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

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

Just Click Here : A Brief Glance at Absurd Electronic Contracts and the Law Failing to Protect Consumers

As e-commerce explodes around the world, consumers’ rights have been left behind. Before the completion of virtually every transaction on the Internet, the onus is placed on consumers to read and agree to an onslaught of terms and conditions. Often hidden in the middle of this extremely lengthy list of terms are massive exemption and limitation of liability clauses that deny consumers most if not all of their rights as “equal” trading partners. The common law principle that all onerous clauses in a contract need to be brought to the attention of the consumer for them to be binding seems to have been lost with the invention of the “click here to agree” button for signing online contracts. As the courts in Canada have not provided clear guidance on this issue thus far, other means must be pursued in order to protect consumers from the near-tyrannical control of unencumbered electronic standard form contracts in e-commerce. This paper will describe the principle of sufficiency of notice as it applies to paper contracts, and then contrast it with the newer jurisprudence that has refused to apply the principle to electronic contracts. The reasons for the refusal will be explored, followed by an examination of why the principle of sufficiency of notice needs to be applied and strengthened to respond to the increasingly onerous provisions hidden in electronic contracts. Finally, some other options for achieving the goal of consumer protection from hidden onerous clauses will be briefly explored. These other options include introducing stiffer consumer protection legislation domestically, the creation of international treaties, developing voluntary standards of contracting, and relying on Internet self-regulation

Genomic analysis of a pre-elimination Malaysian Plasmodium vivax population reveals selective pressures and changing transmission dynamics.

The incidence of Plasmodium vivax infection has declined markedly in Malaysia over the past decade despite evidence of high-grade chloroquine resistance. Here we investigate the genetic changes in a P. vivax population approaching elimination in 51 isolates from Sabah, Malaysia and compare these with data from 104 isolates from Thailand and 104 isolates from Indonesia. Sabah displays extensive population structure, mirroring that previously seen with the emergence of artemisinin-resistant P. falciparum founder populations in Cambodia. Fifty-four percent of the Sabah isolates have identical genomes, consistent with a rapid clonal expansion. Across Sabah, there is a high prevalence of loci known to be associated with antimalarial drug resistance. Measures of differentiation between the three countries reveal several gene regions under putative selection in Sabah. Our findings highlight important factors pertinent to parasite resurgence and molecular cues that can be used to monitor low-endemic populations at the end stages of P. vivax elimination