper 15 km, which suggests that rocks are exhumed to the surface here from the middle crust in a near-vertical path. The continental crust of the westernmost Ryukyu arc is almost as thick (~40 km) as in the adjacent northern Central Range of Taiwan, and it appears to override the leading edge of the Philippine Sea Plate offshore northeastern Taiwan. If we assume that the western Ryukyu arc crust also thickened in the collision, then the mountain belt is wider and less thick in northern Taiwan than in central Taiwan (~50 km), which may be the result of post-collisional extension in the north.

Beschreibung: In this study we derive a spectral model describing the source, propagation and site characteristics of S waves recorded in central Italy. To this end, we compile and analyse a high-quality data set composed of more than 9000 acceleration and velocity waveforms in the local magnitude ( M l ) range 3.0–5.8 recorded at epicentral distances smaller than 120 km. The data set spans the time period from 2008 January 1 to 2013 May 31, and includes also the 2009 L'Aquila (moment magnitude M w 6.1, M l = 5.8) sequence. This data set is suitable for the application of data-driven approaches to derive the empirical functions for source, attenuation and site terms. Therefore, we apply a non-parametric inversion scheme to the acceleration Fourier spectra of the S waves of 261 earthquakes recorded at 129 stations. In a second step, with the aim of defining spectral models suitable for the implementation in numerical simulation codes, we represent the obtained non-parametric source and propagation terms by fitting standard parametric models. The frequency-dependent attenuation with distance r shows a complex trend that we parametrize in terms of geometrical spreading, anelastic attenuation and high-frequency decay parameter k. The geometrical spreading term is described by a piecewise linear model with crossover distances at 10 and 70 km: in the first segment, the spectral ordinates decay as 〈 tex – mathid = " IM 0001" 〉 r – 1.01 while in the second as 〈 tex – mathid = " IM 0002" 〉 r – 1.68 . Beyond 70 km, the attenuation decreases and the spectral amplitude attenuate as 〈 tex – mathid = " IM 0003" 〉 r – 0.64 . The quality factor Q ( f ) and the high-frequency attenuation parameter k , are 〈 tex – mathid = " IM 0004" 〉 Q ( f ) = 290 f 0.16 and k = 0.012 s, respectively, the latter being applied only for frequencies higher than 10 Hz. The source spectra are well described by 2 models, from which seismic moment and stress drops of 231 earthquakes are estimated. We calibrate a new regional relationship between seismic moment and local magnitude that improves the existing ones and extends the validity range to 3.0–5.8. We find a significant stress drop increase with seismic moment for events with M w larger than 3.75, with so-called scaling parameter  close to 1.5. We also observe that the overall offset of the stress-drop scaling is controlled by earthquake depth. We evaluate the performance of the proposed parametric models through the residual analysis of the Fourier spectra in the frequency range 0.5–25 Hz. The results show that the considered stress-drop scaling with magnitude and depth reduces, on average, the standard deviation by 18 per cent with respect to a constant stress-drop model. The overall quality of fit (standard deviation between 0.20 and 0.27, in the frequency range 1–20 Hz) indicates that the spectral model calibrated in this study can be used to predict ground motion in the L'Aquila region.

Beschreibung: Molecular stratification of tumors is essential for developing personalized therapies. Although patient stratification strategies have been successful; computational methods to accurately translate the gene-signature from high-throughput platform to a clinically adaptable low-dimensional platform are currently lacking. Here, we describe PIGExClass (platform-independent isoform-level gene-expression based classification-system), a novel computational approach to derive and then transfer gene-signatures from one analytical platform to another. We applied PIGExClass to design a reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) based molecular-subtyping assay for glioblastoma multiforme (GBM), the most aggressive primary brain tumors. Unsupervised clustering of TCGA (the Cancer Genome Altas Consortium) GBM samples, based on isoform-level gene-expression profiles, recaptured the four known molecular subgroups but switched the subtype for 19% of the samples, resulting in significant ( P = 0.0103) survival differences among the refined subgroups. PIGExClass derived four-class classifier, which requires only 121 transcript-variants, assigns GBM patients’ molecular subtype with 92% accuracy. This classifier was translated to an RT-qPCR assay and validated in an independent cohort of 206 GBM samples. Our results demonstrate the efficacy of PIGExClass in the design of clinically adaptable molecular subtyping assay and have implications for developing robust diagnostic assays for cancer patient stratification.

Beschreibung: In this study, information carried by the ambient seismic field is exploited to extract impulse response functions between two seismic stations using one as a ‘virtual’ source. Interferometry by deconvolution method is used and validated by comparing the extracted ambient noise impulse response waveforms with records of moderate magnitude earthquakes (from M w 4 to 5.8) that occurred close to the virtual source station in Japan. As the information is only available at low frequencies (less than 0.25 Hz), the ambient seismic field approach is coupled to a non-stationary stochastic model to simulate time domain accelerograms up to 50 Hz. This coupling allows the predicted ground motion to have both the deterministic part at low frequencies coming from the source and the crust structure and the high-frequency random contribution from the seismic waves scattering. The resulting combined accelerograms for an M w 5.8 event show a good agreement with observed ground motions from a real earthquake.