Pitfalls and limitations in seismic attribute interpretation of tectonic features

Seismic attributes are routinely used to accelerate and quantify the interpretation of tectonic features in 3D seismic data. Coherence (or variance) cubes delineate the edges of megablocks and faulted strata, curvature delineates folds and flexures, while spectral components delineate lateral changes in thickness and lithology. Seismic attributes are at their best in extracting subtle and easy to overlook features on high-quality seismic data. However, seismic attributes can also exacerbate otherwise subtle effects such as acquisition footprint and velocity pull-up/push-down, as well as small processing and velocity errors in seismic imaging. As a result, the chance that an interpreter will suffer a pitfall is inversely proportional to his or her experience. Interpreters with a history of making conventional maps from vertical seismic sections will have previously encountered problems associated with acquisition, processing, and imaging. Because they know that attributes are a direct measure of the seismic amplitude data, they are not surprised that such attributes “accurately” represent these familiar errors. Less experienced interpreters may encounter these errors for the first time. Regardless of their level of experience, all interpreters are faced with increasingly larger seismic data volumes in which seismic attributes become valuable tools that aid in mapping and communicating geologic features of interest to their colleagues. In terms of attributes, structural pitfalls fall into two general categories: false structures due to seismic noise and processing errors including velocity pull-up/push-down due to lateral variations in the overburden and errors made in attribute computation by not accounting for structural dip. We evaluate these errors using 3D data volumes and find areas where present-day attributes do not provide the images we want

Strong, specific, monodentate G-C base pair recognition by N7-inosine derivatives in the pyrimidine•purine-pyrimidine triple-helical binding motif

The nucleoside analogs 7-(2′-deoxy-α-D-ribofuranosyl)hypoxanthine (β7H, 1), 7-(2′-deoxy-β-D-ribofuranosyl)hypoxanthine (β7H, 2) and 7-(2′-O-methyl-β-Dribofuranosyl)hypoxanthine (β7HOMe, 3) were prepared and incorporated into triplex forming oligodeoxynucleotides, designed to bind to DNA in the parallel (pyrimidine•purine-pyrimidine) motif. By DNase I footprinting techniques and UV-melting curve analysis it was found that, at pH 7.0, the 15mer oligonucleotides d(TTTTTMeCTXTMeCTMeCTMeCT) (MeC = 5-methyldeoxycytidine, X = β7H, β7HOMe) bind to a DNA target duplex forming a H•G-C base triple with equal to slightly increased (10-fold) stability compared to a control oligodeoxynucleotide in which the hypoxanthine residue is replaced by MeC. Remarkably, triplehelix formation is specific to G-C base pairs and up to 40 µM third strand concentration, no stable triplex exhibiting H•A-T, H•T-A or H•C-G base arrangements could be found (target duplex concentration ∼0.1 nM). Multiply substituted sequences containing β7H residues either in an isolated [d(TTTTTβ7HTβ7HTβ7HTβ7HTβ7HT)] or in a contiguous [d(TTTβ7Hβ7Hβ7Hβ7HTTTTβ7HTTT)] manner still form triplexes with their targets of comparable stability as the control (MeC-containing) sequences at pH 7.0 and high salt or spermine containing buffers. General considerations lead to a structural model in which the recognition of the G-C base pair by hypoxanthine takes place via only one H-bond of the N-H of hypoxanthine to N7 of guanine. This model is supported by a molecular dynamics simulation. A general comparison of the triplex forming properties of oligonucleotides containing β7H with those containing MeC or N7-2′-deoxyguanosine (N7G) reveals that monodentate recognition in the former case can energetically compete with bidentate recognition in the latter two case

Reconstructing the colonization history of Indo-Pacific bottlenose dolphins (Tursiops aduncus) in Northwestern Australia

Bottlenose dolphins (Tursiops spp.) are found in waters around Australia, with T. truncatus typically occupying deeper, more oceanic habitat, while T. aduncus occur in shallower, coastal waters. Little is known about the colonization history of T. aduncus along the Western Australian coastline; however, it has been hypothesized that extant populations are the result of an expansion along the coastline originating from a source in the north of Australia. To investigate the history of coastal T. aduncus populations in the area, we generated a genomic SNP dataset using a double-digest restriction-site-associated DNA (ddRAD) sequencing approach. The resulting dataset consisted of 103,201 biallelic SNPs for 112 individuals which were sampled from eleven coastal and two offshore sites between Shark Bay and Cygnet Bay, Western Australia. Our population genomic analyses showed a pattern consistent with the proposed source in the north with significant isolation by distance along the coastline, as well as a reduction in genomic diversity measures along the coastline with Shark Bay showing the most pronounced reduction. Our demographic analysis indicated that the expansion of T. aduncus along the coastline began around the last glacial maximum and progressed southwards with the Shark Bay population being founded only 13 kya. Our results are in line with coastal colonization histories inferred for Tursiops globally, highlighting the ability of delphinids to rapidly colonize novel coastal niches as habitat is released during glacial cycle-related global sea level and temperature changes

Wave equation calculation of most energetic traveltimes and amplitudes for Kirchhoff prestack migration

This work was conceived during a visit by Kurt Marfurt to Seoul National University, sponsored by the Korean Ministry of Science andTechnology.This work was financially supported by the Brain Korea 21 Project of the Ministry of Education of Korea and the National Research Laboratory project of the Ministry of Science and Technology. The authors acknowledge the support of the Korea Institute of Science and Technology Information (KISTI) under the Grand Challenge Support Program and the use of the Supercomputing Center

Elastic modeling and steep dips: unraveling the reflected wavefield

As part of a larger elastic numerical modeling project, we have been investigating how energy reflected from steeply dipping interfaces is recorded using typical multicomponent acquisition geometries. Specifically, we have been interpreting how rcflection events from the flanks of salt dome structures are distributed on 3C and 4C phones for vertical seismic profiles (VSPs) and ocean bottom seismic (OBS) or land surface surveys. The ultimate goal of this investigation is to improve the structural imaging of steeply dipping interfaces and eventually to evaluate the usc of the recorded elastic wavefield for fluid description near these interfaces. In the current work, we focus on a common assumption used when processing converted wave reflection seismic data that most PP energy is recorded on the vertical geophone and/or the hydrophone and that most PS energy is recorded on the horizontal geophones. This is a useful assumption when it is valid, because it eliminates the need for separation of the recorded wavefield into P and S wavetypes. Using two elastic models and different acquisition geometries, we examine the validity of this assumption in the presence of steeply dipping interfaces and discuss the implications for converted-wave and vector imaging of salt flanks

No association between the Plasmodium vivax crt-o MS334 or In9pvcrt polymorphisms and chloroquine failure in a pre-elimination clinical cohort from Malaysia with a large clonal expansion

Increasing reports of resistance to a frontline malaria blood-stage treatment, chloroquine (CQ), raises concerns for the elimination of Plasmodium vivax. The absence of an effective molecular marker of CQ resistance in P. vivax greatly constrains surveillance of this emerging threat. A recent genetic cross between CQ sensitive (CQS) and CQ resistant (CQR) NIH-1993 strains of P. vivax linked a moderate CQR phenotype with two candidate markers in P. vivax CQ resistance transporter gene (pvcrt-o): MS334 and In9pvcrt. Longer TGAAGH motif lengths at MS334 were associated with CQ resistance, as were shorter motifs at the In9pvcrt locus. In this study, high-grade CQR clinical isolates of P. vivax from a low endemic setting in Malaysia were used to investigate the association between the MS334 and In9pvcrt variants and treatment efficacy. Among a total of 49 independent monoclonal P. vivax isolates assessed, high-quality MS334 and In9pvcrt sequences could be derived from 30 (61%) and 23 (47%), respectively. Five MS334 and six In9pvcrt alleles were observed, with allele frequencies ranging from 2 to 76% and 3 to 71%, respectively. None of the clinical isolates had the same variant as the NIH-1993 CQR strain, and none of the variants were associated with CQ treatment failure (all P > 0.05). Multi-locus genotypes (MLGs) at 9 neutral microsatellites revealed a predominant P. vivax strain (MLG6) accounting for 52% of Day 0 infections. The MLG6 strain comprised equal proportions of CQS and CQR infections. Our study reveals complexity in the genetic basis of CQ resistance in the Malaysian P. vivax pre-elimination setting and suggests that the proposed pvcrt-o MS334 and In9pvcrt markers are not reliable markers of CQ treatment efficacy in this setting. Further studies are needed in other endemic settings, applying hypothesis-free genome-wide approaches, and functional approaches to understand the biological impact of the TGAAGH repeats linked to CQ response in a cross are warranted to comprehend and track CQR P. vivax

Development of a TaqMan Allelic Discrimination Assay for detection of Single Nucleotides Polymorphisms associated with anti-malarial drug resistance

<p>Abstract</p> <p>Background</p> <p>Anti-malarial drug resistance poses a threat to current global efforts towards control and elimination of malaria. Several methods are used in monitoring anti-malarial drug resistance. Molecular markers such as single nucleotide polymorphism (SNP) for example are increasingly being used to identify genetic mutations related to anti-malarial drug resistance. Several methods are currently being used in analysis of SNP associated with anti-malarial drug resistance and although each one of these methods has unique strengths and shortcoming, there is still need to improve and/or develop new methods that will close the gap found in the current methods.</p> <p>Methods</p> <p>TaqMan Allelic Discrimination assays for detection of SNPs associated with anti-malarial drug resistance were designed for analysis on Applied Biosystems PCR platform. These assays were designed by submitting SNP sequences associated with anti-malarial drug resistance to Applied Biosystems website. Eleven SNPs associated with resistance to anti-malarial drugs were selected and tested. The performance of each SNP assay was tested by creating plasmid DNAs carrying codons of interests and analysing them for analysis. To test the sensitivity and specificity of each SNP assay, 12 clinical samples were sequenced at codons of interest and used in the analysis. Plasmid DNAs were used to establish the Limit of Detection (LoD) for each assay.</p> <p>Results</p> <p>Data from genetic profiles of the <it>Plasmodium falciparum </it>laboratory strains and sequence data from 12 clinical samples was used as the reference method with which the performance of the SNP assays were compared to. The sensitivity and specificity of each SNP assay was establish at 100%. LoD for each assay was established at 2 GE, equivalent to less than 1 parasite/μL. SNP assays performed well in detecting mixed infection and analysis of clinical samples.</p> <p>Conclusion</p> <p>TaqMan Allelic Discrimination assay provides a good alternative tool in detection of SNPs associated with anti-malarial drug.</p

Efficient calculation of a partial-derivative wavefield using reciprocity for seismic imaging and inversion

Linearized inversion of surface seismic data for a model of the earths subsurface requires estimating the sensitivity of the seismic response to perturbations in the earths subsurface. This sensitivity, or Jacobian, matrix is usually quite expensive to estimate for all but the simplest model parameterizations.We exploit the numerical structure of the finite-element method, modern sparse matrix technology, and source–receiver reciprocity to develop an algorithm that explicitly calculates the Jacobian matrix at only the cost of a forward model solution. Furthermore, we show that we can achieve improved subsurface images using only one inversion iteration through proper scaling of the image by a diagonal approximation of the Hessian matrix, as predicted by the classical Gauss-Newton method. Our method is applicable to the full suite of wave scattering problems amenable to finiteelement forward modeling.We demonstrate our method through some simple 2-D synthetic examples