Quantitation and organic geochemical characterization of petroleum-like materials found on an undisturbed beach of the Padre Island National Seashore

On June 3, 1979 the IXTOC I well in the Bay of Campeche 'blew out' with the subsequent release of 3 to 4 million barrels of oil. A major portion of that oil is known to have escaped recovery or was deliberately dispersed into the environment. This catastrophic source appears to be a major contributor to coastal water petroleum residues of the Gulf. Two questions which arise are: 1) What quantities of this petroleum-like material are being deposited annually on the south Texas beaches? And 2), is there a single source of beach tar (seeps) or are there multiple sources (spilled or dumped crudes as well as seeps)? This study is part of an effort to find answers to these questions.A report submitted to: United States Department of the Interior, National Park Service, Southwest RegionMarine Scienc

The NTD Nanoscope: potential applications and implementations

<p>Abstract</p> <p>Background</p> <p>Nanopore transduction detection (NTD) offers prospects for a number of highly sensitive and discriminative applications, including: (i) single nucleotide polymorphism (SNP) detection; (ii) targeted DNA re-sequencing; (iii) protein isoform assaying; and (iv) biosensing via antibody or aptamer coupled molecules. Nanopore event transduction involves single-molecule biophysics, engineered information flows, and nanopore cheminformatics. The NTD Nanoscope has seen limited use in the scientific community, however, due to lack of information about potential applications, and lack of availability for the device itself. Meta Logos Inc. is developing both pre-packaged device platforms and component-level (unassembled) kit platforms (the latter described here). In both cases a lipid bi-layer workstation is first established, then augmentations and operational protocols are provided to have a nanopore transduction detector. In this paper we provide an overview of the NTD Nanoscope applications and implementations. The NTD Nanoscope Kit, in particular, is a component-level reproduction of the standard NTD device used in previous research papers.</p> <p>Results</p> <p>The NTD Nanoscope method is shown to functionalize a single nanopore with a channel current modulator that is designed to transduce events, such as binding to a specific target. To expedite set-up in new lab settings, the calibration and troubleshooting for the NTD Nanoscope kit components and signal processing software, the NTD Nanoscope Kit, is designed to include a set of test buffers and control molecules based on experiments described in previous NTD papers (the model systems briefly described in what follows). The description of the Server-interfacing for advanced signal processing support is also briefly mentioned.</p> <p>Conclusions</p> <p>SNP assaying, SNP discovery, DNA sequencing and RNA-seq methods are typically limited by the accuracy of the error rate of the enzymes involved, such as methods involving the polymerase chain reaction (PCR) enzyme. The NTD Nanoscope offers a means to obtain higher accuracy as it is a single-molecule method that does not inherently involve use of enzymes, using a functionalized nanopore instead.</p

The core structure of presolar graphite onions

Of the ``presolar particles'' extracted from carbonaceous chondrite dissolution residues, i.e. of those particles which show isotopic evidence of solidification in the neighborhood of other stars prior to the origin of our solar system, one subset has an interesting concentric graphite-rim/graphene-core structure. We show here that single graphene sheet defects in the onion cores (e.g. cyclopentane loops) may be observable edge-on by HREM. This could allow a closer look at models for their formation, and in particular strengthen the possibility that growth of these assemblages proceeds atom-by-atom with the aid of such in-plane defects, under conditions of growth (e.g. radiation fluxes or grain temperature) which discourage the graphite layering that dominates subsequent formation of the rim.Comment: 4 pages, 7 figures, 11 refs, see also http://www.umsl.edu/~fraundor/isocore.htm

Unhealthy Behaviors and the Relationship to Body Mass Index (BMI) in College Students

Please view abstract in the attached PDF file

Laser spectroscopy of hyperfine structure in highly-charged ions: a test of QED at high fields

An overview is presented of laser spectroscopy experiments with cold, trapped, highly-charged ions, which will be performed at the HITRAP facility at GSI in Darmstadt (Germany). These high-resolution measurements of ground state hyperfine splittings will be three orders of magnitude more precise than previous measurements. Moreover, from a comparison of measurements of the hyperfine splittings in hydrogen- and lithium-like ions of the same isotope, QED effects at high electromagnetic fields can be determined within a few percent. Several candidate ions suited for these laser spectroscopy studies are presented.Comment: 5 pages, 1 figure, 1 table. accepted for Canadian Journal of Physics (2006

Physical properties of sediments from Keathley Canyon and Atwater Valley, JIP Gulf of Mexico gas hydrate drilling program

This paper is not subject to U.S. copyright. The definitive version was published in Marine and Petroleum Geology 25 (2008): 896-905, doi:10.1016/j.marpetgeo.2008.01.018.Physical property measurements and consolidation behavior are different between sediments from Atwater Valley and Keathley Canyon in the northern Gulf of Mexico. Void ratio and bulk density of Atwater Valley sediment from a seafloor mound (holes ATM1 and ATM2) show little effective stress (or depth) dependence to 27 meters below seafloor (mbsf), perhaps owing to fluidized transport through the mound itself with subsequent settling onto the seafloor or mound flanks. Off-mound sediments (hole AT13-2) have bulk physical properties that are similar to mound sediments above 27 mbsf, but void ratio and porosity decrease below that depth. Properties of shallow (<50 mbsf) Keathley Canyon sediments (KC151-3) change with increasing effective stress (or depth) compared to Atwater Valley, but vary little below that depth. Organic carbon is present in concentrations between typical near-shore and deep-sea sediments. Organic carbon-to-nitrogen ratios suggest that the organic matter contained in Atwater Valley off-mound and mound sites came from somewhat different sources. The difference in organic carbon-to-nitrogen ratios between Atwater Valley and Keathley Canyon is more pronounced. At Keathley Canyon a more terrigenous source of the organic matter is indicated. Grain sizes are typically silty clay or clay within the two basins reflecting similar transport energy. However, the range in most shallow sediment properties is significantly different between the two basins. Bulk density profiles agree with logging results in Atwater Valley and Keathley Canyon. Agreement between lab-derived and logging-derived properties supports using logging data to constrain bulk physical properties where cores were not collected.Support of this research was provided by the USGS Coastal and Marine Geology Program, the USGS Energy Program, and the National Energy Technology Laboratory

Duration learning for analysis of nanopore ionic current blockades

<p>Abstract</p> <p>Background</p> <p>Ionic current blockade signal processing, for use in nanopore detection, offers a promising new way to analyze single molecule properties, with potential implications for DNA sequencing. The alpha-Hemolysin transmembrane channel interacts with a translocating molecule in a nontrivial way, frequently evidenced by a complex ionic flow blockade pattern. Typically, recorded current blockade signals have several levels of blockade, with various durations, all obeying a fixed statistical profile for a given molecule. Hidden Markov Model (HMM) based duration learning experiments on artificial two-level Gaussian blockade signals helped us to identify proper modeling framework. We then apply our framework to the real multi-level DNA hairpin blockade signal.</p> <p>Results</p> <p>The identified upper level blockade state is observed with durations that are geometrically distributed (consistent with an a physical decay process for remaining in any given state). We show that mixture of convolution chains of geometrically distributed states is better for presenting multimodal long-tailed duration phenomena. Based on learned HMM profiles we are able to classify 9 base-pair DNA hairpins with accuracy up to 99.5% on signals from same-day experiments.</p> <p>Conclusion</p> <p>We have demonstrated several implementations for <it>de novo </it>estimation of duration distribution probability density function with HMM framework and applied our model topology to the real data. The proposed design could be handy in molecular analysis based on nanopore current blockade signal.</p

Social structure and language structure: The new nomothetic approach

Recent studies have taken advantage of newly available, large-scale, cross-linguistic data and new statistical techniques to look at the relationship between language structure and social structure. These ‘nomothetic’ approaches contrast with more traditional approaches and a tension is observed between proponents of each method. We review some nomothetic studies and point out some challenges that must be overcome. However, we argue that nomothetic approaches can contribute to our understanding of the links between social structure and language structure if they address these challenges and are taken as part of a body of mutually supporting evidence. Nomothetic studies are a powerful tool for generating hypotheses that can go on to be corroborated and tested with experimental and theoretical approaches. These studies are highlighting the effect of interaction on language