Application of qPCR Technologies in Stormwater Source Tracking and Determination of Host Contributions of Fecal Indicator Bacteria

2012 S.C. Water Resources Conference - Exploring Opportunities for Collaborative Water Research, Policy and Managemen

Review on wildlife value orientation for ecotourism resource management

Wildlife value orientation (WVO) is important in the management of conflicts in ecotourism, particularly in human and wildlife concerns as human-wildlife conflict reported cases have increased in recent years. Therefore, this article systematically reviews literatures on WVO globally from the context of theoretical approach as well as the effect of modernization on values towards wildlife. The theoretical approach highlights the cognitive hierarchy model and the development of four theories that shapes the cultural thought towards wildlife relevant to ecotourism products. By understanding, through integrated empirical investigation, the values people hold towards wildlife, it enables the development of effective decision makings in handling the conflicts in the realm of ecotourism product or resource management

Nitrogen geochemistry of subducting sediments: new results from the Izu-Bonin-Mariana margin and insights regarding global nitrogen subduction

[1] Toward understanding of the subduction mass balance in the Izu-Bonin-Mariana (IBM) convergent margin, we present an inventory of N and C concentrations and isotopic compositions in sediments obtained on Ocean Drilling Program (ODP) Legs 129 and 185. Samples from Sites 1149, 800, 801, and 802 contain 5 to 661 ppm total N (organic, inorganic combined) with δ15NAir of −0.2 to +8.2‰ (all δ15N values <+2.5‰ from Site 800). At Site 1149, N content is higher in clay-rich layers and lower in chert and carbonate layers, and δ15N shows a distinct down-section decrease from 0 to 120 mbsf (near +8.0 at shallow levels to near +4.0‰). Reduced-C concentration ranges from 0.02 to 0.5 wt.%, with δ13CVPDB of −28.1 to −21.7‰. The down-section decreases in δ15N and N concentration (and variations in concentrations and δ13C of reduced C, and Creduced/N) at Site 1149 could help reconcile differences between δ15N values of modern deep-sea sediments from near the sediment-water interface and values for forearc metasedimentary rocks. At Site 1149, negative shifts in δ15N, from marine organic values (up to ∼+8‰) toward lower values approaching those for the metasedimentary rocks (+1 to +3‰), are most likely caused by complex diagenetic processes, conceivably with minor effects of changes in productivity and differing proportions of marine and terrestrial organic matter. However, the forearc metamorphic suites (e.g., Franciscan Complex) are known to have been deposited nearer continents, and their lower δ15N at least partly reflects larger proportions of lower-δ15N terrestrial organic matter. Subduction at the Izu-Bonin (IB) margin, of a sediment section like that at Site 1149, would deliver an approximate annual subduction flux of 2.5 × 106 g of N and 1.4 × 107 g of reduced C per linear kilometer of trench, with average δ15N of +5.0‰ and δ13C of −24‰. Incorporating the larger C flux of 9.2 × 108 g/yr/linear-km in carbonate-rich layers of 1149B (average δ13C = +2.3‰) provides a total C flux of 9.3 × 108 g/yr/linear-km (δ13C = +1.9‰). Once subducted, sediments are shifted to higher δ15N by N loss during devolatilization, with magnitudes of the shifts depending on the thermal evolution of the margin

Octree-based, GPU implementation of a continuous cellular automaton for the simulation of complex, evolving surfaces

Presently, dynamic surface-based models are required to contain increasingly larger numbers of points and to propagate them over longer time periods. For large numbers of surface points, the octree data structure can be used as a balance between low memory occupation and relatively rapid access to the stored data. For evolution rules that depend on neighborhood states, extended simulation periods can be obtained by using simplified atomistic propagation models, such as the Cellular Automata (CA). This method, however, has an intrinsic parallel updating nature and the corresponding simulations are highly inefficient when performed on classical Central Processing Units (CPUs), which are designed for the sequential execution of tasks. In this paper, a series of guidelines is presented for the efficient adaptation of octree-based, CA simulations of complex, evolving surfaces into massively parallel computing hardware. A Graphics Processing Unit (GPU) is used as a cost-efficient example of the parallel architectures. For the actual simulations, we consider the surface propagation during anisotropic wet chemical etching of silicon as a computationally challenging process with a wide-spread use in microengineering applications. A continuous CA model that is intrinsically parallel in nature is used for the time evolution. Our study strongly indicates that parallel computations of dynamically evolving surfaces simulated using CA methods are significantly benefited by the incorporation of octrees as support data structures, substantially decreasing the overall computational time and memory usage. © 2010 Elsevier B.V. All rights reserved.We thank the anonymous reviewers for their valuable comments and suggestions. This work has been supported by Programa de Becas de Excelencia de la Universidad Politecnica de Valencia (PAID-09-09), MEXT Grant in Aid Research (Kakenhi: Silicon etching (A) 19201026), and the Global COE program of Japan (GCOE, Wakate JSPS Young Scientist Fund).Ferrando Jódar, N.; Gosalvez, M.; Cerdá Boluda, J.; Gadea Gironés, R.; Sato, K. (2011). Octree-based, GPU implementation of a continuous cellular automaton for the simulation of complex, evolving surfaces. Computer Physics Communications. 182(3):628-640. https://doi.org/10.1016/j.cpc.2010.11.004S628640182

Learning biophysically-motivated parameters for alpha helix prediction

<p>Abstract</p> <p>Background</p> <p>Our goal is to develop a state-of-the-art protein secondary structure predictor, with an intuitive and biophysically-motivated energy model. We treat structure prediction as an optimization problem, using parameterizable cost functions representing biological "pseudo-energies". Machine learning methods are applied to estimate the values of the parameters to correctly predict known protein structures.</p> <p>Results</p> <p>Focusing on the prediction of alpha helices in proteins, we show that a model with 302 parameters can achieve a Q_{<it>α </it>}value of 77.6% and an SOV_{<it>α </it>}value of 73.4%. Such performance numbers are among the best for techniques that do not rely on external databases (such as multiple sequence alignments). Further, it is easier to extract biological significance from a model with so few parameters.</p> <p>Conclusion</p> <p>The method presented shows promise for the prediction of protein secondary structure. Biophysically-motivated elementary free-energies can be learned using SVM techniques to construct an energy cost function whose predictive performance rivals state-of-the-art. This method is general and can be extended beyond the all-alpha case described here.</p

Benthic pH gradients across a range of shelf sea sediment types linked to sediment characteristics and seasonal variability

This study used microelectrodes to record pH profiles in fresh shelf sea sediment cores collected across a range of different sediment types within the Celtic Sea. Spatial and temporal variability was captured during repeated measurements in 2014 and 2015. Concurrently recorded oxygen microelectrode profiles and other sedimentary parameters provide a detailed context for interpretation of the pH data. Clear differences in profiles were observed between sediment type, location and season. Notably, very steep pH gradients exist within the surface sediments (10–20 mm), where decreases greater than 0.5 pH units were observed. Steep gradients were particularly apparent in fine cohesive sediments, less so in permeable sandier matrices. We hypothesise that the gradients are likely caused by aerobic organic matter respiration close to the sediment–water interface or oxidation of reduced species at the base of the oxic zone (NH4+, Mn2+, Fe2+, S−). Statistical analysis suggests the variability in the depth of the pH minima is controlled spatially by the oxygen penetration depth, and seasonally by the input and remineralisation of deposited organic phytodetritus. Below the pH minima the observed pH remained consistently low to maximum electrode penetration (ca. 60 mm), indicating an absence of sub-oxic processes generating H+ or balanced removal processes within this layer. Thus, a climatology of sediment surface porewater pH is provided against which to examine biogeochemical processes. This enhances our understanding of benthic pH processes, particularly in the context of human impacts, seabed integrity, and future climate changes, providing vital information for modelling benthic response under future climate scenarios

Theme and variations, musical transposition of prion protein sequences into music and retrotransposition of musical motifs into protein sequences

Prions are a class of protein which are able to propagate their conformational state and have therefore been termed infectious. Prions found in microbes, in particular in fungi constitute good model systems to study the structural basis of prion propagation. A specific prion from the species Podospora anserina termed HET-s is currently the only prion of which the 3D structure was solved. We have identified a series of several hundred variant forms of this prion motif in different fungal genomes. In an approach akin to phenomenological reduction, we aim at a better understanding of the essential characteristics of a prion motif. As a complement or alternative to standard bioinformatics analysis methods that we have applied, we wondered whether an esthetic approach of the question could provide further insights of the biological order governing this system. We engaged into an “art and science” project supported by IdEx-Université de Bordeaux and proposed to a musician (Clément Libes) to transpose the prion protein sequences musically in the form of a classical “theme and variations” approach and in return will synthesize, as peptides, retro-transposed musical motifs that musically fit the original theme. The project is currently at an initial stage but we will present the biological background of the project and the envisioned possible outcome