Efficient computation of seismic traveltimes in anisotropic media and the application in pre-stack depth migration

This study is concerned with the computation of seismic first-arrival traveltimes in anisotropic media using finite difference eikonal methods. For this purpose, different numerical schemes that directly solve the eikonal equation are implemented and assessed numerically. Subsequently, they are used for pre-stack depth migration on synthetic and field data. The thesis starts with a detailed examination of different finite difference methods that have gained popularity in scientific literature for computing seismic traveltimes in isotropic media. The most appropriate for an extension towards anisotropic media are found to be the so-called Fast Marching/Sweeping methods. Both schemes rely on different iteration strategies, but incorporate the same upwind finite difference Godunov schemes that are implemented up to the second order. As a result, the derived methods exhibit high numerical accuracy and perform robustly even in highly contrasted velocity models. Subsequently, the methods are adapted for transversely isotropic media with vertical (VTI) and tilted (TTI) symmetry axes, respectively. Therefore, two different formulations for approximating the anisotropic phase velocities are tested, which are the weakly-anisotropic and the pseudo-acoustic approximation. As expected, the pseudo-acoustic formulation shows superior accuracy especially for strongly anisotropic media. Moreover, it turns out that the tested eikonal schemes are generally more accurate than anisotropic ray tracing approaches, since they do not require an approximation of the group velocity. Numerical experiments are carried out on homogeneous models with varying strengths of anisotropy and the industrial BP 2007 benchmark model. They show that the computed eikonal traveltimes are in good agreement with independent results from finite difference modelling of the isotropic and anisotropic elastic wave equations, and traveltimes estimated by ray-based wavefront construction, respectively. The computational performance of the TI eikonal schemes is largely increased compared to their original isotropic implementations, which is due to the algebraic complexity of the anisotropic phase velocity formulations. At this point, the Fast Marching Method is found to be more efficient on models containing up to 50 million grid points. For larger models, the anisotropic Fast Sweeping implementation gradually becomes advantageous. Here, both techniques perform independently well of the structural complexity of the underlying velocity model. The final step of this thesis is the application of the developed eikonal schemes in pre-stack depth migration. A synthetic experiment over a VTI/TTI layer-cake model demonstrates that the traveltime computation leads to accurate imaging results including a tilted, strongly anisotropic shale layer. The experiment shows further that the estimation of anisotropic velocity models solely from surface reflection data is highly ambiguous. In a second example, the eikonal solvers are applied for depth imaging of two-dimensional field data that were acquired for geothermal exploration in southern Tuscany, Italy. The developed methods also produce clear imaging results in this setting, which illustrates their general applicability for pre-stack depth imaging, particularly in challenging environments

Underground Vertical Seismic Profiling with Conventional and Fiber-Optic Systems for Exploration in the Kylylahti Polymetallic Mine, Eastern Finland

Seismic reflection methods have been used for the exploration of mineral resources for several decades. However, despite their unmatched spatial resolution and depth penetration, they only have played a minor role in mineral discoveries so far. Instead, mining and exploration companies have traditionally focused more on the use of potential field, electric and electromagnetic methods. In this context, we present a case study of an underground Vertical Seismic Profiling (VSP) experiment, which was designed to image a (semi-)massive sulfide deposit located in the Kylylahti polymetallic mine in eastern Finland. For the measurement, we used a conventional VSP with three-component geophones and a novel fiber-optic Distributed Acoustic Sensing (DAS) system. Both systems were deployed in boreholes located nearby the target sulfide deposit, and used in combination with an active seismic source that was fired from within the underground tunnels. With this setup, we successfully recorded seismic reflections from the deposit and its nearby geological contrasts. The recording systems provided data with a good signal-to-noise ratio and high spatial resolution. In addition to the measurements, we generated a realistic synthetic dataset based on a detailed geological model derived from extensive drilling data and petrophysical laboratory analysis. Specific processing and imaging of the acquired and synthetic datasets yielded high-resolution reflectivity images. Joint analysis of these images and cross-validation with lithological logging data from 135 nearby boreholes led to successful interpretation of key geological contacts including the target sulfide mineralization. In conclusion, our experiment demonstrates the value of in-mine VSP measurements for detailed resource delineation in a complex geological setting. In particular, we emphasize the potential benefit of using fiber-optic DAS systems, which provide reflection data at sufficient quality with less logistical effort and a higher acquisition rate. This amounts to a lower total acquisition cost, which makes DAS a valuable tool for future mineral exploration activities.Peer reviewe

Evaluation of the uniformity and stability of T-DNA integration and gene expression in transgenic apple plants

The generation of transgenic apple plants relies on the molecular analysis of transgene integration and expression based on polymerase chain reaction (PCR) analysis, blotting techniques and enzymatic assays on vitro leaves of putative transgenic regenerates. In order to assess the uniformity and the stability of transfer DNA (T-DNA) integration and gene expression, we studied 26 transgenic apple lines carrying the attacin E gene from Hyalophora cecropia , the \u3b2-glucuronidase gene, and the nptII gene. Plants were evaluated using standard molecular techniques, such as PCR, Southern blot, reverse transcription PCR (RT-PCR) and Enzyme Linked Immunosorbent Assay (ELISA), and propagated in vitro on non-selective antibiotic-free media for four years to mimic natural conditions in the field. In some T-lines transgene integration and expression did not remain stable; differences were also found between distinct plants of a single T-line. Individual plants with partially or completely silenced transgenes were identified as well as plants with non-detectable T-DNA. Several lines appeared chimeric or partially silenced. Although most molecular techniques can reliably detect the presence of transgenic cells, they often fail to detect mixtures of transformed and non-transformed cells, or cells with silenced transgenes. This should be taken into consideration, especially in the case of vegetatively propagated trees, where non-transformed or silenced plant parts could mistakenly be used as propagation material

Seismic mineral exploration at different scales in the Outokumpu Ore District, Eastern Finland

Non peer reviewe

Relationship between molecular pathogen detection and clinical disease in febrile children across Europe: a multicentre, prospective observational study

BackgroundThe PERFORM study aimed to understand causes of febrile childhood illness by comparing molecular pathogen detection with current clinical practice.MethodsFebrile children and controls were recruited on presentation to hospital in 9 European countries 2016-2020. Each child was assigned a standardized diagnostic category based on retrospective review of local clinical and microbiological data. Subsequently, centralised molecular tests (CMTs) for 19 respiratory and 27 blood pathogens were performed.FindingsOf 4611 febrile children, 643 (14%) were classified as definite bacterial infection (DB), 491 (11%) as definite viral infection (DV), and 3477 (75%) had uncertain aetiology. 1061 controls without infection were recruited. CMTs detected blood bacteria more frequently in DB than DV cases for N. meningitidis (OR: 3.37, 95% CI: 1.92-5.99), S. pneumoniae (OR: 3.89, 95% CI: 2.07-7.59), Group A streptococcus (OR 2.73, 95% CI 1.13-6.09) and E. coli (OR 2.7, 95% CI 1.02-6.71). Respiratory viruses were more common in febrile children than controls, but only influenza A (OR 0.24, 95% CI 0.11-0.46), influenza B (OR 0.12, 95% CI 0.02-0.37) and RSV (OR 0.16, 95% CI: 0.06-0.36) were less common in DB than DV cases. Of 16 blood viruses, enterovirus (OR 0.43, 95% CI 0.23-0.72) and EBV (OR 0.71, 95% CI 0.56-0.90) were detected less often in DB than DV cases. Combined local diagnostics and CMTs respectively detected blood viruses and respiratory viruses in 360 (56%) and 161 (25%) of DB cases, and virus detection ruled-out bacterial infection poorly, with predictive values of 0.64 and 0.68 respectively.InterpretationMost febrile children cannot be conclusively defined as having bacterial or viral infection when molecular tests supplement conventional approaches. Viruses are detected in most patients with bacterial infections, and the clinical value of individual pathogen detection in determining treatment is low. New approaches are needed to help determine which febrile children require antibiotics.FundingEU Horizon 2020 grant 668303

Impact of infection on proteome-wide glycosylation revealed by distinct signatures for bacterial and viral pathogens

Mechanisms of infection and pathogenesis have predominantly been studied based on differential gene or protein expression. Less is known about posttranslational modifications, which are essential for protein functional diversity. We applied an innovative glycoproteomics method to study the systemic proteome-wide glycosylation in response to infection. The protein site-specific glycosylation was characterized in plasma derived from well-defined controls and patients. We found 3862 unique features, of which we identified 463 distinct intact glycopeptides, that could be mapped to more than 30 different proteins. Statistical analyses were used to derive a glycopeptide signature that enabled significant differentiation between patients with a bacterial or viral infection. Furthermore, supported by a machine learning algorithm, we demonstrated the ability to identify the causative pathogens based on the distinctive host blood plasma glycopeptide signatures. These results illustrate that glycoproteomics holds enormous potential as an innovative approach to improve the interpretation of relevant biological changes in response to infection

Genomic investigations of unexplained acute hepatitis in children

Since its first identification in Scotland, over 1,000 cases of unexplained paediatric hepatitis in children have been reported worldwide, including 278 cases in the UK1. Here we report an investigation of 38 cases, 66 age-matched immunocompetent controls and 21 immunocompromised comparator participants, using a combination of genomic, transcriptomic, proteomic and immunohistochemical methods. We detected high levels of adeno-associated virus 2 (AAV2) DNA in the liver, blood, plasma or stool from 27 of 28 cases. We found low levels of adenovirus (HAdV) and human herpesvirus 6B (HHV-6B) in 23 of 31 and 16 of 23, respectively, of the cases tested. By contrast, AAV2 was infrequently detected and at low titre in the blood or the liver from control children with HAdV, even when profoundly immunosuppressed. AAV2, HAdV and HHV-6 phylogeny excluded the emergence of novel strains in cases. Histological analyses of explanted livers showed enrichment for T cells and B lineage cells. Proteomic comparison of liver tissue from cases and healthy controls identified increased expression of HLA class 2, immunoglobulin variable regions and complement proteins. HAdV and AAV2 proteins were not detected in the livers. Instead, we identified AAV2 DNA complexes reflecting both HAdV-mediated and HHV-6B-mediated replication. We hypothesize that high levels of abnormal AAV2 replication products aided by HAdV and, in severe cases, HHV-6B may have triggered immune-mediated hepatic disease in genetically and immunologically predisposed children

Efficient computation of seismic traveltimes in anisotropic media and the application in pre-stack depth migration

This study is concerned with the computation of seismic first-arrival traveltimes in anisotropic media using finite difference eikonal methods. For this purpose, different numerical schemes that directly solve the eikonal equation are implemented and assessed numerically. Subsequently, they are used for pre-stack depth migration on synthetic and field data. The thesis starts with a detailed examination of different finite difference methods that have gained popularity in scientific literature for computing seismic traveltimes in isotropic media. The most appropriate for an extension towards anisotropic media are found to be the so-called Fast Marching/Sweeping methods. Both schemes rely on different iteration strategies, but incorporate the same upwind finite difference Godunov schemes that are implemented up to the second order. As a result, the derived methods exhibit high numerical accuracy and perform robustly even in highly contrasted velocity models. Subsequently, the methods are adapted for transversely isotropic media with vertical (VTI) and tilted (TTI) symmetry axes, respectively. Therefore, two different formulations for approximating the anisotropic phase velocities are tested, which are the weakly-anisotropic and the pseudo-acoustic approximation. As expected, the pseudo-acoustic formulation shows superior accuracy especially for strongly anisotropic media. Moreover, it turns out that the tested eikonal schemes are generally more accurate than anisotropic ray tracing approaches, since they do not require an approximation of the group velocity. Numerical experiments are carried out on homogeneous models with varying strengths of anisotropy and the industrial BP 2007 benchmark model. They show that the computed eikonal traveltimes are in good agreement with independent results from finite difference modelling of the isotropic and anisotropic elastic wave equations, and traveltimes estimated by ray-based wavefront construction, respectively. The computational performance of the TI eikonal schemes is largely increased compared to their original isotropic implementations, which is due to the algebraic complexity of the anisotropic phase velocity formulations. At this point, the Fast Marching Method is found to be more efficient on models containing up to 50 million grid points. For larger models, the anisotropic Fast Sweeping implementation gradually becomes advantageous. Here, both techniques perform independently well of the structural complexity of the underlying velocity model. The final step of this thesis is the application of the developed eikonal schemes in pre-stack depth migration. A synthetic experiment over a VTI/TTI layer-cake model demonstrates that the traveltime computation leads to accurate imaging results including a tilted, strongly anisotropic shale layer. The experiment shows further that the estimation of anisotropic velocity models solely from surface reflection data is highly ambiguous. In a second example, the eikonal solvers are applied for depth imaging of two-dimensional field data that were acquired for geothermal exploration in southern Tuscany, Italy. The developed methods also produce clear imaging results in this setting, which illustrates their general applicability for pre-stack depth imaging, particularly in challenging environments