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Sample records for dynamically important residues

  1. Large-scale evaluation of dynamically important residues in proteins predicted by the perturbation analysis of a coarse-grained elastic model

    Directory of Open Access Journals (Sweden)

    Tekpinar Mustafa

    2009-07-01

    Full Text Available Abstract Backgrounds It is increasingly recognized that protein functions often require intricate conformational dynamics, which involves a network of key amino acid residues that couple spatially separated functional sites. Tremendous efforts have been made to identify these key residues by experimental and computational means. Results We have performed a large-scale evaluation of the predictions of dynamically important residues by a variety of computational protocols including three based on the perturbation and correlation analysis of a coarse-grained elastic model. This study is performed for two lists of test cases with >500 pairs of protein structures. The dynamically important residues predicted by the perturbation and correlation analysis are found to be strongly or moderately conserved in >67% of test cases. They form a sparse network of residues which are clustered both in 3D space and along protein sequence. Their overall conservation is attributed to their dynamic role rather than ligand binding or high network connectivity. Conclusion By modeling how the protein structural fluctuations respond to residue-position-specific perturbations, our highly efficient perturbation and correlation analysis can be used to dissect the functional conformational changes in various proteins with a residue level of detail. The predictions of dynamically important residues serve as promising targets for mutational and functional studies.

  2. 40 CFR 180.632 - Fenazaquin; import tolerances for residues.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Fenazaquin; import tolerances for... § 180.632 Fenazaquin; import tolerances for residues. (a) General. Import tolerances are established for residues of the insecticide and miticide, fenazaquin, 4-tert-butylphenethyl quinazolin-4-yl ether, in or on...

  3. Dynamical network of residue-residue contacts reveals coupled allosteric effects in recognition, catalysis, and mutation.

    Science.gov (United States)

    Doshi, Urmi; Holliday, Michael J; Eisenmesser, Elan Z; Hamelberg, Donald

    2016-04-26

    Detailed understanding of how conformational dynamics orchestrates function in allosteric regulation of recognition and catalysis remains ambiguous. Here, we simulate CypA using multiple-microsecond-long atomistic molecular dynamics in explicit solvent and carry out NMR experiments. We analyze a large amount of time-dependent multidimensional data with a coarse-grained approach and map key dynamical features within individual macrostates by defining dynamics in terms of residue-residue contacts. The effects of substrate binding are observed to be largely sensed at a location over 15 Å from the active site, implying its importance in allostery. Using NMR experiments, we confirm that a dynamic cluster of residues in this distal region is directly coupled to the active site. Furthermore, the dynamical network of interresidue contacts is found to be coupled and temporally dispersed, ranging over 4 to 5 orders of magnitude. Finally, using network centrality measures we demonstrate the changes in the communication network, connectivity, and influence of CypA residues upon substrate binding, mutation, and during catalysis. We identify key residues that potentially act as a bottleneck in the communication flow through the distinct regions in CypA and, therefore, as targets for future mutational studies. Mapping these dynamical features and the coupling of dynamics to function has crucial ramifications in understanding allosteric regulation in enzymes and proteins, in general.

  4. The functional importance of co-evolving residues in proteins.

    Science.gov (United States)

    Sandler, Inga; Zigdon, Nitzan; Levy, Efrat; Aharoni, Amir

    2014-02-01

    Computational approaches for detecting co-evolution in proteins allow for the identification of protein-protein interaction networks in different organisms and the assignment of function to under-explored proteins. The detection of co-variation of amino acids within or between proteins, moreover, allows for the discovery of residue-residue contacts and highlights functional residues that can affect the binding affinity, catalytic activity, or substrate specificity of a protein. To explore the functional impact of co-evolutionary changes in proteins, a combined experimental and computational approach must be recruited. Here, we review recent studies that apply computational and experimental tools to obtain novel insight into the structure, function, and evolution of proteins. Specifically, we describe the application of co-evolutionary analysis for predicting high-resolution three-dimensional structures of proteins. In addition, we describe computational approaches followed by experimental analysis for identifying specificity-determining residues in proteins. Finally, we discuss studies addressing the importance of such residues in terms of the functional divergence of proteins, allowing proteins to evolve new functions while avoiding crosstalk with existing cellular pathways or forming reproductive barriers and hence promoting speciation.

  5. Dynamic residual stress in thermal sprayed coatings

    Institute of Scientific and Technical Information of China (English)

    Wang Zhiping; Yang Yuanyuan

    2005-01-01

    With the modified Almen method, the forming and development process of residual stress in a thermal sprayed coating has been obtained. The test results identify that the residual stress in a coating is depend on coating material properties, technique and coating thickness. The paper pays much attention to the hysteresis between the coating temperature and residual stress in the coating or between the applied stress and the strain of the coating, and confirms that the fact is resulted from the"Gas Fix" character of a thermal sprayed coating.

  6. Identification of catalytically important residues in yeast transketolase.

    Science.gov (United States)

    Wikner, C; Nilsson, U; Meshalkina, L; Udekwu, C; Lindqvist, Y; Schneider, G

    1997-12-16

    The possible roles of four histidine residues in the active site of yeast transketolase were examined by site-directed mutagenesis. Replacement of the invariant His69 with alanine yielded a mutant enzyme with 1.5% of the specific activity of the wild-type enzyme and with an increased KM for the donor. This residue is located at the bottom of the substrate cleft close to the C1 hydroxyl group of the donor substrate, and the side chain of His69 might be required for recognition of this hydroxyl group and possibly for maintenance of the proper orientation of the reaction intermediate, (alpha, beta-dihydroxyethyl)thiamin diphosphate. Amino acid replacements of His481 by alanine, serine, and glutamine resulted in mutant enzymes with significantly increased KM values for the donor substrate and specific activities of 4.4%, 1.9%, and 5.5% of the wild-type enzyme. The kinetic data suggest that this residue, although close to the C2 carbonyl oxygen of the substrate, is not absolutely required for stabilization of the negative charge that develops at this oxygen in the transition state. This points toward the 4'-NH2 group of the pyrimidine ring of thiamin diphosphate as the major source of charge stabilization. Mutations at positions His30 and His263 result in mutant enzymes severely impaired in catalytic activity (1.5% and less of the activity of wild-type transketolase). The KM value for the donor substrate was increased for the His30Ala mutant but remained unchanged in the His263Ala enzyme. The side chains of both residues interact with the C3 hydroxyl group of the donor substrate, and the results indicate that the two residues act in concert during proton abstraction of the C3 hydroxyl proton during catalysis.

  7. Analysis of binding behavior between dynamic structures of a papain and the peptide consisting of 10 GLY residues

    Science.gov (United States)

    Nishiyama, Katsuhiko

    2010-07-01

    The binding of 10GLY to dynamic structures of papain was investigated by molecular dynamics and docking simulations. The binding free energies and sites were greatly fluctuated depending on the time and the binding was more stable and existed at the near site of active center when the structural changes in the highly flexible residues in papain were larger. Binding stability and sites would be significantly influenced by the highly flexible residues. Analysis of such residues would provide an important guideline for clarification of enzymatic activities and modification of structural dynamics of such residues would allow us to control enzymatic activities.

  8. Thermal decomposition dynamics and severity of microalgae residues in torrefaction.

    Science.gov (United States)

    Chen, Wei-Hsin; Huang, Ming-Yueh; Chang, Jo-Shu; Chen, Chun-Yen

    2014-10-01

    To figure out the torrefaction characteristics and weight loss dynamics of microalgae residues, the thermogravimetric analyses of two microalgae (Chlamydomonas sp. JSC4 and Chlorella sorokiniana CY1) residues are carried out. A parameter of torrefaction severity index (TSI) in the range of 0-1, in terms of weight loss ratio between a certain operation and a reference operation, is defined to indicate the degree of biomass thermal degradation due to torrefaction. The TSI profiles of the two residues are similar to each other; therefore, the parameter may be used to describe the torrefaction extents of various biomass materials. The curvature of TSI profile along light torrefaction is slight, elucidating its slight impact on biomass thermal degradation. The sharp curvature along severe torrefaction in the initial pretreatment period reveals that biomass upgraded with high temperature and short duration is more effective than using low temperature with long duration.

  9. Residual Minimizing Model Reduction for Parameterized Nonlinear Dynamical Systems

    CERN Document Server

    Constantine, Paul G

    2010-01-01

    We present a method for approximating the solution of a parameterized, nonlinear dynamical (or static) system using an affine combination of solutions computed at other points in the input parameter space. The coefficients of the affine combination are computed with a nonlinear least squares procedure that minimizes the residual of the dynamical system. The approximation properties of this residual minimizing scheme are comparable to existing reduced basis and POD-Galerkin model reduction methods, but its implementation requires only independent evaluations of the nonlinear forcing function. We prove some interesting characteristics of the scheme including uniqueness and an interpolatory property, and we present heuristics for mitigating the effects of the ill-conditioning and reducing the overall cost of the method. We apply the method to representative numerical examples from kinetics - a three state system with one parameter controlling the stiffness - and groundwater modeling - a nonlinear parabolic PDE w...

  10. Some Characterization Results on Dynamic Cumulative Residual Tsallis Entropy

    Directory of Open Access Journals (Sweden)

    Madan Mohan Sati

    2015-01-01

    Full Text Available We propose a generalized cumulative residual information measure based on Tsallis entropy and its dynamic version. We study the characterizations of the proposed information measure and define new classes of life distributions based on this measure. Some applications are provided in relation to weighted and equilibrium probability models. Finally the empirical cumulative Tsallis entropy is proposed to estimate the new information measure.

  11. Penetratin-Mediated Transepithelial Insulin Permeation: Importance of Cationic Residues and pH for Complexation and Permeation

    DEFF Research Database (Denmark)

    Kristensen, Mie; Franzyk, Henrik; Klausen, M. T.

    2015-01-01

    Penetratin is a widely used carrier peptide showing promising potential for mucosal delivery of therapeutic proteins. In the present study, the importance of specific penetratin residues and pH was investigated with respect to complexation with insulin and subsequent transepithelial insulin...... permeation. Besides penetratin, three analogues were studied. The carrier peptide-insulin complexes were characterized in terms of size and morphology at pH 5, 6.5, and 7.4 by dynamic light scattering (DLS) and transmission electron microscopy (TEM), respectively. At pH 7.4 mainly very large complexes were...... present, while much smaller complexes dominated at pH 5. Presence of arginine residues in the carrier peptide proved to be a prerequisite for complexation with insulin as well as for enhanced transepithelial insulin permeation in vitro. Rearrangement of tryptophan residues resulted in significantly...

  12. Dissipation dynamic and residue distribution of flusilazole in mandarin.

    Science.gov (United States)

    Wang, Chen; Qiu, Lihong; Zhao, Huiyu; Wang, Kai; Zhang, Hongyan

    2013-11-01

    In this paper, dissipation dynamic and terminal residue of flusilazole in mandarin and soil, as well as residue distribution of flusilazole in mandarin, were studied at three sites in China. Mandarin peel, mandarin pulp, whole mandarin, and soil samples were extracted by acetonitrile, cleaned up with dispersive solid-phase extraction, then analyzed by gas chromatography-mass spectrometry. The dissipation half-lives of flusilazole in mandarin and soil at all three experiment sites were 6.3-8.4 days and 5.5-13.4 days, respectively, with the exception of the soil dissipation at the Hunan site, which showed an increase-decrease process. Flusilazole residue levels in whole mandarin were all below 0.1 mg/kg on 14 days after the last application. Terminal residue study showed that flusilazole was mostly distributed in mandarin peel, which indicates minimal risk for eating mandarin pulp. These results could provide guidance for the proper and safe use of flusilazole on citrus fruits, and further our understanding of pesticide distribution in citrus fruits.

  13. Threonine 89 Is an Important Residue of Profilin-1 That Is Phosphorylatable by Protein Kinase A.

    Directory of Open Access Journals (Sweden)

    David Gau

    Full Text Available Dynamic regulation of actin cytoskeleton is at the heart of all actin-based cellular events. In this study, we sought to identify novel post-translational modifications of Profilin-1 (Pfn1, an important regulator of actin polymerization in cells.We performed in vitro protein kinase assay followed by mass-spectrometry to identify Protein Kinase A (PKA phosphorylation sites of Pfn1. By two-dimensional gel electrophoresis (2D-GE analysis, we further examined the changes in the isoelectric profile of ectopically expressed Pfn1 in HEK-293 cells in response to forskolin (FSK, an activator of cAMP/PKA pathway. Finally, we combined molecular dynamics simulations (MDS, GST pull-down assay and F-actin analyses of mammalian cells expressing site-specific phosphomimetic variants of Pfn1 to predict the potential consequences of phosphorylation of Pfn1.We identified several PKA phosphorylation sites of Pfn1 including Threonine 89 (T89, a novel site. Consistent with PKA's ability to phosphorylate Pfn1 in vitro, FSK stimulation increased the pool of the most negatively charged form of Pfn1 in HEK-293 cells which can be attenuated by PKA inhibitor H89. MDS predicted that T89 phosphorylation destabilizes an intramolecular interaction of Pfn1, potentially increasing its affinity for actin. The T89D phosphomimetic mutation of Pfn1 elicits several changes that are hallmarks of proteins folded into alternative three-dimensional conformations including detergent insolubility, protein aggregation and accelerated proteolysis, suggesting that T89 is a structurally important residue of Pfn1. Expression of T89D-Pfn1 induces actin:T89D-Pfn1 co-clusters and dramatically reduces overall actin polymerization in cells, indicating an actin-sequestering action of T89D-Pfn1. Finally, rendering T89 non-phosphorylatable causes a positive charge shift in the isoelectric profile of Pfn1 in a 2D gel electrophoresis analysis of cell extracts, a finding that is consistent with

  14. Present-day dynamic and residual topography in Central Anatolia

    Science.gov (United States)

    Şengül Uluocak, Ebru; Pysklywec, Russell; Göǧüş, Oǧuz H.

    2016-09-01

    The Central Anatolian orogenic plateau is represented by young volcanism, rapid plateau uplift and distinctive (past and active) tectonic deformation. In this study, we consider observational data in terms of regional present-day geodynamics in the region. The residual topography of Central Anatolia was derived to define the regional isostatic conditions according to Airy isostasy and infer the potential role of `dynamic topography'. 2-D thermomechanical forward models for coupled mantle-lithosphere flow/deformation were conducted along an N-S directional profile through the region (e.g. northern/Pontides, interior and southern/Taurides). These models were based on seismic tomography data that provide estimates about the present-day mantle thermal structure beneath the Anatolian plate. We compare the modelling results with calculated residual topography and independent data sets of geological deformation, gravity and high surface heat flow/widespread geothermal activity. Model results suggest that there is ˜1 km of mantle flow induced dynamic topography associated with the sublithospheric flow driven by the seismically inferred mantle structure. The uprising mantle may have also driven the asthenospheric source of volcanism in the north (e.g. Galatia volcanic province) and the Cappadocia volcanic province in the south while elevating the surface in the last 10 Myr. Our dynamic topography calculations emphasize the role of vertical forcing under other orogenic plateaux underlain by relatively thin crust and low-density asthenospheric mantle.

  15. Present-day dynamic and residual topography in Central Anatolia

    Science.gov (United States)

    Şengül Uluocak, Ebru; Pysklywec, Russell; Göǧüş, Oǧuz H.

    2016-09-01

    The Central Anatolian orogenic plateau is represented by young volcanism, rapid plateau uplift and distinctive (past and active) tectonic deformation. In this study, we consider observational data in terms of regional present-day geodynamics in the region. The residual topography of Central Anatolia was derived to define the regional isostatic conditions according to Airy isostasy and infer the potential role of `dynamic topography'. 2-D thermomechanical forward models for coupled mantle-lithosphere flow/deformation were conducted along an N-S directional profile through the region (e.g. northern/Pontides, interior and southern/Taurides). These models were based on seismic tomography data that provide estimates about the present-day mantle thermal structure beneath the Anatolian plate. We compare the modelling results with calculated residual topography and independent data sets of geological deformation, gravity and high surface heat flow/widespread geothermal activity. Model results suggest that there is ˜1 km of mantle flow induced dynamic topography associated with the sublithospheric flow driven by the seismically inferred mantle structure. The uprising mantle may have also driven the asthenospheric source of volcanism in the north (e.g. Galatia volcanic province) and the Cappadocia volcanic province in the south while elevating the surface in the last 10 Myr. Our dynamic topography calculations emphasize the role of vertical forcing under other orogenic plateaux underlain by relatively thin crust and low-density asthenospheric mantle.

  16. The minimal important difference for residual volume in patients with severe emphysema

    NARCIS (Netherlands)

    Hartman, Jorine E.; ten Hacken, Nick H. T.; Klooster, Karin; Boezen, H. Marike; de Greef, Mathieu H. G.; Slebos, Dirk-Jan

    2012-01-01

    Residual volume (RV) measured by body plethysmography is a routine measurement in clinical pulmonary practice and is often an important outcome variable in clinical trials. However, it is not known what size of improvement can be regarded as being important in severe emphysema patients. Therefore, t

  17. The importance of measuring dynamic visual acuity

    National Research Council Canada - National Science Library

    Muzdalo, Natasa Vujko

    2013-01-01

    .... Beside good eyesight, drivers also have to have good reflexes and short reaction span. The aim of this study was to compare dynamic and static visual acuity in order to observe how they vary among individuals...

  18. [Survey of pesticide residues in imported spices and herbs (1997.4-2011.3)].

    Science.gov (United States)

    Kobayashi, Maki; Ohtsuka, Kenji; Tamura, Yasuhiro; Tomizawa, Sanae; Kinoshita, Teruaki; Kamijo, Kyoko; Iwakoshi, Keiko; Sato, Chizuko; Nagayama, Toshihiro; Takano, Ichiro

    2013-01-01

    A survey of pesticide residues in 313 samples of imported spices and herbs on the Tokyo market from April 1997 to March 2011 was carried out. Thirty-seven kinds of pesticides, including organophosphorus, organochlorine, pyrethroid, carbamate and others, were detected between levels of trace (below 0.01 ppm) and 3.3 ppm from 64 samples. The rate of detection was highest in peel (100%) followed by stem (66.7%), fruit (34.5%), bark (33.3%), flower (31.3%) and leaf (14.7%). No residues were detected in root, seed or whole grass. Organochlorine pesticides were detected in all plant parts. The insecticides were detected in products from all production areas, suggesting that their use is common. Residue levels of these pesticides were calculated as less than 1% of their ADI values, based on the daily intake of spices and herbs. Therefore, these spices and herbs should be safe when consumed in customary amounts.

  19. Scenario Analysis of Tillage, Residue and Fertilization Management Effects on Soil Organic Carbon Dynamics

    Institute of Scientific and Technical Information of China (English)

    WANG Xiao-Bin; CAI Dian-Xiong; W.B.HOOGMOED; O.OENEMA; U.D.PERDOK

    2005-01-01

    Based on data from 10-year field experiments on residue/fertilizer management in the dryland farming region of northern China, Century model was used to simulate the site-specific ecosystem dynamics through adjustment of the model's parameters, and the applicability of the model to propose soil organic carbon (SOC) management temporally and spatially, in cases such as of tillage/residue/fertilization management options, was identified via scenario analysis.Results between simulations and actual measurements were in close agreement when appropriate applications of stover,manure and inorganic fertilizer were combined. Simulations of extreme C/N ratios with added organic materials tended to underestimate the measured effects. Scenarios of changed tillage methods, residue practices and fertilization options showed potential to maintain and enhance SOC in the long run, while increasing inorganic N slowed down the SOC turnover rate but did not create a net C sink without any organic C input. The Century model simulation showed a good relationship between annual C inputs to the soil and the rate of C sequestration in the top 20 cm layer and provided quantitative estimations of changes in parameters crucial for sustainable land use and management. Conservation tillage practices for sustainable land use should be integrated with residue management and appreciable organic and inorganic fertilizer application, adapted according to the local residue resource, soil fertility and production conditions. At least 50%residue return into the soil was needed annually for maintenance of SOC balance, and manure amendment was important for enhancement of SOC in small crop-livestock systems in which crop residue land application was limited.

  20. Functional importance of motif I of pseudouridine synthases: mutagenesis of aligned lysine and proline residues.

    Science.gov (United States)

    Spedaliere, C J; Hamilton, C S; Mueller, E G

    2000-08-01

    On the basis of sequence alignments, the pseudouridine synthases were grouped into four families that share no statistically significant global sequence similarity, though some common sequence motifs were discovered [Koonin, E. V. (1996) Nucleic Acids. Res. 24, 2411-2415; Gustafsson, C., Reid, R., Greene, P. J., and Santi, D. V. (1996) Nucleic Acids Res. 24, 3756-3762]. We have investigated the functional significance of these alignments by substituting the nearly invariant lysine and proline residues in Motif I of RluA and TruB, pseudouridine synthases belonging to different families. Contrary to our expectations, the altered enzymes display only very mild kinetic impairment. Substitution of the aligned lysine and proline residues does, however, reduce structural stability, consistent with a temperature sensitive phenotype that results from substitution of the cognate proline residue in Cbf5p, a yeast homologue of TruB [Zerbarjadian, Y., King, T., Fournier, M. J., Clarke, L., and Carbon, J. (1999) Mol. Cell. Biol. 19, 7461-7472]. Together, our data support a functional role for Motif I, as predicted by sequence alignments, though the effect of substituting the highly conserved residues was milder than we anticipated. By extrapolation, our findings also support the assignment of pseudouridine synthase function to certain physiologically important eukaryotic proteins that contain Motif I, including the human protein dyskerin, alteration of which leads to the disease dyskeratosis congenita.

  1. Studies on the analysis of pesticide residues in foods (XL) PCB (polychlorinated biphenyls) residues in imported smelt fished from the Canadian Great Lakes

    National Research Council Canada - National Science Library

    Sekita, H; Sasaki, K; Kawamura, Y; Takeda, M; Uchiyama, M

    1987-01-01

    The inspection of PCB (polychlorinated biphenyls) residues in pond smelt samples imported from Canada in June, 1983, fished from Lake Erie, one of the Great Lakes, was performed by gas chromatography with ECD...

  2. Toward accurate prediction of pKa values for internal protein residues: the importance of conformational relaxation and desolvation energy.

    Science.gov (United States)

    Wallace, Jason A; Wang, Yuhang; Shi, Chuanyin; Pastoor, Kevin J; Nguyen, Bao-Linh; Xia, Kai; Shen, Jana K

    2011-12-01

    Proton uptake or release controls many important biological processes, such as energy transduction, virus replication, and catalysis. Accurate pK(a) prediction informs about proton pathways, thereby revealing detailed acid-base mechanisms. Physics-based methods in the framework of molecular dynamics simulations not only offer pK(a) predictions but also inform about the physical origins of pK(a) shifts and provide details of ionization-induced conformational relaxation and large-scale transitions. One such method is the recently developed continuous constant pH molecular dynamics (CPHMD) method, which has been shown to be an accurate and robust pK(a) prediction tool for naturally occurring titratable residues. To further examine the accuracy and limitations of CPHMD, we blindly predicted the pK(a) values for 87 titratable residues introduced in various hydrophobic regions of staphylococcal nuclease and variants. The predictions gave a root-mean-square deviation of 1.69 pK units from experiment, and there were only two pK(a)'s with errors greater than 3.5 pK units. Analysis of the conformational fluctuation of titrating side-chains in the context of the errors of calculated pK(a) values indicate that explicit treatment of conformational flexibility and the associated dielectric relaxation gives CPHMD a distinct advantage. Analysis of the sources of errors suggests that more accurate pK(a) predictions can be obtained for the most deeply buried residues by improving the accuracy in calculating desolvation energies. Furthermore, it is found that the generalized Born implicit-solvent model underlying the current CPHMD implementation slightly distorts the local conformational environment such that the inclusion of an explicit-solvent representation may offer improvement of accuracy.

  3. Substrate specificity of papain dynamic structures for peptides consisting of 8-10 GLY residues

    Science.gov (United States)

    Nishiyama, Katsuhiko

    2011-01-01

    We investigated the substrate specificity of papain dynamic structures for peptides of 8-10 glycine residues (8-10GLY) via molecular dynamics and docking simulations. The substrate specificity of papain for 8-10GLY fluctuated considerably with time. There were several residues that were different among those that had a significant impact on binding (RESIDUES_IMPACT) with 10GLY, 9GLY, and 8GLY. Modification of these different residues should allow for control of substrate specificity, providing a framework for modifying substrate specificity in papain and other enzymes.

  4. Life cycle assessment and residue leaching: the importance of parameter, scenario and leaching data selection.

    Science.gov (United States)

    Allegrini, E; Butera, S; Kosson, D S; Van Zomeren, A; Van der Sloot, H A; Astrup, T F

    2015-04-01

    Residues from industrial processes and waste management systems (WMSs) have been increasingly reutilised, leading to landfilling rate reductions and the optimisation of mineral resource utilisation in society. Life cycle assessment (LCA) is a holistic methodology allowing for the analysis of systems and products and can be applied to waste management systems to identify environmental benefits and critical aspects thereof. From an LCA perspective, residue utilisation provides benefits such as avoiding the production and depletion of primary materials, but it can lead to environmental burdens, due to the potential leaching of toxic substances. In waste LCA studies where residue utilisation is included, leaching has generally been neglected. In this study, municipal solid waste incineration bottom ash (MSWI BA) was used as a case study into three LCA scenarios having different system boundaries. The importance of data quality and parameter selection in the overall LCA results was evaluated, and an innovative method to assess metal transport into the environment was applied, in order to determine emissions to the soil and water compartments for use in an LCA. It was found that toxic impacts as a result of leaching were dominant in systems including only MSWI BA utilisation, while leaching appeared negligible in larger scenarios including the entire waste system. However, leaching could not be disregarded a priori, due to large uncertainties characterising other activities in the scenario (e.g. electricity production). Based on the analysis of relevant parameters relative to leaching, and on general results of the study, recommendations are provided regarding the use of leaching data in LCA studies. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. Life cycle assessment and residue leaching: The importance of parameter, scenario and leaching data selection

    Energy Technology Data Exchange (ETDEWEB)

    Allegrini, E., E-mail: elia@env.dtu.dk [Technical University of Denmark, Department of Environmental Engineering, Building 115, 2800 Lyngby (Denmark); Butera, S. [Technical University of Denmark, Department of Environmental Engineering, Building 115, 2800 Lyngby (Denmark); Kosson, D.S. [Vanderbilt University, Department of Civil and Environmental Engineering, Box 1831 Station B, Nashville, TN 37235 (United States); Van Zomeren, A. [Energy Research Centre of the Netherlands (ECN), Department of Environmental Risk Assessment, P.O. Box 1, 1755 ZG Petten (Netherlands); Van der Sloot, H.A. [Hans van der Sloot Consultancy, Dorpsstraat 216, 1721 BV Langedijk (Netherlands); Astrup, T.F. [Technical University of Denmark, Department of Environmental Engineering, Building 115, 2800 Lyngby (Denmark)

    2015-04-15

    Highlights: • Relevance of metal leaching in waste management system LCAs was assessed. • Toxic impacts from leaching could not be disregarded. • Uncertainty of toxicity, due to background activities, determines LCA outcomes. • Parameters such as pH and L/S affect LCA results. • Data modelling consistency and coverage within an LCA are crucial. - Abstract: Residues from industrial processes and waste management systems (WMSs) have been increasingly reutilised, leading to landfilling rate reductions and the optimisation of mineral resource utilisation in society. Life cycle assessment (LCA) is a holistic methodology allowing for the analysis of systems and products and can be applied to waste management systems to identify environmental benefits and critical aspects thereof. From an LCA perspective, residue utilisation provides benefits such as avoiding the production and depletion of primary materials, but it can lead to environmental burdens, due to the potential leaching of toxic substances. In waste LCA studies where residue utilisation is included, leaching has generally been neglected. In this study, municipal solid waste incineration bottom ash (MSWI BA) was used as a case study into three LCA scenarios having different system boundaries. The importance of data quality and parameter selection in the overall LCA results was evaluated, and an innovative method to assess metal transport into the environment was applied, in order to determine emissions to the soil and water compartments for use in an LCA. It was found that toxic impacts as a result of leaching were dominant in systems including only MSWI BA utilisation, while leaching appeared negligible in larger scenarios including the entire waste system. However, leaching could not be disregarded a priori, due to large uncertainties characterising other activities in the scenario (e.g. electricity production). Based on the analysis of relevant parameters relative to leaching, and on general results

  6. Identification of amino acid residues in PEPHC1 important for binding to the tumor-specific receptor EGFRvIII

    DEFF Research Database (Denmark)

    Hansen, Charlotte Lund; Hansen, Paul Robert; Pedersen, Nina

    2008-01-01

    to identify the amino acid residues important for binding of PEPHC1 to EGFRvIII. The results indicate that the amino acid residues at the N-terminus of PEPHC1 are essential for the binding to the mutated receptor. One analog, [Ala(12)]PEPHC1, showed higher selective binding to EGFRvIII than PEPHC1...

  7. Life cycle assessment and residue leaching: The importance of parameter, scenario and leaching data selection

    DEFF Research Database (Denmark)

    Allegrini, Elisa; Butera, Stefania; Kosson, D.S.

    2015-01-01

    boundaries. The importance of data quality and parameter selection in the overall LCA results was evaluated, and an innovative method to assess metal transport into the environment was applied, in order to determine emissions to the soil and water compartments for use in an LCA. It was found that toxic...... of systems and products and can be applied to waste management systems to identify environmental benefits and critical aspects thereof. From an LCA perspective, residue utilisation provides benefits such as avoiding the production and depletion of primary materials, but it can lead to environmental burdens...... in the scenario (e.g. electricity production). Based on the analysis of relevant parameters relative to leaching, and on general results of the study, recommendations are provided regarding the use of leaching data in LCA studies....

  8. Predicting important residues and interaction pathways in proteins using Gaussian Network Model: binding and stability of HLA proteins.

    Directory of Open Access Journals (Sweden)

    Turkan Haliloglu

    Full Text Available A statistical thermodynamics approach is proposed to determine structurally and functionally important residues in native proteins that are involved in energy exchange with a ligand and other residues along an interaction pathway. The structure-function relationships, ligand binding and allosteric activities of ten structures of HLA Class I proteins of the immune system are studied by the Gaussian Network Model. Five of these models are associated with inflammatory rheumatic disease and the remaining five are properly functioning. In the Gaussian Network Model, the protein structures are modeled as an elastic network where the inter-residue interactions are harmonic. Important residues and the interaction pathways in the proteins are identified by focusing on the largest eigenvalue of the residue interaction matrix. Predicted important residues match those known from previous experimental and clinical work. Graph perturbation is used to determine the response of the important residues along the interaction pathway. Differences in response patterns of the two sets of proteins are identified and their relations to disease are discussed.

  9. Impact of river-tide dynamics on the residual water level slope and residual sediment transport in the Pearl River channel networks

    Science.gov (United States)

    Cai, Huayang; Zhang, Zihao; Yang, Qingshu; Ou, Suying

    2016-04-01

    Large-scale delta systems, such as the Rhine-Meuse delta, the Mississippi River delta, the Mekong delta, the Yangtze delta and the Pearl River delta etc., usually feature a typical channel networks, where individual channels are interrelated through a networks system, resulting in both longitudinal and transverse variations of residual water level slope (averaged over a lunar day) caused by the river-tide interplay. Enhancing our insight of river-tide dynamics in these channel networks has vital importance for the protection and management of estuarine environment since river-tide interplay is closely related to sediment transport, water quality, water utilization and estuarine ecosystem. In this study, we investigate the impact of river-tide dynamics on the temporal-spatial changes of flow and suspended sediment load in terms of residual water level slope and residual sediment transport in the Pearl River channel networks, which is one of the complex channel networks in the world. Making use of a nonstationary harmonic analysis (NS_TIDE), the continuous time series observations of velocity covering a spring-neap cycle in 1999 (representing flood season) and 2001 (representing dry season) collected from around 60 stations in the Pearl River channel networks have been used to extract the temporal-spatial changes in residual velocity and tidal properties (including amplitudes and phases) as a function of variable river flow debouching into the delta. On the basis of harmonic analysis, the tidally averaged friction is decomposed into contributions made by riverine forcing alone, river-tide interaction and tidal asymmetry using Chebyshev polynomials approach. It is shown that river flow enhances friction via river-tide interaction, which increases the residual water level slope that influences the distribution of suspended sediment load in the Pearl River channel networks.

  10. Dynamic organization of the mitochondrial protein import machinery.

    Science.gov (United States)

    Straub, Sebastian P; Stiller, Sebastian B; Wiedemann, Nils; Pfanner, Nikolaus

    2016-11-01

    Mitochondria contain elaborate machineries for the import of precursor proteins from the cytosol. The translocase of the outer mitochondrial membrane (TOM) performs the initial import of precursor proteins and transfers the precursors to downstream translocases, including the presequence translocase and the carrier translocase of the inner membrane, the mitochondrial import and assembly machinery of the intermembrane space, and the sorting and assembly machinery of the outer membrane. Although the protein translocases can function as separate entities in vitro, recent studies revealed a close and dynamic cooperation of the protein import machineries to facilitate efficient transfer of precursor proteins in vivo. In addition, protein translocases were found to transiently interact with distinct machineries that function in the respiratory chain or in the maintenance of mitochondrial membrane architecture. Mitochondrial protein import is embedded in a regulatory network that ensures protein biogenesis, membrane dynamics, bioenergetic activity and quality control.

  11. The importance of the non-active site and non-periodical structure located histidine residue respect to the structure and function of exo-inulinase.

    Science.gov (United States)

    Arjomand, Maryam Rezaei; Ahmadian, Gholamreza; Habibi-Rezaei, Mehran; Hassanzadeh, Malihe; Karkhane, Ali Asghar; Moosavi-Movahedi, Ali Akbar; Amanlou, Massoud

    2017-05-01

    Here, we have studied the role of a histidine residue with the lowest solvent accessibility among other histidine residues at the end of a short connecting structure ((189)AELH(192)) of the catalytic domain of the exo-inulinase through creation of H192A mutant. Site-directed mutagenesis method was applied to create the mutant enzyme. Molecular dynamics (MD) simulations, spectroscopic, calorimetric and kinetics analysis were used to study the structural and functional consequences of His192 substitution. Accordingly, the thermo-stabilities and catalytic performance were decreased upon H192A mutation. In silico and experimental approaches evidently confirm that His192 residue of exo-inulinase possesses structural and functional importance regardless of the lack of direct interaction with the substrate or involvement in the catalytic activity of exo-inulinase. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. H2r: Identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments

    Directory of Open Access Journals (Sweden)

    Zwick Matthias

    2008-03-01

    Full Text Available Abstract Background A multiple sequence alignment (MSA generated for a protein can be used to characterise residues by means of a statistical analysis of single columns. In addition to the examination of individual positions, the investigation of co-variation of amino acid frequencies offers insights into function and evolution of the protein and residues. Results We introduce conn(k, a novel parameter for the characterisation of individual residues. For each residue k, conn(k is the number of most extreme signals of co-evolution. These signals were deduced from a normalised mutual information (MI value U(k, l computed for all pairs of residues k, l. We demonstrate that conn(k is a more robust indicator than an individual MI-value for the prediction of residues most plausibly important for the evolution of a protein. This proposition was inferred by means of statistical methods. It was further confirmed by the analysis of several proteins. A server, which computes conn(k-values is available at http://www-bioinf.uni-regensburg.de. Conclusion The algorithms H2r, which analyses MSAs and computes conn(k-values, characterises a specific class of residues. In contrast to strictly conserved ones, these residues possess some flexibility in the composition of side chains. However, their allocation is sensibly balanced with several other positions, as indicated by conn(k.

  13. Identification of key residues in the A-Raf kinase important for phosphoinositide lipid binding specificity.

    Science.gov (United States)

    Johnson, Lindsey M; James, Kristy M; Chamberlain, M Dean; Anderson, Deborah H

    2005-03-01

    Raf kinases are involved in regulating cellular signal transduction pathways in response to a wide variety of external stimuli. Upstream signals generate activated Ras-GTP, important for the relocalization of Raf kinases to the membrane. Upon full activation, Raf kinases phosphorylate and activate downstream kinase in the mitogen-activated protein kinase (MAPK) signaling pathway. The Raf family of kinases has three members, Raf-1, B-Raf, and A-Raf. The ability of Raf-1 and B-Raf to bind phosphatidylserine (PS) and phosphatidic acid (PA) has been show to facilitate Raf membrane associations and regulate Raf kinase activity. We have characterized the lipid binding properties of A-Raf, as well as further characterized those of Raf-1. Both A-Raf and Raf-1 were found to bind to 3-, 4-, and 5-monophosphorylated phosphoinositides [PI(3)P, PI(4)P, and PI(5)P] as well as phosphatidylinositol 3,5-bisphosphate [PI(3,5)P(2)]. In addition, A-Raf also bound specifically to phosphatidylinositol 4,5- and 3,4-bisphosphates [PI(4,5)P(2) and PI(3,4)P(2)] and to PA. A mutational analysis of A-Raf localized the PI(4,5)P(2) binding site to two basic residues (K50 and R52) within the Ras binding domain. Additionally, an A-Raf mutant lacking the first 199 residues [i.e., the entire conserved region 1 (CR1) domain] bound the same phospholipids as full-length Raf-1. This suggests that a second region of A-Raf between amino acids 200 and 606 was responsible for interactions with the monophosphorylated PIs and PI(3,5)P(2). These results raise the possibility that Raf-1 and A-Raf bind to specific phosphoinositides as a mechanism to localize them to particular membrane microdomains rich in these phospholipids. Moreover, the differences in their lipid binding profiles could contribute to their proposed isoform-specific Raf functions.

  14. CFD (Computational Fluid Dynamics) simulators and thermal cracking of heavy oil and ultraheavy residues using microreactor

    Energy Technology Data Exchange (ETDEWEB)

    Jardini, Andre L.; Bineli, Aulus R.R.; Viadana, Adriana M.; Maciel, Maria Regina Wolf; Maciel Filho, Rubens [State University of Campinas (UNICAMP), SP (Brazil). School of Chemical Engineering; Medina, Lilian C.; Gomes, Alexandre de O. [PETROBRAS S.A., Rio de Janeiro, RJ (Brazil). Centro de Pesquisas (CENPES); Barros, Ricardo S. [University Foundation Jose Bonifacio (FUJB), Rio de Janeiro, RJ (Brazil)

    2008-07-01

    In this paper, the design of microreactor with microfluidics channels has been carried out in Computer Aided Design Software (CAD) and constructed in rapid prototyping system to be used in chemical reaction processing of the heavy oil fractions. The flow pattern properties of microreactor (fluid dynamics, mixing behavior) have been considered through CFD (computational fluid dynamics) simulations. CFD calculations are also used to study the design and specification of new microreactor developments. The potential advantages of using a microreactor include better control of reaction conditions, improved safety and portability. A more detailed crude assay of the raw national oil, whose importance was evidenced by PETROBRAS/CENPES allows establishing the optimum strategies and processing conditions, aiming at a maximum utilization of the heavy oil fractions, towards valuable products. These residues are able to be processed in microreactor, in which conventional process like as hydrotreating, catalytic and thermal cracking may be carried out in a much more intensified fashion. The whole process development involves a prior thermal study to define the possible operating conditions for a particular task, the microreactor design through computational fluid dynamics and construction using rapid prototyping. This gives high flexibility for process development, shorter time, and costumer/task oriented process/product development. (author)

  15. Transforming Government Service: The Importance of Dynamic Capabilities

    DEFF Research Database (Denmark)

    Pedersen, Keld

    2017-01-01

    both aiming at realizing this strategy by reengineering back office processes and implement one-stop shopping. The research contributes to the e-government literature by identifying key differences between the two cases in terms of dynamic capabilities, by identifying the importance......The Danish government has defined an ambitious e-government strategy aiming to increase both citizen centricity and the efficiency of government service production and delivery. This research uses dynamic capability theory to compare a highly successful and a less successful e-government program...

  16. Dynamics of mature pea residue nitrogen turnover in unplanted soil under field conditions

    DEFF Research Database (Denmark)

    Jensen, E.S.

    1994-01-01

    mineralizable after 2 yr of decomposition, indicating that the remaining residue N-15 was present in rather recalcitrant soil organic matter. After 90 days of decomposition N-15 unaccounted for corresponded to 10% of the input, increasing to 20-30% after 2-3 yr of decomposition. The main part of the N......The dynamics of N-15-labelled mature, pea (Pisum sativum L.) residue turnover in soil were studied in two 3 yr experiments, using residue sizes of decomposition there was a sharp decline in the amount of N-15 in organic...... to the biomass N-15, but the size of the potentially-mineralizable N-15 pool was much smaller than the biomass N-15 pool. After 3 yr of decomposition, 28% (Expt 1) and 45% (Expt 2) of the residue N-15 input was present in the topsoil in organic forms. Only 1-2% of the residual organic N-15 was potentially...

  17. 3D Dynamic Finite Element Analysis of the Nonuniform Residual Stress in Ultrasonic Impact Treatment Process

    Science.gov (United States)

    Hu, Shengsun; Guo, Chaobo; Wang, Dongpo; Wang, Zhijiang

    2016-09-01

    The nonuniform distributions of the residual stress were simulated by a 3D finite element model to analyze the elastic-plastic dynamic ultrasonic impact treatment (UIT) process of multiple impacts on the 2024 aluminum alloy. The evolution of the stress during the impact process was discussed. The successive impacts during the UIT process improve the uniformity of the plastic deformation and decrease the maximum compressive residual stress beneath the former impact indentations. The influences of different controlled parameters, including the initial impact velocity, pin diameter, pin tip, device moving, and offset distances, on the residual stress distributions were analyzed. The influences of the controlled parameters on the residual stress distributions are apparent in the offset direction due to the different surface coverage in different directions. The influences can be used to understand the UIT process and to obtain the desired residual stress by optimizing the controlled parameters.

  18. Dynamics of pear-pathogenic Stemphylium vesicarium in necrotic plant residues in Dutch pear orchards

    NARCIS (Netherlands)

    Köhl, J.; Jong, de P.F.; Kastelein, P.; Groenenboom-de Haas, de B.H.; Anbergen, R.H.N.; Balkhoven, H.; Wubben, J.P.

    2013-01-01

    Brown spot disease on pear caused by Stemphylium vesicarium may affect leaves and fruits. Inoculum sources present on orchard floors play an important role in the epidemiology of pear brown spot. The pathogen can overwinter on plant residues and multiply and spread on the residues during the growing

  19. Dynamically important magnetic fields near accreting supermassive black holes.

    Science.gov (United States)

    Zamaninasab, M; Clausen-Brown, E; Savolainen, T; Tchekhovskoy, A

    2014-06-05

    Accreting supermassive black holes at the centres of active galaxies often produce 'jets'--collimated bipolar outflows of relativistic particles. Magnetic fields probably play a critical role in jet formation and in accretion disk physics. A dynamically important magnetic field was recently found near the Galactic Centre black hole. If this is common and if the field continues to near the black hole event horizon, disk structures will be affected, invalidating assumptions made in standard models. Here we report that jet magnetic field and accretion disk luminosity are tightly correlated over seven orders of magnitude for a sample of 76 radio-loud active galaxies. We conclude that the jet-launching regions of these radio-loud galaxies are threaded by dynamically important fields, which will affect the disk properties. These fields obstruct gas infall, compress the accretion disk vertically, slow down the disk rotation by carrying away its angular momentum in an outflow and determine the directionality of jets.

  20. Residues in the Nucleosome Acidic Patch Regulate Histone Occupancy and Are Important for FACT Binding in Saccharomyces cerevisiae.

    Science.gov (United States)

    Hodges, Amelia J; Gloss, Lisa M; Wyrick, John J

    2017-07-01

    The essential histone chaperone FACT plays a critical role in DNA replication, repair, and transcription, primarily by binding to histone H2A-H2B dimers and regulating their assembly into nucleosomes. While FACT histone chaperone activity has been extensively studied, the exact nature of the H2A and H2B residues important for FACT binding remains controversial. In this study, we characterized the functions of residues in the histone H2A and H2B acidic patch, which is important for binding many chromatin-associated factors. We found that mutations in essential acidic patch residues cause a defect in histone occupancy in yeast, even though most of these histone mutants are expressed normally in yeast and form stable nucleosomes in vitro Instead, we show that two acidic patch residues, H2B L109 and H2A E57, are important for histone binding to FACT in vivo We systematically screened mutants in other H2A and H2B residues previously suspected to be important for FACT binding and confirmed the importance of H2B M62 using an in-vivo FACT-binding assay. Furthermore, we show that, like deletion mutants in FACT subunits, an H2A E57 and H2B M62 double mutant is lethal in yeast. In summary, we show that residues in the nucleosome acidic patch promote histone occupancy and are important for FACT binding to H2A-H2B dimers in yeast. Copyright © 2017 by the Genetics Society of America.

  1. Field evaluations of residual pesticide applications and misting system on militarily relevant materials against medically important mosquitoes in Thailand

    Science.gov (United States)

    A key strategy to reduce insect-borne disease is to reduce contact between disease vectors and hosts. In the current study, residual pesticide application and misting system were applied on militarily relevant materials and evaluated against medically important mosquitoes. Field evaluations were car...

  2. Structural analysis of a penicillin V acylase from Pectobacterium atrosepticum confirms the importance of two Trp residues for activity and specificity.

    Science.gov (United States)

    Avinash, Vellore Sunder; Panigrahi, Priyabrata; Chand, Deepak; Pundle, Archana; Suresh, Cheravakattu Gopalan; Ramasamy, Sureshkumar

    2016-02-01

    Penicillin V acylases (PVA) catalyze the deacylation of the beta-lactam antibiotic phenoxymethylpenicillin (Pen V). They are members of the Ntn hydrolase family and possess an N-terminal cysteine as the main catalytic nucleophile residue. They form the evolutionarily related cholylglycine hydrolase (CGH) group which includes bile salt hydrolases (BSH) responsible for bile deconjugation. Even though a few PVA and BSH structures have been reported, no structure of a functional PVA from Gram-negative bacteria is available. Here, we report the crystal structure of a highly active PVA from Gram-negative Pectobacterium atrosepticum (PaPVA) at 2.5Å resolution. Structural comparison with PVAs from Gram-positive bacteria revealed that PaPVA had a distinctive tetrameric structure and active site organization. In addition, mutagenesis of key active site residues and biochemical characterization of the resultant variants elucidated the role of these residues in substrate binding and catalysis. The importance of residue Trp23 and Trp87 side chains in binding and correct positioning of Pen V by PVAs was confirmed using mutagenesis and substrate docking with a 15ns molecular dynamics simulation. These results establish the unique nature of Gram-negative CGHs and necessitate further research about their substrate spectrum.

  3. Residue dynamics of procymidone in leeks and soil in greenhouses by smoke generator application.

    Science.gov (United States)

    Chen, Li; Li, Xue-Sheng; Wang, Zheng-Quan; Pan, Can-Ping; Jin, Ru-Chen

    2010-01-01

    A modified QuEChERS-GC-MS method for analysis of procymidone residue in leeks and soil was developed and validated. Procymidone residue dynamics and residues in supervised field trials at GAP conditions in leeks and soil in greenhouses were studied. Leek samples were treated under microwave radiation for 1min before homogenization, followed by extracting with acetonitrile and clean-up with reverse solid phase dispersion by primary and secondary amine (PSA). Procymidone residue was determined by GC-MS in selected ion monitoring (SIM) mode. At fortification levels of 0.02, 0.2 and 2mg/kg in leeks and soil, it was shown that recoveries ranged from 74.9% to 100.8% with relative standard deviations of 1.3-8.5%. At four geographical experimental plots, procymidone residue in leeks and soil showed a relatively fast dissipation rate, with half-lives of 4.52-8.76 days for leeks and 3.76-5.65 days for soil. At pre-harvest intervals of 21-30 days, procymidone residue ranged from 0.033 to 0.17mg/kg in leeks, and 0.020-1.75mg/kg in soil. Residues persistence varied in leeks and soil in four field trials, suggesting that it might be affected by some physical and chemical factors, growth dilution factor, soil characteristics and microorganisms.

  4. Dynamic Investigation of Interface Stress on Below-Knee Residual Limb in a Prosthetic Socket

    Institute of Scientific and Technical Information of China (English)

    贾晓红; 张明; 王人成; 金德闻

    2004-01-01

    The dynamic effects of inertial loads on the interface stresses between a residual limb and the trans-tibial prosthetic socket were investigated. A 3-D nonlinear finite element model, based on the actual geometry of the residual limb, including internal bones and socket liner, was developed to study the mechanical interaction between the socket and the residual limb during walking. To simulate the friction/slip boundary conditions between the skin and liner, automated surface-to-surface contact was used. The results show that interface pressure and shear stress have a similar double-peaked waveform shape in the stance phase. The average difference in interface stresses between the cases with and without consideration of inertial forces is 8.4% in the stance phase and 20.1% in the swing phase. The results suggest that the dynamic effects of inertial loads on interface stress distribution during walking must be considered in prosthetic socket design.

  5. Important aspects of residue sampling in drilling dikes; Aspectos importantes para a amostragem de residuos em diques de perfuracao

    Energy Technology Data Exchange (ETDEWEB)

    Silva, Gilvan Ferreira da [PETROBRAS, Rio de Janeiro (Brazil). Centro de Pesquisas. Div. de Explotacao

    1989-12-31

    This paper describes the importance of sampling in the evaluation of physical and chemical properties of residues found in drilling dikes, considering the later selection of treatment methods or discard of these residues. We present the fundamental concepts of applied statistics, which are essential to the elaboration of sampling plans, with views of obtaining exact and precise results. Other types of samples are also presented, as well as sampling equipment and methods for storage and preservation of the samples. As a conclusion, we the example of the implementation of a sampling plan. (author) 3 refs., 9 figs., 3 tabs.

  6. Complement factor 5a receptor chimeras reveal the importance of lipid-facing residues in transport competence

    DEFF Research Database (Denmark)

    Klco, Jeffery M; Sen, Saurabh; Hansen, Jakob L

    2009-01-01

    . Despite relatively conservative substitutions, the lipid-facing chimeras (TM1, TM2, TM4, TM5, TM6 or TM7) were retained in the endoplasmic reticulum/cis-Golgi network. With the exception of the TM7 chimera that did not bind ligand, the lipid-facing chimeras bound ligand with low affinity, but similar...... oligomerization studies demonstrated energy transfer between the wild-type complement factor 5a receptor and the lipid-facing chimeras, suggesting that the lipid-facing residues within a single TM segment are not essential for oligomerization. These studies highlight the importance of the lipid-facing residues...

  7. Scenario analysis of tillage, residue and fertilization management effects on soil organic carbon dynamics

    NARCIS (Netherlands)

    Wang Xiaobin,; Cai Diangxiong,; Hoogmoed, W.B.; Oenema, O.; Perdok, U.D.

    2005-01-01

    Based on data from 10-year field experiments on residue/fertilizer management in the dryland farming region of northern China, Century model was used to simulate the site-specific ecosystem dynamics through adjustment of the model's parameters, and the applicability of the model to propose soil orga

  8. The clinical importance of dynamic lung hyperinflation in COPD.

    Science.gov (United States)

    O'Donnell, Denis E; Laveneziana, Pierantonio

    2006-12-01

    Lung hyperinflation commonly accompanies expiratory flow-limitation in patients with Chronic Obstructive Pulmonary Disease (COPD) and contributes importantly to dyspnea and activity limitation. It is not surprising, therefore, that lung hyperinflation has become an important therapeutic target in symptomatic COPD patients. There is increasing evidence that acute dynamic increases in lung hyperinflation, under conditions of worsening expiratory flow-limitation and increased ventilatory demand (or both) can seriously stress cardiopulmonary reserves, particularly in patients with more advanced disease. Our understanding of the physiological mechanisms of dynamic lung hyperinflation during both physical activity and exacerbations in COPD continues to grow, together with an appreciation of its serious negative mechanical and sensory consequences. In this review, we will discuss the basic pathophysiology of COPD during rest, exercise and exacerbation so as to better understand how this can be pharmacologically manipulated for the patient's benefit. Finally, we will review current concepts of the mechanisms of symptom relief and improved exercise endurance following pharmacological lung volume reduction.

  9. Structural insights into the evolution of a non-biological protein: importance of surface residues in protein fold optimization.

    Directory of Open Access Journals (Sweden)

    Matthew D Smith

    Full Text Available Phylogenetic profiling of amino acid substitution patterns in proteins has led many to conclude that most structural information is carried by interior core residues that are solvent inaccessible. This conclusion is based on the observation that buried residues generally tolerate only conserved sequence changes, while surface residues allow more diverse chemical substitutions. This notion is now changing as it has become apparent that both core and surface residues play important roles in protein folding and stability. Unfortunately, the ability to identify specific mutations that will lead to enhanced stability remains a challenging problem. Here we discuss two mutations that emerged from an in vitro selection experiment designed to improve the folding stability of a non-biological ATP binding protein. These mutations alter two solvent accessible residues, and dramatically enhance the expression, solubility, thermal stability, and ligand binding affinity of the protein. The significance of both mutations was investigated individually and together, and the X-ray crystal structures of the parent sequence and double mutant protein were solved to a resolution limit of 2.8 and 1.65 A, respectively. Comparative structural analysis of the evolved protein to proteins found in nature reveals that our non-biological protein evolved certain structural features shared by many thermophilic proteins. This experimental result suggests that protein fold optimization by in vitro selection offers a viable approach to generating stable variants of many naturally occurring proteins whose structures and functions are otherwise difficult to study.

  10. Efficient quantification of the importance of contacts for the dynamical stability of proteins.

    Science.gov (United States)

    Hamacher, Kay

    2011-04-15

    Understanding the stability of the native state and the dynamics of a protein is of great importance for all areas of biomolecular design. The efficient estimation of the influence of individual contacts between amino acids in a protein structure is a first step in the reengineering of a particular protein for technological or pharmacological purposes. At the same time, the functional annotation of molecular evolution can be facilitated by such insight. Here, we use a recently suggested, information theoretical measure in biomolecular design - the Kullback-Leibler-divergence - to quantify and therefore rank residue-residue contacts within proteins according to their overall contribution to the molecular mechanics. We implement this protocol on the basis of a reduced molecular model, which allows us to use a well-known lemma of linear algebra to speed up the computation. The increase in computational performance is around 10(1)- to 10(4)-fold. We applied the method to two proteins to illustrate the protocol and its results. We found that our method can reliably identify key residues in the molecular mechanics and the protein fold in comparison to well-known properties in the serine protease inhibitor. We found significant correlations to experimental results, e.g., dissociation constants and Φ values.

  11. Aflatoxin B1 residues in imported and local broiler, s breast and thigh muscle in Kurdistan region

    Directory of Open Access Journals (Sweden)

    E.P. Candlan

    2015-06-01

    Full Text Available Residues of Aflatoxins and their metabolites might be present in meat and other products of animals receiving Aflatoxin contaminated feeds which could subsequently create health problems in man. Eighty nine imported (Iran/Khosh pokht; (Turkey/Yam-tapilic, Lades, Senplic, Kapidac, Kozoa, Oznesilpilic and (Brazil, hilal, Sadia, and 90 locally produced (Hoshiar poultry farm, Nihad poultry farm, Hokar poultry farm, Mansoor poultry farm, AL-Shimal poultry house, Mardin poultry house and AL-Eetimad poultry slaughterhouse broiler breast and thigh muscle samples were examined for residual Aflatoxin B1 using ELIZA test. Results revealed that out of 89 imported samples only 21 (23.59% were positive, but only 2 (2.24% were rejected, while the remaining 87 samples (97.75% were acceptable. Concerning the local samples, results showed that 19 samples (21.11% were positive, but 10 (11.11% were rejected, while the remaining 80 samples (88.88% were accepted. The public health importance of residual AFB1 in broiler meat samples was discussed.

  12. Isomerization of Asp residues plays an important role in αA-crystallin dissociation.

    Science.gov (United States)

    Takata, Takumi; Fujii, Noriko

    2016-03-01

    Aged cataract formation is caused by the accumulative precipitation of lens proteins incorporating diverse post-translational modifications. α-Crystallin, a major structural and functional lens protein, consists of a large polymeric structure that is dissociated and insolubilized with accumulative post-translational modifications. One such modification, isomerization of Asp, was recently identified in αB-crystallin monomers derived from aged lens. However, the distributions of Asp isomers in each lens fraction remain unknown. Here, α-crystallin fractions from aged lens were separated into heteropolymeric and monomeric forms to determine the Asp isomerization ratios in each fraction. Lens of four different ages were homogenized and centrifuged, and the soluble fraction was applied to size-exclusion chromatography. The heteropolymeric α-crystallin and monomeric crystallin fractions were obtained and concentrated. After trypsin digestion, each fraction was independently applied to liquid chromatography equipped with mass spectrometry to extract α-crystallin-derived peptides containing Asp isomers. The results showed that Asp58, Asp84 and Asp151 of αA-crystallin were highly isomerized in the monomeric fraction, but not isomerized to the same level in the heteropolymeric fraction. Each type of Asp isomerization increased in an age-dependent manner, was site-specific and was similar to previous results from lens water-insoluble fractions. These results imply that isomerization of Asp residues leads to dissociation of αA-crystallin from the heteropolymeric state and induces insolubilization in aged lens. Taken together, our findings suggest that isomerization of Asp might disrupt the higher order polymeric state of α-crystallin, resulting in decreased solubility and function, ultimately contributing to lens protein impairment and cataract formation with aging. © 2015 Federation of European Biochemical Societies.

  13. Effect of the secondary structure of carbohydrate residues of alpha 1-acid glycoprotein (orosomucoid) on the local dynamics of Trp residues.

    Science.gov (United States)

    Albani, Jihad René

    2004-01-01

    We studied in this work the relation between the secondary structure of the carbohydrate residues of alpha1-acid glycoprotein and the local motions of Trp residues of the protein. We measured for this purpose the fluorescence emission intensity and anisotropy of the Trp residues between -46 and +30 degrees of the sialylated and asialylated protein. Our results indicate that, in both forms, the global profile of the emission intensity with temperature shows that Trp residues display static and collisional interaction with the neighboring amino acids. However, the profile of the asialylated form is more structured than that observed for the sialylated protein. The Y-plot analysis of the emission-anisotropy results indicated that the frictional resistance to rotation of the surface Trp residue is less important in the sialylated protein than in the asialylated form. This result is in good agreement with the fact that, in the asialylated conformation, the carbohydrate residues are closer to the protein surface than in the sialylated form, thereby increasing the contact of the surface Trp residue with the neighboring amino acids. Also, the interaction between the carbohydrate residues and the surface Trp residue contributes to the modification of the frictional resistance to rotation of the fluorophore.

  14. Predicting functional residues in Plasmodium falciparum plasmepsins by combining sequence and structural analysis with molecular dynamics simulations.

    Science.gov (United States)

    Valiente, Pedro A; Batista, Paulo R; Pupo, Amaury; Pons, Tirso; Valencia, Alfonso; Pascutti, Pedro G

    2008-11-01

    Plasmepsins are aspartic proteases involved in the initial steps of the hemoglobin degradation pathway, a critical stage in the Plasmodium falciparum life cycle during human infection. Thus, they are attractive targets for novel therapeutic compounds to treat malaria, which remains one of the world's biggest health problems. The three-dimensional structures available for P. falciparum plasmepsins II and IV make structure-based drug design of antimalarial compounds that focus on inhibiting plasmepsins possible. However, the structural flexibility of the plasmepsin active site cavity combined with insufficient knowledge of the functional residues and of those determining the specificity of parasitic enzymes is a drawback when designing specific inhibitors. In this study, we have combined a sequence and structural analysis with molecular dynamics simulations to predict the functional residues in P. falciparum plasmepsins. The careful analysis of X-ray structures and 3D models carried out here suggests that residues Y17, V105, T108, L191, L242, Q275, and T298 are important for plasmepsin function. These seven amino acids are conserved across the malarial strains but not in human aspartic proteases. Residues V105 and T108 are localized in a flap of an interior pocket and they only establish contacts with a specific non-peptide achiral inhibitor. We also observed a rapid conformational change in the L3 region of plasmepsins that closes the active site of the enzyme, which explains earlier experimental findings. These results shed light on the role of V105 and T108 residues in plasmepsin specificities, and they should be useful in structure-based design of novel, selective inhibitors that may serve as antimalarial drugs.

  15. Dynamics of difenoconazole and propiconazole residues on pomegranate over 2 years under field conditions.

    Science.gov (United States)

    Mohapatra, Soudamini

    2016-03-01

    Residue dynamics of difenoconazole and propiconazole on pomegranate was studied after application at the recommended and double doses of 125 and 250 g active ingredient (a.i.) ha(-1) during August-October 2012. The study was repeated during the same period in 2013. QuEChERS method, in conjunction with gas chromatography (GC), was used for analysis of the fungicides after carrying out the method validation. The recoveries of the fungicides from pomegranate and soil were between 80.3 and 96.2 %; the limit of detection (LOD) and limit of quantification (LOQ) were 0.016 and 0.05 mg kg(-1), respectively. The uncertainties of measurement were between 9.7 and 16.3 %. The initial residue deposits of difenoconazole were 0.875 and 1.205 mg kg(-1) from treatment at the recommended dose and 1.54 and 1.672 mg kg(-1) from treatment at the double dose from the first- and second-year studies. Propiconazole residues were 0.663 and 0.864 mg kg(-1) from recommended dose treatments and 1.474 and 2.045 mg kg(-1) from double dose treatments from the first- and second-year studies. The half-lives of degradation of difenoconazole were 6.4-8.4 days and propiconazole 7.9-8.5 days over the 2 years. Residues of difenoconazole and propiconazole remained on the pomegranate fruit surface and did not move to the edible part (aril). The pre-harvest intervals (PHIs), the time required for the residues to reduce below their respective EU maximum residue limits (MRLs), were 25.4 and 30.8 days for difenoconazole and 33.3 and 43.8 days for propiconazole from treatments at the recommended and double doses, respectively. Keeping in view consumer safety, the longer PHI from the two studies has been selected.

  16. Importance of Dynamic Inflow Model Predictive Control of Wind Turbines

    DEFF Research Database (Denmark)

    Odgaard, Peter Fogh; Knudsen, Torben; Overgaard, Anders;

    2015-01-01

    The efficiency of including dynamic inflow in the model based design of wind turbine controller has been discussed for many years in the wind energy community with out getting to a safe conclusion. This paper delivers a good argument in favor of including dynamic inflow. The main contributions...

  17. Relative-Residual-Based Dynamic Schedule for Belief Propagation Decoding of LDPC Codes

    Institute of Scientific and Technical Information of China (English)

    Huang Jie; Zhang Lijun

    2011-01-01

    Two Relative-Residual-based Dynamic Schedules (RRDS) for Belief Propagation (BP) decoding of Low-Density Parity-Check (LDPC) codes are proposed,in which the Variable code-RRDS (VN-RRDS) is a greediness-reduced version of the Check code-RRDS (CN-RRDS).The RRDS only processes the variable (or check) node,which has the maximum relative residual among all the variable (or check) nodes in each decoding iteration,thus keeping less greediness and decreased complexity in comparison with the edge-based Variable-to-Check Residual Belief Propagation (VC-RBP) algorithm.Moreover,VN-RRDS propagates first the message which has the largest residual based on all check equations.For different types of LDPC codes,simulation results show that the convergence rate of RRDS is higher than that of VC-RBP while keeping very low computational complexity.Furthermore,VN-RRDS achieves faster convergence as well as better performance than CN-RRDS.

  18. Exploiting Oceanic Residual Depth to Quantify Present-day Dynamic Topography at the Earth's Surface

    Science.gov (United States)

    Hoggard, Mark; White, Nicky

    2014-05-01

    Convective circulation within the mantle causes vertical motions at the Earth's surface. This dynamic topography is time dependent and occurs on wavelengths of 1000s km with maximum amplitudes of ±2 km. Convective simulation models have been used extensively to make predictions of dynamic topography and have thus far out-paced observational constraints. Here, the well-established relationship between seafloor subsidence and age is used to produce a global map of residual depth anomalies in the oceanic realm. Care is taken to remove other causes of topography, including an isostatic correction for sedimentary loading that takes compaction into account, a correction for variable oceanic crustal thickness, and lithospheric thickening with age away from mid-ocean ridge spreading centres. A dataset including over 1000 seismic reflection profiles and 300 modern wide-angle refraction experiments has been amassed, primarily on old ocean floor adjacent to the continents. Calculation of residual depth yields a map of present-day dynamic topography with amplitudes significantly larger than the errors associated with the corrections. One of the most interesting results occurs along the west coast of Africa, where two full 2000 km wavelengths of dynamic topography have been captured with amplitudes ±1 km that correlate well with the long-wavelength free air gravity anomaly. Comparison with predictive models reveal poor to moderate correlations. This is a direct result of the limited resolution of the mantle tomography models used to set-up convection simulations and also the currently poor understanding of viscosity structure within the Earth. It is hoped that this residual depth dataset should provide an excellent surface boundary constraint for future convective simulation.

  19. Molecular dynamics studies unravel role of conserved residues responsible for movement of ions into active site of DHBPS

    Science.gov (United States)

    Shinde, Ranajit Nivrutti; Karthikeyan, Subramanian; Singh, Balvinder

    2017-01-01

    3,4-dihydroxy-2-butanone-4-phosphate synthase (DHBPS) catalyzes the conversion of D-ribulose 5-phosphate (Ru5P) to L-3,4-dihydroxy-2-butanone-4-phosphate in the presence of Mg2+. Although crystal structures of DHBPS in complex with Ru5P and non-catalytic metal ions have been reported, structure with Ru5P along with Mg2+ is still elusive. Therefore, mechanistic role played by Mg2+ in the structure of DHBPS is poorly understood. In this study, molecular dynamics simulations of DHBPS-Ru5P complex along with Mg2+ have shown entry of Mg2+ from bulk solvent into active site. Presence of Mg2+ in active site has constrained conformations of Ru5P and has reduced flexibility of loop-2. Formation of hydrogen bonds among Thr-108 and residues - Gly-109, Val-110, Ser-111, and Asp-114 are found to be critical for entry of Mg2+ into active site. Subsequent in silico mutations of residues, Thr-108 and Asp-114 have substantiated the importance of these interactions. Loop-4 of one monomer is being proposed to act as a “lid” covering the active site of other monomer. Further, the conserved nature of residues taking part in the transfer of Mg2+ suggests the same mechanism being present in DHBPS of other microorganisms. Thus, this study provides insights into the functioning of DHBPS that can be used for the designing of inhibitors.

  20. Dynamics of novel insecticide HNPC-A9908 residue in vegetable-field ecosystem

    Institute of Scientific and Technical Information of China (English)

    OU Xiao-ming; YU Shu-ying; FAN De-fang; WANG Xiao-guang

    2006-01-01

    HNPC-A9908 (o-(3-phenoxybenzyl)-2-methylthio-1-(4-chlorophenyl) propyl ketone oxime), a novel oxime insecticide, is a highly effective and broad-spectrum insecticide which can be widely used to control many species of foliar insects on various crops. A study was conducted to evaluate the fate of HNPC-A9908 and study the degradation dynamics of HNPC-A9908 residue in vegetable field ecosystem. The results showed that degradation of HNPC-A9908 was much faster in vegetable pakchoi than in soil, and its half-life in pakchoi and soil was 1.32 and 3.75 d, respectively. The final residue of HNPC-A9908 in pakchoi was at the undetectable level to 0.122 mg/kg. As a conclusion, a dosage of 90 g/hm2 was suggested and considered to be safe to human beings and animals.

  1. Surface residues dynamically organize water bridges to enhance electron transfer between proteins

    CERN Document Server

    de la Lande, Aurélien; Řezáč, Jan; Sanders, Barry C; Salahub, Dennis R; 10.1073/pnas.0914457107

    2010-01-01

    Cellular energy production depends on electron transfer (ET) between proteins. In this theoretical study, we investigate the impact of structural and conformational variations on the electronic coupling between the redox proteins methylamine dehydrogenase and amicyanin from Paracoccus denitrificans. We used molecular dynamics simulations to generate configurations over a duration of 40ns (sampled at 100fs intervals) in conjunction with an ET pathway analysis to estimate the ET coupling strength of each configuration. In the wild type complex, we find that the most frequently occurring molecular configurations afford superior electronic coupling due to the consistent presence of a water molecule hydrogen-bonded between the donor and acceptor sites. We attribute the persistence of this water bridge to a "molecular breakwater" composed of several hydrophobic residues surrounding the acceptor site. The breakwater supports the function of nearby solvent-organizing residues by limiting the exchange of water molecul...

  2. Tyr-199 and charged residues of pharaonis Phoborhodopsin are important for the interaction with its transducer.

    Science.gov (United States)

    Sudo, Yuki; Iwamoto, Masayuki; Shimono, Kazumi; Kamo, Naoki

    2002-01-01

    pharaonis Phoborhodopsin (ppR; also pharaonis sensory rhodopsin II, psRII) is a retinal protein in Natronobacterium pharaonis and is a receptor of negative phototaxis. It forms a complex with its transducer, pHtrII, in membranes and transmits light signals by protein-protein interaction. Tyr-199 is conserved completely in phoborhodopsins among a variety of archaea, but it is replaced by Val (for bacteriorhodopsin) and Phe (for sensory rhodopsin I). Previously, we (Sudo, Y., M. Iwamoto, K. Shimono, and N. Kamo, submitted for publication) showed that analysis of flash-photolysis data of a complex between D75N and the truncated pHtrII (t-Htr) give a good estimate of the dissociation constant K(D) in the dark. To investigate the importance of Tyr-199, K(D) of double mutants of D75N/Y199F or D75N/Y199V with t-Htr was estimated by flash-photolysis and was approximately 10-fold larger than that of D75N, showing the significant contribution of Tyr-199 to binding. The K(D) of the D75N/t-Htr complex increased with decreasing pH, and the data fitted well with the Henderson-Hasselbach equation with a single pK(a) of 3.86 +/- 0.02. This suggests that certain deprotonated carboxyls at the surface of the transducer (possibly Asp-102, Asp-104, and Asp-106) are needed for the binding. PMID:12080131

  3. The reverse logistics importance in the management of residues of plastic packaging of lubricants and the program jogue limpo

    Directory of Open Access Journals (Sweden)

    Everaldo Francisco da Silva

    2017-07-01

    Full Text Available This article aims to demonstrate the importance of the Reverse Logistics in the management of solid residues through the Jogue Limpo program, an initiative dedicated to the destination and recycling of lubricant packaging. In the current context, where natural resources are scarce, the environmental issue is a factor of differentiation in business, so the destination of the waste we produce along the production chain and the possibility of reuse and mitigation of possible environmental impacts are extremely important for the society. The article seeks to show how the Reverse Logistics is the means to interconnect stakeholders for the correct destination and reuse of resources, as well as the benefits of this initiative for the society.

  4. Oceanic residual depth measurements, the plate cooling model, and global dynamic topography

    Science.gov (United States)

    Hoggard, Mark J.; Winterbourne, Jeff; Czarnota, Karol; White, Nicky

    2017-03-01

    Convective circulation of the mantle causes deflections of the Earth's surface that vary as a function of space and time. Accurate measurements of this dynamic topography are complicated by the need to isolate and remove other sources of elevation, arising from flexure and lithospheric isostasy. The complex architecture of continental lithosphere means that measurement of present-day dynamic topography is more straightforward in the oceanic realm. Here we present an updated methodology for calculating oceanic residual bathymetry, which is a proxy for dynamic topography. Corrections are applied that account for the effects of sedimentary loading and compaction, for anomalous crustal thickness variations, for subsidence of oceanic lithosphere as a function of age and for non-hydrostatic geoid height variations. Errors are formally propagated to estimate measurement uncertainties. We apply this methodology to a global database of 1936 seismic surveys located on oceanic crust and generate 2297 spot measurements of residual topography, including 1161 with crustal corrections. The resultant anomalies have amplitudes of ±1 km and wavelengths of ˜1000 km. Spectral analysis of our database using cross-validation demonstrates that spherical harmonics up to and including degree 30 (i.e., wavelengths down to 1300 km) are required to accurately represent these observations. Truncation of the expansion at a lower maximum degree erroneously increases the amplitude of inferred long-wavelength dynamic topography. There is a strong correlation between our observations and free-air gravity anomalies, magmatism, ridge seismicity, vertical motions of adjacent rifted margins, and global tomographic models. We infer that shorter wavelength components of the observed pattern of dynamic topography may be attributable to the presence of thermal anomalies within the shallow asthenospheric mantle.

  5. Dynamics, Residue and Risk Assessment of Nitenpyram in Rice and Paddy Field

    Directory of Open Access Journals (Sweden)

    YUAN Xue-xia

    2016-09-01

    Full Text Available Residues dynamics, final residual levels and dietary intake risk of nitenpyram in rice and paddy field were investigated in three dif-ferent regions of China(Shandong, Henan and Anhui. A method was illustrated to detect nitenpyram residues in paddy, plant, brown rice, paddy water and soil. The residues in paddy and rice were extracted with methanol+phosphate buffer(0.2 mol·L-1, pH=7.0(60+40, adjust pH to 2.5, then cleaned up with solid phase extraction column and 0.22 μm filter membrane, and then analyzed by HPLC with an ul-traviolet detector at 260 nm. When spiked 0.05, 0.5, 1.0 mg·kg-1, the recoveries of nitenpyram in paddy plant and brown rice were 78.4%~94.7% and 84.0%~94.2%, respectively. The residues in paddy water and soil were extracted with phosphate buffer (0.2 mol·L-1, pH=7.0, when spiked 0.01, 0.5, 1.0 mg·kg-1, the recoveries of nitenpyram in paddy water and soil were 84.6%~98.0% and 93.7%~97.1%, respective-ly, which indicated this method match the requirement of the detection. Two years results showed that nitenpyram belongs to easily degraded pesticides, because all half-lives were below 1.4 d in rice plant, as well as below 4.2 d in paddy water. Final residual levels of nitenpyram in rice were all below 0.05 mg·kg-1,which was far below the Japanese maximum residue limit(0.5 mg·kg-1. The risk quotients (RQs were low for different populations in China, which indicated its low risk in rice. Therefore, the rice with nitenpyram applied, according to the recom-mend method, 45 g·hm-2 application once, with 21 days collection interval, was safe.

  6. A new dynamical diffraction-based technique of residual stress measurements in thin films

    CERN Document Server

    Agamalian, M; Kaiser, H; Rehm, C; Werner, S A

    2002-01-01

    The recently discovered dynamical diffraction effect 'neutron camel' was used for residual stress measurements in a thick Si (111) crystal coated with a 2000 A-thick Ni film. The observed asymmetry of the back-face rocking curve corresponds to the bending radius of propor to 19 km and the tension force applied to the Ni film is propor to 90 N/m. Relative deformation of the Si crystallographic cells in the vicinity of diffractive surfaces is vertical stroke partial deriv u sub z /partial deriv z vertical stroke approx 1.6 x 10 sup - sup 6. (orig.)

  7. Site-directed mutagenesis of HgcA and HgcB reveals amino acid residues important for mercury methylation.

    Science.gov (United States)

    Smith, Steven D; Bridou, Romain; Johs, Alexander; Parks, Jerry M; Elias, Dwayne A; Hurt, Richard A; Brown, Steven D; Podar, Mircea; Wall, Judy D

    2015-05-01

    Methylmercury is a potent neurotoxin that is produced by anaerobic microorganisms from inorganic mercury by a recently discovered pathway. A two-gene cluster, consisting of hgcA and hgcB, encodes two of the proteins essential for this activity. hgcA encodes a corrinoid protein with a strictly conserved cysteine proposed to be the ligand for cobalt in the corrinoid cofactor, whereas hgcB encodes a ferredoxin-like protein thought to be an electron donor to HgcA. Deletion of either gene eliminates mercury methylation by the methylator Desulfovibrio desulfuricans ND132. Here, site-directed mutants of HgcA and HgcB were constructed to determine amino acid residues essential for mercury methylation. Mutations of the strictly conserved residue Cys93 in HgcA, the proposed ligand for the corrinoid cobalt, to Ala or Thr completely abolished the methylation capacity, but a His substitution produced measurable methylmercury. Mutations of conserved amino acids near Cys93 had various impacts on the methylation capacity but showed that the structure of the putative "cap helix" region harboring Cys93 is crucial for methylation function. In the ferredoxin-like protein HgcB, only one of two conserved cysteines found at the C terminus was necessary for methylation, but either cysteine sufficed. An additional, strictly conserved cysteine, Cys73, was also determined to be essential for methylation. This study supports the previously predicted importance of Cys93 in HgcA for methylation of mercury and reveals additional residues in HgcA and HgcB that facilitate the production of this neurotoxin.

  8. Sensing actin dynamics: Structural basis for G-actin-sensitive nuclear import of MAL

    Energy Technology Data Exchange (ETDEWEB)

    Hirano, Hidemi; Matsuura, Yoshiyuki, E-mail: matsuura.yoshiyuki@d.mbox.nagoya-u.ac.jp

    2011-10-22

    Highlights: {yields} MAL has a bipartite NLS that binds to Imp{alpha} in an extended conformation. {yields} Mutational analyses verified the functional significance of MAL-Imp{alpha} interactions. {yields} Induced folding and NLS-masking by G-actins inhibit nuclear import of MAL. -- Abstract: The coordination of cytoskeletal actin dynamics with gene expression reprogramming is emerging as a crucial mechanism to control diverse cellular processes, including cell migration, differentiation and neuronal circuit assembly. The actin-binding transcriptional coactivator MAL (also known as MRTF-A/MKL1/BSAC) senses G-actin concentration and transduces Rho GTPase signals to serum response factor (SRF). MAL rapidly shuttles between the cytoplasm and the nucleus in unstimulated cells but Rho-induced depletion of G-actin leads to MAL nuclear accumulation and activation of transcription of SRF:MAL-target genes. Although the molecular and structural basis of actin-regulated nucleocytoplasmic shuttling of MAL is not understood fully, it is proposed that nuclear import of MAL is mediated by importin {alpha}/{beta} heterodimer, and that G-actin competes with importin {alpha}/{beta} for the binding to MAL. Here we present structural, biochemical and cell biological evidence that MAL has a classical bipartite nuclear localization signal (NLS) in the N-terminal 'RPEL' domain containing Arg-Pro-X-X-X-Glu-Leu (RPEL) motifs. The NLS residues of MAL adopt an extended conformation and bind along the surface groove of importin-{alpha}, interacting with the major- and minor-NLS binding sites. We also present a crystal structure of wild-type MAL RPEL domain in complex with five G-actins. Comparison of the importin-{alpha}- and actin-complexes revealed that the binding of G-actins to MAL is associated with folding of NLS residues into a helical conformation that is inappropriate for importin-{alpha} recognition.

  9. Fungicide residues in grapes determined the dynamics of Saccharomyces cerevisiae strains during spontaneous wine fermentation

    Directory of Open Access Journals (Sweden)

    Čuš Franc

    2011-01-01

    Full Text Available Impact of three fungicides against B. cinerea (iprodione, pyrimethanil and f ludioxonil plus cyprodinil on the population of Saccharomyces cerevisiae strains during the spontaneous alcoholic fermentation was studied. With regard to the use of fungicides in the vineyard at two stages of the grapevine growth we followed four different spontaneous fermentations: control, iprodione, pyrimethanil and f ludioxonil plus cyprodinil. The fungicide residues in the grapes were determined by GC/MS system and the fermentations were followed by changes in yeast, sugar, and ethanol concentrations using colony counting and HPLC. The karyotype analysis of 473 isolates was done by pulsed-field gel electrophoresis. The fungicide residues in the grapes at the harvest were below the maximum residue limits. Isolates of S. cerevisiae were classified into 15 karyotype groups. The duration of the processes and the populations of the karyotypes differed between the fermentations. The iprodione and control fermentations lasted 36 days with the prevalence of karyotype A while the fludioxonil plus cyprodinil fermentation lasted 50 days and karyotype D led the process. In the pyrimethanil fermentation, none of the karyotypes prevailed in the must and the fermentation lasted much longer than others did (68 days. The results showed that the fungicide residues have an influence on the fermentation kinetics and selection of S. cerevisiae strains during the spontaneous alcoholic fermentation and therefore should be considered as an important factor that may indirectly influence the formation of fermentation aroma in the wine produced by such process.

  10. Load transfer mechanics between trans-tibial prosthetic socket and residual limb--dynamic effects.

    Science.gov (United States)

    Jia, Xiaohong; Zhang, Ming; Lee, Winson C C

    2004-09-01

    The effects of inertial loads on the interface stresses between trans-tibial residual limb and prosthetic socket were investigated. The motion of the limb and prosthesis was monitored using a Vicon motion analysis system and the ground reaction force was measured by a force platform. Equivalent loads at the knee joint during walking were calculated in two cases with and without consideration of the material inertia. A 3D nonlinear finite element (FE) model based on the actual geometry of residual limb, internal bones and socket liner was developed to study the mechanical interaction between socket and residual limb during walking. To simulate the friction/slip boundary conditions between the skin and liner, automated surface-to-surface contact was used. The prediction results indicated that interface pressure and shear stress had the similar double-peaked waveform shape in stance phase. The average difference in interface stresses between the two cases with and without consideration of inertial forces was 8.4% in stance phase and 20.1% in swing phase. The maximum difference during stance phase is up to 19%. This suggests that it is preferable to consider the material inertia effect in a fully dynamic FE model.

  11. On-matrix derivatization for dynamic headspace sampling of nonvolatile surface residues.

    Science.gov (United States)

    Harvey, Scott D; Wahl, Jon H

    2012-09-21

    The goal of this study is to extend sampling by the field and laboratory emission cell (FLEC) dynamic headspace technique to applications that target nonvolatile residues. On-matrix derivatization of residues to render analytes stable and more volatile is explored to achieve this goal. Results show that on-matrix derivatizations of nerve agent hydrolysis products (monoalkyl methylphosphonic acids and methylphosphonic acid [MPA]) with diazomethane were successful on glass and painted wallboard (at the 10-μg level). It also was successful on the more difficult concrete (at the 500-μg level) and carpet (at the 20-μg level), substrates that cannot be successfully sampled using swipe techniques. Analysis of additional chemical warfare (CW)-associated residues can be approached by on-matrix derivatization with trifluoroacetic anhydride (TFAA). For example, amines (used as stabilizers or present as decomposition products of the nerve agent VX) or thiodiglycol (hydrolysis product of sulfur mustard) could be sampled as their TFAA derivatives from glass, painted wallboard, and concrete (at the 40-μg level), as well as carpet (at the 80-μg level) surfaces. Although the amine and thiodiglycol are semi-volatile and could be sampled directly, derivatization improves the recovery and chromatographic behavior of these analytes.

  12. Damage of composite structures: Detection technique, dynamic response and residual strength

    Science.gov (United States)

    Lestari, Wahyu

    2001-10-01

    Reliable and accurate health monitoring techniques can prevent catastrophic failures of structures. Conventional damage detection methods are based on visual or localized experimental methods and very often require prior information concerning the vicinity of the damage or defect. The structure must also be readily accessible for inspections. The techniques are also labor intensive. In comparison to these methods, health-monitoring techniques that are based on the structural dynamic response offers unique information on failure of structures. However, systematic relations between the experimental data and the defect are not available and frequently, the number of vibration modes needed for an accurate identification of defects is much higher than the number of modes that can be readily identified in the experiment. These motivated us to develop an experimental data based detection method with systematic relationships between the experimentally identified information and the analytical or mathematical model representing the defective structures. The developed technique use changes in vibrational curvature modes and natural frequencies. To avoid misinterpretation of the identified information, we also need to understand the effects of defects on the structural dynamic response prior to developing health-monitoring techniques. In this thesis work we focus on two type of defects in composite structures, namely delamination and edge notch like defect. Effects of nonlinearity due to the presence of defect and due to the axial stretching are studied for beams with delamination. Once defects are detected in a structure, next concern is determining the effects of the defects on the strength of the structure and its residual stiffness under dynamic loading. In this thesis, energy release rate due to dynamic loading in a delaminated structure is studied, which will be a foundation toward determining the residual strength of the structure.

  13. Dynamic importance of unsteady effects in glottal flow aerodynamics

    Science.gov (United States)

    Krane, Michael; Peltier, Joel; Medvitz, Richard

    2008-11-01

    Finite element computations of flow through a constriction are used to illuminate the role of unsteady flow dynamics in glottal flow and voice production. Unsteady computations were performed for a series of prescribed idealized vocal fold wall motions over reduced frequencies f*=0, 0.04 and 0.08, which correspond to quasi-steady, adult male and adult female speaking voices, respectively. Glottal resistance and estimates of the relative magnitudes of the various terms of the integral momentum equation are presented. Results suggest that glottal flow is inherently unsteady.

  14. The nociceptin receptor (NOPR) and its interaction with clinically important agonist molecules: a membrane molecular dynamics simulation study.

    Science.gov (United States)

    Kothandan, Gugan; Gadhe, Changdev G; Balupuri, Anand; Ganapathy, Jagadeesan; Cho, Seung Joo

    2014-12-01

    The nociceptin receptor (NOPR) is an orphan G protein-coupled receptor that contains seven transmembrane helices. NOPR has a distinct mechanism of activation, though it shares a significant homology with other opioid receptors. Previously there have been reports on homology modeling of NOPR and also molecular dynamics simulation studies for a short period. Recently the crystal structure of NOPR was reported. In this study, we analyzed the time dependent behavior of NOPR docked with clinically important agonist molecules such as NOP (natural agonist) peptide and compound 10 (SCH-221510 derivative) using molecular dynamics simulations (MDS) for 100 ns. Molecular dynamics simulations of NOPR-agonist complexes allowed us to refine the system and to also identify stable structures with better binding modes. Structure activity relationships (SAR) for SCH221510 derivatives were investigated and reasons for the activities of these derivatives were determined. Our molecular dynamics trajectory analysis of NOPR-peptide and NOPR-compound 10 complexes found residues to be crucial for binding. Mutagenesis studies on the residues identified from our analysis could prove useful. Our results could also provide useful information in the structure-based drug design of novel and potent agonists targeting NOPR.

  15. Future Arctic ozone recovery: the importance of chemistry and dynamics

    Science.gov (United States)

    Bednarz, Ewa M.; Maycock, Amanda C.; Abraham, N. Luke; Braesicke, Peter; Dessens, Olivier; Pyle, John A.

    2016-09-01

    Future trends in Arctic springtime total column ozone, and its chemical and dynamical drivers, are assessed using a seven-member ensemble from the Met Office Unified Model with United Kingdom Chemistry and Aerosols (UM-UKCA) simulating the period 1960-2100. The Arctic mean March total column ozone increases throughout the 21st century at a rate of ˜ 11.5 DU decade-1, and is projected to return to the 1980 level in the late 2030s. However, the integrations show that even past 2060 springtime Arctic ozone can episodically drop by ˜ 50-100 DU below the corresponding long-term ensemble mean for that period, reaching values characteristic of the near-present-day average level. Consistent with the global decline in inorganic chlorine (Cly) over the century, the estimated mean halogen-induced chemical ozone loss in the Arctic lower atmosphere in spring decreases by around a factor of 2 between the periods 2001-2020 and 2061-2080. However, in the presence of a cold and strong polar vortex, elevated halogen-induced ozone losses well above the corresponding long-term mean continue to occur in the simulations into the second part of the century. The ensemble shows a significant cooling trend in the Arctic winter mid- and upper stratosphere, but there is less confidence in the projected temperature trends in the lower stratosphere (100-50 hPa). This is partly due to an increase in downwelling over the Arctic polar cap in winter, which increases transport of ozone into the polar region as well as drives adiabatic warming that partly offsets the radiatively driven stratospheric cooling. However, individual winters characterised by significantly suppressed downwelling, reduced transport and anomalously low temperatures continue to occur in the future. We conclude that, despite the projected long-term recovery of Arctic ozone, the large interannual dynamical variability is expected to continue in the future, thereby facilitating episodic reductions in springtime ozone columns

  16. Dynamics of Hydrophobic Core Phenylalanine Residues Probed by Solid-State Deuteron NMR

    Energy Technology Data Exchange (ETDEWEB)

    Vugmeyster, Liliya; Ostrovsky, Dmitry; Villafranca, Toni; Sharp, Janelle; Xu, Wei; Lipton, Andrew S.; Hoatson, Gina; Vold, Robert L.

    2015-11-03

    We conducted a detailed investigation of the dynamics of two phenylalanine side chains in the hydrophobic core of the villin headpiece subdomain protein (HP36) in the hydrated powder state over the 298–80 K temperature range. We utilized static deuteron NMR measurements of longitudinal relaxation and line shapes supplemented with computational modeling. The temperature dependence of the relaxation times reveals the presence of two main mechanisms that can be attributed to the ring-flips, dominating at high temperatures, and small-angle fluctuations, dominating at low temperatures. The relaxation is non- exponential at all temperatures with the extent of non-exponentiality increasing from higher to lower temperatures. This behavior suggests a distribution of conformers with unique values of activation energies. The central values of the activation energies for the ring-flipping motions are among the smallest reported for aromatic residues in peptides and proteins and point to a very mobile hydrophobic core. The analysis of the widths of the distributions, in combination with the earlier results on the dynamics of flanking methyl groups (Vugmeyster et al., J. Phys. Chem. 2013, 117, 6129–6137), suggests that the hydrophobic core undergoes concerted fluctuations. There is a pronounced effect of dehydration on the ring-flipping motions, which shifts the distribution toward more rigid conformers. The cross-over temperature between the regions of dominance of the small-angle fluctuations and ring-flips shifts from 195 K in the hydrated protein to 278 K in the dry one. This result points to the role of solvent in the onset of the concerted fluctuations of the core and highlights aromatic residues as markers of the protein dynamical transitions.

  17. Changes in the relative importance of dynamic risk factors for recidivism during adolescence

    NARCIS (Netherlands)

    C.E. van der Put; G.J.J.M. Stams; M. Hoeve; M. Deković; H.J.M. Spanjaard; P.H. van der Laan; R.P. Barnoski

    2012-01-01

    This study examined which dynamic risk factors for recidivism play an important role during adolescence. The sample consisted of 13,613 American juveniles who had committed a criminal offense. The results showed that the importance of almost all dynamic risk factors, both in the social environment d

  18. Sorting of LPXTG peptides by archetypal sortase A: role of invariant substrate residues in modulating the enzyme dynamics and conformational signature of a productive substrate.

    Science.gov (United States)

    Biswas, Tora; Pawale, Vijaykumar S; Choudhury, Devapriya; Roy, Rajendra P

    2014-04-22

    Transpeptidase sortase catalyzes the covalent anchoring of surface proteins to the cell wall in Gram-positive bacteria. Sortase A (SrtA) of Staphylococcus aureus is a prototype enzyme and considered a bona fide drug target because several substrate proteins are virulence-related and implicated in pathogenesis. Besides, SrtA also works as a versatile tool in protein engineering. Surface proteins destined for cell wall anchoring contain a LPXTG sequence located in their C-terminus which serves as a substrate recognition motif for SrtA. Recent studies have implicated substrate-induced conformational dynamics in SrtA. In the present work, we have explored the roles of invariant Leu and Pro residues of the substrate in modulating the enzyme dynamics with a view to understand the selection process of a catalytically competent substrate. Overall results of molecular dynamics simulations and experiments carried out with noncanonical substrates and site-directed mutagenesis reveal that the kinked conformation due to Pro in LPXTG is obligatory for productive binding but does not per se control the enzyme dynamics. The Leu residue of the substrate appears to play the crucial role of an anchor to the beta6-beta7 loop directing the conformational transition of the enzyme from an "open" to a "closed" state subsequent to which the Pro residue facilitates the consummation of binding through predominant engagement of the loop and catalytic motif residues in hydrophobic interactions. Collectively, our study provides insights about specificity, tolerance, and conformational sorting of substrate by SrtA. These results have important implications in designing newer substrates and inhibitors for this multifaceted enzyme.

  19. Topology of eukaryotic type II membrane proteins: importance of N-terminal positively charged residues flanking the hydrophobic domain.

    Science.gov (United States)

    Parks, G D; Lamb, R A

    1991-02-22

    We have tested the role of different charged residues flanking the sides of the signal/anchor (S/A) domain of a eukaryotic type II (N(cyt)C(exo)) integral membrane protein in determining its topology. The removal of positively charged residues on the N-terminal side of the S/A yields proteins with an inverted topology, while the addition of positively charged residues to only the C-terminal side has very little effect on orientation. Expression of chimeric proteins composed of domains from a type II protein (HN) and the oppositely oriented membrane protein M2 indicates that the HN N-terminal domain is sufficient to confer a type II topology and that the M2 N-terminal ectodomain can direct a type II topology when modified by adding positively charged residues. These data suggest that eukaryotic membrane protein topology is governed by the presence or absence of an N-terminal signal for retention in the cytoplasm that is composed in part of positive charges.

  20. Residues in the central β-hairpin of the DNA helicase of bacteriophage T7 are important in DNA unwinding

    NARCIS (Netherlands)

    Satapathy, Ajit K.; Kochaniak, Anna B.; Mukherjee, Sourav; Crampton, Donald J.; Oijen, Antoine van; Richardson, Charles C.

    2010-01-01

    The ring-shaped helicase of bacteriophage T7 (gp4), the product of gene 4, has basic β-hairpin loops lining its central core where they are postulated to be the major sites of DNA interaction. We have altered multiple residues within the β-hairpin loop to determine their role during dTTPase-driven

  1. Conformational dynamics in substrate-binding domains influences transport in the ABC importer GlnPQ

    NARCIS (Netherlands)

    Gouridis, Giorgos; Schuurman-Wolters, Geesina; Ploetz, Evelyn; Husada, Florence; Vietrov, Ruslan; de Boer, Marijn; Cordes, Thorben; Poolman, Bert

    2015-01-01

    The conformational dynamics in ABC transporters is largely elusive. The ABC importer GlnPQ from Lactococcus lactis has different covalently linked substrate-binding domains (SBDs), thus making it an excellent model system to elucidate the dynamics and role of the SBDs in transport. We demonstrate by

  2. Analysis of Amino Acid Residues of Potential Importance for Phosphati-dylserine Specificity of P4-type ATPase ATP8A2

    DEFF Research Database (Denmark)

    Mogensen, Louise; Vestergaard, Anna Lindeløv; Mikkelsen, Stine

    The asymmetric structure of the plasma membrane is maintained through internalization of phos-pholipids by the family of P4-ATPases by a poorly characterized mechanism. Studies in yeast point towards a non-classical pathway involving important residues of a two-gate mechanism [1]. Glycine-230 and...

  3. Identification of residues in the heme domain of soluble guanylyl cyclase that are important for basal and stimulated catalytic activity.

    Directory of Open Access Journals (Sweden)

    Padmamalini Baskaran

    Full Text Available Nitric oxide signals through activation of soluble guanylyl cyclase (sGC, a heme-containing heterodimer. NO binds to the heme domain located in the N-terminal part of the β subunit of sGC resulting in increased production of cGMP in the catalytic domain located at the C-terminal part of sGC. Little is known about the mechanism by which the NO signaling is propagated from the receptor domain (heme domain to the effector domain (catalytic domain, in particular events subsequent to the breakage of the bond between the heme iron and Histidine 105 (H105 of the β subunit. Our modeling of the heme-binding domain as well as previous homologous heme domain structures in different states point to two regions that could be critical for propagation of the NO activation signal. Structure-based mutational analysis of these regions revealed that residues T110 and R116 in the αF helix-β1 strand, and residues I41 and R40 in the αB-αC loop mediate propagation of activation between the heme domain and the catalytic domain. Biochemical analysis of these heme mutants allows refinement of the map of the residues that are critical for heme stability and propagation of the NO/YC-1 activation signal in sGC.

  4. Talin contains a C-terminal calpain2 cleavage site important in focal adhesion dynamics.

    Directory of Open Access Journals (Sweden)

    Neil Bate

    Full Text Available Talin is a large (∼2540 residues dimeric adaptor protein that associates with the integrin family of cell adhesion molecules in cell-extracellular matrix junctions (focal adhesions; FAs, where it both activates integrins and couples them to the actin cytoskeleton. Calpain2-mediated cleavage of talin between the head and rod domains has previously been shown to be important in FA turnover. Here we identify an additional calpain2-cleavage site that removes the dimerisation domain from the C-terminus of the talin rod, and show that an E2492G mutation inhibits calpain cleavage at this site in vitro, and increases the steady state levels of talin1 in vivo. Expression of a GFP-tagged talin1 E2492G mutant in CHO.K1 cells inhibited FA turnover and the persistence of cell protrusion just as effectively as a L432G mutation that inhibits calpain cleavage between the talin head and rod domains. Moreover, incorporation of both mutations into a single talin molecule had an additive effect clearly demonstrating that calpain cleavage at both the N- and C-terminal regions of talin contribute to the regulation of FA dynamics. However, the N-terminal site was more sensitive to calpain cleavage suggesting that lower levels of calpain are required to liberate the talin head and rod fragments than are needed to clip off the C-terminal dimerisation domain. The talin head and rod liberated by calpain2 cleavage have recently been shown to play roles in an integrin activation cycle important in FA turnover and in FAK-dependent cell cycle progression respectively. The half-life of the talin head is tightly regulated by ubiquitination and we suggest that removal of the C-terminal dimerisation domain from the talin rod may provide a mechanism both for terminating the signalling function of the talin rod and indeed for inactivating full-length talin thereby promoting FA turnover at the rear of the cell.

  5. Influence of biochar and plant growth on organic matter dynamics in a reclaimed mine residue

    Science.gov (United States)

    Moreno-Barriga, Fabián; Díaz, Vicente; Alberto, Jose; Faz, Ángel; Zornoza, Raúl

    2016-04-01

    This study aims at assessing the impact of biochar and marble waste amendment and the development of vegetation in acidic mine wastes on organic matter dynamics. For this purpose, a mine residue was collected in a tailing pond from the Sierra Minera of Cartagena-La Unión (SE Spain), and a greenhouse experiment was established for 120 days. Marble waste (MW) was added in a rate of 200 g kg-1 as a source of calcium carbonate to increase the pH from 3 to 7.5-8 (average pH in the native soils of the area). We added biochar as a source of organic carbon and nutrients, in two different rates, 50 g kg-1 (BC1) and 100 g kg-1 (BC2). To assess the influence of vegetation growth on the creation of a technosoil from mine residues and its impact on organic matter dynamics, the plant species Piptatherum miliaceum (PM) was planted in half the pots with the different amendments. Thus, five treatments were established: unamended and unplanted control (CT), BC1, BC2, BC1+PM and BC2+PM. Results showed that the different treatments had no significant effect on aggregates stability, microbial biomass carbon and the emission of N2O and CH4. So, it seems that longer periods are needed to increase the stability of aggregates and microbial populations, since even the combined use of biochar, marble waste and vegetation was not enough to increase these properties in 120 days. Nonetheless, it was positive that the addition of biochar and the release of root exudates did not trigger the emission of greenhouse gases. Organic carbon significantly increased with the addition of biochar, with values similar to the dose applied, indicating high stability and low mineralization of the amendment. The addition of amendments significantly increased arylesterase activity, while the growth of the plant was needed to significantly increase β-glucosidase activity. The soluble carbon significantly decreased in BC1 and BC2 with regards to CT, while no significant differences were observed among CT and

  6. Short-term dynamics of culturable bacteria in a soil amended with biotransformed dry olive residue.

    Science.gov (United States)

    Siles, J A; Pascual, J; González-Menéndez, V; Sampedro, I; García-Romera, I; Bills, G F

    2014-03-01

    Dry olive residue (DOR) transformation by wood decomposing basidiomycetes (e.g. Coriolopsis floccosa) is a possible strategy for eliminating the liabilities related to the use of olive oil industry waste as an organic soil amendment. The effects of organic fertilization with DOR on the culturable soil microbiota are largely unknown. Therefore, the objectives of this study were to measure the short-term effects of DOR and C. floccosa-transformed DOR on the culturable bacterial soil community, while at the same time documenting the bacterial diversity of an agronomic soil in the southeastern Iberian Peninsula. The control soil was compared with the same soil treated with DOR and with C. floccosa-transformed DOR for 0, 30 and 60 days. Impact was measured from total viable cells and CFU counts, as well as the isolation and characterization of 900 strains by fatty acid methyl ester profiles and 16S rRNA partial sequencing. The bacterial diversity was distributed between Actinobacteria, Alphaproteobacteria, Gammaproteobacteria, Betaproteobacteria, Bacilli, Sphingobacteria and Cytophagia. Analysis of the treatments and controls demonstrated that soil amendment with untransformed DOR produced important changes in bacterial density and diversity. However, when C. floccosa-transformed DOR was applied, bacterial proliferation was observed but bacterial diversity was less affected, and the distribution of microorganisms was more similar to the unamended soil.

  7. Importance of clustered 2'-O-(2-aminoethyl) residues for the gene targeting activity of triple helix-forming oligonucleotides.

    Science.gov (United States)

    Puri, Nitin; Majumdar, Alokes; Cuenoud, Bernard; Miller, Paul S; Seidman, Michael M

    2004-02-10

    We are developing triple helix-forming oligonucleotides (TFOs) as gene targeting reagents in living mammalian cells. We have described psoralen-linked TFOs with 2'-O-methyl and 2'-O-(2-aminoethyl) (2'-AE) substitutions that are active in a gene knockout assay in cultured cells. The assay is based on mutagenesis by psoralen, a photoactive DNA cross-linker. Previous work showed that TFOs with three or four 2'-AE residues were disproportionately more active than those with one or two substitutions. Here we demonstrate that for optimal bioactivity the 2'-AE residues must be clustered rather than dispersed. We have further characterized bioactive and inactive TFOs in an effort to identify biochemical and biophysical correlates of biological activity. While thermal stability is a standard monitor of TFO biophysical activity, we find that T(m) values do not distinguish bioactive and inactive TFOs. In contrast, measurements of TFO association rates appear to correlate well with bioactivity, in that triplex formation occurs disproportionately faster with the TFOs containing three or four 2'-AE residues. We asked if extending the incubation time prior to photoactivation would enhance the bioactivity of a TFO with a slow on rate relative to the TFO with a faster association rate. However, there was no change in bioactivity differential. These results are compatible with a model in which TFO binding in vivo is followed by relatively rapid elution by cellular functions, similar to that described for transcription factors. Under these circumstances, TFOs with faster on rates would be favored because they would be more likely to be in triplexes at the time of photoactivation.

  8. Exploring the molecular mechanism of cross-resistance to HIV-1 integrase strand transfer inhibitors by molecular dynamics simulation and residue interaction network analysis.

    Science.gov (United States)

    Xue, Weiwei; Jin, Xiaojie; Ning, Lulu; Wang, Meixia; Liu, Huanxiang; Yao, Xiaojun

    2013-01-28

    The rapid emergence of cross-resistance to the integrase strand transfer inhibitors (INSTIs) has become a serious problem in the therapy of human immunodeficiency virus type 1 (HIV-1) infection. Understanding the detailed molecular mechanism of INSTIs cross-resistance is therefore critical for the development of new effective therapy against cross-resistance. On the basis of the homology modeling constructed structure of tetrameric HIV-1 intasome, the detailed molecular mechanism of the cross-resistance mutation E138K/Q148K to three important INSTIs (Raltegravir (RAL, FDA approved in 2007), Elvitegravir (EVG, FDA approved in 2012), and Dolutegravir (DTG, phase III clinical trials)) was investigated by using molecular dynamics (MD) simulation and residue interaction network (RIN) analysis. The results from conformation analysis and binding free energy calculation can provide some useful information about the detailed binding mode and cross-resistance mechanism for the three INSTIs to HIV-1 intasome. Binding free energy decomposition analysis revealed that Pro145 residue in the 140s 1oop (Gly140 to Gly149) of the HIV-1 intasome had strong hydrophobic interactions with INSTIs and played an important role in the binding of INSTIs to HIV-1 intasome active site. A systematic comparison and analysis of the RIN proves that the communications between the residues in the resistance mutant is increased when compared with that of the wild-type HIV-1 intasome. Further analysis indicates that residue Pro145 may play an important role and is relevant to the structure rearrangement in HIV-1 intasome active site. In addition, the chelating ability of the oxygen atoms in INSTIs (e.g., RAL and EVG) to Mg(2+) in the active site of the mutated intasome was reduced due to this conformational change and is also responsible for the cross-resistance mechanism. Notably, the cross-resistance mechanism we proposed could give some important information for the future rational design of novel

  9. Direct prediction of residual dipolar couplings of small molecules in a stretched gel by stochastic molecular dynamics simulations.

    Science.gov (United States)

    Frank, Andreas O; Freudenberger, J Christoph; Shaytan, Alexey K; Kessler, Horst; Luy, Burkhard

    2015-03-01

    Residual dipolar couplings are highly useful NMR parameters for calculating and refining molecular structures, dynamics, and interactions. For some applications, however, it is inevitable that the preferred orientation of a molecule in an alignment medium is calculated a priori. Several methods have been developed to predict molecular orientations and residual dipolar couplings. Being beneficial for macromolecules and selected small-molecule applications, such approaches lack sufficient accuracy for a large number of organic compounds for which the fine structure and eventually the flexibility of all involved molecules have to be considered or are limited to specific, well-studied liquid crystals. We introduce a simplified model for detailed all-atom molecular dynamics calculations with a polymer strand lined up along the principal axis as a new approach to simulate the preferred orientation of small to medium-sized solutes in polymer-based, gel-type alignment media. As is shown by a first example of strychnine in a polystyrene/CDCl3 gel, the simulations potentially enable the accurate prediction of residual dipolar couplings taking into account structural details and dynamic averaging effects of both the polymer and the solute.

  10. Importance of the Roughness and Residual Stresses of Dental Implants on Fatigue and Osseointegration Behavior. In Vivo Study in Rabbits.

    Science.gov (United States)

    Velasco, Eugenio; Monsalve-Guil, Loreto; Jimenez, Alvaro; Ortiz, Iván; Moreno-Muñoz, Jesús; Nuñez-Marquez, Enrique; Pegueroles, Marta; Pérez, Román A; Gil, Francisco Javier

    2016-12-01

    This study focuses on the fatigue behavior and bone-implant attachment for the more usual surfaces of the different CP-titanium dental implants. The implants studied were: as-received (CTR), acid etching (AE), spark-anodization (SA), and with a grit-blasted surface (GB). Residual stresses were determined by means of X-ray diffraction. The fatigue tests were carried out at 37°C on 160 dental implants, and the stress-failure (S-N) curve was determined. The fatigue tests showed that the grit-blasting process improved fatigue life. This is a consequence of the layer of compressive residual stresses that the treatment generates in titanium surfaces. Further, our aim was to assess and compare the short- and midterm bone regenerative potential and mechanical retention of the implants in bone of New Zealand rabbits. The mechanical retention after 4 and 10 weeks of implantation was evaluated with histometric and pull-out tests, respectively, as a measure of the osseointegration of the implants. The results demonstrated that the GB treatment produced microrough that accelerated bone tissue regeneration and increased mechanical retention in the bone bed at short periods of implantation in comparison with all other implants tested. The GB surface produced an improvement in mechanical long-time behavior and improved bone growth. These types of treated implants can have great potential in clinical applications, as evidenced by the outcomes of the current study.

  11. Dynamic of population-dynamics in a medically important snail species Lymnaea (Radix Luteola (Lamarck

    Directory of Open Access Journals (Sweden)

    T. K. Misra

    1993-09-01

    Full Text Available The life-cycle parameters of the snail Lymnaea (Radix luteola and the factors influencing the same have been studied under laboratory conditions. Ins each month, from July 1990 to June 1991, a batch of 100 zero-day old individual were considered for studies. The snails of April batch survived for 19.42 days while those in December batch survived for 87.45 days. The May batch individual though survived for 65.67 days gained maximum shell size (15.84 mm in length and body weight (419.87 mg. All individuals of April batch died prior to attainment of sexual maturity. In the remaining 11 batches the snails became sexually mature between 32 and 53 days. At this stage, they were with varying shell lengths, 9.3 mm to 13,11 mm in respect to batches. The reproduction period varied from 1-67 days. An individual laid, on an average, 0,25 (March batch to 443.67 (May batch eggs in its life-span. A batch of such snails would leave 24312, 22520, 720268, 80408, 76067, 418165, 214, 9202, 0, 0, 2459386 and 127894 individuals at the end of 352nd day. Since the environmental conditions were almost similar the 'dynamic' of population dynamics seems to be involved with the 'strain' of the snail individuals of the batches concerned.

  12. Decomposition Dynamics and Changes in Chemical Composition of Wheat Straw Residue under Anaerobic and Aerobic Conditions.

    Science.gov (United States)

    Gao, Hongjian; Chen, Xi; Wei, Junling; Zhang, Yajie; Zhang, Ligan; Chang, Jiang; Thompson, Michael L

    2016-01-01

    Soil aeration is a crucial factor that regulates crop residue decomposition, and the chemical composition of decomposing crop residues may change the forms and availability of soil nutrients, such as N and P. However, to date, differences in the chemical composition of crop straw residues after incorporation into soil and during its decomposition under anaerobic vs. aerobic conditions have not been well documented. The objective of the present study was to assess changes in the C-containing functional groups of wheat straw residue during its decomposition in anaerobic and aerobic environments. A 12-month incubation experiment was carried out to investigate the temporal variations of mass, carbon, and nitrogen loss, as well as changes in the chemical composition of wheat (Triticum aestivum L) straw residues under anaerobic and aerobic conditions by measuring C-containing functional groups using solid state nuclear magnetic resonance (NMR) spectroscopy. The residual mass, carbon content, and nitrogen content of the straw residue sharply declined during the initial 3 months, and then slowly decreased during the last incubation period from 3 to 12 months. The decomposition rate constant (k) for mass loss under aerobic conditions (0.022 d-1) was higher than that under anaerobic conditions (0.014 d-1). The residual mass percentage of cellulose and hemicellulose in the wheat straw gradually declined, whereas that of lignin gradually increased during the entire 12-month incubation period. The NMR spectra of C-containing functional groups in the decomposing straw under both aerobic and anaerobic conditions were similar at the beginning of the incubation as well as at 1 month, 6 months, and 12 months. The main alterations in C-containing functional groups during the decomposition of wheat straw were a decrease in the relative abundances of O-alkyl C and an increase in the relative abundances of alkyl C, aromatic C and COO/N-C = O functional groups. The NMR signals of alkyl C

  13. Mechanism of the Orotidine 5’-Monophosphate Decarboxylase-Catalyzed Reaction: Importance of Residues in the Orotate Binding Site†

    Science.gov (United States)

    Iiams, Vanessa; Desai, Bijoy J.; Fedorov, Alexander A.; Fedorov, Elena V.; Almo, Steven C.; Gerlt, John A.

    2011-01-01

    The reaction catalyzed by orotidine 5’-monophosphate decarboxylase (OMPDC) is accompanied by exceptional values for the rate enhancement [kcat/knon = 7.1 × 1016] and catalytic proficiency [(kcat/KM)/knon = 4.8 × 1022 M−1]. Although a stabilized vinyl carbanion/carbene intermediate is located on the reaction coordinate, the structural strategies by which the reduction in the activation energy barrier is realized remain incompletely understood. This laboratory recently reported that “substrate destabilization” by Asp 70 in the OMPDC from Methanothermobacter thermoautotrophicus (MtOMPDC) lowers the activation energy barrier by ~5 kcal/mol (contributing ~2.7 × 103 to the rate enhancement) [K. K. Chan, B. M. Wood, A. A. Fedorov, E. V. Fedorov, H. J. Imker, T. L. Amyes, J. P. Richard, S. C. Almo, and J. A. Gerlt (2009) Biochemistry 48, 5518–31]. We now report that substitutions of hydrophobic residues in a pocket proximal to the carboxylate group of the substrate (Ile 96, Leu 123, and Val 155) with neutral hydrophilic residues decrease the value of kcat by as much as 400-fold but have minimal effect on the value of kex for exchange of H6 of the FUMP product analog with solvent deuterium; we hypothesize that this pocket destabilizes the substrate by preventing hydration of the substrate carboxylate group. We also report that substitutions for Ser 127 that is proximal to O4 of the orotate ring decrease the value of kcat/KM, with the S127P substitution that eliminates hydrogen-bonding interactions with O4 producing a 2.5 × 106-fold reduction in the value of kcat/KM; this effect is consistent with delocalization of the negative charge of the carbanionic intermediate on O4 to produce an anionic carbene intermediate and thereby provide a structural strategy for stabilization of the intermediate. These observations provide additional information on the identities of the active site residues that contribute to the rate enhancement and, therefore, insights into the

  14. 吡虫啉在枸杞中的残留动态%Residues Dynamics of Imidacloprid in Lycium

    Institute of Scientific and Technical Information of China (English)

    张艳; 王晓菁; 牛艳; 吴燕

    2012-01-01

    To evaluate residues dynamics of imidacloprid in lycium, field trials for imidacloprid residue in lycium were conducted in Ningxia, Neimenggu and Gansu. The results showed that the residues and degradation dynamics of imidacloprid in lycium completely fitted to the first-order reaction kinetic equation. The half-life of degradation for imidacloprid was 3. 0 to 3. 4 d in fresh lycium berries,2. 9 to 5. 0 d in dry fruits. According to the recommended application dosage, the final residue ranged from 0. 004 2 to 0. 403 mg/kg of imidacloprid in lycium. The maximum residue limit was recommended 1 mg/kg in lycium.%为了评价吡虫啉在枸杞上使用后的残留动态,在宁夏、内蒙古和甘肃同时进行残留动态试验.结果表明,吡虫啉在枸杞中的残留消解完全符合一级反应动力学方程式,在枸杞鲜果上的半衰期为3.0~3.4 d,在枸杞干果上的半衰期为2.9~5.0 d;按推荐剂量施用的情况下,在枸杞中的残留为0.004 2~0.403mg/kg.吡虫啉在枸杞中最高残留限量(MRL值)推荐值为1 mg/kg.

  15. Residues of a proposed gate region in type I ATP-binding cassette import systems are crucial for function as revealed by mutational analysis.

    Science.gov (United States)

    Weidlich, Daniela; Wiesemann, Nicole; Heuveling, Johanna; Wardelmann, Kristina; Landmesser, Heidi; Sani, Katayoun Behnam; Worth, Catherine L; Preissner, Robert; Schneider, Erwin

    2013-09-01

    The type I ATP-binding cassette (ABC) importer for positively charged amino acids of the thermophilic bacterium Geobacillus stearothermophilus consists of the extracellular solute binding protein, ArtJ, and a homodimer each of the transmembrane subunit, ArtM, and the nucleotide-binding and -hydrolyzing subunit, ArtP. We have investigated the functional consequences of mutations affecting conserved residues from two peptide regions in ArtM, recently proposed to form a 'gate' by which access of a substrate to the translocation path is controlled (Hollenstein et al., 2007 [14]). Transporter variants were reconstituted into proteoliposomes and assayed for ArtJ/arginine-stimulated ATPase activity. Replacement of residues from region 1 (Arg-63, Pro-66) caused no or only moderate reduction in ATPase activity. In contrast, mutating residues from gate region 2 (Lys-159, Leu-163) resulted in a substantial increase in ATPase activity which, however, as demonstrated for variants ArtM(K159I) and ArtM(K159E), is not coupled to transport. Replacing homologous residues in the closely related histidine transporter of Salmonella enterica serovar Typhimurium (HisJ-QMP2) caused different phenotypes. Mutation to isoleucine of HisQ(K163) or HisM(H172), both homologous to ArtM(K159), abolished ATPase activity. The mutations most likely caused a structural change as revealed by limited proteolysis. In contrast, substantial, albeit reduced, enzymatic activity was observed with variants of HisQ(L167→G) or HisM(L176→G), both homologous to ArtM(L163). Our study provides the first experimental evidence in favor of a crucial role of residues from the proposed gate region in type I ABC importer function. Copyright © 2013 Elsevier B.V. All rights reserved.

  16. Microtubule Dynamicity Is More Important than Stability in Memory Formation: an In Vivo Study.

    Science.gov (United States)

    Atarod, Deyhim; Eskandari-Sedighi, Ghazaleh; Pazhoohi, Farid; Karimian, Seyed Morteza; Khajeloo, Mojtaba; Riazi, Gholam Hossein

    2015-06-01

    It has been shown that microtubule (MT) activity and dynamics can have huge impacts on synaptic plasticity and memory formation. This is mainly due to various functions of MTs in neurons; MTs are involved in dendritic spine formation, axonal transportation, neuronal polarity, and receptor trafficking. Recent studies from our group and other labs have suggested the possible role of brain MT dynamicity and activity in memory; however, there is a need for more detailed studies regarding this aspect. In this study, we have tried to evaluate the importance of microtubule dynamicity rather than stability in memory formation in vivo. In order to investigate the role of MT stability in memory formation, we treated mice with paclitaxel-a classic microtubule-stabilizing agent. We then studied the behavior of treated animals using Morris water maze (MWM) test. To measure the effect of injected paclitaxel on MT polymerization kinetics, we conducted polymerization assays on brain extracts of the same paclitaxel-treated animals. Our results show that paclitaxel treatment affects animals' memory in a negative way and treated animals behave poorly in MWM compared to control group. In addition, our kinetics studies show that MT stability is significantly increased in brain extracts from paclitaxel-treated mice, but MT dynamics is reduced. Thus, we suggest that dynamicity is a very important feature of MT protein structures, and regarding memory formation, dynamicity is more important than stability and high activity.

  17. Effective Boolean dynamics analysis to identify functionally important genes in large-scale signaling networks.

    Science.gov (United States)

    Trinh, Hung-Cuong; Kwon, Yung-Keun

    2015-11-01

    Efficiently identifying functionally important genes in order to understand the minimal requirements of normal cellular development is challenging. To this end, a variety of structural measures have been proposed and their effectiveness has been investigated in recent literature; however, few studies have shown the effectiveness of dynamics-based measures. This led us to investigate a dynamic measure to identify functionally important genes, and the effectiveness of which was verified through application on two large-scale human signaling networks. We specifically consider Boolean sensitivity-based dynamics against an update-rule perturbation (BSU) as a dynamic measure. Through investigations on two large-scale human signaling networks, we found that genes with relatively high BSU values show slower evolutionary rate and higher proportions of essential genes and drug targets than other genes. Gene-ontology analysis showed clear differences between the former and latter groups of genes. Furthermore, we compare the identification accuracies of essential genes and drug targets via BSU and five well-known structural measures. Although BSU did not always show the best performance, it effectively identified the putative set of genes, which is significantly different from the results obtained via the structural measures. Most interestingly, BSU showed the highest synergy effect in identifying the functionally important genes in conjunction with other measures. Our results imply that Boolean-sensitive dynamics can be used as a measure to effectively identify functionally important genes in signaling networks.

  18. Dynamics and regulation of nuclear import and nuclear movements of HIV-1 complexes

    Science.gov (United States)

    Burdick, Ryan C.; Chen, Jianbo; Sastri, Jaya; Hu, Wei-Shau

    2017-01-01

    The dynamics and regulation of HIV-1 nuclear import and its intranuclear movements after import have not been studied. To elucidate these essential HIV-1 post-entry events, we labeled viral complexes with two fluorescently tagged virion-incorporated proteins (APOBEC3F or integrase), and analyzed the HIV-1 dynamics of nuclear envelope (NE) docking, nuclear import, and intranuclear movements in living cells. We observed that HIV-1 complexes exhibit unusually long NE residence times (1.5±1.6 hrs) compared to most cellular cargos, which are imported into the nuclei within milliseconds. Furthermore, nuclear import requires HIV-1 capsid (CA) and nuclear pore protein Nup358, and results in significant loss of CA, indicating that one of the viral core uncoating steps occurs during nuclear import. Our results showed that the CA-Cyclophilin A interaction regulates the dynamics of nuclear import by delaying the time of NE docking as well as transport through the nuclear pore, but blocking reverse transcription has no effect on the kinetics of nuclear import. We also visualized the translocation of viral complexes docked at the NE into the nucleus and analyzed their nuclear movements and determined that viral complexes exhibited a brief fast phase (HIV-1 complexes quickly tether to chromatin at or near their sites of integration in both wild-type cells and cells in which LEDGF/p75 was deleted using CRISPR/cas9, indicating that the tethering interactions do not require LEDGF/p75. These studies provide novel insights into the dynamics of viral complex-NE association, regulation of nuclear import, viral core uncoating, and intranuclear movements that precede integration site selection. PMID:28827840

  19. Determination and dynamics of difenoconazole residues in Chinese cabbage and soil

    Institute of Scientific and Technical Information of China (English)

    Zhi Hua Wang; Tong Yang; Dong Mei Qin; Yong Gong; Ying Ji

    2008-01-01

    An analytical method was developed using a solid phase extraction (SPE) cleanup and gas chromatography for detecting the residues of difenoconazole in Chinese cabbage and soil. The recovery and the relative standard deviation of this method in Chinese cabbage was 87.6-99.0%, 1.71-10.50%, respectively; in soil was 92.4-95.5%, 4.93-10.70%, respectively. Further degradation of difenoconazole residue in Chinese cabbage and soil was studied to evaluate residue behavior and environmental safety of difenoconazole. Degradation rate of difenoconazole in both Chinese cabbage and soil followed the first order kinetics with the half-lives of 6.6-7.8 and 54.2-55.0 days, respectively.

  20. Post-Transition State Dynamics in Gas Phase Reactivity: Importance of Bifurcations and Rotational Activation.

    Science.gov (United States)

    Martín-Sómer, Ana; Yáñez, Manuel; Hase, William L; Gaigeot, Marie-Pierre; Spezia, Riccardo

    2016-03-01

    Beyond the established use of thermodynamic vs kinetic control to explain chemical reaction selectivity, the concept of bifurcations on a potential energy surface (PES) is proving to be of pivotal importance with regard to selectivity. In this article, we studied by means of post-transition state (TS) direct dynamics simulations the effect that vibrational and rotational excitation at the TS may have on selectivity on a bifurcating PES. With this aim, we studied the post-TS unimolecular reactivity of the [Ca(formamide)](2+) ion, for which Coulomb explosion and neutral loss reactions compete. The PES exhibits different kinds of nonintrinsic reaction coordinate (IRC) dynamics, among them PES bifurcations, which direct the trajectories to multiple reaction paths after passing the TS. Direct dynamics simulations were used to distinguish between the bifurcation non-IRC dynamics and non-IRC dynamics arising from atomistic motions directing the trajectories away from the IRC. Overall, we corroborated the idea that kinetic selectivity often does not reduce to a simple choice between paths with different barrier heights and instead dynamical behavior after passing the TS may be crucial. Importantly, rotational excitation may play a pivotal role on the reaction selectivity favoring nonthermodynamic products.

  1. Residual HIV-1 DNA Flap-independent nuclear import of cPPT/CTS double mutant viruses does not support spreading infection

    Directory of Open Access Journals (Sweden)

    Iglesias Candela

    2011-11-01

    Full Text Available Abstract Background The human immunodeficiency virus type 1 (HIV-1 central DNA Flap is generated during reverse transcription as a result of (+ strand initiation at the central polypurine tract (cPPT and termination after a ca. 100 bp strand displacement at the central termination sequence (CTS. The central DNA Flap is a determinant of HIV-1 nuclear import, however, neither cPPT nor CTS mutations entirely abolish nuclear import and infection. Therefore, to determine whether or not the DNA Flap is essential for HIV-1 nuclear import, we generated double mutant (DM viruses, combining cPPT and CTS mutations to abolish DNA Flap formation. Results The combination of cPPT and CTS mutations reduced the proportion of viruses forming the central DNA Flap at the end of reverse transcription and further decreased virus infectivity in one-cycle titration assays. The most affected DM viruses were unable to establish a spreading infection in the highly permissive MT4 cell line, nor in human primary peripheral blood mononuclear cells (PBMCs, indicating that the DNA Flap is required for virus replication. Surprisingly, we found that DM viruses still maintained residual nuclear import levels, amounting to 5-15% of wild-type virus, as assessed by viral DNA circle quantification. Alu-PCR quantification of integrated viral genome also indicated 5-10% residual integration levels compared to wild-type virus. Conclusion This work establishes that the central DNA Flap is required for HIV-1 spreading infection but points to a residual DNA Flap independent nuclear import, whose functional significance remains unclear since it is not sufficient to support viral replication.

  2. Molecular dynamics simulations of mutated Mycobacterium tuberculosis L-alanine dehydrogenase to illuminate the role of key residues.

    Science.gov (United States)

    Ling, Baoping; Bi, Siwei; Sun, Min; Jing, Zhihong; Li, Xiaoping; Zhang, Rui

    2014-05-01

    L-Alanine dehydrogenase from Mycobacterium tuberculosis (L-MtAlaDH) catalyzes the NADH-dependent interconversion of l-alanine and pyruvate, and it is considered to be a potential target for the treatment of tuberculosis. The experiment has verified that amino acid replacement of the conserved active-site residues which have strong stability and no great changes in biological evolutionary process, such as His96 and Asp270, could lead to inactive mutants [Ågren et al., J. Mol. Biol. 377 (2008) 1161-1173]. However, the role of these conserved residues in catalytic reaction still remains unclear. Based on the crystal structures, a series of mutant structures were constructed to investigate the role of the conserved residues in enzymatic reaction by using molecular dynamics simulations. The results show that whatever the conserved residues were mutated, the protein can still convert its conformation from open state to closed state as long as NADH is present in active site. Asp270 maintains the stability of nicotinamide ring and ribose of NADH through hydrogen bond interactions, and His96 is helpful to convert the protein conformation by interactions with Gln271, whereas, they would lead to the structural rearrangement in active site and lose the catalytic activity when they were mutated. Additionally, we deduce that Met301 plays a major role in catalytic reaction due to fixing the nicotinamide ring of NADH to prevent its rotation, and we propose that Met301 would be mutated to the hydrophobic residue with large steric hindrance in side chain to test the activity of the protein in future experiment.

  3. Residual dynamics of thiacloprid in medical herbs marjoram, thyme, and camomile in soil

    Institute of Scientific and Technical Information of China (English)

    YU Yun-long; WU Jia-lun; STAHLER Matthias; PESTEMER Wilfried

    2007-01-01

    Thiacloprid is a new insecticide of the chloronicotinyl family. To assess its risk after application, residual characteristics of thiacloprid in marjoram, thyme, and camomile and in soil were studied under field conditions. The active ingredient was extracted from the plant material using a mixture of acetone-water. After filtration, the extract was concentrated to the aqueous phase, diluted with water, and portioned against ethyl acetate on a matrix solid phase dispersion column. Thiacloprid was extracted from soil using a mixture of methanol-water, filtered, and reextracted (clean up) with dichloromethane. The residues were quantified using HPLC-MS-MS. The methods were validated by recovery experiments. Thiacloprid residues in marjoram, thyme, and camomile and in soil persisted beyond 10, 14, 14, and 21 d but no residues were detected after 14, 21, 21, and 28 d, respectively. The data obtained in this study indicated that the biexponential model is more suitable than the first-order function to describe the decline of thiacloprid in fresh marjoram, fresh thyme, and dried camomile flowers with half-life (t1/2) of 1.1, 0.7, and 1.2 d, respectively. However, both the first-order function and biexponential model were found to be applicable for dissipation of thiacloprid in soil with almost the same t1/2 values of 3.5 and 3.6 d.The results indicated that thiacloprid dissipates rapidly and does not accumulate in the tested herbs and in soil.

  4. Continuum electrostatic calculations of the pKa of ionizable residues in an ion channel: dynamic vs. static input structure.

    Science.gov (United States)

    Aguilella-Arzo, M; Aguilella, V M

    2010-04-01

    We have computed the pK(a)'s of the ionizable residues of a protein ion channel, the Staphylococcus aureus toxin alpha-hemolysin, by using two types of input structures, namely the crystal structure of the heptameric alpha-hemolysin and a set of over four hundred snapshots from a 4.38 ns Molecular Dynamics simulation of the protein inserted in a phospholipid planar bilayer. The comparison of the dynamic picture provided by the Molecular Simulation with the static one based on the X-ray crystal structure of the protein embedded in a lipid membrane allows analyzing the influence of the fluctuations in the protein structure on its ionization properties. We find that the use of the dynamic structure provides interesting information about the sensitivity of the computed pK(a) of a given residue to small changes in the local structure. The calculated pK(a) are consistent with previous indirect estimations obtained from single-channel conductance and selectivity measurements.

  5. Positioning of cysteine residues within the N-terminal portion of the BST-2/tetherin ectodomain is important for functional dimerization of BST-2.

    Science.gov (United States)

    Welbourn, Sarah; Kao, Sandra; Du Pont, Kelly E; Andrew, Amy J; Berndsen, Christopher E; Strebel, Klaus

    2015-02-06

    BST-2/tetherin is a cellular host factor capable of restricting the release of a variety of enveloped viruses, including HIV-1. Structurally, BST-2 consists of an N-terminal cytoplasmic domain, a transmembrane domain, an ectodomain, and a C-terminal membrane anchor. The BST-2 ectodomain encodes three cysteine residues in its N-terminal half, each of which can contribute to the formation of cysteine-linked dimers. We previously reported that any one of the three cysteine residues is sufficient to produce functional BST-2 dimers. Here we investigated the importance of cysteine positioning on the ectodomain for functional dimerization of BST-2. Starting with a cysteine-free monomeric form of BST-2, individual cysteine residues were reintroduced at various locations throughout the ectodomain. The resulting BST-2 variants were tested for expression, dimerization, surface presentation, and inhibition of HIV-1 virus release. We found significant flexibility in the positioning of cysteine residues, although the propensity to form cysteine-linked dimers generally decreased with increasing distance from the N terminus. Interestingly, all BST-2 variants, including the one lacking all three ectodomain cysteines, retained the ability to form non-covalent dimers, and all of the BST-2 variants were efficiently expressed at the cell surface. Importantly, not all BST-2 variants capable of forming cysteine-linked dimers were functional, suggesting that cysteine-linked dimerization of BST-2 is necessary but not sufficient for inhibiting virus release. Our results expose new structural constraints governing the functional dimerization of BST-2, a property essential to its role as a restriction factor tethering viruses to the host cell.

  6. Importance of a Conserved Lys/Arg Residue for Ligand/PDZ Domain Interactions as Examined by Protein Semisynthesis

    DEFF Research Database (Denmark)

    Pedersen, Søren W; Moran, Griffin E; Sereikaité, Vita

    2016-01-01

    drug targets for diseases (in the brain in particular), so understanding the molecular details of PDZ domain interactions is of fundamental importance. PDZ domains bind to a protein partner at either a C-terminal peptide or internal peptide motifs. Here, we examined the importance of a conserved Lys......PDZ domains are ubiquitous small protein domains that are mediators of numerous protein-protein interactions, and play a pivotal role in protein trafficking, synaptic transmission, and the assembly of signaling-transduction complexes. In recent years, PDZ domains have emerged as novel and exciting...

  7. Water-soluble LYNX1 residues important for interaction with muscle-type and/or neuronal nicotinic receptors.

    Science.gov (United States)

    Lyukmanova, Ekaterina N; Shulepko, Mikhail A; Buldakova, Svetlana L; Kasheverov, Igor E; Shenkarev, Zakhar O; Reshetnikov, Roman V; Filkin, Sergey Y; Kudryavtsev, Denis S; Ojomoko, Lucy O; Kryukova, Elena V; Dolgikh, Dmitry A; Kirpichnikov, Mikhail P; Bregestovski, Piotr D; Tsetlin, Victor I

    2013-05-31

    Human LYNX1, belonging to the Ly6/neurotoxin family of three-finger proteins, is membrane-tethered with a glycosylphosphatidylinositol anchor and modulates the activity of nicotinic acetylcholine receptors (nAChR). Recent preparation of LYNX1 as an individual protein in the form of water-soluble domain lacking glycosylphosphatidylinositol anchor (ws-LYNX1; Lyukmanova, E. N., Shenkarev, Z. O., Shulepko, M. A., Mineev, K. S., D'Hoedt, D., Kasheverov, I. E., Filkin, S. Y., Krivolapova, A. P., Janickova, H., Dolezal, V., Dolgikh, D. A., Arseniev, A. S., Bertrand, D., Tsetlin, V. I., and Kirpichnikov, M. P. (2011) NMR structure and action on nicotinic acetylcholine receptors of water-soluble domain of human LYNX1. J. Biol. Chem. 286, 10618-10627) revealed the attachment at the agonist-binding site in the acetylcholine-binding protein (AChBP) and muscle nAChR but outside it, in the neuronal nAChRs. Here, we obtained a series of ws-LYNX1 mutants (T35A, P36A, T37A, R38A, K40A, Y54A, Y57A, K59A) and examined by radioligand analysis or patch clamp technique their interaction with the AChBP, Torpedo californica nAChR and chimeric receptor composed of the α7 nAChR extracellular ligand-binding domain and the transmembrane domain of α1 glycine receptor (α7-GlyR). Against AChBP, there was either no change in activity (T35A, T37A), slight decrease (K40A, K59A), and even enhancement for the rest mutants (most pronounced for P36A and R38A). With both receptors, many mutants lost inhibitory activity, but the increased inhibition was observed for P36A at α7-GlyR. Thus, there are subtype-specific and common ws-LYNX1 residues recognizing distinct targets. Because ws-LYNX1 was inactive against glycine receptor, its "non-classical" binding sites on α7 nAChR should be within the extracellular domain. Micromolar affinities and fast washout rates measured for ws-LYNX1 and its mutants are in contrast to nanomolar affinities and irreversibility of binding for α-bungarotoxin and similar

  8. Water-soluble LYNX1 Residues Important for Interaction with Muscle-type and/or Neuronal Nicotinic Receptors*

    Science.gov (United States)

    Lyukmanova, Ekaterina N.; Shulepko, Mikhail A.; Buldakova, Svetlana L.; Kasheverov, Igor E.; Shenkarev, Zakhar O.; Reshetnikov, Roman V.; Filkin, Sergey Y.; Kudryavtsev, Denis S.; Ojomoko, Lucy O.; Kryukova, Elena V.; Dolgikh, Dmitry A.; Kirpichnikov, Mikhail P.; Bregestovski, Piotr D.; Tsetlin, Victor I.

    2013-01-01

    Human LYNX1, belonging to the Ly6/neurotoxin family of three-finger proteins, is membrane-tethered with a glycosylphosphatidylinositol anchor and modulates the activity of nicotinic acetylcholine receptors (nAChR). Recent preparation of LYNX1 as an individual protein in the form of water-soluble domain lacking glycosylphosphatidylinositol anchor (ws-LYNX1; Lyukmanova, E. N., Shenkarev, Z. O., Shulepko, M. A., Mineev, K. S., D'Hoedt, D., Kasheverov, I. E., Filkin, S. Y., Krivolapova, A. P., Janickova, H., Dolezal, V., Dolgikh, D. A., Arseniev, A. S., Bertrand, D., Tsetlin, V. I., and Kirpichnikov, M. P. (2011) NMR structure and action on nicotinic acetylcholine receptors of water-soluble domain of human LYNX1. J. Biol. Chem. 286, 10618–10627) revealed the attachment at the agonist-binding site in the acetylcholine-binding protein (AChBP) and muscle nAChR but outside it, in the neuronal nAChRs. Here, we obtained a series of ws-LYNX1 mutants (T35A, P36A, T37A, R38A, K40A, Y54A, Y57A, K59A) and examined by radioligand analysis or patch clamp technique their interaction with the AChBP, Torpedo californica nAChR and chimeric receptor composed of the α7 nAChR extracellular ligand-binding domain and the transmembrane domain of α1 glycine receptor (α7-GlyR). Against AChBP, there was either no change in activity (T35A, T37A), slight decrease (K40A, K59A), and even enhancement for the rest mutants (most pronounced for P36A and R38A). With both receptors, many mutants lost inhibitory activity, but the increased inhibition was observed for P36A at α7-GlyR. Thus, there are subtype-specific and common ws-LYNX1 residues recognizing distinct targets. Because ws-LYNX1 was inactive against glycine receptor, its “non-classical” binding sites on α7 nAChR should be within the extracellular domain. Micromolar affinities and fast washout rates measured for ws-LYNX1 and its mutants are in contrast to nanomolar affinities and irreversibility of binding for α-bungarotoxin and

  9. SARS-coronavirus spike S2 domain flanked by cysteine residues C822 and C833 is important for activation of membrane fusion.

    Science.gov (United States)

    Madu, Ikenna G; Belouzard, Sandrine; Whittaker, Gary R

    2009-10-25

    The S2 domain of the coronavirus spike (S) protein is known to be responsible for mediating membrane fusion. In addition to a well-recognized cleavage site at the S1-S2 boundary, a second proteolytic cleavage site has been identified in the severe acute respiratory syndrome coronavirus (SARS-CoV) S2 domain (R797). C-terminal to this S2 cleavage site is a conserved region flanked by cysteine residues C822 and C833. Here, we investigated the importance of this well conserved region for SARS-CoV S-mediated fusion activation. We show that the residues between C822-C833 are well conserved across all coronaviruses. Mutagenic analysis of SARS-CoV S, combined with cell-cell fusion and pseudotyped virion infectivity assays, showed a critical role for the core-conserved residues C822, D830, L831, and C833. Based on available predictive models, we propose that the conserved domain flanked by cysteines 822 and 833 forms a loop structure that interacts with components of the SARS-CoV S trimer to control the activation of membrane fusion.

  10. Determination and dynamics of ethylicin residues in cotton-field ecosystem.

    Science.gov (United States)

    Chen, Zilei; Zhang, Hong; Ding, Ruiyan; Wang, Wenzheng; Wang, Wenbo; Li, Huidong

    2012-10-01

    In this work, we developed an efficient method to determine the ethylicin content in soil, cotton plant and cotton seed, and we also studied the fate of ethylicin in the cotton field ecosystem. The residual ethylicin was analyzed by GC-ECD. The limit of quantification was 0.005 mg/kg for soil, 0.01 mg/kg for the plant and cotton seed. The kinetics study of ethylicin residue showed that the ethylicin concentration in plant and soil can be regressively quantified as C = 1.0762e(-0.2529t) and C = 0.5535e(-0.1333t), representing a half-live of 2.7 and 5.2 days, respectively. As a conclusion, a dosage of 354 g a.i. ha(-1) was recommended, which could be considered as safe to human beings and animals.

  11. Protonation of a Glutamate Residue Modulates the Dynamics of the Drug Transporter EmrE

    OpenAIRE

    Gayen, Anindita; Leninger, Maureen; Traaseth, Nathaniel J.

    2016-01-01

    Secondary active transport proteins play a central role in conferring bacterial multidrug resistance. In this work, we investigated the proton-coupled transport mechanism for the Escherichia coli drug efflux pump EmrE using nuclear magnetic resonance (NMR) spectroscopy. Our results show that the global conformational motions necessary for transport are modulated in an allosteric fashion by the protonation state of a membrane-embedded glutamate residue. These observations directly correlate wi...

  12. Protonation of a Glutamate Residue Modulates the Dynamics of the Drug Transporter EmrE

    OpenAIRE

    Gayen, Anindita; Leninger, Maureen; Traaseth, Nathaniel J.

    2016-01-01

    Secondary active transport proteins play a central role in conferring bacterial multidrug resistance. In this work, we investigated the proton-coupled transport mechanism for the Escherichia coli drug efflux pump EmrE using nuclear magnetic resonance (NMR) spectroscopy. Our results show that the global conformational motions necessary for transport are modulated in an allosteric fashion by the protonation state of a membrane-embedded glutamate residue. These observations directly correlate wi...

  13. Hepatocellular carcinoma treated with transarterial chemoembolization: Dynamic perfusion-CT in the assessment of residual tumor

    Institute of Scientific and Technical Information of China (English)

    Davide; Ippolito; Pietro; Andrea; Bonaff; ini; Laura; Ratti; Laura; Antolini; Rocco; Corso; Ferruccio; Fazio; Sandro; Sironi

    2010-01-01

    AIM: To asses the value of computed tomography (CT)-perfusion in the detection of residual hepatocellular carcinoma (HCC) vascularization after transarterial chemoembolization (TACE). METHODS: Thirty-two consecutive patients were pro-spectively included in this study. All patients had liver cirrhosis and a conf irmed HCC lesion which was treated with TACE. One month after treatment, perfusion measurements of treated lesions were carried out. The CTperfusion (CT-p) protocol was performed with 16 slice multid...

  14. Determination of acetamiprid residues in zucchini grown under greenhouse conditions: application to behavioral dynamics.

    Science.gov (United States)

    Park, Ji-Yeon; Choi, Jeong-Heui; Kim, Bo-Mee; Park, Jong-Hyouk; Cho, Soon-Kil; Ghafar, M W; Abd El-Aty, A M; Shim, Jae-Han

    2011-01-01

    A simple analytical method was developed for the determination of acetamiprid residues in zucchini and zucchini leaves grown under greenhouse conditions using liquid chromatography. Residues were confirmed via tandem mass spectrometry in positive-ion electrospray ionization mode. The calibration curves were linear with correlation coefficients in excess of 0.999. The limits of detection and limits of quantification were 0.01 and 0.03 µg/g and 0.02 and 0.06 µg/g, for the zucchini and zucchini leaves, respectively. For validation purposes, recoveries studies were carried out at low and high levels, yielding recovery rates ranged from 85.7 to 92.2% in zucchini and from 90.5 to 101.9% in zucchini leaves, with a relative standard deviation of zucchini leaves were substantially higher than in the zucchini plant itself. No residues were detected at 7 days post-application. The results of this study suggest that acetamiprid is acceptable for application in/on zucchini under the recommended dosage conditions.

  15. On-matrix Derivatization for Dynamic Headspace Sampling of Nonvolatile Surface Residues

    Energy Technology Data Exchange (ETDEWEB)

    Harvey, Scott D.; Wahl, Jon H.

    2012-09-01

    The goal of this study is to extend sampling by the field and laboratory emission cell (FLEC) purge-and-trap technique to applications that target nonvolatile residues. On-matrix derivatization of residues to render analytes stable and more volatile is explored to achieve this goal. Results show that on-matrix derivatizations of nerve agent hydrolysis products (monoalkyl methylphosphonic acids and methylphosphonic acid [MPA]) with diazomethane were successful on glass and painted wallboard (at the 10-µg level). It also was successful on the more difficult concrete (at the 500-µg level) and carpet (at the 20-µg level) substrates that cannot be successfully sampled using swipe techniques. Analysis of additional chemical warfare (CW)-associated residues can be approached by on-matrix derivatization with trifluoroacetic anhydride (TFAA). For example, amines (used as stabilizers or present as decomposition products of the nerve agent VX) or thiodiglycol (hydrolysis product of sulfur mustard) could be sampled as their TFAA derivatives from glass, painted wallboard, and concrete (at the 40-µg level), as well as carpet (at the 80-µg level) surfaces. Although the amine and thiodiglycol are semi-volatile and could be sampled directly, derivatization improves the recovery and chromatographic behavior of these analytes.

  16. Effects of Maize Residue Removal and Tillage on Soil Erosion, Carbon, and Macronutrient Dynamics

    Science.gov (United States)

    Beniston, J.; Shipitalo, M.; Lal, R.; Dayton, E. A.; Hopkins, D.; Jones, F. S.; Joynes, A.; Dungait, J.

    2013-12-01

    Erosion by water is a principal process of soil degradation in agricultural lands. Soil erosion influences the storage and fluxes of C and key macronutrients N and P in soil surface layers. No till (NT) crop management significantly reduces erosion on susceptible landscapes. The selective removal of crop residues for bio-energy production from no-till systems has been suggested as a secondary crop, but the effect of this practice on the conservation benefits of NT has not been quantified. Therefore, this study was initiated in spring 2012 to examine the effects of soil management practices on erosion and associated macronutrient fluxes on erodible soils subjected to a high intensity simulated rain storm at the North Appalachian Experimental Watershed (NAEW) in Coshocton, OH, U.S.A. The soil management practices evaluated included: long term no-till with 100% crop residue (NT100) , no-till with 50% crop reside (NT50), NT with complete crop residue removal (NT0), long term conventional tillage (CT), and long term no-tillage plots that were cultivated (TNT) with a rototiller before the rainfall application. A field rainfall simulator was utilized to apply rainfall at an intensity of 7 cm hr-1 to a 4 m2 area of each plot for 30 minutes. Total runoff from the NT0 plots (22.1 mm) was almost double compared with the NT 50% (13.3 mm), CT (12.8 mm) and TNT (12.8 mm) plots and was more than 5 times greater than the NT100 plots (4.4mm). CT and NT0 plots produced 40 (2.7 Mg ha-1) and 20 times (1.4 Mg ha-1) more soil loss, respectively, than NT100 plots (0.07 Mg ha-1). Tillage of the no-till (TNT) soil produced the largest sediment-bound fluxes of C and N, while sediment-bound P fluxes were largest in the CT soils. Natural abundance δ13C and δ15N values were distinct between eroded sediments and the source topsoils and suggested enhanced loss of older (>28 yrs) C residues in CT plots. All observations suggest NT management provides greater resilience to soils than CT during

  17. Residual and Dynamic Range of Retinal Nerve Fiber Layer Thickness in Glaucoma: Comparison of Three OCT Platforms

    Science.gov (United States)

    Mwanza, Jean-Claude; Kim, Hanna Y.; Budenz, Donald L.; Warren, Joshua L.; Margolis, Michael; Lawrence, Scott D.; Jani, Pooja D.; Thompson, Garrett S.; Lee, Richard K.

    2015-01-01

    Purpose To estimate visual field (VF) sensitivity at which retinal nerve fiber layer (RNFL) thinning reaches the measurement floor and at which RNFL stops thinning (change points), the dynamic range of RNFL thickness, and the number of steps from normal to RNFL floor among three optical coherence tomography (OCT) devices. Methods Glaucomatous patients (n = 58) and healthy subjects (n = 55–60) prospectively underwent VF testing and RNFL thickness measurement with Cirrus, Spectralis, and RTVue. Change points and corresponding RNFL thicknesses were estimated with simple linear regression (SLR) and Bayesian change point (BCP) analyses. The dynamic range and number of steps to RNFL floor were determined. Results The average VF change points and corresponding residual thickness at the time RNFL stopped thinning were −22.2 dB and 57.0 μm (Cirrus), −25.3 dB and 49.2 μm (Spectralis), and −24.6 dB and 64.7 μm (RTVue). The RNFL dynamic ranges derived from SLR values were wider on Spectralis (52.6 μm) than on Cirrus (35.4 μm) and RTVue (35.5 μm); the corresponding number of steps to reach the RNFL floor were 9.0 on Cirrus, 10.6 on Spectralis, and 8.3 on RTVue. Conclusions The relative VF sensitivity at which average RNFL thickness reaches the measurement floor, the residual layer thickness, and RNFL dynamic measurement range differ among the three devices. However, the number of steps from normal to the RNFL thickness floor is comparable. PMID:26436887

  18. The importance of temperature fluctuations in understanding mosquito population dynamics and malaria risk

    Science.gov (United States)

    Nelson, William A.; Paaijmans, Krijn P.; Thomas, Matthew B.; Bjørnstad, Ottar N.

    2017-01-01

    Temperature is a key environmental driver of Anopheles mosquito population dynamics; understanding its central role is important for these malaria vectors. Mosquito population responses to temperature fluctuations, though important across the life history, are poorly understood at a population level. We used stage-structured, temperature-dependent delay-differential equations to conduct a detailed exploration of the impacts of diurnal and annual temperature fluctuations on mosquito population dynamics. The model allows exploration of temperature-driven temporal changes in adult age structure, giving insights into the population’s capacity to vector malaria parasites. Because of temperature-dependent shifts in age structure, the abundance of potentially infectious mosquitoes varies temporally, and does not necessarily mirror the dynamics of the total adult population. In addition to conducting the first comprehensive theoretical exploration of fluctuating temperatures on mosquito population dynamics, we analysed observed temperatures at four locations in Africa covering a range of environmental conditions. We found both temperature and precipitation are needed to explain the observed malaria season in these locations, enhancing our understanding of the drivers of malaria seasonality and how temporal disease risk may shift in response to temperature changes. This approach, tracking both mosquito abundance and age structure, may be a powerful tool for understanding current and future malaria risk.

  19. Analysis of antigenically important residues in human influenza A virus in terms of B-cell epitopes.

    Science.gov (United States)

    Lees, William D; Moss, David S; Shepherd, Adrian J

    2011-09-01

    In this paper we undertake an analysis of the antigenicity of influenza A virus hemagglutinin. We developed a novel computational approach to the identification of antigenically active regions and showed that the amino acid substitutions between successive predominant seasonal strains form clusters that are consistent, in terms of both their location and their size, with the properties of B-cell epitopes in general and with those epitopes that have been identified experimentally in influenza A virus hemagglutinin to date. Such an interpretation provides a biologically plausible framework for an understanding of the location of antigenically important substitutions that is more specific than the canonical "antigenic site" model and provides an effective basis for deriving models that predict antigenic escape in the H3N2 subtype. Our results support recent indications that antibodies binding to the "stalk" region of hemagglutinin are found in the human population and exert evolutionary pressure on the virus. Our computational approach provides a possible method for identifying antigenic escape through evolution in this region, which in some cases will not be identified by the hemagglutinin inhibition assay.

  20. Dynamics of imports of sheep meat in Brazil: analysis of temporal components

    Directory of Open Access Journals (Sweden)

    João Garibaldi Almeida Viana

    2015-07-01

    Full Text Available The sheep production is an important livestock activity in Brazil. Its production stretches away into the country, a source of income and livelihood. On the demand side, there is an increase in domestic consumption, driven by the increased purchasing power of the population. To meet the growing demand, Brazil access international markets through of sheep meat imports. In this context, the work aims to analyze the dynamics of sheep meat imports in Brazil from 2000 to 2012, giving particular attention to the tendency and seasonality of the quantity imported. The data of volume and value of imports were collected from the system AliceWeb. Statistical analysis followed the multiplicative time series model. Identified an upward tendency of sheep meat import, with annual growth of 5.09% in the period. Still, the total quantity commercialized, there is the purchase of sheep bone cuts. There was the seasonal behavior in the import of sheep meat, focusing primarily in the months of the end of the year, with import volumes 68% higher than the average of the total amount. The main trading partner of Brazil is the Uruguay, market responsible for at least 80% of the annual volume of import.

  1. Histidine and Aspartic Acid Residues Important for Immunoglobulin G Endopeptidase Activity of the Group A Streptococcus Opsonophagocytosis-Inhibiting Mac Protein

    Science.gov (United States)

    Lei, Benfang; Liu, Mengyao; Meyers, Elishia G.; Manning, Heather M.; Nagiec, Michael J.; Musser, James M.

    2003-01-01

    The secreted Mac protein made by serotype M1 group A Streptococcus (GAS) (designated Mac5005) inhibits opsonophagocytosis and killing of GAS by human polymorphonuclear neutrophils. This protein also has cysteine endopeptidase activity against human immunoglobulin G (IgG). Site-directed mutagenesis was used to identify histidine and aspartic acid residues important for Mac IgG endopeptidase activity. Replacement of His262 with Ala abolished Mac5005 IgG endopeptidase activity. Asp284Ala and Asp286Ala mutant proteins had compromised enzymatic activity, whereas 21 other Asp-to-Ala mutant proteins cleaved human IgG at the apparent wild-type level. The results suggest that His262 is an active-site residue and that Asp284 and Asp286 are important for the enzymatic activity or structure of Mac protein. These Mac mutants provide new information about structure-activity relationships in this protein and will assist study of the mechanism of inhibition of opsonophagocytosis and killing of GAS by Mac. PMID:12704162

  2. The Impact of Imports on the Dynamics of the Regional Manufacturing Industry Development

    Directory of Open Access Journals (Sweden)

    Igor Olegovich Botkin

    2016-09-01

    Full Text Available The aim of the study is to identify regions with the highest dependence on imports and assess the impact of imports on the dynamics of the manufacturing industry’s growth. The methodological framework of the study involves the use of well-known processing methods of regional static data. The paper presents an empirical study of imports volume and structure in the regional manufacturing industry for the period from 2005 to 2014, and groups them on the basis of the assessment of sustainability indicators. At the regional level, intermediate imports are characterized by a high heterogeneity both in absolute and relative terms. The significant volumes of imports are concentrated in few regions with a high industrial concentration. It allows to allocate regions with the greatest risks for the manufacturing sector in negative external environment. The study demonstrates the relationship of the intermediate imports with the growth dynamics of the manufacturing industry in a certain set of macroeconomic conditions, assuming the economic growth with the stable exchange rate and relatively high growth rate of the producer prices on the domestic market. We also found a positive impact of imports on the growth rate of manufacturing industry in this period due to the effects of market substitution. Thus, the limitation of import substitution in specialized regions at preservation of the basic external factors is emphasized. The obtained results can be used for strategic planning at various levels of management, defining the model and direction for growth of the industrial sector of the region and improving the methodological tools for further empirical research.

  3. Importance of explicit salt ions for protein stability in molecular dynamics simulation.

    Science.gov (United States)

    Ibragimova, G T; Wade, R C

    1998-06-01

    The accurate and efficient treatment of electrostatic interactions is one of the challenging problems of molecular dynamics simulation. Truncation procedures such as switching or shifting energies or forces lead to artifacts and significantly reduced accuracy. The particle mesh Ewald (PME) method is one approach to overcome these problems by providing a computationally efficient means of calculating all long-range electrostatic interactions in a periodic simulation box by use of fast Fourier transformation techniques. For the application of the PME method to the simulation of a protein with a net charge in aqueous solution, counterions are added to neutralize the system. The usual procedure is to add charge-balancing counterions close to charged residues to neutralize the protein surface. In the present article, we show that for MD simulation of a small protein of marginal stability, the YAP-WW domain, explicit modeling of 0.2 M ionic strength (in addition to the charge-balancing counterions) is necessary to maintain a stable protein structure. Without explicit ions throughout the periodic simulation box, the charge-balancing counterions on the protein surface diffuse away from the protein, resulting in destruction of the beta-sheet secondary structure of the WW domain.

  4. Protonation of a glutamate residue modulates the dynamics of the drug transporter EmrE.

    Science.gov (United States)

    Gayen, Anindita; Leninger, Maureen; Traaseth, Nathaniel J

    2016-03-01

    Secondary active transport proteins play a central role in conferring bacterial multidrug resistance. In this work, we investigated the proton-coupled transport mechanism for the Escherichia coli drug efflux pump EmrE using NMR spectroscopy. Our results show that the global conformational motions necessary for transport are modulated in an allosteric fashion by the protonation state of a membrane-embedded glutamate residue. These observations directly correlate with the resistance phenotype for wild-type EmrE and the E14D mutant as a function of pH. Furthermore, our results support a model in which the pH gradient across the inner membrane of E. coli may be used on a mechanistic level to shift the equilibrium of the transporter in favor of an inward-open resting conformation poised for drug binding.

  5. DNA polymerase conformational dynamics and the role of fidelity-conferring residues: Insights from computational simulations

    Directory of Open Access Journals (Sweden)

    Massimiliano eMeli

    2016-05-01

    Full Text Available Herein we investigate the molecular bases of DNA polymerase I conformational dynamics that underlie the replication fidelity of the enzyme. Such fidelity is determined by conformational changes that promote the rejection of incorrect nucleotides before the chemical ligation step. We report a comprehensive atomic resolution study of wild type and mutant enzymes in different bound states and starting from different crystal structures, using extensive molecular dynamics (MD simulations that cover a total timespan of ~ 5 microseconds. The resulting trajectories are examined via a combination of novel methods of internal dynamics and energetics analysis, aimed to reveal the principal molecular determinants for the (destabilization of a certain conformational state. Our results show that the presence of fidelity-decreasing mutations or the binding of incorrect nucleotides in ternary complexes tend to favor transitions from closed towards open structures, passing through an ensemble of semi-closed intermediates. The latter ensemble includes the experimentally observed ajar conformation which, consistent with previous experimental observations, emerges as a molecular checkpoint for the selection of the correct nucleotide to incorporate. We discuss the implications of our results for the understanding of the relationships between the structure, dynamics and function of DNA polymerase I at the atomistic level.

  6. Conformational dynamics in substrate-binding domains influences transport in the ABC importer GlnPQ.

    Science.gov (United States)

    Gouridis, Giorgos; Schuurman-Wolters, Gea K; Ploetz, Evelyn; Husada, Florence; Vietrov, Ruslan; de Boer, Marijn; Cordes, Thorben; Poolman, Bert

    2015-01-01

    The conformational dynamics in ABC transporters is largely elusive. The ABC importer GlnPQ from Lactococcus lactis has different covalently linked substrate-binding domains (SBDs), thus making it an excellent model system to elucidate the dynamics and role of the SBDs in transport. We demonstrate by single-molecule spectroscopy that the two SBDs intrinsically transit from open to closed ligand-free conformation, and the proteins capture their amino acid ligands via an induced-fit mechanism. High-affinity ligands elicit transitions without changing the closed-state lifetime, whereas low-affinity ligands dramatically shorten it. We show that SBDs in the closed state compete for docking onto the translocator, but remarkably the effect is strongest without ligand. We find that the rate-determining steps depend on the SBD and the amino acid transported. We conclude that the lifetime of the closed conformation controls both SBD docking to the translocator and substrate release.

  7. The dynamical importance of binary systems in young massive star clusters

    CERN Document Server

    de Grijs, Richard; Geller, Aaron M

    2015-01-01

    Characterization of the binary fractions in star clusters is of fundamental importance for many fields in astrophysics. Observations indicate that the majority of stars are found in binary systems, while most stars with masses greater than $0.5 M_\\odot$ are formed in star clusters. In addition, since binaries are on average more massive than single stars, in resolved star clusters these systems are thought to be good tracers of (dynamical) mass segregation. Over time, dynamical evolution through two-body relaxation will cause the most massive objects to migrate to the cluster center, while the relatively lower-mass objects remain in or migrate to orbits at greater radii. This process will globally dominate a cluster's stellar distribution. However, close encounters involving binary systems may disrupt `soft' binaries. This process will occur more frequently in a cluster's central, dense region than in its periphery, which may mask the effects of mass segregation. Using high resolution Hubble Space Telescope o...

  8. Impact of static and dynamic A-form heterogeneity on the determination of RNA global structural dynamics using NMR residual dipolar couplings

    Energy Technology Data Exchange (ETDEWEB)

    Musselman, Catherine [University of Michigan, Department of Chemistry, Biophysics Research Division, and Program in Bioinformatics (United States); Pitt, Stephen W. [Johnson and Johnson Inc (United States); Gulati, Kush; Foster, Lesley L.; Andricioaei, Ioan; Al-Hashimi, Hashim M. [University of Michigan, Department of Chemistry, Biophysics Research Division, and Program in Bioinformatics (United States)], E-mail: hashimi@umich.edu

    2006-12-15

    We examined how static and dynamic deviations from the idealized A-form helix propagate into errors in the principal order tensor parameters determined using residual dipolar couplings (rdcs). A 20-ns molecular dynamics (MD) simulation of the HIV-1 transactivation response element (TAR) RNA together with a survey of spin relaxation studies of RNA dynamics reveals that pico-to-nanosecond local motions in non-terminal Watson-Crick base-pairs will uniformly attenuate base and sugar one bond rdcs by {approx}7%. Gaussian distributions were generated for base and sugar torsion angles through statistical comparison of 40 RNA X-ray structures solved to <3.0 A resolution. For a typical number ({>=}11) of one bond C-H base and sugar rdcs, these structural deviations together with rdc uncertainty (1.5 Hz) lead to average errors in the magnitude and orientation of the principal axis of order that are <9% and <4 deg., respectively. The errors decrease to <5% and <4 deg. for {>=}17 rdcs. A protocol that allows for estimation of error in A-form order tensors due to both angular deviations and rdc uncertainty (Aform-RDC) is validated using theoretical simulations and used to analyze rdcs measured previously in TAR in the free state and bound to four distinct ligands. Results confirm earlier findings that the two TAR helices undergo large changes in both their mean relative orientation and dynamics upon binding to different targets.

  9. Deciphering the mechanism behind the varied binding activities of COXIBs through Molecular Dynamic Simulations, MM-PBSA binding energy calculations and per-residue energy decomposition studies.

    Science.gov (United States)

    Chaudhary, Neha; Aparoy, Polamarasetty

    2017-03-01

    COX-2 is a well-known drug target in inflammatory disorders. COX-1/COX-2 selectivity of NSAIDs is crucial in assessing the gastrointestinal side effects associated with COX-1 inhibition. Celecoxib, rofecoxib, and valdecoxib are well-known specific COX-2 inhibiting drugs. Recently, polmacoxib, a COX-2/CA-II dual inhibitor has been approved by the Korean FDA. These COXIBs have similar structure with diverse activity range. Present study focuses on unraveling the mechanism behind the 10-fold difference in the activities of these sulfonamide-containing COXIBs. In order to obtain insights into their binding with COX-2 at molecular level, molecular dynamics simulations studies, and MM-PBSA approaches were employed. Further, per-residue decomposition of these energies led to the identification of crucial amino acids and interactions contributing to the differential binding of COXIBs. The results clearly indicated that Leu338, Ser339, Arg499, Ile503, Phe504, Val509, and Ser516 (Leu352, Ser353, Arg513, Ile517, Phe518, Val523, and Ser530 in PGHS-1 numbering) were imperative in determining the activity of these COXIBs. The binding energies and energy contribution of various residues were similar in all the three simulations. The results suggest that hydrogen bond interaction between the hydroxyl group of Ser516 and five-membered ring of diarylheterocycles augments the affinity in COXIBs. The SAR of the inhibitors studied and the per-residue energy decomposition values suggested the importance of Ser516. Additionally, the positive binding energy obtained with Arg106 explains the binding of COXIBs in hydrophobic channel deep in the COX-2 active site. The findings of the present work would aid in the development of potent COX-2 inhibitors.

  10. Relative importance of natural disturbances and habitat degradation on snail kite population dynamics

    Science.gov (United States)

    Martin, J.; Kitchens, W.M.; Cattau, Christopher E.; Oli, M.K.

    2008-01-01

    Natural disturbances and habitat degradation are major factors influencing the dynamics and persistence of many wildlife populations, yet few large-scale studies have explored the relative influence of these factors on the dynamics and persistence of animal populations. We used longterm demographic data and matrix population models to examine the potential effects of habitat degradation and natural disturbances on the dynamics of the endangered snail kite Rostrhamus sociabilis in Florida, USA. We found that estimates of stochastic population growth rate were low (0.90). Population growth rate (??) during the first half or our study period (1992 to 1998) was substantially greater than during the second half (1999 to 2005). These 2 periods were characterized by contrasting hydrological conditions. Although ?? was most sensitive to changes in adult survival, the analysis of life table response experiments revealed that a reduction in fertility of kites accounted for >80% of the observed decline in population growth rate. We examined the possibility that the reduction in ?? was caused by (1) habitat degradation due to management, (2) an increase in frequency of moderate drying events in recent years, and (3) both habitat degradation and an increase in frequency of moderate drying events. Our results suggest that both factors could potentially contribute to a large decrease in population growth rate. Our study highlights the importance of simultaneously considering short- and long-term effects of disturbances when modeling population dynamics. Indeed, focusing exclusively on one type of effect may be misleading to both our understanding of the ecological dynamics of the system and to management. The relevance of our results to management is heightened because the snail kite has been selected as a key performance measure of one of the most ambitious ecosystem restoration projects ever undertaken. ?? Inter-Research 2008.

  11. The importance of progressive senescence in the biomass dynam of giant kelp (Macrocystis pyrifera).

    Science.gov (United States)

    Rodriguez, Gabriel E; Rassweiler, Andrew; Reed, Daniel C; Holbrook, Sally J

    2013-08-01

    Temporal variation in primary producer biomass has profound effects on the structure and function of the surrounding ecological community. The giant kelp (Macrocystis pyrifera) exhibits strong intra-annual variation in biomass density, which is better explained by the demographic rates of fronds than by those of whole plants. To better understand the processes controlling the dynamics of giant kelp fronds we collected monthly time-series data of frond initiation and survival. These data were used to determine how frond loss and frond initiation rates were predicted by factors thought to affect the growth and survival of Macrocystis, including external environmental factors (i.e., wave height, day length, temperature, nutrient concentration, and neighborhood density) and intrinsic biological characteristics (i.e., frond age, plant size, and nutritional status). Our results revealed that frond dynamics were better explained by intrinsic biological processes rather than external environmental factors. A metric of frond age structure that incorporated progressive senescence was the best predictor of frond loss rate, accounting for 58% of the explained variation in frond loss. A similar analysis revealed that frond age structure was also the single best predictor of frond initiation rate, accounting for 46% of the explained variation. To further examine the importance of senescence in biomass dynamics, we used frond age-dependent mortality and frond initiation rates to predict biomass in subsequent months and found that the model explained 73% of the observed variation in biomass at our sites. Vegetation dynamics of many species including giant kelp are often considered largely in the context of external controls on resource availability and physical disturbance. Our results indicate that investigations of the processes controlling vegetation dynamics may benefit greatly from the inclusion of intrinsic biological factors such as age-dependent mortality and growth, which

  12. Identification of Residues Important for the Activity of Haloferax volcanii AglD, a Component of the Archaeal N-Glycosylation Pathway

    Directory of Open Access Journals (Sweden)

    Lina Kaminski

    2010-01-01

    Full Text Available In Haloferax volcanii, AglD adds the final hexose to the N-linked pentasaccharide decorating the S-layer glycoprotein. Not knowing the natural substrate of the glycosyltransferase, together with the challenge of designing assays compatible with hypersalinity, has frustrated efforts at biochemical characterization of AglD activity. To circumvent these obstacles, an in vivo assay designed to identify amino acid residues important for AglD activity is described. In the assay, restoration of AglD function in an Hfx. volcanii aglD deletion strain transformed to express plasmid-encoded versions of AglD, generated through site-directed mutagenesis at positions encoding residues conserved in archaeal homologues of AglD, is reflected in the behavior of a readily detectable reporter of N-glycosylation. As such Asp110 and Asp112 were designated as elements of the DXD motif of AglD, a motif that interacts with metal cations associated with nucleotide-activated sugar donors, while Asp201 was predicted to be the catalytic base of the enzyme.

  13. Identification of residues important for the activity of Haloferax volcanii AglD, a component of the archaeal N-glycosylation pathway.

    Science.gov (United States)

    Kaminski, Lina; Eichler, Jerry

    2010-05-06

    In Haloferax volcanii, AglD adds the final hexose to the N-linked pentasaccharide decorating the S-layer glycoprotein. Not knowing the natural substrate of the glycosyltransferase, together with the challenge of designing assays compatible with hypersalinity, has frustrated efforts at biochemical characterization of AglD activity. To circumvent these obstacles, an in vivo assay designed to identify amino acid residues important for AglD activity is described. In the assay, restoration of AglD function in an Hfx. volcanii aglD deletion strain transformed to express plasmid-encoded versions of AglD, generated through site-directed mutagenesis at positions encoding residues conserved in archaeal homologues of AglD, is reflected in the behavior of a readily detectable reporter of N-glycosylation. As such Asp110 and Asp112 were designated as elements of the DXD motif of AglD, a motif that interacts with metal cations associated with nucleotide-activated sugar donors, while Asp201 was predicted to be the catalytic base of the enzyme.

  14. Stabilization of secondary structure elements by specific combinations of hydrophilic and hydrophobic amino acid residues is more important for proteins encoded by GC-poor genes.

    Science.gov (United States)

    Khrustalev, Vladislav Victorovich; Barkovsky, Eugene Victorovich

    2012-12-01

    Stabilization of secondary structure elements by specific combinations of hydrophobic and hydrophilic amino acids has been studied by the way of analysis of pentapeptide fragments from twelve partial bacterial proteomes. PDB files describing structures of proteins from species with extremely high and low genomic GC-content, as well as with average G + C were included in the study. Amino acid residues in 78,009 pentapeptides from alpha helices, beta strands and coil regions were classified into hydrophobic and hydrophilic ones. The common propensity scale for 32 possible combinations of hydrophobic and hydrophilic amino acid residues in pentapeptide has been created: specific pentapeptides for helix, sheet and coil were described. The usage of pentapeptides preferably forming alpha helices is decreasing in alpha helices of partial bacterial proteomes with the increase of the average genomic GC-content in first and second codon positions. The usage of pentapeptides preferably forming beta strands is increasing in coil regions and in helices of partial bacterial proteomes with the growth of the average genomic GC-content in first and second codon positions. Due to these circumstances the probability of coil-sheet and helix-sheet transitions should be increased in proteins encoded by GC-rich genes making them prone to form amyloid in certain conditions. Possible causes of the described fact that importance of alpha helix and coil stabilization by specific combinations of hydrophobic and hydrophilic amino acids is growing with the decrease of genomic GC-content have been discussed.

  15. Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction

    Science.gov (United States)

    Lipska, Agnieszka G.; Seidman, Steven R.; Sieradzan, Adam K.; Giełdoń, Artur; Liwo, Adam; Scheraga, Harold A.

    2016-05-01

    The folding of the N-terminal part of the B-domain of staphylococcal protein A (PDB ID: 1BDD, a 46-residue three-α-helix bundle) and the formin-binding protein 28 WW domain (PDB ID: 1E0L, a 37-residue three-stranded anti-parallel β protein) was studied by means of Langevin dynamics with the coarse-grained UNRES force field to assess the influence of hydrodynamic interactions on protein-folding pathways and kinetics. The unfolded, intermediate, and native-like structures were identified by cluster analysis, and multi-exponential functions were fitted to the time dependence of the fractions of native and intermediate structures, respectively, to determine bulk kinetics. It was found that introducing hydrodynamic interactions slows down both the formation of an intermediate state and the transition from the collapsed structures to the final native-like structures by creating multiple kinetic traps. Therefore, introducing hydrodynamic interactions considerably slows the folding, as opposed to the results obtained from earlier studies with the use of Gō-like models.

  16. Diagnostics of many-particle electronic states: non-stationary currents and residual charge dynamics

    Science.gov (United States)

    Maslova, N. S.; Mantsevich, V. N.; Arseyev, P. I.

    2017-01-01

    We propose the method for identifying many particle electronic states in the system of coupled quantum dots (impurities) with Coulomb correlations. We demonstrate that different electronic states can be distinguished by the complex analysis of localized charge dynamics and non-stationary characteristics. We show that localized charge time evolution strongly depends on the properties of initial state and analyze different time scales in charge kinetics for initially prepared singlet and triplet states. We reveal the conditions for existence of charge trapping effects governed by the selection rules for electron transitions between the states with different occupation numbers.

  17. Carbon and nitrogen dynamics in agroforestry systems. Temporal patterns of some important soil processes

    Energy Technology Data Exchange (ETDEWEB)

    Nyberg, Gert [Swedish Univ. of Agricultural Sciences, Umeaa (Sweden). Dept. of Forest Ecology

    2001-07-01

    The ameliorative effects of different tree species on soils in some agroforestry systems were studied. The temporal pattern of nutrient release from tree organic material is important to achieve synchrony with crop uptake. When, as in many tropical agroforestry systems, trees (C{sub 3}-plants) are planted on C{sub 4}-carbon dominated soils, the difference of around 12-16 per mille in natural abundance of {sup 13}C between C{sub 3} and C{sub 4} plants makes the natural abundance of {sup 13}C a particularly sensitive indicator of the influence of trees on the soil. An increase of 3-5% of the percentage C was proven to derive from trees by this method, only five years after planting. By using the difference of around 10 per mille in natural abundance of {sup 13}C between the endogenous soil C (mainly C{sub 4}) and the applied C (C{sub 3}) in green manure experiments, the contributions of the two C sources to soil respiration can be calculated. The microbial response to the additions of leaves was an immediate increase in respiration. This non-destructive method allows repeated measurements of the actual rate of C mineralisation and facilitates decomposition studies with high temporal resolution in the field. The mineralisation of N was also very rapid and the concentration of NH{sub 4}{sup +} in the soil correlated well with respiration of added C. In our studies, 3-4% of the added C was respired daily, for the first 10 days after addition of Sesbania sesban leaves. Although respiration rates decline with time, we estimated 70-90% to be respired in as short time as 40 days. Weight losses of around 80% after 52 days, from high quality residues in litter bags, also indicate substantial C losses. Measurable build-up of soil organic matter is, hence, unlikely. For immediate soil fertility, addition of high quality green manure may, however, be a viable management option. To achieve synchrony with crop demand, caution is needed in management as large amounts of N are

  18. Importance of soil thermal regime in terrestrial ecosystem carbon dynamics in the circumpolar north

    Science.gov (United States)

    Jiang, Yueyang; Zhuang, Qianlai; Sitch, Stephen; O'Donnell, Jonathan A.; Kicklighter, David; Sokolov, Andrei; Melillo, Jerry

    2016-07-01

    In the circumpolar north (45-90°N), permafrost plays an important role in vegetation and carbon (C) dynamics. Permafrost thawing has been accelerated by the warming climate and exerts a positive feedback to climate through increasing soil C release to the atmosphere. To evaluate the influence of permafrost on C dynamics, changes in soil temperature profiles should be considered in global C models. This study incorporates a sophisticated soil thermal model (STM) into a dynamic global vegetation model (LPJ-DGVM) to improve simulations of changes in soil temperature profiles from the ground surface to 3 m depth, and its impacts on C pools and fluxes during the 20th and 21st centuries. With cooler simulated soil temperatures during the summer, LPJ-STM estimates ~ 0.4 Pg C yr- 1 lower present-day heterotrophic respiration but ~ 0.5 Pg C yr- 1 higher net primary production than the original LPJ model resulting in an additional 0.8 to 1.0 Pg C yr- 1 being sequestered in circumpolar ecosystems. Under a suite of projected warming scenarios, we show that the increasing active layer thickness results in the mobilization of permafrost C, which contributes to a more rapid increase in heterotrophic respiration in LPJ-STM compared to the stand-alone LPJ model. Except under the extreme warming conditions, increases in plant production due to warming and rising CO2, overwhelm the e nhanced ecosystem respiration so that both boreal forest and arctic tundra ecosystems remain a net C sink over the 21st century. This study highlights the importance of considering changes in the soil thermal regime when quantifying the C budget in the circumpolar north.

  19. A cluster of aspartic residues in the extracellular loop II of PAR 4 is important for thrombin interaction and activation of platelets.

    Science.gov (United States)

    Sánchez Centellas, Daniel; Gudlur, Sushanth; Vicente-Carrillo, Alejandro; Ramström, Sofia; Lindahl, Tomas L

    2017-06-01

    Thrombin activates platelets via proteolytic cleavage of protease-activated receptors (PARs) 1 and 4. The two PARs have distinct but complementary roles. The mechanisms responsible for PAR1 activation by thrombin have been extensively studied. However, much less is known regarding thrombin activation of PAR4, especially the potential involvement of regions of PAR4 other than the N-terminal, which is bound to the catalytic site of thrombin. We have studied PAR4 in S. cerevisiae strain MMY12, an expression system in which the GPCR receptors are connected to a Lac Z reporter gene resulting in increased β-galactosidase activity. This approach was used to assess PAR4 mutants to evaluate the contribution of different aspartic residues in facilitating PAR4 activation. Furthermore, peptides mimicking parts of the PAR4 N-terminal and the second extracellular loop (ECLII) were tested for their ability to inhibit platelet activation by thrombin. Binding of these peptides to γ-thrombin was studied by monitoring the decrease in tryptophan fluorescence intensity of thrombin. We conclude that not only the N-terminal but also the electronegative aspartic residues D224, D230 and D235 (located in ECLII) are be important for PAR4 binding to thrombin. We further suggest that they play a role for the tethered ligand binding to the receptor, as mutations also affected activation in response to a PAR4-activating peptide mimicking the new N-terminal formed after cleavage. This agrees with previous results on PAR1 and thrombin binding. We suggest that the ECLII of PAR4 could be a potential target for antithrombotic drug development. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. The tyrosine 343 residue of nucleophosmin (NPM)-anaplastic lymphoma kinase (ALK) is important for its interaction with SHP1, a cytoplasmic tyrosine phosphatase with tumor suppressor functions.

    Science.gov (United States)

    Hegazy, Samar A; Wang, Peng; Anand, Mona; Ingham, Robert J; Gelebart, Pascal; Lai, Raymond

    2010-06-25

    The cytoplasmic tyrosine phosphatase SHP1 has been shown to inhibit the oncogenic fusion protein nucleophosmin (NPM)-anaplastic lymphoma kinase (ALK), and loss of SHP1 contributes to NPM-ALK-mediated tumorigenesis. In this study, we aimed to further understand how SHP1 interacts and regulates NPM-ALK. We employed an in vitro model in which GP293 cells were transfected with various combinations of NPM-ALK (or mutants) and SHP1 (or mutants) expression vectors. We found that SHP1 co-immunoprecipitated with NPM-ALK, but not the enzymatically inactive NPM-ALK(K210R) mutant, or the mutant in which all three functionally important tyrosine residues (namely, Tyr(338), Tyr(342), and Tyr(343)) in the kinase activation loop (KAL) of ALK were mutated. Interestingly, whereas mutation of Tyr(338) or Tyr(342) did not result in any substantial change in the NPM-ALK/SHP1 binding (assessed by co-immunoprecipitation), mutation of Tyr(343) abrogated this interaction. Furthermore, the NPM-ALK/SHP1 binding was readily detectable when each of the remaining 8 tyrosine residues known to be phosphorylated were mutated. Although the expression of SHP1 effectively reduced the level of tyrosine phosphorylation of NPM-ALK, it did not affect that of the NPM-ALK(Y343F) mutant. In soft agar clonogenic assay, SHP1 expression significantly reduced the tumorigenicity of NPM-ALK but not that of NPM-ALK(Y343F). In conclusion, we identified Tyr(343) of NPM-ALK as the crucial site for mediating the NPM-ALK/SHP1 interaction. Our results also support the notion that the tumor suppressor effects of SHP1 on NPM-ALK are dependent on its ability to bind to this oncogenic protein.

  1. Mutation of putative N-linked glycosylation sites on the human nucleotide receptor P2X7 reveals a key residue important for receptor function.

    Science.gov (United States)

    Lenertz, Lisa Y; Wang, Ziyi; Guadarrama, Arturo; Hill, Lindsay M; Gavala, Monica L; Bertics, Paul J

    2010-06-08

    The nucleotide receptor P2X(7) is an immunomodulatory cation channel and a potential therapeutic target. P2X(7) is expressed in immune cells such as monocytes and macrophages and is activated by extracellular ATP following tissue injury or infection. Ligand binding to P2X(7) can stimulate ERK1/2, the transcription factor CREB, enzymes linked to the production of reactive oxygen species and interleukin-1 isoforms, and the formation of a nonspecific pore. However, little is known about the biochemistry of P2X(7), including whether the receptor is N-linked glycosylated and if this modification affects receptor function. Here we provide evidence that P2X(7) is sensitive to the glycosidases EndoH and PNGase F and that the human receptor appears glycosylated at N187, N202, N213, N241, and N284. Mutation of N187 results in weakened P2X(7) agonist-induced phosphorylation of ERK1/2, CREB, and p90 ribosomal S6 kinase, as well as a decreased level of pore formation. In further support of a role for glycosylation in receptor function, treatment of RAW 264.7 macrophages with the N-linked glycosylation synthesis inhibitor tunicamycin attenuates P2X(7) agonist-induced, but not phorbol ester-induced, ERK1/2 phosphorylation. Interestingly, residue N187 belongs to an N-linked glycosylation consensus sequence found in six of the seven P2X family members, suggesting this site is fundamentally important to P2X receptor function. To address the mechanism whereby N187 mutation attenuates receptor activity, we developed a live cell proteinase K digestion assay that demonstrated altered cell surface expression of P2X(7) N187A. This is the first report to map human P2X(7) glycosylation sites and reveal residue N187 is critical for receptor trafficking and function.

  2. Dynamic response and residual stress fields of Ti6Al4V alloy under shock wave induced by laser shock peening

    Science.gov (United States)

    Sun, Rujian; Li, Liuhe; Zhu, Ying; Zhang, Lixin; Guo, Wei; Peng, Peng; Li, Bo; Guo, Chao; Liu, Lei; Che, Zhigang; Li, Weidong; Sun, Jianfei; Qiao, Hongchao

    2017-09-01

    Laser shock peening (LSP), an innovative surface treatment technique, generates compressive residual stress on the surface of metallic components to improve their fatigue performance, wear resistance and corrosion resistance. To illustrate the dynamic response during LSP and residual stress fields after LSP, this study conducted FEM simulations of LSP in a Ti6Al4V alloy. Results showed that when power density was 7 GW cm-2, a plastic deformation occurred at 10 ns during LSP and increased until the shock pressure decayed below the dynamic yield strength of Ti6Al4V after 60 ns. A maximum tensile region appeared beneath the surface at around 240 ns, forming a compressive-tensile-compressive stress sandwich structure with a thickness of 98, 1020 and 606 μm for each layer. After the model became stabilized, the value of the surface residual compressive stress was 564 MPa at the laser spot center. Higher value of residual stress across the surface and thicker compressive residual stress layers were achieved by increasing laser power density, impact times and spot sizes during LSP. A ‘Residual stress hole’ occurred with a high laser power density of 9 GW cm-2 when laser pulse duration was 10 ns, or with a long laser pulse duration of 20 ns when laser power density was 7 GW cm-2 for Ti6Al4V. This phenomenon occurred because of the permanent reverse plastic deformation generated at laser spot center.

  3. Antibody VH and VL recombination using phage and ribosome display technologies reveals distinct structural routes to affinity improvements with VH-VL interface residues providing important structural diversity.

    Science.gov (United States)

    Groves, Maria A T; Amanuel, Lily; Campbell, Jamie I; Rees, D Gareth; Sridharan, Sudharsan; Finch, Donna K; Lowe, David C; Vaughan, Tristan J

    2014-01-01

    In vitro selection technologies are an important means of affinity maturing antibodies to generate the optimal therapeutic profile for a particular disease target. Here, we describe the isolation of a parent antibody, KENB061 using phage display and solution phase selections with soluble biotinylated human IL-1R1. KENB061 was affinity matured using phage display and targeted mutagenesis of VH and VL CDR3 using NNS randomization. Affinity matured VHCDR3 and VLCDR3 library blocks were recombined and selected using phage and ribosome display protocol. A direct comparison of the phage and ribosome display antibodies generated was made to determine their functional characteristics.In our analyses, we observed distinct differences in the pattern of beneficial mutations in antibodies derived from phage and ribosome display selections, and discovered the lead antibody Jedi067 had a ~3700-fold improvement in KD over the parent KENB061. We constructed a homology model of the Fv region of Jedi067 to map the specific positions where mutations occurred in the CDR3 loops. For VL CDR3, positions 94 to 97 carry greater diversity in the ribosome display variants compared with the phage display. The positions 95a, 95b and 96 of VLCDR3 form part of the interface with VH in this model. The model shows that positions 96, 98, 100e, 100f, 100 g, 100h, 100i and 101 of the VHCDR3 include residues at the VH and VL interface. Importantly, Leu96 and Tyr98 are conserved at the interface positions in both phage and ribosome display indicating their importance in maintaining the VH-VL interface. For antibodies derived from ribosome display, there is significant diversity at residues 100a to 100f of the VH CDR3 compared with phage display. A unique deletion of isoleucine at position 102 of the lead candidate, Jedi067, also occurs in the VHCDR3.As anticipated, recombining the mutations via ribosome display led to a greater structural diversity, particularly in the heavy chain CDR3, which in turn

  4. Effect of the N-terminal residues on the quaternary dynamics of human adult hemoglobin

    Science.gov (United States)

    Chang, Shanyan; Mizuno, Misao; Ishikawa, Haruto; Mizutani, Yasuhisa

    2016-05-01

    The protein dynamics of human hemoglobin following ligand photolysis was studied by time-resolved resonance Raman spectroscopy. The time-resolved spectra of two kinds of recombinant hemoglobin expressed in Escherichia coli, normal recombinant hemoglobin and the α(V1M)/β(V1M) double mutant, were compared with those of human adult hemoglobin (HbA) purified from blood. A frequency shift of the iron-histidine stretching [ν(Fe-His)] band was observed in the time-resolved spectra of all three hemoglobin samples, indicative of tertiary and quaternary changes in the protein following photolysis. The spectral changes of the α(V1M)/β(V1M) double mutant were distinct from those of HbA in the tens of microseconds region, whereas the spectral changes of normal recombinant hemoglobin were similar to those of HbA isolated from blood. These results demonstrated that a structural change in the N-termini is involved in the second step of the quaternary structure change of hemoglobin. We discuss the implications of these results for understanding the allosteric pathway of HbA.

  5. Determination of benzene residues in recycled polyethylene terephthalate (PETE) by dynamic headspace-gas chromatography.

    Science.gov (United States)

    Komolprasert, V; Hargraves, W A; Armstrong, D J

    1994-01-01

    A dynamic headspace-gas chromatography (HS/GC) method was developed to quantitate benzene in recycled PETE material derived from 21 PETE beverage bottles. The analytical system consisted of a purge-and-trap apparatus which was interfaced directly with a gas chromatograph/flame ionization detector. Cryofocusing and non-cryofocusing GC systems were used. The technique was applied to spiked PETE test samples which were prepared at various benzene concentrations ranging from 100 ppb to 117 ppm. The initial spiked benzene concentration in the PETE test samples was determined gravimetrically. The HS/GC technique was limited by the slow desorption rate of benzene from the PETE matrix; as a result, multipurges were performed at 60 degrees C. Regression analysis was done on the multipurge data to develop a desorption model which would predict the total amount of benzene in the PETE. The calculated results agreed with the experimental recoveries within +/- 10%. Recovery depended on the initial benzene level in the PETE and ranged from 70 to 90% after the first five purges.

  6. Involvement of the catalytically important Asp54 residue of Mycobacterium smegmatis DevR in protein-protein interactions between DevR and DevS.

    Science.gov (United States)

    Lee, Ha-Na; Lee, Na-On; Ko, In-Jeong; Kim, Si Wouk; Kang, Beom Sik; Oh, Jeong-Il

    2013-06-01

    The DevSR two-component system in Mycobacterium smegmatis consists of the DevS histidine kinase and the DevR response regulator. It is a regulatory system that is involved in the adaptation of mycobacteria to hypoxic and NO stresses. Using the yeast two-hybrid assay and pull-down assay, it was demonstrated that the phosphoaccepting Asp (Asp54) of DevR is important for protein-protein interactions between DevR and DevS. The negative charge of Asp54 of DevR was shown to play an important role in protein-protein interactions between DevR and DevS. When the Lys104 residue, which is involved in transmission of conformational changes induced by phosphorylation of the response regulator, was replaced with Ala, the mutant form of DevR was not phosphorylated by DevS and functionally inactive in vivo. However, the K104A mutation in DevR only slightly affected protein-protein interactions between DevR and DevS. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  7. Perspective: On the importance of hydrodynamic interactions in the subcellular dynamics of macromolecules

    Science.gov (United States)

    Skolnick, Jeffrey

    2016-01-01

    An outstanding challenge in computational biophysics is the simulation of a living cell at molecular detail. Over the past several years, using Stokesian dynamics, progress has been made in simulating coarse grained molecular models of the cytoplasm. Since macromolecules comprise 20%-40% of the volume of a cell, one would expect that steric interactions dominate macromolecular diffusion. However, the reduction in cellular diffusion rates relative to infinite dilution is due, roughly equally, to steric and hydrodynamic interactions, HI, with nonspecific attractive interactions likely playing rather a minor role. HI not only serve to slow down long time diffusion rates but also cause a considerable reduction in the magnitude of the short time diffusion coefficient relative to that at infinite dilution. More importantly, the long range contribution of the Rotne-Prager-Yamakawa diffusion tensor results in temporal and spatial correlations that persist up to microseconds and for intermolecular distances on the order of protein radii. While HI slow down the bimolecular association rate in the early stages of lipid bilayer formation, they accelerate the rate of large scale assembly of lipid aggregates. This is suggestive of an important role for HI in the self-assembly kinetics of large macromolecular complexes such as tubulin. Since HI are important, questions as to whether continuum models of HI are adequate as well as improved simulation methodologies that will make simulations of more complex cellular processes practical need to be addressed. Nevertheless, the stage is set for the molecular simulations of ever more complex subcellular processes. PMID:27634243

  8. Determining important regulatory relations of amino acids from dynamic network analysis of plasma amino acids.

    Science.gov (United States)

    Shikata, Nahoko; Maki, Yukihiro; Nakatsui, Masahiko; Mori, Masato; Noguchi, Yasushi; Yoshida, Shintaro; Takahashi, Michio; Kondo, Nobuo; Okamoto, Masahiro

    2010-01-01

    The changes in the concentrations of plasma amino acids do not always follow the flow-based metabolic pathway network. We have previously shown that there is a control-based network structure among plasma amino acids besides the metabolic pathway map. Based on this network structure, in this study, we performed dynamic analysis using time-course data of the plasma samples of rats fed single essential amino acid deficient diet. Using S-system model (conceptual mathematical model represented by power-law formalism), we inferred the dynamic network structure which reproduces the actual time-courses within the error allowance of 13.17%. By performing sensitivity analysis, three of the most dominant relations in this network were selected; the control paths from leucine to valine, from methionine to threonine, and from leucine to isoleucine. This result is in good agreement with the biological knowledge regarding branched-chain amino acids, and suggests the biological importance of the effect from methionine to threonine.

  9. Channel is more important than effectiveness in spreading dynamics on multiplex networks

    CERN Document Server

    Li, Ming; Peng, Dan; Jia, Chun-Xiao; Wang, Bing-Hong

    2016-01-01

    The multiplex networks are often used as a platform that various pathogens or information spread on. In this paper we consider a spread process that only one kind of pathogen or information spreads over different layers simultaneously, such as opinion or rumor spreads online and offline. We study this model as a special bond percolation, and develop a theoretical method to obtain the epidemic threshold and the corresponding outbreak size, which are in agreement with the simulation results well. Through simulation and theoretical studies on Poisson and scale-free degree distribution multiplex networks, we find that though the overlapping of links can increase the epidemic effectiveness between the individuals connected by such links, the epidemic threshold could also increase with the increasing of overlapping, i.e., the overlapping suppresses the spreading process. This indicates the epidemic channel could play a more important role in the spreading dynamics than the epidemic probability.

  10. The importance of the pre-exponential factor in semiclassical molecular dynamics

    Science.gov (United States)

    Di Liberto, Giovanni; Ceotto, Michele

    2016-10-01

    This paper deals with the critical issue of approximating the pre-exponential factor in semiclassical molecular dynamics. The pre-exponential factor is important because it accounts for the quantum contribution to the semiclassical propagator of the classical Feynman path fluctuations. Pre-exponential factor approximations are necessary when chaotic or complex systems are simulated. We introduced pre-exponential factor approximations based either on analytical considerations or numerical regularization. The approximations are tested for power spectrum calculations of more and more chaotic model systems and on several molecules, for which exact quantum mechanical values are available. The results show that the pre-exponential factor approximations introduced are accurate enough to be safely employed for semiclassical simulations of complex systems.

  11. Spatial and temporal dynamics of root exudation: how important is heterogeneity in allelopathic interactions?

    Science.gov (United States)

    Weidenhamer, Jeffrey D; Mohney, Brian K; Shihada, Nader; Rupasinghe, Maduka

    2014-08-01

    Understanding allelopathy has been hindered by the lack of methods available to monitor the dynamics of allelochemicals in the soil. Previous work has demonstrated the feasibility of using polydimethylsiloxane (PDMS) microtubing (silicone tubing microextraction, or STME) to construct sampling devices to monitor the release of lipophilic allelochemicals from plant roots. The objective of this study was to use such sampling devices to intensively monitor thiophene fluxes beneath marigolds over several weeks to gain insight into the magnitude of temporal and spatial heterogeneity in these fluxes. Marigolds were grown in rhizoboxes (20.5 x 20.5 x 3.0 cm) with 16 individual STME samplers per box. Thiophene sampling and HPLC analysis began 45 days after planting. At the end of the study, roots around each sampler were analyzed by HPLC. Results confirmed the tremendous spatial and temporal heterogeneity in thiophene production seen in our previous studies. STME probes show that thiophene concentrations generally increase over time; however, these effects were sampling-port specific. When sampling ports were monitored at 12 h intervals, fluxes at each port ranged from 0 to 2,510 ng day(-1). Fluxes measured over daylight hr averaged 29 % higher than those measured overnight. Fluxes were less than 1 % on average of the total thiophene content of surrounding roots. While the importance of such heterogeneity, or "patchiness", in the root zone has been recognized for soil nutrients, the potential importance in allelopathic interactions has seldom been considered. The reasons for this variability are unclear, but are being investigated. Our results demonstrate that STME can be used as a tool to provide a more finely-resolved picture of allelochemical dynamics in the root zone than has previously been available.

  12. Experimental design to monitor the influence of crop residue management on the dynamics of soil water content

    Science.gov (United States)

    Chélin, Marie; Hiel, Marie-Pierre; Parvin, Nargish; Bodson, Bernard; Degré, Aurore; Nguyen, Frédéric; Garré, Sarah

    2015-04-01

    Choices related to crop residue management affecting soil structure determine spatio-temporal dynamics of water content and eventually crop yields. In this contribution, we will discuss the experimental design we adopted to study the influence of agricultural management strategies (tillage and residue management) on the soil water dynamics under maize in a Cutanic Siltic Luvisol in Gembloux, Belgium. Three different treatments will be studied: a conventional ploughing realized either in December 2014 or just before sowing in April 2015, and a strip tillage in April 2015. A bare soil under conventional ploughing will also be monitored in order to better understand the influence of the plant over the growing season. In order to limit soil disturbance, we opted for the use of electrical resistivity tomography (ERT) and we use the bulk electrical conductivity as a proxy for soil moisture content. ERT will be collected every week on a surface of two square meters corresponding to three rows of seven maize plants through surface stainless steel electrodes. Five additional sticks with stainless steel electrodes will be vertically inserted into the soil up to 1.50 m to get more detailed information near to the central maize row. In each of the monitoring plots, two time-domain reflectometry (TDR) probes will be installed for data validation. In order to calibrate the relationship between electrical resistivity and soil water content under highly variable field conditions (changes in soil structure, variable weather conditions, plant growth, fertilization), a trench will be dug, in which a set of four electrodes, one TDR probe and one temperature sensor will be placed at four different depths. In addition, two suction cups will be installed in each of the plots to quantify changes in ion composition and electrical conductivity of the soil solution at two different depths. Within the framework of the multidisciplinary research platform AgricultureIsLife, regular assessment

  13. The highly conserved aspartic acid residue between hypervariable regions 1 and 2 of human immunodeficiency virus type 1 gp120 is important for early stages of virus replication.

    Science.gov (United States)

    Wang, W K; Essex, M; Lee, T H

    1995-01-01

    Between hypervariable regions V1 and V2 of human immunodeficiency virus type 1 (HIV-1) gp120 lies a cluster of relatively conserved residues. The contribution of nine charged residues in this region to virus infectivity was evaluated by single-amino-acid substitutions in an infectious provirus clone. Three of the HIV-1 mutants studied had slower growth kinetics than the wild-type virus. The delay was most pronounced in a mutant with an alanine substituted for an aspartic acid residue at position 180. This aspartic acid is conserved by all HIV-1 isolates with known nucleotide sequences. Substitutions with three other residues at this position, including a negatively charged glutamic acid, all affected virus infectivity. The defect identified in these mutants suggests that this aspartic acid residue is involved in the early stages of HIV-1 replication. PMID:7983752

  14. MODELING OF WORLD'S SYSTEMICALLY IMPORTANT ECONOMIES IMPACT ON THE DYNAMICS OF MACROECONOMIC INDICATORS IN UKRAINE

    Directory of Open Access Journals (Sweden)

    O. Bazhenova

    2015-03-01

    Full Text Available This paper develops the vector autoregression model of the Ukraine’s economy for exploring the dynamics of key indicators of the domestic economy in response to the shocks from systemically important economies. The foreign variables in the model are growth rates of real GDP, consumer price indices in the advanced economies and in countries of emerging and developing Asia and oil price. The results suggest that the shocks from the “large” economies are absorbed by the domestic economy for a long time. A significant part of the variability of real GDP growth index in Ukraine is due to external factors. Inflation in advanced countries has the most significant influence on this variability (among other external shocks that confirms inflation import from these economies. At the same time the price of oil does not significantly contribute to the explanation of the mentioned variability. Given the euro area share increase in foreign trade and China’s impact on metal market conditions this paper also explores the influence of these economies’ indicators (notably production indices and consumer price indices on Ukraine’s economy.

  15. Long-term dynamics of adaptive evolution in a globally important phytoplankton species to ocean acidification

    Science.gov (United States)

    Schlüter, Lothar; Lohbeck, Kai T.; Gröger, Joachim P.; Riebesell, Ulf; Reusch, Thorsten B. H.

    2016-01-01

    Marine phytoplankton may adapt to ocean change, such as acidification or warming, because of their large population sizes and short generation times. Long-term adaptation to novel environments is a dynamic process, and phenotypic change can take place thousands of generations after exposure to novel conditions. We conducted a long-term evolution experiment (4 years = 2100 generations), starting with a single clone of the abundant and widespread coccolithophore Emiliania huxleyi exposed to three different CO2 levels simulating ocean acidification (OA). Growth rates as a proxy for Darwinian fitness increased only moderately under both levels of OA [+3.4% and +4.8%, respectively, at 1100 and 2200 μatm partial pressure of CO2 (Pco2)] relative to control treatments (ambient CO2, 400 μatm). Long-term adaptation to OA was complex, and initial phenotypic responses of ecologically important traits were later reverted. The biogeochemically important trait of calcification, in particular, that had initially been restored within the first year of evolution was later reduced to levels lower than the performance of nonadapted populations under OA. Calcification was not constitutively lost but returned to control treatment levels when high CO2–adapted isolates were transferred back to present-day control CO2 conditions. Selection under elevated CO2 exacerbated a general decrease of cell sizes under long-term laboratory evolution. Our results show that phytoplankton may evolve complex phenotypic plasticity that can affect biogeochemically important traits, such as calcification. Adaptive evolution may play out over longer time scales (>1 year) in an unforeseen way under future ocean conditions that cannot be predicted from initial adaptation responses. PMID:27419227

  16. How important is a detailed hydrological representation when modelling soil carbon dynamics in Chinese red soils.

    Science.gov (United States)

    Oyesiku-Blakemore, Joseph; Verrot, Lucile; Geris, Josie; Zhang, Ganlin; Peng, Xinhua; Hallett, Paul; Smith, Jo

    2017-04-01

    Soil carbon and nitrogen processing are strongly influenced by the hydrology of soils. When simulating these processes models represent soil hydrology in some way. The hydrological components of soil carbon and nitrogen models vary greatly in their complexity, as does the burden of simulation time and data requirements. Hydrology specific models, such as Hydrus, have more detailed representations of soil hydrology than those used in some soil carbon and nitrogen models, such as ECOSSE, and can provide a more accurate and precise description of the movement and content of water in soil. Moisture content is one of the key variables controlling the processing of carbon and nitrogen in soil models. A higher soil moisture content results in increased methane production through the anaerobic decomposition of soil carbon pools. It also alters the rate at which aerobic decomposition occurs, with low and high soil moisture contents limiting the decomposition of SOC. An inaccurate estimate of soil moisture will introduce errors in the estimated rates of model SOC transformations, which would result in errors in the simulated SOC. In order to shed light on this uncertainty we use the same input data to simulate soil moisture contents in a Red Soil region of China, using both the ECOSSE model and Hydrus 2D. We compare the simulations of both models with measurements of soil moisture at the site and each other. We highlight where the models differ and identify the conditions under which errors are likely to occur. We then simulate SOC dynamics using the ECOSSE model and its original hydrology with the ECOSSE model simulations using the Hydrus 2D simulations. This shows the importance of including a detailed representation of soil moisture when simulating soil organic matter dynamics.

  17. Immediate postarousal sleep dynamics: an important determinant of sleep stability in obstructive sleep apnea.

    Science.gov (United States)

    Younes, Magdy; Hanly, Patrick J

    2016-04-01

    Arousability from sleep is increasingly recognized as an important determinant of the clinical spectrum of sleep disordered breathing (SDB). Patients with SDB display a wide range of arousability. The reason for these differences is not known. We hypothesized that differences in the speed with which sleep deepens following arousals/awakenings (postarousal sleep dynamics) is a major determinant of these differences in arousability in patients with SDB. We analyzed 40 preexisting clinical polysomnography records from patients with a range of SDB severity (apnea-hypopnea index 5-135/h). Sleep depth was determined every 3 s using the odds ratio product (ORP) method, a continuous index of sleep depth (0 = deep sleep, 2.5 = full wakefulness) that correlates strongly (r = 0.98) with arousability (Younes M, Ostrowski M, Soiferman M, Younes H, Younes M, Raneri J, and Hanly P. Sleep 38: 641-654, 2015). Time course of ORP was determined from end of arousal until the next arousal. All arousals were analyzed (142 ± 65/polysomnogram). ORP increased from 0.58 ± 0.32 during sleep to 1.67 ± 0.35 during arousals. ORP immediately (first 9 s) following arousals/awakenings (ORP-9) ranged from 0.21(very deep sleep) to 1.71 (highly arousable state) in different patients. In patients with high ORP-9, sleep deepened slowly (over minutes) beyond 9 s but only if no arousals/awakenings recurred. ORP-9 correlated strongly with average non-rapid eye movement sleep depth (r = 0.87, P sleep architecture. We conclude that postarousal sleep dynamics are highly variable among patients with sleep-disordered breathing and largely determine average sleep depth and continuity.

  18. Wind-driven residual circulation and related oxygen and nutrient dynamics in the Gulf of Finland (Baltic Sea) in winter

    Science.gov (United States)

    Lips, Urmas; Laanemets, Jaan; Lips, Inga; Liblik, Taavi; Suhhova, Irina; Suursaar, Ülo

    2017-08-01

    Establishment of distinct circulation patterns in the Gulf of Finland was observed by a targeted measurement campaign in winter 2013-2014. Strong and long enough up-estuary wind events caused a collapse of vertical stratification and development of a barotropic flow system consisting of an outflow in the open part and inflow along the coasts. In the periods without such unidirectional wind forcing, but when the water column remained weakly stratified, the residual barotropic inflow in the open gulf and outflow along the coasts was observed. In the case of moderate wind forcing, the three-layer vertical stratification and flow structure developed in the gulf. It is shown that the along-gulf expansion of the fresher water tongue in the surface layer as well as the up-estuary penetration of the saltwater wedge in the near-bottom layer followed well the long-term (monthly) changes in the cumulative along-gulf wind stress. The dynamics of the near-bottom saltwater wedge determined the extent of hypoxic bottoms and, as suggested by the firm correlation between the near-bottom phosphate concentration and salinity, the nutrient conditions in the near-bottom layer. The lateral transport of phosphorus, strengthened vertical stratification in the Northern Baltic Proper and suggested increase in the frequency of stratification collapses in the Gulf of Finland in winter predict that the eutrophication effects would not diminish significantly in this estuary in the nearest future.

  19. Molecular dynamic simulations of Escherichia coli L-asparaginase to illuminate its role in deamination of asparagine and glutamine residues.

    Science.gov (United States)

    Erva, Rajeswara Reddy; Rajulapati, Satish Babu; Potla Durthi, Chandrasai; Bhatia, Mayuri; Pola, Madhuri

    2016-06-01

    Acute lymphocytic leukemia (ALL) is an outrageous disease worldwide. L-Asparagine (L-Asn) and L-Glutamine (L-Gln) deamination play a crucial role in ALL treatment. Role of Elspar(®) (L-asparaginase from Escherichia coli) in regulation of L-Asn and L-Gln has been confirmed by the other researchers through experimental studies. Therapeutic research against ALL remained elusive with the lack of information on molecular interactions of Elspar(®) with amino acid substrates. In the present study, using different docking tools binding cavities, key residues in binding and ligand binding mechanisms were identified. For the apo state enzyme and ligand bound state complexes, MD simulations were performed. Trajectory analysis for 30 ns run confirmed the kinship of L-Asn with L-asparaginase enzyme in the dynamic system with less stability in comparison to L-Gln docked complex. Overall findings strongly supported the bi-functional nature of the enzyme drug. A good number of conformational changes were observed with 1NNS structure due to ligand binding. Results of present study give much more information on structural and functional aspects of E. coli L-asparaginase upon the interaction with its ligands which may be useful in designing effective therapeutics for ALL.

  20. The valine and lysine residues in the conserved FxVTxK motif are important for the function of phylogenetically distant plant cellulose synthases.

    Science.gov (United States)

    Slabaugh, Erin; Scavuzzo-Duggan, Tess; Chaves, Arielle; Wilson, Liza; Wilson, Carmen; Davis, Jonathan K; Cosgrove, Daniel J; Anderson, Charles T; Roberts, Alison W; Haigler, Candace H

    2016-05-01

    Cellulose synthases (CESAs) synthesize the β-1,4-glucan chains that coalesce to form cellulose microfibrils in plant cell walls. In addition to a large cytosolic (catalytic) domain, CESAs have eight predicted transmembrane helices (TMHs). However, analogous to the structure of BcsA, a bacterial CESA, predicted TMH5 in CESA may instead be an interfacial helix. This would place the conserved FxVTxK motif in the plant cell cytosol where it could function as a substrate-gating loop as occurs in BcsA. To define the functional importance of the CESA region containing FxVTxK, we tested five parallel mutations in Arabidopsis thaliana CESA1 and Physcomitrella patens CESA5 in complementation assays of the relevant cesa mutants. In both organisms, the substitution of the valine or lysine residues in FxVTxK severely affected CESA function. In Arabidopsis roots, both changes were correlated with lower cellulose anisotropy, as revealed by Pontamine Fast Scarlet. Analysis of hypocotyl inner cell wall layers by atomic force microscopy showed that two altered versions of Atcesa1 could rescue cell wall phenotypes observed in the mutant background line. Overall, the data show that the FxVTxK motif is functionally important in two phylogenetically distant plant CESAs. The results show that Physcomitrella provides an efficient model for assessing the effects of engineered CESA mutations affecting primary cell wall synthesis and that diverse testing systems can lead to nuanced insights into CESA structure-function relationships. Although CESA membrane topology needs to be experimentally determined, the results support the possibility that the FxVTxK region functions similarly in CESA and BcsA.

  1. The Importance of Grain Size to Mantle Dynamics and Seismological Observations: A Multidisciplinary Approach

    Science.gov (United States)

    Gassmöller, Rene; Dannberg, Juliane; Eilon, Zach; Moulik, Pritwiraj; Myhill, Robert; Faul, Ulrich

    2016-04-01

    Dynamic models of Earth's convecting mantle usually implement flow laws with constant grain size, stress-independent viscosity and a limited treatment of variations associated with changes in mineral assemblage. These simplifications greatly reduce computational requirements but preclude effects such as shear localisation and transient changes in rheology associated with phase transitions, which have the potential to fundamentally change flow patterns in the mantle. Here we use the finite-element code ASPECT [Bangerth et al., 2013] to model grain size evolution and the interplay between grain size, stress and strain rate in the convecting mantle. We include the simultaneous and competing effects of dynamic recrystallisation resulting from work done by dislocation creep, grain growth in multiphase assemblages and recrystallisation at phase transitions. Grain size variations also affect seismic properties of mantle materials. We apply published formalisms [Jackson & Faul, 2010; McCarthy et al., 2011; Takei et al., 2014] to relate intrinsic variables (P, T, and grain size) from our numerical models to seismic velocity (Vs) and attenuation (Q). We investigate these formalisms for consistency with seismic observations at conditions beyond the range of the experiments upon which they are based; this requires constraining the range of pre-factors and activation volumes relevant for the lower mantle. Our calculations use thermodynamically self-consistent anharmonic elastic moduli determined for the mineral assemblages in the mantle using HeFESTo [Stixrude and Lithgow-Bertelloni, 2013]. We investigate the effect of realistically heterogeneous grain sizes by computing synthetic seismological data; these highlight the frequency-dependent sensitivity of seismic waves to grain size, which is important when interpreting Vs and Q observations in terms of mineral assemblage and temperature. Our models show that grain size evolution can lead to lateral viscosity variations of six

  2. Internal Representation of Task Rules by Recurrent Dynamics: The Importance of the Diversity of Neural Responses

    Science.gov (United States)

    Rigotti, Mattia; Rubin, Daniel Ben Dayan; Wang, Xiao-Jing; Fusi, Stefano

    2010-01-01

    Neural activity of behaving animals, especially in the prefrontal cortex, is highly heterogeneous, with selective responses to diverse aspects of the executed task. We propose a general model of recurrent neural networks that perform complex rule-based tasks, and we show that the diversity of neuronal responses plays a fundamental role when the behavioral responses are context-dependent. Specifically, we found that when the inner mental states encoding the task rules are represented by stable patterns of neural activity (attractors of the neural dynamics), the neurons must be selective for combinations of sensory stimuli and inner mental states. Such mixed selectivity is easily obtained by neurons that connect with random synaptic strengths both to the recurrent network and to neurons encoding sensory inputs. The number of randomly connected neurons needed to solve a task is on average only three times as large as the number of neurons needed in a network designed ad hoc. Moreover, the number of needed neurons grows only linearly with the number of task-relevant events and mental states, provided that each neuron responds to a large proportion of events (dense/distributed coding). A biologically realistic implementation of the model captures several aspects of the activity recorded from monkeys performing context-dependent tasks. Our findings explain the importance of the diversity of neural responses and provide us with simple and general principles for designing attractor neural networks that perform complex computation. PMID:21048899

  3. Internal representation of task rules by recurrent dynamics: the importance of the diversity of neural responses

    Directory of Open Access Journals (Sweden)

    Mattia Rigotti

    2010-10-01

    Full Text Available Neural activity of behaving animals, especially in the prefrontal cortex, is highly heterogeneous, with selective responses to diverse aspects of the executed task. We propose a general model of recurrent neural networks that perform complex rule-based tasks, and we show that the diversity of neuronal responses plays a fundamental role when the behavioral responses are context dependent. Specifically, we found that when the inner mental states encoding the task rules are represented by stable patterns of neural activity (attractors of the neural dynamics, the neurons must be selective for combinations of sensory stimuli and inner mental states. Such mixed selectivity is easily obtained by neurons that connect with random synaptic strengths both to the recurrent network and to neurons encoding sensory inputs. The number of randomly connected neurons needed to solve a task is on average only three times as large as the number of neurons needed in a network designed ad hoc. Moreover, the number of needed neurons grows only linearly with the number of task-relevant events and mental states, provided that each neuron responds to a large proportion of events (dense/distributed coding. A biologically realistic implementation of the model captures several aspects of the activity recorded from monkeys performing context dependent tasks. Our findings explain the importance of the diversity of neural responses and provide us with simple and general principles for designing attractor neural networks that perform complex computation.

  4. Quantitative conformational analysis of the core region of N-glycans using residual dipolar couplings, aqueous molecular dynamics, and steric alignment

    Energy Technology Data Exchange (ETDEWEB)

    Almond, Andrew; Duus, Jens O. [Carlsberg Laboratory (Denmark)

    2001-08-15

    A method is described for quantitatively investigating the dynamic conformation of small oligosaccharides containing an {alpha}(1{sup {yields}}6) linkage. It was applied to the oligosaccharide Man-{alpha}(1{sup {yields}}3) {l_brace}Man-{alpha} (1{sup {yields}}6){r_brace}Man-{alpha}-O-Me, which is a core region frequently observed in N-linked glycans. The approach tests an aqueous molecular dynamics simulation, capable of predicting microscopic dynamics, against experimental residual dipolar couplings, by assuming that alignment is caused purely by steric hindrance. The experimental constraints were heteronuclear and homonuclear residual dipolar couplings, and in particular those within the {alpha}(1{sup {yields}}6) linkage itself. Powerful spin-state-selective pulse sequences and editing schemes were used to obtain the most relevant couplings for testing the model. Molecular dynamics simulations in water over a period of 50 ns were not able to predict the correct rotamer population at the {alpha}(1{sup {yields}}6) linkage to agree with the experimental data. However, this sampling problem could be corrected using a simple maximum likelihood optimisation, indicating that the simulation was modelling local dynamics correctly. The maximum likelihood prediction of the residual dipolar couplings was found to be an almost equal population of the gg and gt rotamer conformations at the {alpha}(1{sup {yields}}6) linkage, and the tg conformation was predicted to be unstable and unpopulated in aqueous solution. In this case all twelve measured residual dipolar couplings could be satisfied. This conformer population could also be used to make predictions of scalar couplings with the use of a previously derived empirical equation, and is qualitatively in agreement with previous predictions based on NMR, X-ray crystallography and optical data.

  5. Neutron Scattering of Residual Hydrogen in 1,4-Dioxane-D8 Liquid. Understanding Measurements with Molecular Dynamics Simulations

    Energy Technology Data Exchange (ETDEWEB)

    de Almeida, Valmor F. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Liu, Hongjun [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Herwig, Kenneth W. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Kidder, Michelle [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2016-01-25

    That incoherent scattering from protiated molecular liquids adds a constant background to the measured scattering intensity is well known, but less appreciated is the fact that coherent scattering is also induced by the presence of hydrogen in a deuterated liquid. In fact, the scattering intensity can be very sensitive, in the small-q region, with respect to the amounts and distribution of residual H in the system. We used 1,4-dioxane liquid to demonstrate that the partial structure factors of the HD and DD atom pairs contribute significantly to inter-molecular scattering and that uncertainty in the extent of deuteration account for discrepancies between simulations and measurements. Both contributions to uncertainty have similar magnitudes: scattering interference of the hydrogen-deuterium pair, and complementary interference from the deuterium-deuterium pair by virtue of chemical inhomogeneity. This situation arises in practice since deuteration of liquids is often 99% or less. A combined experimental and extensive computational study of static thermal neutron scattering of 1,4-dioxane demonstrates the foregoing. We show, through simulations, that the reason for the differences is the content of protiated dioxane (vendors quote 1%). We estimate that up to 5% (at 298K and at 343K) protiated mole fraction may be involved in generating the scattering differences. Finally, we find that the particular distribution of hydrogen in the protiated molecules affects the results significantly; here we considered molecules to be either fully protiated or fully deuterated. This scenario best reconciles the computational and experimental results, and leads us to speculate that the deuteration synthesis process tends to leave a molecule either fully deuterated or fully protiated. Although we have used 1,4-dioxane as a model liquid, the effects described in this study extend to similar liquids and similar systematic experimental/computational studies can be performed to either

  6. Dynamic Range of Vertebrate Retina Ganglion Cells: Importance of Active Dendrites and Coupling by Electrical Synapses

    Science.gov (United States)

    Publio, Rodrigo; Ceballos, Cesar Celis; Roque, Antonio C.

    2012-01-01

    The vertebrate retina has a very high dynamic range. This is due to the concerted action of its diverse cell types. Ganglion cells, which are the output cells of the retina, have to preserve this high dynamic range to convey it to higher brain areas. Experimental evidence shows that the firing response of ganglion cells is strongly correlated with their total dendritic area and only weakly correlated with their dendritic branching complexity. On the other hand, theoretical studies with simple neuron models claim that active and large dendritic trees enhance the dynamic range of single neurons. Theoretical models also claim that electrical coupling between ganglion cells via gap junctions enhances their collective dynamic range. In this work we use morphologically reconstructed multi-compartmental ganglion cell models to perform two studies. In the first study we investigate the relationship between single ganglion cell dynamic range and number of dendritic branches/total dendritic area for both active and passive dendrites. Our results support the claim that large and active dendrites enhance the dynamic range of a single ganglion cell and show that total dendritic area has stronger correlation with dynamic range than with number of dendritic branches. In the second study we investigate the dynamic range of a square array of ganglion cells with passive or active dendritic trees coupled with each other via dendrodendritic gap junctions. Our results suggest that electrical coupling between active dendritic trees enhances the dynamic range of the ganglion cell array in comparison with both the uncoupled case and the coupled case with cells with passive dendrites. The results from our detailed computational modeling studies suggest that the key properties of the ganglion cells that endow them with a large dynamic range are large and active dendritic trees and electrical coupling via gap junctions. PMID:23144767

  7. Dynamic range of vertebrate retina ganglion cells: importance of active dendrites and coupling by electrical synapses.

    Science.gov (United States)

    Publio, Rodrigo; Ceballos, Cesar Celis; Roque, Antonio C

    2012-01-01

    The vertebrate retina has a very high dynamic range. This is due to the concerted action of its diverse cell types. Ganglion cells, which are the output cells of the retina, have to preserve this high dynamic range to convey it to higher brain areas. Experimental evidence shows that the firing response of ganglion cells is strongly correlated with their total dendritic area and only weakly correlated with their dendritic branching complexity. On the other hand, theoretical studies with simple neuron models claim that active and large dendritic trees enhance the dynamic range of single neurons. Theoretical models also claim that electrical coupling between ganglion cells via gap junctions enhances their collective dynamic range. In this work we use morphologically reconstructed multi-compartmental ganglion cell models to perform two studies. In the first study we investigate the relationship between single ganglion cell dynamic range and number of dendritic branches/total dendritic area for both active and passive dendrites. Our results support the claim that large and active dendrites enhance the dynamic range of a single ganglion cell and show that total dendritic area has stronger correlation with dynamic range than with number of dendritic branches. In the second study we investigate the dynamic range of a square array of ganglion cells with passive or active dendritic trees coupled with each other via dendrodendritic gap junctions. Our results suggest that electrical coupling between active dendritic trees enhances the dynamic range of the ganglion cell array in comparison with both the uncoupled case and the coupled case with cells with passive dendrites. The results from our detailed computational modeling studies suggest that the key properties of the ganglion cells that endow them with a large dynamic range are large and active dendritic trees and electrical coupling via gap junctions.

  8. Importance of Residues Outside the Cation Binding Pocket for Na+ and K+ Binding to the Na+/K+-ATPase

    DEFF Research Database (Denmark)

    Christiansen, Line; Toustrup-Jensen, Mads Schak; Einholm, Anja P.;

    Mutagenesis studies have identified several oxygen-containing residues in the transmembrane region which are important for the coordination of Na+ and/or K+. These were later confirmed by the high-resolution crystal structures of the Na+/K+-ATPase with bound Na+ or K+. However, more information......-established that K+ antagonizes ouabain binding, and vice versa. Furthermore, recent crystal structures have shown that ouabain binds in an extracellular cavity created by residues of transmembrane helices 4, 5, and 6 (3). This cavity, which is lined by Phe785 and Phe788, as well as Phe318, Arg882, and Asp886, may...... aromatic ring, while Arg882 and Asp886 were mutated to leucine and alanine, respectively, to investigate the importance of charge and size of the residues. All three mutants could sustain growth and proliferation under ouabain pressure. However, the mutants exhibited a reduced turnover number. All three...

  9. Importance of Fabric and Phyllosilicates for the Strength and Dynamics of the Middle Crust

    Science.gov (United States)

    Montesi, L. G.

    2011-12-01

    From the height of mountains to the recurrence of earthquakes, the strength of the lithosphere influences directly tectonic activity and patterns. Yet, strength remain a point of contention. On the one hand, laboratory experiments predicting stresses that are about ten times larger than estimates based on geodynamics observations such as stress direction, effective viscosity, and postseismic signals. On the other hand, stress estimates based on grain size in natural samples are in remarkable agreements with laboratory flow laws [Bürgmann and Dresen, AREPS, 2008; Behr and Platt, EPSL, 2011]. How can these discordant estimates be reconciled? I propose here that large-scale tectonic signals are strongly influenced by the presence of phyllosilicates in ductile shear zones. Shear zones in polymineral rocks display intense layering. In a layered aggregate, the weakest phase controls the aggregate strength - if its abundance is sufficient for it to be interconnected. Phyllosilicates, such as micas, are notoriously difficult to test experimentally but several studies [Kronenberg, JGR, 1990; Mariani et al., JSG, 2006] have confirmed a low activation energy and high non-linearity that makes the strength of phyllosilicate essentially independent of stress and depth. If deformation zones were sufficiently layered for phyllosilicates to dominate their rheology, the strength of the middle crust would be between 1 and 40 MPa, which is compatible with geodynamics estimates. In addition, micas have important dynamical implications. As their rheology is highly non-linear, changing the fabric from one in which micas are dispersed to one in which they are present in layers is accompanied by a dramatic increase in shear rate at constant stress, which can explain the generation of ductile shear zones. These shear zones would be very sensitive to even minor perturbations in stress and therefore generate rapid postseismic transient signals as observed following many earthquakes of

  10. Comparisons of Interfacial Phe, Tyr, and Trp Residues as Determinants of Orientation and Dynamics for GWALP Transmembrane Peptides

    OpenAIRE

    Sparks, Kelsey A.; Gleason, Nicholas J.; Gist, Renetra; Langston, Rebekah; Greathouse, Denise V.; Koeppe, Roger E.

    2014-01-01

    Aromatic amino acids often flank the transmembrane alpha helices of integral membrane proteins. By favoring locations within the membrane–water interface of the lipid bilayer, aromatic residues Trp, Tyr, and sometimes Phe may serve as anchors to help stabilize a transmembrane orientation. In this work, we compare the influence of interfacial Trp, Tyr, or Phe residues upon the properties of tilted helical transmembrane peptides. For such comparisons, it has been critical to start with no more ...

  11. Explaining Managers' Residual Rights by the "Theory of Relative Importance of Factors"%用“要素相对重要性理论”解释经营者剩余权

    Institute of Scientific and Technical Information of China (English)

    张东明

    2012-01-01

    Enterprise residual rights are considered to be the most important in modem enterprise ,residual rightsallocation will directly affect the efficiency of corporate shareholder and operator properly has become the key governance, therefore, how to configure residual rights between issue in the study of corporate governance. The traditional incentive theory thought that, Due to the limited rationality and opportunism, operators often take hidden action. The best way to avoid is to give the operator a certain amount of residual claim, at the same time, thebest constraints may come from the outside, for example the manager market. Thus, they formed the incentive and re- straint mechanism for the managers. It is within a certain range to be plausible, but why have managers not residual claim just in a development of enterprise? The incentive and constraint theorv further work frnm H~rt nntl ath~r,~ la,~tton the asset specificity theory research results,they denied the enterprise residual claim,that the highest power in the enterprise should be the residual rights of control, and who has the fight of control must be those who invested assets specificity higher elements of the owner, but the attendant problem is that investment, asset specificity low factor owner or has no special assets owner does not have any residual control right? Empirical evidence once again rejected thisconclusion. More eclectic views come from the theory of distribution according to essential factor, but marginal distri- bution logic and the surplus product distribution way of the theory still remains deliberate. Incentive theory cannot explain why the same business human cap,tat early m me emerp,-l~z ~a,, ,,uL ~ sidual claim,in the absence of conscious enterprise residual control right exists,cannot explain why not the owner of the company is owned enterprise residual control right;asset specificity theory cannot face the Japanese Enterprise Employees Union involved in the control of problem

  12. Dynamic contrast-enhanced MRI in patients with muscle-invasive transitional cell carcinoma of the bladder can distinguish between residual tumour and post-chemotherapy effect

    Energy Technology Data Exchange (ETDEWEB)

    Donaldson, Stephanie B., E-mail: Stephanie.donaldson1@nhs.net [School of Cancer and Enabling Sciences, University of Manchester, Oxford Road, Manchester M13 9PL (United Kingdom); Christie Medical Physics and Engineering, The Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX (United Kingdom); Bonington, Suzanne C., E-mail: suzi.bonington@christie.nhs.uk [Department of Radiology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX (United Kingdom); Kershaw, Lucy E., E-mail: lucy.kershaw@christie.nhs.uk [Christie Medical Physics and Engineering, The Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX (United Kingdom); Cowan, Richard, E-mail: richard.cowan@christie.nhs.uk [Department of Clinical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX (United Kingdom); Lyons, Jeanette, E-mail: jeanette.lyons@christie.nhs.uk [Department of Clinical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX (United Kingdom); Elliott, Tony, E-mail: tony.elliott@christie.nhs.uk [Department of Clinical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX (United Kingdom); Carrington, Bernadette M., E-mail: bernadette.carrington@christie.nhs.uk [Department of Radiology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX (United Kingdom)

    2013-12-01

    Introduction: Treatment of muscle-invasive bladder cancer with chemotherapy results in haemorrhagic inflammation, mimicking residual tumour on conventional MR images and making interpretation difficult. The aim of this study was to use dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) to estimate descriptive and tracer kinetic parameters post-neoadjuvant chemotherapy and to investigate whether parameters differed in areas of residual tumour and chemotherapy-induced haemorrhagic inflammation (treatment effect, Tr-Eff). Methods and materials: Twenty-one patients underwent DCE-MRI scans with 2.5 s temporal resolution before and following neoadjuvant chemotherapy. Regions-of-interest (ROIs) were defined in areas suspicious of residual tumour on T{sub 2}-weighted MRI scans. Data were analysed semi-quantitatively and with a two-compartment exchange model to obtain parameters including relative signal intensity (rSI{sub 80s}) and plasma perfusion (F{sub p}) respectively. The bladder was subsequently examined histologically after cystectomy for evidence of residual tumour and/or Tr-Eff. Differences in parameters measured in areas of residual tumour and Tr-Eff were examined using Student's t-test. Results: Twenty-four abnormal sites were defined after neoadjuvant chemotherapy. On pathology, 10 and 14 areas were identified as residual tumour and Tr-Eff respectively. Median rSI{sub 80s} and F{sub p} were significantly higher in areas of residual tumour than Tr-Eff (rSI{sub 80s} = 2.9 vs 1.7, p < 0.001; F{sub p} = 20.7 vs 9.1 ml/100 ml/min, p = 0.03). The sensitivity and specificity for differentiating residual tumour from Tr-Eff were 70% and 100% (rSI{sub 80s}), 60% and 86% (F{sub p}), and 75% and 100% when combined. Conclusion: DCE-MRI parameters obtained post-treatment are capable of distinguishing between residual tumour and treatment effect in patients treated for bladder cancer with neoadjuvant chemotherapy.

  13. The importance of including dynamic soil-structure interaction into wind turbine simulation codes

    DEFF Research Database (Denmark)

    Damgaard, Mads; Andersen, Lars Vabbersgaard; Ibsen, Lars Bo

    2014-01-01

    A rigorous numerical model, describing a wind turbine structure and subsoil, may contain thousands of degrees of freedom, making the approach computationally inefficient for fast time domain analysis. In order to meet the requirements of real-time calculations, the dynamic impedance of the founda......A rigorous numerical model, describing a wind turbine structure and subsoil, may contain thousands of degrees of freedom, making the approach computationally inefficient for fast time domain analysis. In order to meet the requirements of real-time calculations, the dynamic impedance...... is examined. The optimal order of the models is determined and implemented into the aeroelastic code HAWC2, where the dynamic response of a 5.0 MW wind turbine is evaluated. In contrast to the fore-aft vibrations, the inclusion of soil-structure interaction is shown to be critical for the side-side vibrations...

  14. Crystal structure of a four-layer aggregate of engineered TMV CP implies the importance of terminal residues for oligomer assembly.

    Science.gov (United States)

    Li, Xiangyang; Song, Baoan; Chen, Xi; Wang, Zhenchao; Zeng, Mengjiao; Yu, Dandan; Hu, Deyu; Chen, Zhuo; Jin, Linhong; Yang, Song; Yang, Caiguang; Chen, Baoen

    2013-01-01

    Crystal structures of the tobacco mosaic virus (TMV) coat protein (CP) in its helical and disk conformations have previously been determined at the atomic level. For the helical structure, interactions of proteins and nucleic acids in the main chains were clearly observed; however, the conformation of residues at the C-terminus was flexible and disordered. For the four-layer aggregate disk structure, interactions of the main chain residues could only be observed through water-mediated hydrogen bonding with protein residues. In this study, the effects of the C-terminal peptides on the interactions of TMV CP were investigated by crystal structure determination. The crystal structure of a genetically engineered TMV CP was resolved at 3.06 Å. For the genetically engineered TMV CP, a six-histidine (His) tag was introduced at the N-terminus, and the C-terminal residues 155 to 158 were truncated (N-His-TMV CP(19)). Overall, N-His-TMV CP(19) protein self-assembled into the four-layer aggregate form. The conformations of residues Gln36, Thr59, Asp115 and Arg134 were carefully analyzed in the high radius and low radius regions of N-His-TMV CP(19), which were found to be significantly different from those observed previously for the helical and four-layer aggregate forms. In addition, the aggregation of the N-His-TMV CP(19) layers was found to primarily be mediated through direct hydrogen-bonding. Notably, this engineered protein also can package RNA effectively and assemble into an infectious virus particle. The terminal sequence of amino acids influences the conformation and interactions of the four-layer aggregate. Direct protein-protein interactions are observed in the major overlap region when residues Gly155 to Thr158 at the C-terminus are truncated. This engineered TMV CP is reassembled by direct protein-protein interaction and maintains the normal function of the four-layer aggregate of TMV CP in the presence of RNA.

  15. Crystal structure of a four-layer aggregate of engineered TMV CP implies the importance of terminal residues for oligomer assembly.

    Directory of Open Access Journals (Sweden)

    Xiangyang Li

    Full Text Available BACKGROUND: Crystal structures of the tobacco mosaic virus (TMV coat protein (CP in its helical and disk conformations have previously been determined at the atomic level. For the helical structure, interactions of proteins and nucleic acids in the main chains were clearly observed; however, the conformation of residues at the C-terminus was flexible and disordered. For the four-layer aggregate disk structure, interactions of the main chain residues could only be observed through water-mediated hydrogen bonding with protein residues. In this study, the effects of the C-terminal peptides on the interactions of TMV CP were investigated by crystal structure determination. METHODOLOGY/PRINCIPAL FINDINGS: The crystal structure of a genetically engineered TMV CP was resolved at 3.06 Å. For the genetically engineered TMV CP, a six-histidine (His tag was introduced at the N-terminus, and the C-terminal residues 155 to 158 were truncated (N-His-TMV CP(19. Overall, N-His-TMV CP(19 protein self-assembled into the four-layer aggregate form. The conformations of residues Gln36, Thr59, Asp115 and Arg134 were carefully analyzed in the high radius and low radius regions of N-His-TMV CP(19, which were found to be significantly different from those observed previously for the helical and four-layer aggregate forms. In addition, the aggregation of the N-His-TMV CP(19 layers was found to primarily be mediated through direct hydrogen-bonding. Notably, this engineered protein also can package RNA effectively and assemble into an infectious virus particle. CONCLUSION: The terminal sequence of amino acids influences the conformation and interactions of the four-layer aggregate. Direct protein-protein interactions are observed in the major overlap region when residues Gly155 to Thr158 at the C-terminus are truncated. This engineered TMV CP is reassembled by direct protein-protein interaction and maintains the normal function of the four-layer aggregate of TMV CP in the

  16. The importance of including dynamic soil-structure interaction into wind turbine simulation codes

    DEFF Research Database (Denmark)

    Damgaard, Mads; Andersen, Lars Vabbersgaard; Ibsen, Lars Bo

    2014-01-01

    is examined. The optimal order of the models is determined and implemented into the aeroelastic code HAWC2, where the dynamic response of a 5.0 MW wind turbine is evaluated. In contrast to the fore-aft vibrations, the inclusion of soil-structure interaction is shown to be critical for the side-side vibrations......A rigorous numerical model, describing a wind turbine structure and subsoil, may contain thousands of degrees of freedom, making the approach computationally inefficient for fast time domain analysis. In order to meet the requirements of real-time calculations, the dynamic impedance...

  17. Protein–Mineral Interactions: Molecular Dynamics Simulations Capture Importance of Variations in Mineral Surface Composition and Structure

    Energy Technology Data Exchange (ETDEWEB)

    Andersen, Amity; Reardon, Patrick N.; Chacon, Stephany S.; Qafoku, Nikolla P.; Washton, Nancy M.; Kleber, Markus

    2016-06-21

    Molecular dynamics simulations, conventional and metadynamics, were performed to determine the interaction of model protein Gb1 over kaolinite (001), Na+-montmorillonite (001), Ca2+-montmorillonite (001), goethite (100), and Na+-birnessite (001) mineral surfaces. Gb1, a small (56 residue) protein with a well-characterized solution-state nuclear magnetic resonance (NMR) structure and having α-helix, four-fold β-sheet, and hydrophobic core features, is used as a model protein to study protein soil mineral interactions and gain insights on structural changes and potential degradation of protein. From our simulations, we observe little change to the hydrated Gb1 structure over the kaolinite, montmorillonite, and goethite surfaces relative to its solvated structure without these mineral surfaces present. Over the Na+-birnessite basal surface, however, the Gb1 structure is highly disturbed as a result of interaction with this birnessite surface. Unraveling of the Gb1 β-sheet at specific turns and a partial unraveling of the α-helix is observed over birnessite, which suggests specific vulnerable residue sites for oxidation or hydrolysis possibly leading to fragmentation.

  18. Robust dynamic myocardial perfusion CT deconvolution for accurate residue function estimation via adaptive-weighted tensor total variation regularization: a preclinical study

    Science.gov (United States)

    Zeng, Dong; Gong, Changfei; Bian, Zhaoying; Huang, Jing; Zhang, Xinyu; Zhang, Hua; Lu, Lijun; Niu, Shanzhou; Zhang, Zhang; Liang, Zhengrong; Feng, Qianjin; Chen, Wufan; Ma, Jianhua

    2016-11-01

    Dynamic myocardial perfusion computed tomography (MPCT) is a promising technique for quick diagnosis and risk stratification of coronary artery disease. However, one major drawback of dynamic MPCT imaging is the heavy radiation dose to patients due to its dynamic image acquisition protocol. In this work, to address this issue, we present a robust dynamic MPCT deconvolution algorithm via adaptive-weighted tensor total variation (AwTTV) regularization for accurate residue function estimation with low-mA s data acquisitions. For simplicity, the presented method is termed ‘MPD-AwTTV’. More specifically, the gains of the AwTTV regularization over the original tensor total variation regularization are from the anisotropic edge property of the sequential MPCT images. To minimize the associative objective function we propose an efficient iterative optimization strategy with fast convergence rate in the framework of an iterative shrinkage/thresholding algorithm. We validate and evaluate the presented algorithm using both digital XCAT phantom and preclinical porcine data. The preliminary experimental results have demonstrated that the presented MPD-AwTTV deconvolution algorithm can achieve remarkable gains in noise-induced artifact suppression, edge detail preservation, and accurate flow-scaled residue function and MPHM estimation as compared with the other existing deconvolution algorithms in digital phantom studies, and similar gains can be obtained in the porcine data experiment.

  19. On the importance of excited state dynamic response electron correlation in polarizable embedding methods

    DEFF Research Database (Denmark)

    Eriksen, Janus J.; Sauer, Stephan P. A.; Mikkelsen, Kurt Valentin

    2012-01-01

    We investigate the effect of including a dynamic reaction field at the lowest possible ab inito wave function level of theory, namely the Hartree-Fock (HF) Self-Consistent Field (SCF) level within the Polarizable Embedding (PE) formalism. We formulate HF based PE within the linear response theory...

  20. Bioefficacy, residue dynamics and safety assessment of the combination fungicide trifloxystrobin 25% + tebuconazole 50%-75 WG in managing early blight of tomato (Lycopersicon esculentum Mill.).

    Science.gov (United States)

    Saha, Sujoy; Purath, Ahammed Shabeer Thekkum; Jadhav, Manjusha R; Loganathan, M; Banerjee, Kaushik; Rai, A B

    2014-01-01

    This paper reports the in vitro and in vivo bioefficacy of a combination fungicide trifloxystrobin (25%) + tebuconazole (50%) against early blight disease of tomato (Lycopersicon esculentum Mill.) caused by Alternaria solani and their corresponding pre-harvest intervals (PHI) with reference to the maximum residue limits (European Union). Bioefficacy of the test fungicide combination revealed that in vitro conditions manifested the best control (75.1%) at 350 mg kg(-1) against 76.2% control under field conditions. A sample preparation method based on ethyl acetate extraction and estimation by LC-MS multiple reaction monitoring (MRM) was validated in tomato fruits at 0.01 mg/kg and dissipation studies were conducted in field at single and double doses. The residues of both the compounds on all the sampling days were below the European Union maximum residue limits (EU-MRLs) and the maximum permissible intakes (MPIs) were calculated on the basis of prescribed acceptable daily intake (ADI). The combined bioefficacy and residue dynamics information will support label-claim of this fungicide combination for the management of early blight in tomato.

  1. On the relative importance of second-order terms in relativistic dissipative fluid dynamics

    CERN Document Server

    Molnár, E; Denicol, G S; Rischke, D H

    2013-01-01

    In Denicol et al., Phys. Rev. D 85, 114047 (2012), the equations of motion of relativistic dissipative fluid dynamics were derived from the relativistic Boltzmann equation. These equations contain a multitude of terms of second order in Knudsen number, in inverse Reynolds number, or their product. Terms of second order in Knudsen number give rise to non-hyperbolic (and thus acausal) behavior and must be neglected in (numerical) solutions of relativistic dissipative fluid dynamics. The coefficients of the terms which are of the order of the product of Knudsen and inverse Reynolds numbers have been explicitly computed in the above reference, in the limit of a massless Boltzmann gas. Terms of second order in inverse Reynolds number arise from the collision term in the Boltzmann equation, upon expansion to second order in deviations from the single-particle distribution function in local thermodynamical equilibrium. In this work, we compute these second-order terms for a massless Boltzmann gas with constant scatt...

  2. Aggregate size and structure determination of nanomaterials in physiological media: importance of dynamic evolution

    Science.gov (United States)

    Afrooz, A. R. M. Nabiul; Hussain, Saber M.; Saleh, Navid B.

    2014-12-01

    Most in vitro nanotoxicological assays are performed after 24 h exposure. However, in determining size and shape effect of nanoparticles in toxicity assays, initial characterization data are generally used to describe experimental outcome. The dynamic size and structure of aggregates are typically ignored in these studies. This brief communication reports dynamic evolution of aggregation characteristics of gold nanoparticles. The study finds that gradual increase in aggregate size of gold nanospheres (AuNS) occurs up to 6 h duration; beyond this time period, the aggregation process deviates from gradual to a more abrupt behavior as large networks are formed. Results of the study also show that aggregated clusters possess unique structural conformation depending on nominal diameter of the nanoparticles. The differences in fractal dimensions of the AuNS samples likely occurred due to geometric differences, causing larger packing propensities for smaller sized particles. Both such observations can have profound influence on dosimetry for in vitro nanotoxicity analyses.

  3. The importance of being supercoiled: how DNA mechanics regulate dynamic processes.

    Science.gov (United States)

    Baranello, Laura; Levens, David; Gupta, Ashutosh; Kouzine, Fedor

    2012-07-01

    Through dynamic changes in structure resulting from DNA-protein interactions and constraints given by the structural features of the double helix, chromatin accommodates and regulates different DNA-dependent processes. All DNA transactions (such as transcription, DNA replication and chromosomal segregation) are necessarily linked to strong changes in the topological state of the double helix known as torsional stress or supercoiling. As virtually all DNA transactions are in turn affected by the torsional state of DNA, these changes have the potential to serve as regulatory signals detected by protein partners. This two-way relationship indicates that DNA dynamics may contribute to the regulation of many events occurring during cell life. In this review we will focus on the role of DNA supercoiling in the cellular processes, with particular emphasis on transcription. Besides giving an overview on the multiplicity of factors involved in the generation and dissipation of DNA torsional stress, we will discuss recent studies which give new insight into the way cells use DNA dynamics to perform functions otherwise not achievable. This article is part of a Special Issue entitled: Chromatin in time and space. Published by Elsevier B.V.

  4. Sex, social status and physiological stress in primates: the importance of social and glucocorticoid dynamics.

    Science.gov (United States)

    Cavigelli, Sonia A; Caruso, Michael J

    2015-05-26

    Social status has been associated with health consequences, although the mechanisms by which status affects health are relatively unknown. At the physiological level, many studies have investigated the potential relationship between social behaviour/rank and physiological stress, with a particular focus on glucocorticoid (GC) production. GCs are of interest because of their experimentally established influence on health-related processes such as metabolism and immune function. Studies in a variety of species, in both naturalistic and laboratory settings, have led to complex outcomes. This paper reviews findings from primates and rodents and proposes a psychologically and physiologically relevant framework in which to study the relationship between social status and GC function. We (i) compare status-specific GC production between male and female primates, (ii) review the functional significance of different temporal patterns of GC production, (iii) propose ways to assess these temporal dynamics, and (iv) present novel hypotheses about the relationship between social status and GC temporal dynamics, and potential fitness and health implications. To understand whether GC production mediates social status-related fitness disparities, we must consider social contest conditions and the temporal dynamics of GC production. This framework will provide greater insights into the relationship between social status, physiological stress and health.

  5. Residual stresses within sprayed coatings

    Institute of Scientific and Technical Information of China (English)

    JIANG Yi; XU Bin-shi; WANG Hai-dou

    2005-01-01

    Some important developments of residual stress researches for coating-based systems were studied. The following topics were included the sources of residual stresses in coatings: error analysis of Stoney's equation in the curvature method used for the measurement of coating residual stress, the modeling of residual stress and some analytical models for predicting the residual stresses in coatings. These topics should provide some important insights for the fail-safe design of the coating-based systems.

  6. Assessment of a design to monitor the influence of crop residue management on the dynamics of soil water content with ERT

    Science.gov (United States)

    Chelin, Marie; Hiel, Marie-Pierre; Hermans, Thomas; Binley, Andrew; Garre, Sarah

    2016-04-01

    Choices related to crop residue management affect the soil structure. As a consequence, they may determine the spatio-temporal dynamics of water content and eventually the crop yields. In order to better understand the influence of these strategies on hydraulic processes occurring at the plot scale, we opted for the use electrical resistivity tomography (ERT). This approach presents the advantage to limit soil disturbance but is still faced to important challenges when applied in an agricultural field context. Especially changing soil-electrode contact has to be considered, as it can lead to bad quality data, especially for setups with small electrodes and small inter-electrode distance. The objective of this study was to test the efficiency of a high-resolution 3-D field measurement design to properly assess the dynamics of soil water content. ERT measurements were conducted in a Cutanic Siltic Luvisol in Gembloux, Belgium, on two plots of 2m2 ploughed in Oct 2014 at a depth of 25 cm and sown with maize in April 2015. The plants were removed on one of the plots in order to obtain a bare soil reference. A grid of 98 surface stainless steel electrodes was layed-out on each plot and four sticks supporting each eight stainless steel electrodes were vertically inserted into the soil up to 1.20 m to get more detailed information in depth. The experiments were performed between Jul and Oct 2015, in order to get measurements both in dry and wet periods. For surface and borehole monitoring, a dipole-dipole array configuration including in-line and cross-line measurements was adopted. Normal and reciprocal measurements were performed systematically to assess the data quality: only the datasets with a mean reciprocal error lower than 3% were considered for the data inversion. This contribution will show the first inverted results showing the complexity of experimental design and data analysis for high-resolution, timelapse ERT in field conditions. Based on these results, we

  7. Accurately characterizing the importance of wave‐particle interactions in radiation belt dynamics: The pitfalls of statistical wave representations

    Science.gov (United States)

    Mann, Ian R.; Rae, I. Jonathan; Sibeck, David G.; Watt, Clare E. J.

    2016-01-01

    Abstract Wave‐particle interactions play a crucial role in energetic particle dynamics in the Earth's radiation belts. However, the relative importance of different wave modes in these dynamics is poorly understood. Typically, this is assessed during geomagnetic storms using statistically averaged empirical wave models as a function of geomagnetic activity in advanced radiation belt simulations. However, statistical averages poorly characterize extreme events such as geomagnetic storms in that storm‐time ultralow frequency wave power is typically larger than that derived over a solar cycle and Kp is a poor proxy for storm‐time wave power. PMID:27867798

  8. Accurately characterizing the importance of wave-particle interactions in radiation belt dynamics: The pitfalls of statistical wave representations.

    Science.gov (United States)

    Murphy, Kyle R; Mann, Ian R; Rae, I Jonathan; Sibeck, David G; Watt, Clare E J

    2016-08-01

    Wave-particle interactions play a crucial role in energetic particle dynamics in the Earth's radiation belts. However, the relative importance of different wave modes in these dynamics is poorly understood. Typically, this is assessed during geomagnetic storms using statistically averaged empirical wave models as a function of geomagnetic activity in advanced radiation belt simulations. However, statistical averages poorly characterize extreme events such as geomagnetic storms in that storm-time ultralow frequency wave power is typically larger than that derived over a solar cycle and Kp is a poor proxy for storm-time wave power.

  9. Dynamic contrast-enhanced MRI for automatic detection of foci @]@of residual or recurrent disease after prostatectomy

    Energy Technology Data Exchange (ETDEWEB)

    Parra, N.A.; Orman, Amber; Abramowitz, Matthew; Pollack, Alan; Stoyanova, Radka [University of Miami Miller School of Medicine, Department of Radiation Oncology, Miami, FL (United States); Padgett, Kyle [University of Miami Miller School of Medicine, Department of Radiation Oncology, Miami, FL (United States); University of Miami Miller School of Medicine, Department of Radiology, Miami, FL (United States); Casillas, Victor [University of Miami Miller School of Medicine, Department of Radiology, Miami, FL (United States); Punnen, Sanoj [University of Miami Miller School of Medicine, Department of Urology, Miami, FL (United States)

    2017-01-15

    This study aimed to develop an automated procedure for identifying suspicious foci of residual/recurrent disease in the prostate bed using dynamic contrast-enhanced-MRI (DCE-MRI) in prostate cancer patients after prostatectomy. Data of 22 patients presenting for salvage radiotherapy (RT) with an identified gross tumor volume (GTV) in the prostate bed were analyzed retrospectively. An unsupervised pattern recognition method was used to analyze DCE-MRI curves from the prostate bed. Data were represented as a product of a number of signal-vs.-time patterns and their weights. The temporal pattern, characterized by fast wash-in and gradual wash-out, was considered the ''tumor'' pattern. The corresponding weights were thresholded based on the number (1, 1.5, 2, 2.5) of standard deviations away from the mean, denoted as DCE1.0,.., DCE2.5, and displayed on the T2-weighted MRI. The resultant four volumes were compared with the GTV and maximum pre-RT prostate-specific antigen (PSA) level. Pharmacokinetic modeling was also carried out. Principal component analysis determined 2-4 significant patterns in patients' DCE-MRI. Analysis and display of the identified suspicious foci was performed in commercial software (MIM Corporation, Cleveland, OH, USA). In general, DCE1.0/DCE1.5 highlighted larger areas than GTV. DCE2.0 and GTV were significantly correlated (r = 0.60, p < 0.05). DCE2.0/DCA2.5 were also significantly correlated with PSA (r = 0.52, 0.67, p < 0.05). K{sup trans} for DCE2.5 was statistically higher than the GTV's K{sup trans} (p < 0.05), indicating that the automatic volume better captures areas of malignancy. A software tool was developed for identification and visualization of the suspicious foci in DCE-MRI from post-prostatectomy patients and was integrated into the treatment planning system. (orig.) [German] Entwicklung eines automatischen Analyseverfahrens, um nach Prostatektomie mittels dynamischer kontrastmittelverstaerkter

  10. Interactions between residue placement and earthworm ecological strategy affect aggregate turnover and N2O dynamics in agricultural soil

    NARCIS (Netherlands)

    Giannopoulos, G.; Pulleman, M.M.; Groenigen, van J.W.

    2010-01-01

    Previous laboratory studies using epigeic and anecic earthworms have shown that earthworm activity can considerably increase nitrous oxide (N2O) emissions from crop residues in soils. However, the universality of this effect across earthworm functional groups and its underlying mechanisms remain unc

  11. Functional analysis of CedA based on its structure: residues important in binding of DNA and RNA polymerase and in the cell division regulation.

    Science.gov (United States)

    Abe, Yoshito; Fujisaki, Naoki; Miyoshi, Takanori; Watanabe, Noriko; Katayama, Tsutomu; Ueda, Tadashi

    2016-02-01

    DnaAcos, a mutant of the initiator DnaA, causes overinitiation of chromosome replication in Escherichia coli, resulting in inhibition of cell division. CedA was found to be a multi-copy suppressor which represses the dnaAcos inhibition of cell division. However, functional mechanism of CedA remains elusive except for previously indicated possibilities in binding to DNA and RNA polymerase. In this study, we searched for the specific sites of CedA in binding of DNA and RNA polymerase and in repression of cell division inhibition. First, DNA sequence to which CedA preferentially binds was determined. Next, the several residues and β4 region in CedA C-terminal domain was suggested to specifically interact with the DNA. Moreover, we found that the flexible N-terminal region was required for tight binding to longer DNA as well as interaction with RNA polymerase. Based on these results, several cedA mutants were examined in ability for repressing dnaAcos cell division inhibition. We found that the N-terminal region was dispensable and that Glu32 in the C-terminal domain was required for the repression. These results suggest that CedA has multiple roles and residues with different functions are positioned in the two regions.

  12. A new look at the Dynamic Similarity Hypothesis: the importance of swing phase

    Directory of Open Access Journals (Sweden)

    David A. Raichlen

    2013-08-01

    The Dynamic Similarity Hypothesis (DSH suggests that when animals of different size walk at similar Froude numbers (equal ratios of inertial and gravitational forces they will use similar size-corrected gaits. This application of similarity theory to animal biomechanics has contributed to fundamental insights in the mechanics and evolution of a diverse set of locomotor systems. However, despite its popularity, many mammals fail to walk with dynamically similar stride lengths, a key element of gait that determines spontaneous speed and energy costs. Here, we show that the applicability of the DSH is dependent on the inertial forces examined. In general, the inertial forces are thought to be the centripetal force of the inverted pendulum model of stance phase, determined by the length of the limb. If instead we model inertial forces as the centripetal force of the limb acting as a suspended pendulum during swing phase (determined by limb center of mass position, the DSH for stride length variation is fully supported. Thus, the DSH shows that inter-specific differences in spatial kinematics are tied to the evolution of limb mass distribution patterns. Selection may act on morphology to produce a given stride length, or alternatively, stride length may be a “spandrel” of selection acting on limb mass distribution.

  13. The importance of temporal stress variation and dynamic disequilibrium for the initiation of plate tectonics

    Science.gov (United States)

    Stamenković, V.; Höink, T.; Lenardic, A.

    2016-06-01

    We use 1-D thermal history models and 3-D numerical experiments to study the impact of dynamic thermal disequilibrium and large temporal variations of normal and shear stresses on the initiation of plate tectonics. Previous models that explored plate tectonics initiation from a steady state, single plate mode of convection concluded that normal stresses govern the initiation of plate tectonics, which based on our 1-D model leads to plate yielding being more likely with increasing interior heat and planet mass for a depth-dependent Byerlee yield stress. Using 3-D spherical shell mantle convection models in an episodic regime allows us to explore larger temporal stress variations than can be addressed by considering plate failure from a steady state stagnant lid configuration. The episodic models show that an increase in convective mantle shear stress at the lithospheric base initiates plate failure, which leads with our 1-D model to plate yielding being less likely with increasing interior heat and planet mass. In this out-of-equilibrium and strongly time-dependent stress scenario, the onset of lithospheric overturn events cannot be explained by boundary layer thickening and normal stresses alone. Our results indicate that in order to understand the initiation of plate tectonics, one should consider the temporal variation of stresses and dynamic disequilibrium.

  14. Importance of soil thermal dynamics on land carbon sequestration in Northern Eurasia during the 21st century

    Science.gov (United States)

    Kicklighter, David; Monier, Erwan; Sokolov, Andrei; Zhuang, Qianlai; Melillo, Jerry

    2015-04-01

    Recent modeling studies have suggested that carbon sinks in pan-arctic ecosystems may be weakening partially as a result of warming-induced increases in soil organic matter (SOM) decomposition and the exposure of previously frozen SOM to decomposition. This weakening of carbon sinks is likely to continue in the future as vast amount of carbon in permafrost soils is vulnerable to thaw. Here, we examine the importance of considering soil thermal dynamics when determining the effects of climate change and land-use change on carbon dynamics in Northern Eurasia during the 21st century. This importance is assessed by comparing results for a "business as usual" scenario between a version of the Terrestrial Ecosystem Model that does not consider soil thermal dynamics (TEM 4.4) and a version that does consider these dynamics (TEM 6.0). In this scenario, which is similar to the IPCC Representative Concentration Pathways (RCP) 8.5 scenario, the net area covered by food crops and pastures in Northern Eurasia is assumed to remain relatively constant over the 21st century, but the area covered by secondary forests is projected to double as a result of timber harvest and the abandonment of land associated with displacement of agricultural land. Enhanced decomposition from the newly exposed SOM from permafrost thaw also increases nitrogen availability for plant production so that the loss of carbon from the enhanced decomposition is partially compensated by enhanced uptake and storage of atmospheric carbon dioxide in vegetation. Our results indicate that consideration of soil thermal dynamics have a large influence on how simulated terrestrial carbon dynamics in Northern Eurasia respond to changes in climate, atmospheric chemistry (e.g., carbon dioxide fertilization, ozone pollution, nitrogen deposition) and disturbances.

  15. The importance of incorporating functional habitats into conservation planning for highly mobile species in dynamic systems.

    Science.gov (United States)

    Webb, Matthew H; Terauds, Aleks; Tulloch, Ayesha; Bell, Phil; Stojanovic, Dejan; Heinsohn, Robert

    2017-10-01

    The distribution of mobile species in dynamic systems can vary greatly over time and space. Estimating their population size and geographic range can be problematic and affect the accuracy of conservation assessments. Scarce data on mobile species and the resources they need can also limit the type of analytical approaches available to derive such estimates. We quantified change in availability and use of key ecological resources required for breeding for a critically endangered nomadic habitat specialist, the Swift Parrot (Lathamus discolor). We compared estimates of occupied habitat derived from dynamic presence-background (i.e., presence-only data) climatic models with estimates derived from dynamic occupancy models that included a direct measure of food availability. We then compared estimates that incorporate fine-resolution spatial data on the availability of key ecological resources (i.e., functional habitats) with more common approaches that focus on broader climatic suitability or vegetation cover (due to the absence of fine-resolution data). The occupancy models produced significantly (P < 0.001) smaller (up to an order of magnitude) and more spatially discrete estimates of the total occupied area than climate-based models. The spatial location and extent of the total area occupied with the occupancy models was highly variable between years (131 and 1498 km(2) ). Estimates accounting for the area of functional habitats were significantly smaller (2-58% [SD 16]) than estimates based only on the total area occupied. An increase or decrease in the area of one functional habitat (foraging or nesting) did not necessarily correspond to an increase or decrease in the other. Thus, an increase in the extent of occupied area may not equate to improved habitat quality or function. We argue these patterns are typical for mobile resource specialists but often go unnoticed because of limited data over relevant spatial and temporal scales and lack of spatial data on the

  16. Mathematical modeling of the intracellular protein dynamics: the importance of active transport along microtubules.

    Science.gov (United States)

    Szymańska, Zuzanna; Parisot, Martin; Lachowicz, Mirosław

    2014-12-21

    In this paper we propose a mathematical model of protein and mRNA transport inside a cell. The spatio-temporal model takes into account the active transport along microtubules in the cytoplasm as well as diffusion and is able to reproduce the oscillatory changes in protein concentration observed in many experimental data. In the model the protein and the mRNA interact with each other that allows us to classify the model as a simple gene regulatory network. The proposed model is generic and may be adapted to specific signaling pathways. On the basis of numerical simulations, we formulate a new hypothesis that the oscillatory dynamics is allowed by the mRNA active transport along microtubules from the nucleus to distant locations.

  17. The importance of cantilever dynamics in the interpretation of Kelvin probe force microscopy.

    Science.gov (United States)

    Satzinger, Kevin J; Brown, Keith A; Westervelt, Robert M

    2012-09-15

    A realistic interpretation of the measured contact potential difference (CPD) in Kelvin probe force microscopy (KPFM) is crucial in order to extract meaningful information about the sample. Central to this interpretation is a method to include contributions from the macroscopic cantilever arm, as well as the cone and sharp tip of a KPFM probe. Here, three models of the electrostatic interaction between a KPFM probe and a sample are tested through an electrostatic simulation and compared with experiment. In contrast with previous studies that treat the KPFM cantilever as a rigid object, we allow the cantilever to bend and rotate; accounting for cantilever bending provides the closest agreement between theory and experiment. We demonstrate that cantilever dynamics play a major role in CPD measurements and provide a simulation technique to explore this phenomenon.

  18. HPLC/UV analysis of chlorfenapyr residues in cabbage and soil to study the dynamics of different formulations.

    Science.gov (United States)

    Cao, Yongsong; Chen, Jiuxin; Wang, Yuelong; Liang, Ji; Chen, Lihua; Lu, Yitong

    2005-11-01

    The chlorfenapyr analysis method of residue, its degradation and final residue in soil and cabbage were studied. Residues of chlorfenapyr were extracted from soil and cabbage with acetone/water, purified by liquid/liquid partition and chromatographic column, concentrated to a small volume, and then determined by HPLC equipped with UV detector. The mean accuracy of analytical method were 93.3% and 90.6% in soil and cabbage, respectively; the precision (repeatability) in cabbage ranging from 1.7% to 11.8%, in soil ranging from 2.8% to 11.2%; the precision (reproducibility) in cabbage ranged from 2.2% to 12.1%, in soil it ranged from 2.4% to 11.5%. The minimum detectable amount of chlorfenapyr was 0.65 ng, the minimum detectable concentration was 0.0162 mg kg-1. The degradation of chlorfenapyr formulations in soil and cabbage was determined. The results showed that chlorfenapyr nanoformulation and suspension concentration degradation in soil coincided with C=0.2538 e-0.1612t, C=0.537 e-0.1754t, respectively; the half-lives were about 4.3 d and 3.9 d, respectively. Two kinds of chlorfenapyr formulation degradation in cabbage coincided with C=4.0431 e-0.3103t, C=6.9611 e-0.2686t respectively; the half-lives were about 2.2 d and 2.6, d, respectively. When chlorfenapyr formulations were applied according to the double recommended dose, the final residues in cabbage were much lower than the USA EPA's maximum residue limit of 1 mg kg-1 in vegetables. The degradation rate of chlorfenapyr nanoformulation was faster than that of suspension concentration, and the former residue was also less in soil. Therefore, a harvest interval should be more than 5 d, and a dosage of 900 mL/hm2 was suggested for chlorfenapyr suspension concentration, which could be considered as safe to human beings and animals. Chlorfenapyr nanoformulation was safer than suspension concentration, its harvest interval and dosage can attain a high level.

  19. Amino acid residues important for substrate specificity of the amino acid permeases Can I p and Gnp I p in Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Regenberg, Birgitte; Kielland-Brandt, M.C.

    2001-01-01

    Deletion of the general amino acid permease gene GAP1 abolishes uptake of L-citrulline in Saccharomyces cerevisiae, resulting in the inability to grow on L-citrulline as sole nitrogen source. Selection for suppressor mutants that restored growth on L-citrulline led to isolation of 21 mutations...... in the arginine permease gene CAN1. One similar mutation was found in the glutamine-asparagine permease gene GNP1. L-[C-14]citrulline uptake measurements confirmed that suppressor mutations in CAN1 conferred uptake of this amino acid, while none of the mutant permeases had lost the ability to transport L-[C-14......]arginine. Substrate specificity seemed to remain narrow in most cases, and broad substrate specificity was only observed in the cases where mutations affect two proline residues (P148 and P313) that are both conserved in the amino acid-polyamine-choline (APC) transporter superfamily. We found mutations...

  20. Proteomics reveals the importance of the dynamic redistribution of the subcellular location of proteins in breast cancer cells.

    Science.gov (United States)

    Pinto, Gabriella; Alhaiek, Abdulrab Ahmed M; Godovac-Zimmermann, Jasminka

    2015-02-01

    At the molecular level, living cells are enormously complicated complex adaptive systems in which intertwined genomic, transcriptomic, proteomic and metabolic networks all play a crucial role. At the same time, cells are spatially heterogeneous systems in which subcellular compartmentalization of different functions is ubiquitous and requires efficient cross-compartmental communication. Dynamic redistribution of multitudinous proteins to different subcellular locations in response to cellular functional state is increasingly recognized as a crucial characteristic of cellular function that seems to be at least as important as overall changes in protein abundance. Characterization of the subcellular spatial dynamics of protein distribution is a major challenge for proteomics and recent results with MCF7 breast cancer cells suggest that this may be of particular importance for cancer cells.

  1. Indonesia Rejoining OPEC: Dynamics of the Oil Importer and Exporter Countries

    OpenAIRE

    Badaruddin, Muhammad

    2015-01-01

    Reactivation of Indonesia's full membership to the Organization of the Petroleum Exporting Countries (OPEC) triggered discussion surrounding global petroleum governance. The country which decided to suspend its full membership at the end of 2008, currently labelled as net oil importer. However, in OPEC terms Indonesia never really left, instead of the organization termed it as a "suspension". Departing from the abovementioned context and perspectives, purpose of this essay is to answer the qu...

  2. Future forest aboveground carbon dynamics in the central United States: the importance of forest demographic processes

    Science.gov (United States)

    Jin, Wenchi; He, Hong S.; Thompson, Frank R.; Wang, Wen J.; Fraser, Jacob S.; Shifley, Stephen R.; Hanberry, Brice B.; Dijak, William D.

    2017-01-01

    The Central Hardwood Forest (CHF) in the United States is currently a major carbon sink, there are uncertainties in how long the current carbon sink will persist and if the CHF will eventually become a carbon source. We used a multi-model ensemble to investigate aboveground carbon density of the CHF from 2010 to 2300 under current climate. Simulations were done using one representative model for each of the simple, intermediate, and complex demographic approaches (ED2, LANDIS PRO, and LINKAGES, respectively). All approaches agreed that the current carbon sink would persist at least to 2100. However, carbon dynamics after current carbon sink diminishes to zero differ for different demographic modelling approaches. Both the simple and the complex demographic approaches predicted prolonged periods of relatively stable carbon densities after 2100, with minor declines, until the end of simulations in 2300. In contrast, the intermediate demographic approach predicted the CHF would become a carbon source between 2110 and 2260, followed by another carbon sink period. The disagreement between these patterns can be partly explained by differences in the capacity of models to simulate gross growth (both birth and subsequent growth) and mortality of short-lived, relatively shade-intolerant tree species. PMID:28165483

  3. Importance of Age on the Dynamic Mechanical Behavior of Intertubular and Peritubular Dentin

    Science.gov (United States)

    Ryou, Heonjune; Romberg, Elaine; Pashley, David H.; Tay, Franklin R.; Arola, Dwayne

    2014-01-01

    An experimental evaluation of human coronal dentin was performed using nanoscopic Dynamic Mechanical Analysis (nanoDMA). The primary objectives were to quantify any unique changes in mechanical behavior of intertubular and peritubular dentin with age, and to evaluate the microstructure and mechanical behavior of the mineral deposited within the lumens. Specimens of coronal dentin were evaluated by nanoDMA using single indents and in scanning mode via scanning probe microscopy. Results showed that there were no significant differences in the storage modulus or complex modulus between the two age groups (18–25 versus 54–83 yrs) for either the intertubular or peritubular tissue. However, there were significant differences in the dampening behavior between the young and old dentin, as represented in the loss modulus and tanδ responses. For both the intertubular and peritubular components, the capacity for dampening was significantly lower in the old group. Scanning based nanoDMA showed that the tubules of old dentin exhibit a gradient in elastic behavior, with decrease in elastic modulus from the cuff to the center of tubules filled with newly deposited mineral. PMID:25498296

  4. Population dynamics of Acartia pacifica (Copepoda:Calanoida):the importance of benthic-pelagic coupling

    Institute of Scientific and Technical Information of China (English)

    JIANG Xiaodong; WANG Guizhong; LI Shaojing

    2006-01-01

    The seasonal occurrence of Acartia pacifica (Copepoda: Calanoida) and their resting eggs in the sediment of Xiamen Bay were documented between October 2002 and September 2003. The number of viable eggs in the sediment increased from January to May with the increase in the number of planktonic females. When the population of A. Pacifica disappeared from the water column, the number of eggs in the sediment began to decrease and reached a low value due to lack of input. The peak of nauplii abundance occurred when the hatching potential of eggs from the sediment was high under the natural environment from February to June. The hatching of resting eggs of A. Pacifica was essentially temperature-dependent after suspension, while photoperiod regimes had no significant effect on the hatching. The mean density of subitaneous eggs was 1.122 0 g/cm3 with a standard deviation (SD) of 0.000 2 g/cm3. The mean density of diapause eggs was 1.151 2 g/cm3 with a SD of 0.000 1 g/cm3. The sinking rates of subitaneous eggs ranged from 19.55 to 26.17 m/d, while those of diapause eggs ranged from 30.29 to 31.28 m/d. The comparison of the egg deposition time and egg hatching time suggested that in most cases virtually all subitaneous eggs of A. Pacifica would settle to the bottom before their hatching even though the eggs have high potential to hatch. The evidence was provided that the seasonal dynamics of A. Pacifica is accompanied by benthic-pelagic coupling.

  5. Chemical modification of Penicillium 1,2-alpha-D-mannosidase by water-soluble carbodi-imide: identification of a catalytically important aspartic acid residue.

    Science.gov (United States)

    Yoshida, T; Maeda, K; Kobayashi, M; Ichishima, E

    1994-01-01

    1,2-alpha-D-Mannosidase from Penicillium citrinum was inactivated by chemical modification with 1-ethyl-3-(3-dimethylamino-propyl)carbodi-imide (EDC). Most of the activity was lost after modification in the absence of a nucleophile, glycine ethyl ester. 1-Deoxymannojirimycin (dMM), a competitive inhibitor of the enzyme, showed partial protection against the inactivation. After the modification by EDC without the presence of a nucleophile, proteolytic digests of the enzyme were analysed by reversed-phase h.p.l.c. and a unique peptide was shown to decrease when dMM was present during the modification. The peptide was absent from the digests of unmodified enzyme. The amino acid sequence of the peptide (A; Ile-Gly-Pro) was identical in part with that of the adjacent peptide (B; Ile-Gly-Pro-Asp-Ser-Trp-Gly-Trp-Asp-Pro-Lys). When cholecystokinin tetrapeptide (Trp-Met-Asp-Phe-NH2) was modified by EDC alone, the modified peptide could be separated from unmodified peptide by reversed-phase h.p.i.c., and Edman degradation was stopped before the modified aspartic acid residue. This suggested that, in the enzyme, peptide A was derived from peptide B by the modification. Consequently, Asp-4 in peptide B was assumed to be masked by dMM during the modification, and to be involved in the interaction of the enzyme with its substrate. PMID:7945271

  6. Identifying folding nucleus based on residue contact networks of proteins.

    Science.gov (United States)

    Li, Jie; Wang, Jun; Wang, Wei

    2008-06-01

    In the native structure of a protein, all the residues are tightly parked together in a specific order following its folding and every residue contacts with some spatially neighbor residues. A residue contact network can be constructed by defining the residues as nodes and the native contacts as edges. During the folding of small single-domain proteins, there is a set of contacts (or bonds), defined as the folding nucleus (FN), which is formed around the transition state, i.e., a rate-limiting barrier located at about the middle between the unfolded states and the native state on the free energy landscape. Such a FN plays an essential role in the folding dynamics and the residues, which form the related contacts called as folding nucleus residues (FNRs). In this work, the FNRs in proteins are identified by using quantities which characterize the topology of residue contact networks of proteins. By comparing the specificities of residues with the network quantities K(R), L(R), and D(R), up to 90% FNRs of six typical proteins found experimentally are identified. It is found that the FNRs behave the full-closeness centrals rather than degree or closeness centers in the residue contact network, implying that they are important to the folding cooperativity of proteins. Our study shows that the FNRs can be identified solely from the native structures of proteins based on the analysis of residue contact network without any knowledge of the transition state ensemble. (c) 2008 Wiley-Liss, Inc.

  7. Long-term stability of FeSO4 and H2SO4 treated chromite ore processing residue (COPR): Importance of H(+) and SO4(2).

    Science.gov (United States)

    Wang, Xin; Zhang, Jingdong; Wang, Linling; Chen, Jing; Hou, Huijie; Yang, Jiakuan; Lu, Xiaohua

    2017-01-05

    In this study, the long-term stability of Cr(VI) in the FeSO4 and H2SO4 (FeSO4-H2SO4) treated chromite ore processing residue (COPR) after 400 curing days and the stabilization mechanisms were investigated. FeSO4-H2SO4 treatment significantly reduced toxicity characteristic leaching procedure (TCLP) and synthetic precipitation leaching procedure (SPLP) Cr(VI) concentrations to lower than the regulatory limit of 1.5mgL(-1) (HJ/T 301-2007, China EPA) even for the samples curing 400days, achieving an outstanding long-term stability. Our independent leaching tests revealed that H(+) and SO4(2-) have synergistic effect on promoting the release of Cr(VI), which would make Cr(VI) easier accessed by Fe(II) during stabilization. The contributions of H(+) and SO4(2-) to Cr(VI) release ratio were 25%-44% and 19%-38%, respectively, as 5mol H2SO4 per kg COPR was used. X-ray powder diffraction (XRD), X-ray photoelectron spectroscopy (XPS) and alkaline digestion analyses were also employed to interpret the possible stabilization mechanism. Cr(VI) released from COPR solid was reduced to Cr(III) by Fe(II), and then formed stable FexCr(1-x)(OH)3 precipitate. This study provides a facile and reliable scheme for COPR stabilization, and verifies the excellent long-term stability of the FeSO4-H2SO4 treated COPR.

  8. Functional importance of a pair of conserved glutamic acid residues and of Ca(2+) binding in the cbb(3)-type oxygen reductases from Rhodobacter sphaeroides and Vibrio cholerae.

    Science.gov (United States)

    Ouyang, Hanlin; Han, Huazhi; Roh, Jung H; Hemp, James; Hosler, Jonathan P; Gennis, Robert B

    2012-09-18

    The cbb(3)-type cytochrome c oxidases are members of the family of heme-copper proton pumping respiratory oxygen reductases. The structure of the cbb(3)-type oxidase from Pseudomonas stutzeri reveals that, in addition to the six redox-active metal centers (two b-type hemes, three c-type hemes, and Cu(B)), the enzyme also contains at least one Ca(2+). The calcium bridges two propionate carboxyls at the interface between the low-spin heme b and the active-site heme b(3) and, in addition, is ligated to a serine in subunit CcoO and by a glutamate in subunit CcoN. The glutamate that is ligated to Ca(2+) is one of a pair of glutamic acid residues that has previously been suggested to be part of a proton exit pathway for pumped protons. In this work, mutations of these glutamates are investigated in the cbb(3)-type oxidases from Vibrio cholerae and Rhodobacter sphaeroides. Metal analysis shows that each of these wild-type enzymes contains Ca(2+). Mutations of the glutamate expected to ligate the Ca(2+) in each of these enzymes (E126 in V. cholerae and E180 in R. sphaeroides) result in a loss of activity as well as a loss of Ca(2+). Mutations of the nearby glutamate (E129 in V. cholerae and E183 in R. sphaeroides) also resulted in a loss of oxidase activity and a loss of Ca(2+). It is concluded that the Ca(2+) is essential for assembly of the fully functional enzyme and that neither of the glutamates is likely to be part of a pathway for pumped protons within the cbb(3)-type oxygen reductases. A more likely role for these glutamates is the maintenance of the structural integrity of the active conformation of the enzyme.

  9. Assessing the importance of demographic parameters for population dynamics using Bayesian integrated population modeling.

    Science.gov (United States)

    Eacker, Daniel R; Lukacs, Paul M; Proffitt, Kelly M; Hebblewhite, Mark

    2017-06-01

    To successfully respond to changing habitat, climate or harvest, managers need to identify the most effective strategies to reverse population trends of declining species and/or manage harvest of game species. A classic approach in conservation biology for the last two decades has been the use of matrix population models to determine the most important vital rates affecting population growth rate (λ), that is, sensitivity. Ecologists quickly realized the critical role of environmental variability in vital rates affecting λ by developing approaches such as life-stage simulation analysis (LSA) that account for both sensitivity and variability of a vital rate. These LSA methods used matrix-population modeling and Monte Carlo simulation methods, but faced challenges in integrating data from different sources, disentangling process and sampling variation, and in their flexibility. Here, we developed a Bayesian integrated population model (IPM) for two populations of a large herbivore, elk (Cervus canadensis) in Montana, USA. We then extended the IPM to evaluate sensitivity in a Bayesian framework. We integrated known-fate survival data from radio-marked adults and juveniles, fecundity data, and population counts in a hierarchical population model that explicitly accounted for process and sampling variance. Next, we tested the prevailing paradigm in large herbivore population ecology that juvenile survival of neonates modeling in a Bayesian framework can provide multiple advantages. Our Bayesian LSA framework will provide a useful approach to addressing conservation challenges across a variety of species and data types. © 2017 by the Ecological Society of America.

  10. Estimation of failure probabilities of linear dynamic systems by importance sampling

    Indian Academy of Sciences (India)

    Anna Ivanova Olsen; Arvid Naess

    2006-08-01

    An iterative method for estimating the failure probability for certain time-variant reliability problems has been developed. In the paper, the focus is on the displacement response of a linear oscillator driven by white noise. Failure is then assumed to occur when the displacement response exceeds a critical threshold. The iteration procedure is a two-step method. On the first iteration, a simple control function promoting failure is constructed using the design point weighting principle. After time discretization, two points are chosen to construct a compound deterministic control function. It is based on the time point when the first maximum of the homogenous solution has occurred and on the point at the end of the considered time interval. An importance sampling technique is used in order to estimate the failure probability functional on a set of initial values of state space variables and time. On the second iteration, the concept of optimal control function can be implemented to construct a Markov control which allows much better accuracy in the failure probability estimate than the simple control function. On both iterations, the concept of changing the probability measure by the Girsanov transformation is utilized. As a result the CPU time is substantially reduced compared with the crude Monte Carlo procedure.

  11. Androgen action via testicular arteriole smooth muscle cells is important for Leydig cell function, vasomotion and testicular fluid dynamics.

    Directory of Open Access Journals (Sweden)

    Michelle Welsh

    Full Text Available Regulation of blood flow through the testicular microvasculature by vasomotion is thought to be important for normal testis function as it regulates interstitial fluid (IF dynamics which is an important intra-testicular transport medium. Androgens control vasomotion, but how they exert these effects remains unclear. One possibility is by signalling via androgen receptors (AR expressed in testicular arteriole smooth muscle cells. To investigate this and determine the overall importance of this mechanism in testis function, we generated a blood vessel smooth muscle cell-specific AR knockout mouse (SMARKO. Gross reproductive development was normal in SMARKO mice but testis weight was reduced in adulthood compared to control littermates; this reduction was not due to any changes in germ cell volume or to deficits in testosterone, LH or FSH concentrations and did not cause infertility. However, seminiferous tubule lumen volume was reduced in adult SMARKO males while interstitial volume was increased, perhaps indicating altered fluid dynamics; this was associated with compensated Leydig cell failure. Vasomotion was impaired in adult SMARKO males, though overall testis blood flow was normal and there was an increase in the overall blood vessel volume per testis in adult SMARKOs. In conclusion, these results indicate that ablating arteriole smooth muscle AR does not grossly alter spermatogenesis or affect male fertility but does subtly impair Leydig cell function and testicular fluid exchange, possibly by locally regulating microvascular blood flow within the testis.

  12. The Importance of Three-Body Interactions in Molecular Dynamics Simulations of Water with the Fragment Molecular Orbital Method

    Energy Technology Data Exchange (ETDEWEB)

    Pruitt, Spencer R.; Nakata, Hiroya; Nagata, Takeshi; Mayes, Maricris; Alexeev, Yuri; Fletcher, Graham D.; Fedorov, Dmitri G; Kitaura, Kazuo; Gordon, M

    2016-04-12

    The analytic first derivative with respect to nuclear coordinates is formulated and implemented in the framework of the three-body fragment molecular orbital (FMO) method. The gradient has been derived and implemented for restricted Hartree-Fock, second-order Møller-Plesset perturbation, and density functional theories. The importance of the three-body fully analytic gradient is illustrated through the failure of the two-body FMO method during molecular dynamics simulations of a small water cluster. The parallel implementation of the fragment molecular orbital method, its parallel efficiency, and its scalability on the Blue Gene/Q architecture up to 262,144 CPU cores, are also discussed.

  13. Dynamic properties of single pump, dispersion-compensating Raman/EDFA hybrid amplifier recycling residual Raman pump.

    Science.gov (United States)

    Lee, Ju; Chang, You; Han, Young-Geun; Kim, Sang; Lee, Sang

    2004-12-27

    We experimentally investigate transient effects of our proposed single pump, dispersion-compensating Raman/EDFA hybrid amplifier recycling residual Raman pump in a cascaded EDF under the situation of multi-channel add/drop, and then demonstrate the use of a FBG based all-optical gain-clamping technique to efficiently suppress the output transients. The results show that the proposed hybrid amplifier has a significantly long transient response time of ~ 2 ms compared to the previous reported value of the conventional separate pump, Raman/EDFA hybrid amplifiers due to both the low-pumping regime operation of 14XX nm pumped EDFA section and the additional pump transit time through the 12.6 km long dispersion compensating fiber to reach the EDF. However, using a simple gain-clamping method we obtain an almost, transient-free operation.

  14. Residuation theory

    CERN Document Server

    Blyth, T S; Sneddon, I N; Stark, M

    1972-01-01

    Residuation Theory aims to contribute to literature in the field of ordered algebraic structures, especially on the subject of residual mappings. The book is divided into three chapters. Chapter 1 focuses on ordered sets; directed sets; semilattices; lattices; and complete lattices. Chapter 2 tackles Baer rings; Baer semigroups; Foulis semigroups; residual mappings; the notion of involution; and Boolean algebras. Chapter 3 covers residuated groupoids and semigroups; group homomorphic and isotone homomorphic Boolean images of ordered semigroups; Dubreil-Jacotin and Brouwer semigroups; and loli

  15. The role of dynamic contrast-enhanced MRI in differentiation of local recurrence and residual soft-tissue tumor versus post-treatment changes.

    Science.gov (United States)

    Lehotska, V; Tothova, L; Valkovic, L

    2013-01-01

    To evaluate the reliability of dynamic contrast-enhanced MRI in the diagnosis of local recurrence of malignant soft-tissue tumors after receiving treatment. From March 2002 till December 2009 we performed dynamic contrast enhanced MRI in 95 patients with soft-tissue tumor after receiving treatment (surgery, radiotherapy, chemotherapy). Patients were classified according to five types of TIC. The recurrent disease was suspected in 47 patients and the biopsy was recommended. In 8 cases (TIC II), the biopsy was performed due to long-term post-treatment changes. Histological results proved STT recurrence in 45 patients; in 10 patients (8 with TIC II), biopsy revealed hypervascular granulation tissue, florid inflammation and reactive changes. The sensitivity for dynamic contrast-enhanced MR examination was 100 %, specificity 80 %, positive predictive value (PPV) 95.7 % and negative predictive value (NPV) 100 %. Our results indicate that TICs III, IV and V raise high suspicion of local tumor recurrence and require percutaneous imaging-guided biopsy. TIC of type II usually represents a pseudomass and the biopsy should be performed only in selected cases with increased risk of recurrent disease based on multidisciplinary approach. On the basis of literature review as well as our experiences we created a reliable algorithm proposed for diagnosing the residual or recurrent soft-tissue tumors (Tab. 2, Fig. 6, Ref. 20).

  16. All-atom molecular dynamics simulations reveal significant differences in interaction between antimycin and conserved amino acid residues in bovine and bacterial bc1 complexes.

    Science.gov (United States)

    Kokhan, Oleksandr; Shinkarev, Vladimir P

    2011-02-02

    Antimycin A is the most frequently used specific and powerful inhibitor of the mitochondrial respiratory chain. We used all-atom molecular dynamics (MD) simulations to study the dynamic aspects of the interaction of antimycin A with the Q(i) site of the bacterial and bovine bc(1) complexes embedded in a membrane. The MD simulations revealed considerable conformational flexibility of antimycin and significant mobility of antimycin, as a whole, inside the Q(i) pocket. We conclude that many of the differences in antimycin binding observed in high-resolution x-ray structures may have a dynamic origin and result from fluctuations of protein and antimycin between multiple conformational states of similar energy separated by low activation barriers, as well as from the mobility of antimycin within the Q(i) pocket. The MD simulations also revealed a significant difference in interaction between antimycin and conserved amino acid residues in bovine and bacterial bc(1) complexes. The strong hydrogen bond between antimycin and conserved Asp-228 (bovine numeration) was observed to be frequently broken in the bacterial bc(1) complex and only rarely in the bovine bc(1) complex. In addition, the distances between antimycin and conserved His-201 and Lys-227 were consistently larger in the bacterial bc(1) complex. The observed differences could be responsible for a weaker interaction of antimycin with the bacterial bc(1) complex.

  17. Molecular dynamics and residual entropy in the soft crystal, SmE phase, of 4-butyl-4'-isothiocyano-1,1'-biphenyl.

    Science.gov (United States)

    Ishimaru, Shin'ichi; Saito, Kazuya; Ikeuchi, Satoaki; Massalska-Arodz, Maria; Witko, Waclaw

    2005-05-26

    Molecular dynamics and resulting disorder in the soft crystal, smectic E (SmE) phase, were studied in detail for the title compound, 4-butyl-4'-isothiocyano-1,1'-biphenyl (4TCB), by (1)H NMR spectroscopy and adiabatic calorimetry. The ordered crystal phase of 4TCB was realized for the first time under ambient pressure after long two-step annealing and used as the reference state in the analysis of the experimental results. Four motional modes were identified in the SmE phase through the analysis of the (1)H NMR T(1). The residual entropy was determined as ca. 6 J K(-1) mol(-1). This magnitude implies that most of the disorder in the SmE phase at high temperatures is removed on cooling except for the head-to-tail disorder of the rod-shaped 4TCB molecule. Standard thermodynamic functions are tabulated below 375 K.

  18. Thermophilic Dry Methane Fermentation of Distillation Residue Eluted from Ethanol Fermentation of Kitchen Waste and Dynamics of Microbial Communities.

    Science.gov (United States)

    Huang, Yu-Lian; Tan, Li; Wang, Ting-Ting; Sun, Zhao-Yong; Tang, Yue-Qin; Kida, Kenji

    2017-01-01

    Thermophilic dry methane fermentation is advantageous for feedstock with high solid content. Distillation residue with 65.1 % moisture content was eluted from ethanol fermentation of kitchen waste and subjected to thermophilic dry methane fermentation, after adjusting the moisture content to 75 %. The effect of carbon to nitrogen (C/N) ratio on thermophilic dry methane fermentation was investigated. Results showed that thermophilic dry methane fermentation could not be stably performed for >10 weeks at a C/N ratio of 12.6 and a volatile total solid (VTS) loading rate of 1 g/kg sludge/d; however, it was stably performed at a C/N ratio of 19.8 and a VTS loading rate of 3 g/kg sludge/d with 83.4 % energy recovery efficiency. Quantitative PCR analysis revealed that the number of bacteria and archaea decreased by two orders of magnitude at a C/N ratio of 12.6, whereas they were not influenced at a C/N ratio of 19.8. Microbial community analysis revealed that the relative abundance of protein-degrading bacteria increased and that of organic acid-oxidizing bacteria and acetic acid-oxidizing bacteria decreased at a C/N ratio of 12.6. Therefore, there was accumulation of NH4(+) and acetic acid, which inhibited thermophilic dry methane fermentation.

  19. Alkaline proteinase inhibitor of Pseudomonas aeruginosa: a mutational and molecular dynamics study of the role of N-terminal residues in the inhibition of Pseudomonas alkaline proteinase.

    Science.gov (United States)

    Feltzer, Rhona E; Trent, John O; Gray, Robert D

    2003-07-11

    Alkaline proteinase inhibitor of Pseudomonas aeruginosa is a 11.5-kDa, high affinity inhibitor of the serralysin class of zinc-dependent proteinases secreted by several Gram-negative bacteria. X-ray crystallography of the proteinase-inhibitor complex reveals that five N-terminal inhibitor residues occupy the extended substrate binding site of the enzyme and that the catalytic zinc is chelated by the alpha-amino and carbonyl groups of the N-terminal residue of the inhibitor. In this study, we assessed the effect of alteration of inhibitor residues 2-5 on its affinity for Pseudomonas alkaline proteinase (APR) as derived from the ratio of the dissociation and associate rate constants for formation of the enzyme-inhibitor complex. The largest effect was observed at position Ser-2, which occupies the S1' pocket of the enzyme and donates a hydrogen bond to the carboxyl group of the catalytic Glu-177 of the proteinase. Substitution of Asp, Arg, or Trp at this position increased the dissociation constant KD by 35-, 180-, and 13-fold, respectively. Mutation at positions 3-5 of the trunk also resulted in a reduction in enzyme-inhibitor affinity, with the exception of an I4W mutant, which exhibited a 3-fold increase in affinity. Molecular dynamics simulation of the complex formation between the catalytic domain of APR and the S2D mutant showed that the carboxyl of Asp-2 interacts with the catalytic zinc, thereby partially neutralizing the negative charge that otherwise would clash with the carboxyl group of Glu-177 of APR. Simulation of the interaction between the alkaline proteinase and the I4W mutant revealed a major shift in the loop comprised of residues 189-200 of the enzyme that allowed formation of a stacking interaction between the aromatic rings of Ile-4 of the inhibitor and Tyr-158 of the proteinase. This new interaction could account for the observed increase in enzyme-inhibitor affinity.

  20. Carbon dynamics in the future forest: the importance of long-term successional legacy and climate-fire interactions.

    Science.gov (United States)

    Loudermilk, E Louise; Scheller, Robert M; Weisberg, Peter J; Yang, Jian; Dilts, Thomas E; Karam, Sarah L; Skinner, Carl

    2013-11-01

    Understanding how climate change may influence forest carbon (C) budgets requires knowledge of forest growth relationships with regional climate, long-term forest succession, and past and future disturbances, such as wildfires and timber harvesting events. We used a landscape-scale model of forest succession, wildfire, and C dynamics (LANDIS-II) to evaluate the effects of a changing climate (A2 and B1 IPCC emissions; Geophysical Fluid Dynamics Laboratory General Circulation Models) on total forest C, tree species composition, and wildfire dynamics in the Lake Tahoe Basin, California, and Nevada. The independent effects of temperature and precipitation were assessed within and among climate models. Results highlight the importance of modeling forest succession and stand development processes at the landscape scale for understanding the C cycle. Due primarily to landscape legacy effects of historic logging of the Comstock Era in the late 1880s, C sequestration may continue throughout the current century, and the forest will remain a C sink (Net Ecosystem Carbon Balance > 0), regardless of climate regime. Climate change caused increases in temperatures limited simulated C sequestration potential because of augmented fire activity and reduced establishment ability of subalpine and upper montane trees. Higher temperatures influenced forest response more than reduced precipitation. As the forest reached its potential steady state, the forest could become C neutral or a C source, and climate change could accelerate this transition. The future of forest ecosystem C cycling in many forested systems worldwide may depend more on major disturbances and landscape legacies related to land use than on projected climate change alone.

  1. Computational and Spectroscopic Investigations of the Molecular Scale Structure and Dynamics of Geologically Important Fluids and Mineral-Fluid Interfaces

    Energy Technology Data Exchange (ETDEWEB)

    R. James Kirkpatrick; Andrey G. Kalinichev

    2008-11-25

    Research supported by this grant focuses on molecular scale understanding of central issues related to the structure and dynamics of geochemically important fluids, fluid-mineral interfaces, and confined fluids using computational modeling and experimental methods. Molecular scale knowledge about fluid structure and dynamics, how these are affected by mineral surfaces and molecular-scale (nano-) confinement, and how water molecules and dissolved species interact with surfaces is essential to understanding the fundamental chemistry of a wide range of low-temperature geochemical processes, including sorption and geochemical transport. Our principal efforts are devoted to continued development of relevant computational approaches, application of these approaches to important geochemical questions, relevant NMR and other experimental studies, and application of computational modeling methods to understanding the experimental results. The combination of computational modeling and experimental approaches is proving highly effective in addressing otherwise intractable problems. In 2006-2007 we have significantly advanced in new, highly promising research directions along with completion of on-going projects and final publication of work completed in previous years. New computational directions are focusing on modeling proton exchange reactions in aqueous solutions using ab initio molecular dynamics (AIMD), metadynamics (MTD), and empirical valence bond (EVB) approaches. Proton exchange is critical to understanding the structure, dynamics, and reactivity at mineral-water interfaces and for oxy-ions in solution, but has traditionally been difficult to model with molecular dynamics (MD). Our ultimate objective is to develop this capability, because MD is much less computationally demanding than quantum-chemical approaches. We have also extended our previous MD simulations of metal binding to natural organic matter (NOM) to a much longer time scale (up to 10 ns) for

  2. CME Dynamics Using STEREO and LASCO Observations: The Relative Importance of Lorentz Forces and Solar Wind Drag

    Science.gov (United States)

    Sachdeva, Nishtha; Subramanian, Prasad; Vourlidas, Angelos; Bothmer, Volker

    2017-09-01

    We seek to quantify the relative contributions of Lorentz forces and aerodynamic drag on the propagation of solar coronal mass ejections (CMEs). We use Graduated Cylindrical Shell (GCS) model fits to a representative set of 38 CMEs observed with the Solar and Heliospheric Observatory (SOHO) and the Solar and Terrestrial Relations Observatory (STEREO) spacecraft. We find that the Lorentz forces generally peak between 1.65 and 2.45 R⊙ for all CMEs. For fast CMEs, Lorentz forces become negligible in comparison to aerodynamic drag as early as 3.5 - 4 R⊙. For slow CMEs, however, they become negligible only by 12 - 50 R⊙. For these slow events, our results suggest that some of the magnetic flux might be expended in CME expansion or heating. In other words, not all of it contributes to the propagation. Our results are expected to be important in building a physical model for understanding the Sun-Earth dynamics of CMEs.

  3. Bubble column reactor fluid dynamic study at pilot plant scale for residue and extra heavy crude oil upgrading technology

    Energy Technology Data Exchange (ETDEWEB)

    Sardella, R.; Medina, H. [Infrastructure and Upgrading Department PDVSA-Intevep (Venezuela); Zacarias, L.; Paiva, M. [Refining Department. PDVSA-Intevep (Venezuela)

    2011-07-01

    Bubble column reactors are used in several applications because of their simplicity and low cost; a new technology was developed to convert extra heavy crude oil into upgraded crude using a bubble column reactor. To design this kind of reactor, a lot of parameters like flow regime, gas hold up and dispersion coefficient have to be taken into account. This study aimed at determining the fluid dynamic behaviour of a bubble column working under Aquaconversion operating conditions. Experiments were undertaken on air-tap water and air-light oil systems under atmospheric conditions with various gas superficial velocities and liquid flowrates. Results showed that gas hold up increases with superficial gas velocity but is independent of liquid flowrate and that both systems tested work at the same flow regimes. This paper showed that under the experimental conditions used, this reactor tends to be a complete mixing reactor.

  4. Inter-domain communication mechanisms in an ABC importer: a molecular dynamics study of the MalFGK2E complex.

    Science.gov (United States)

    Oliveira, A Sofia F; Baptista, António M; Soares, Cláudio M

    2011-08-01

    ATP-Binding Cassette transporters are ubiquitous membrane proteins that convert the energy from ATP-binding and hydrolysis into conformational changes of the transmembrane region to allow the translocation of substrates against their concentration gradient. Despite the large amount of structural and biochemical data available for this family, it is still not clear how the energy obtained from ATP hydrolysis in the ATPase domains is "transmitted" to the transmembrane domains. In this work, we focus our attention on the consequences of hydrolysis and inorganic phosphate exit in the maltose uptake system (MalFGK(2)E) from Escherichia coli. The prime goal is to identify and map the structural changes occurring during an ATP-hydrolytic cycle. For that, we use extensive molecular dynamics simulations to study three potential intermediate states (with 10 replicates each): an ATP-bound, an ADP plus inorganic phosphate-bound and an ADP-bound state. Our results show that the residues presenting major rearrangements are located in the A-loop, in the helical sub-domain, and in the "EAA motif" (especially in the "coupling helices" region). Additionally, in one of the simulations with ADP we were able to observe the opening of the NBD dimer accompanied by the dissociation of ADP from the ABC signature motif, but not from its corresponding P-loop motif. This work, together with several other MD studies, suggests a common communication mechanism both for importers and exporters, in which ATP-hydrolysis induces conformational changes in the helical sub-domain region, in turn transferred to the transmembrane domains via the "coupling helices".

  5. Inter-domain communication mechanisms in an ABC importer: a molecular dynamics study of the MalFGK2E complex.

    Directory of Open Access Journals (Sweden)

    A Sofia F Oliveira

    2011-08-01

    Full Text Available ATP-Binding Cassette transporters are ubiquitous membrane proteins that convert the energy from ATP-binding and hydrolysis into conformational changes of the transmembrane region to allow the translocation of substrates against their concentration gradient. Despite the large amount of structural and biochemical data available for this family, it is still not clear how the energy obtained from ATP hydrolysis in the ATPase domains is "transmitted" to the transmembrane domains. In this work, we focus our attention on the consequences of hydrolysis and inorganic phosphate exit in the maltose uptake system (MalFGK(2E from Escherichia coli. The prime goal is to identify and map the structural changes occurring during an ATP-hydrolytic cycle. For that, we use extensive molecular dynamics simulations to study three potential intermediate states (with 10 replicates each: an ATP-bound, an ADP plus inorganic phosphate-bound and an ADP-bound state. Our results show that the residues presenting major rearrangements are located in the A-loop, in the helical sub-domain, and in the "EAA motif" (especially in the "coupling helices" region. Additionally, in one of the simulations with ADP we were able to observe the opening of the NBD dimer accompanied by the dissociation of ADP from the ABC signature motif, but not from its corresponding P-loop motif. This work, together with several other MD studies, suggests a common communication mechanism both for importers and exporters, in which ATP-hydrolysis induces conformational changes in the helical sub-domain region, in turn transferred to the transmembrane domains via the "coupling helices".

  6. Comparison of bacterial community structure and dynamics during the thermophilic composting of different types of solid wastes: anaerobic digestion residue, pig manure and chicken manure.

    Science.gov (United States)

    Song, Caihong; Li, Mingxiao; Jia, Xuan; Wei, Zimin; Zhao, Yue; Xi, Beidou; Zhu, Chaowei; Liu, Dongming

    2014-09-01

    This study investigated the impact of composting substrate types on the bacterial community structure and dynamics during composting processes. To this end, pig manure (PM), chicken manure (CM), a mixture of PM and CM (PM + CM), and a mixture of PM, CM and anaerobic digestion residue (ADR) (PM + CM + ADR) were selected for thermophilic composting. The bacterial community structure and dynamics during the composting process were detected and analysed by polymerase chain reaction-denaturing gradient gel electrophoresis (DGGE) coupled with a statistic analysis. The physical-chemical analyses indicated that compared to single-material composting (PM, CM), co-composting (PM + CM, PM + CM + ADR) could promote the degradation of organic matter and strengthen the ability of conserving nitrogen. A DGGE profile and statistical analysis demonstrated that co-composting, especially PM + CM + ADR, could improve the bacterial community structure and functional diversity, even in the thermophilic stage. Therefore, co-composting could weaken the screening effect of high temperature on bacterial communities. Dominant sequencing analyses indicated a dramatic shift in the dominant bacterial communities from single-material composting to co-composting. Notably, compared with PM, PM + CM increased the quantity of xylan-degrading bacteria and reduced the quantity of human pathogens.

  7. Contact structure, mobility, environmental impact and behaviour: the importance of social forces to infectious disease dynamics and disease ecology.

    Science.gov (United States)

    Arthur, Ronan F; Gurley, Emily S; Salje, Henrik; Bloomfield, Laura S P; Jones, James H

    2017-05-05

    Human factors, including contact structure, movement, impact on the environment and patterns of behaviour, can have significant influence on the emergence of novel infectious diseases and the transmission and amplification of established ones. As anthropogenic climate change alters natural systems and global economic forces drive land-use and land-cover change, it becomes increasingly important to understand both the ecological and social factors that impact infectious disease outcomes for human populations. While the field of disease ecology explicitly studies the ecological aspects of infectious disease transmission, the effects of the social context on zoonotic pathogen spillover and subsequent human-to-human transmission are comparatively neglected in the literature. The social sciences encompass a variety of disciplines and frameworks for understanding infectious diseases; however, here we focus on four primary areas of social systems that quantitatively and qualitatively contribute to infectious diseases as social-ecological systems. These areas are social mixing and structure, space and mobility, geography and environmental impact, and behaviour and behaviour change. Incorporation of these social factors requires empirical studies for parametrization, phenomena characterization and integrated theoretical modelling of social-ecological interactions. The social-ecological system that dictates infectious disease dynamics is a complex system rich in interacting variables with dynamically significant heterogeneous properties. Future discussions about infectious disease spillover and transmission in human populations need to address the social context that affects particular disease systems by identifying and measuring qualitatively important drivers.This article is part of the themed issue 'Opening the black box: re-examining the ecology and evolution of parasite transmission'.

  8. The Crystal Structure of the Fifth Scavenger Receptor Cysteine-Rich Domain of Porcine CD163 Reveals an Important Residue Involved in Porcine Reproductive and Respiratory Syndrome Virus Infection.

    Science.gov (United States)

    Ma, Hongfang; Jiang, Longguang; Qiao, Songlin; Zhi, Yubao; Chen, Xin-Xin; Yang, Yanyan; Huang, Xiaojing; Huang, Mingdong; Li, Rui; Zhang, Gai-Ping

    2017-02-01

    Porcine reproductive and respiratory syndrome (PRRS) has become an economically critical factor in swine industry since its worldwide spread in the 1990s. Infection by its causative agent, PRRS virus (PRRSV), was proven to be mediated by an indispensable receptor, porcine CD163 (pCD163), and the fifth scavenger receptor cysteine-rich domain (SRCR5) is essential for virus infection. However, the structural details and specific residues of pCD163 SRCR5 involved in infection have not been defined yet. In this study, we prepared recombinant pCD163 SRCR5 in Drosophila melanogaster Schneider 2 (S2) cells and determined its crystal structure at a high resolution of 2.0 Å. This structure includes a markedly long loop region and shows a special electrostatic potential, and these are significantly different from those of other members of the scavenger receptor cysteine-rich superfamily (SRCR-SF). Subsequently, we carried out structure-based mutational studies to identify that the arginine residue at position 561 (Arg561) in the long loop region is important for PRRSV infection. Further, we showed Arg561 probably takes effect on the binding of pCD163 to PRRSV during virus invasion. Altogether the current work provides the first view of the CD163 SRCR domain, expands our knowledge of the invasion mechanism of PRRSV, and supports a molecular basis for prevention and control of the virus. PRRS has caused huge economic losses to pig farming. The syndrome is caused by PRRSV, and PRRSV infection has been shown to be mediated by host cell surface receptors. One of them, pCD163, is especially indispensable, and its SRCR5 domain has been further demonstrated to play a significant role in virus infection. However, its structural details and the residues involved in infection are unknown. In this study, we determined the crystal structure of pCD163 SRCR5 and then carried out site-directed mutational studies based on the crystal structure to elucidate which residue is important. Our

  9. Molecular Dynamics Modeling of the Effect of Axial and Transverse Compression on the Residual Tensile Properties of Ballistic Fiber

    Directory of Open Access Journals (Sweden)

    Sanjib C. Chowdhury

    2017-02-01

    Full Text Available Ballistic impact induces multiaxial loading on Kevlar® and polyethylene fibers used in protective armor systems. The influence of multiaxial loading on fiber failure is not well understood. Experiments show reduction in the tensile strength of these fibers after axial and transverse compression. In this paper, we use molecular dynamics (MD simulations to explain and develop a fundamental understanding of this experimental observation since the property reduction mechanism evolves from the atomistic level. An all-atom MD method is used where bonded and non-bonded atomic interactions are described through a state-of-the-art reactive force field. Monotonic tension simulations in three principal directions of the models are conducted to determine the anisotropic elastic and strength properties. Then the models are subjected to multi-axial loads—axial compression, followed by axial tension and transverse compression, followed by axial tension. MD simulation results indicate that pre-compression distorts the crystal structure, inducing preloading of the covalent bonds and resulting in lower tensile properties.

  10. 螺螨酯在柑橘和土壤中残留及消解动态%Residue and Dissipation Dynamics of Spirodiclofen in Orange and Soil

    Institute of Scientific and Technical Information of China (English)

    谢莉; 杨仁斌; 傅强; 肖少怀; 柳王荣

    2012-01-01

    In order to evaluate environmental safety of spirodiclofen in orange and soil, establish the use standard in orange, the field trials on the dissipation and final residue of spirodiclofen were carried out in Changsha, Hangzhou during 2010-2011. The results showed that, the average recoveries of spirodiclofen from orange and soil sample at three spiked levels of 0.05 mg/kg, 0.5 mg/kg and 1 mg/kg, ranged from 82.2% to 110% with variation coefficient from 2.55% to 9.84% . Degradation dynamics of spirodiclofen based on first-order reaction dynamic equations in orange and soil, the half-lives of spirodiclofen were 5.18-8.49 days, 5.19-7.85 days. The final residue of spirodiclofen in peel, pulp and soil were not detected (<0.0035 mg/kg), not detected (<0.0035 mg/kg)-0.1978 mg/kg, not detected (<0.0035 mg/kg)-0.2401 mg/kg, lower than the provisions of maximum residue limit of 0.5 mg/kg in EU. According to application dosage and times of spirodiclofen for reference the maximum residue limits (0.5 mg/kg) by EU, orange was safe to eat after spirodiclofen being sprayed after 20 days.%为了评价螺螨酯在柑橘和土壤中的安全性,建立其在柑橘中的使用规范,于2010、2011年在长沙、杭州进行田间试验,研究螺螨酯在柑橘和土壤中的最终残留和消解动态.结果表明:螺螨酯在柑橘和土壤中的添加回收率为82.2%~110%,相对标准偏差为2.55%~9.84%;螺螨酯在柑橘和土壤中的最低检出限均为0.0035 mg/kg.螺螨酯在柑橘和土壤中的消解均符合一级动力学方程,消解半衰期分别为5.18~8.49天,5.19~7.85天.螺螨酯最终残留在橘肉、橘皮和土壤中的质量分数分别是未检出(<0.0035 mg/kg),未检出(<0.0035 mg/kg)~0.1978 mg/kg,未检出(<0.0035 mg/kg)~0.2401 mg/kg,均低于欧盟规定的在柑橘上的最大残留限量0.5 mg/kg.参考欧盟制定的柑橘中螺螨酯的最大残留限量(0.5 mg/kg),按推荐施药剂量和次数施用螺螨酯,

  11. Product PCNPsurv or the "reduced" evaporation residue cross section σER/σfusion for "hot" fusion reactions studied with the dynamical cluster-decay model

    Science.gov (United States)

    Chopra, Sahila; Kaur, Arshdeep; Hemdeep, Gupta, Raj K.

    2016-04-01

    The product PCNPsurv of compound nucleus (CN) fusion probability PCN and survival probability Psurv is calculated to determine the reduced evaporation residue cross section σER/σfusion , denoted σERreduced, with (total) fusion cross section σfusion given as a sum of CN-formation cross section σCN and non-CN cross section σnCN for each reaction, where σCN is the sum of evaporation residue cross section σER and fusion-fission cross section σff and σnCN, if not measured, is estimated empirically as the difference between measured and calculated σfusion. Our calculations of PCN and Psurv, based on the dynamical cluster-decay model, were successfully made for some 17 "hot" fusion reactions, forming different CN of mass numbers ACN˜100 -300 , with deformations of nuclei up to hexadecapole deformations and "compact" orientations for both coplanar (Φc=0∘ ) and noncoplanar (Φc≠0∘ ) configurations, using various different nuclear interaction potentials. Interesting variations of σERreduced with CN excitation energy E*, fissility parameter χ , CN mass ACN, and Coulomb parameter Z1Z2 show that, independent of entrance channel, different isotopes of CN, and nuclear interaction potentials used, the dominant quantity in the product is Psurv, which classifies all the studied CN into three groups of weakly fissioning, radioactive, and strongly fissioning superheavy nuclei, with relative magnitudes of σERreduced˜1 , ˜10-6 , and ˜10-11 , which, like for PCN, get further grouped in two dependencies of (i) weakly fissioning and strongly fissioning superheavy nuclei decreasing with increasing E* and (ii) radioactive nuclei increasing with increasing E*.

  12. Residual Dynamics of Thiamethoxam in Potato Roots%噻虫嗪种衣剂在马铃薯根中的残留动态分析

    Institute of Scientific and Technical Information of China (English)

    张海英; 陆磊; 胡梅; 郭建国; 刘永刚

    2011-01-01

    An analytical method was developed for determining residues in roots of potatoes grown from the seeds coated with thiamethoxam. This method was characterized by recovery rates between 89.33% and 91.80%, LOD at 0.001 g and sensitivity of 0.001 mg / kg. The residual dynamics of thiamethoxam in potato roots by two different approaches of seed coating was studied in the experiment. The results showed that the degradation rates of thiamethoxam were slow in potato roots by two different approaches of seed coating. The half-lives of thiamethoxam was 17.96 d in roots of potatoes grown from the seeds which were dressed with medicine before cutting, and the half-lives of thiamethoxam was 15.13 d in roots of potatoes from seeds which were cut before dressing with medicine. In a word, thiamethoxam had a long residual activity, but the activity would not exist for a long time in the potato roots.%建立一种高效液相色谱分析方法,用于测定马铃薯根中噻虫嗪种衣剂的残留量,该方法的添加回收率为89.33%~91.80%,最低检出量为0.001 g,最低检出质量分数为0.001 mg/kg。该试验还通过运用两种不同的包衣方式,研究了噻虫嗪在马铃薯根中的残留消解动态。试验结果表明,在两种不同的包衣方式下,噻虫嗪在马铃薯根中的消解速度都较为缓慢,先包衣后切块的半衰期为17.96 d,而先切块后包衣的半衰期为15.13 d,两者持效期都较长,但不会长期存在于马铃薯根中。

  13. Histidine at residue 99 and the transmembrane region of the precursor membrane prM protein are important for the prM-E heterodimeric complex formation of Japanese encephalitis virus.

    Science.gov (United States)

    Lin, Ying-Ju; Wu, Suh-Chin

    2005-07-01

    The formation of the flavivirus prM-E complex is an important step for the biogenesis of immature virions, which is followed by a subsequent cleavage of prM to M protein through cellular protease to result in the production and release of mature virions. In this study, the intracellular formation of the prM-E complex of Japanese encephalitis virus was investigated by baculovirus coexpression of prM and E in trans in Sf9 insect cells as analyzed by anti-E antibody immunoprecipitation and sucrose gradient sedimentation analysis. A series of carboxyl-terminally truncated prM mutant baculoviruses was constructed to demonstrate that the truncations of the transmembrane (TM) region resulted in a reduction of the formation of the stable prM-E complex by approximately 40% for the TM1 (at residues 130 to 147 [prM130-147]) truncation and 20% for TM2 (at prM153-167) truncation. Alanine-scanning site-directed mutagenesis on the prM99-103 region indicated that the His99 residue was the critical prM binding element for stable prM-E heterodimeric complex formation. The single amino acid mutation at the His99 residue of prM abolishing the prM-E interaction was not due to reduced expression or different subcellular location of the mutant prM protein involved in prM-E interactions as characterized by pulse-chase labeling and confocal scanning microscopic analysis. Recombinant subviral particles were detected in the Sf9 cell culture supernatants by baculovirus coexpression of prM and E proteins but not with the prM H99A mutant. Sequence alignment analysis was further conducted with different groups of flaviviruses to show that the prM H99 residues are generally conserved. Our findings are the first report to characterize the minimum binding elements of the prM protein that are involved in prM-E interactions of flaviviruses. This information, concerning a molecular framework for the prM protein, is considered to elucidate the structure/function relationship of the prM-E complex

  14. The importance of using dynamical a-priori profiles for infrared O3 retrievals : the case of IASI.

    Science.gov (United States)

    Peiro, H.; Emili, E.; Le Flochmoen, E.; Barret, B.; Cariolle, D.

    2016-12-01

    MOCAGE+MLS PR than CLIM PR. We found biases of 6% instead of 33% in SH showing that the a priori plays an important role within O3 infrared-retrievals. Improvements of IASI retrievals have been obtained in the free troposphere and low stratosphere, inserting dynamical a priori profiles from a CTM in SOFRID. Possible advancements would be to insert dynamical COV in SOFRID.

  15. Numerical modeling of tides in the Great Bay Estuarine System: dynamical balance and spring-neap residual modulation

    Science.gov (United States)

    McLaughlin, J. W.; Bilgili, A.; Lynch, D. R.

    2003-05-01

    The Great Bay Estuarine System, in New Hampshire, USA, has been the focus area for an attempt to develop a robust finite element method model for estuarine hydrodynamics. Past studies used a nonlinear, time stepping, kinematic model with limited success (Ip et al. Advances in fluid mechanics III, WIT, Southampton (2000) 569; Bilgili et al. J. Geophys. Res. - Oceans 107 (2002); Ertürk et al. Estuar. Coast. Shelf Sci. 47 (1998) 119). We add dynamic physics (that is, local accelerations) for deep-water areas and keep kinematic physics (that is, without local and advective accelerations), with the inclusion of a porous medium beneath the open channel, for shallow and dewatering areas. The choice of which physics set to apply is made on an elemental depth dependent basis. The addition of the local acceleration terms for deep-water areas is seen to greatly improve accuracy in matching of tidal phasing over previous studies. Simulations involving M 2/M 4/M 6 tidal constituents result in strong agreement to observed data from the 1975 Great Bay field program (Swift & Brown, Estuar. Coast. Shelf Sci. 17 (1983) 297), in terms of both tidal heights and cross-section averaged velocities. Comparisons with 10 tidal elevation observation stations and four cross-section averaged current transects show good agreement, displaying average normalized root mean square misfit values of 0.08 and 0.25, respectively. Study of the simulated momentum balance shows the size of the contributions from acceleration terms to be on the order of a third the size of the contributions from the pressure gradient and bottom stress terms. Although relatively small, they are observed to peak at the crucial time of tidal reversal. Application of the model for long-term simulation using an M 2/N 2/S 2 forcing shows the ability to realistically capture the spring-neap cycle. The tidally rectified flow is generally described as a constant spatial pattern with overall amplitude modulation following the

  16. Residue Dynamics of Oxyfluorfen in Garlic and Soil%乙氧氟草醚在大蒜和土壤中的残留动态

    Institute of Scientific and Technical Information of China (English)

    王峰恩; 李瑞菊; 方丽萍; 李腾

    2014-01-01

    To evaluate the environmental pollution and the food safety of applying oxyfluorfen in garlic production , the residue and digestion dynamics of oxyfluorfen in garlic and soil were studied by field experi-ment.The samples were extracted by acetone/ethyl acetate , heated by microwave , purified by Florsil column , and then analyzed by gas chromatograph -mass spectrometer ( GC-MS) .The results showed that the linear relationship of oxyfluorfen in the range of 0 .01 ~1 .0 mg/L was good with the correlation coefficient of 0 .9980 .The fortified recovery in garlic , plants and soil ranged from 85 .2% to 104 .1% with the relative standard deviation (RSD) of 1.8%~9.6%.The residual quantity in garlic plants was too low to observe the digestion dynamic .Whereas , the digestion dynamic in soil was clear .The half-life period was 15 .4~18 .6 days, and the residue was digested more than 90%on the 42th day after application.Spraying 30%oxyfluor-fen and prometryn WP at the dosage of 900 g a.i./hm2 and 1 350 g a.i./hm2 respectively, the residual quan-tities of oxyfluorfen in garlic and garlic sprout were both less than the limit of detection ( LOD) of 0.01 mg/kg, and the maximum residue level (MRL) in Japan and Iarael of 0.05 mg/kg.In conclusion, to control weeds in garlic field, spraying 30%oxyfluorfen and prometryn WP at the dosage of 450~900 g a.i./hm2 be-fore seed germination , the products were safe .%采用田间试验方法研究了乙氧氟草醚在大蒜和土壤中的残留和降解情况,以评价大蒜生产中乙氧氟草醚残留对环境的污染程度以及所得产品的食用安全性。样品经丙酮/乙酸乙酯提取,微波加热处理,弗罗里硅土柱净化,气相色谱-质谱联用仪检测。结果显示,乙氧氟草醚在0.01~1.0 mg/L范围内线性关系良好,相关系数为0.9980,在大蒜及其植株和土壤中的添加回收率为85.2%~104.1%,相对标准偏差为1.8%~9.6%。在大蒜植株中残留量

  17. Residue Dynamics of Mancozeb in Chilli ( Capsicum annuum Linn) and Soil%代森锰锌在辣椒和土壤中的残留动态

    Institute of Scientific and Technical Information of China (English)

    简韬; 杨仁斌; 杨周宁; 付强; 周杨

    2011-01-01

    [目的]研究代森锰锌在辣椒及土壤中的残留动态.[方法]于2008 ~ 2009年在长沙、广州和北京三地分别开展田间施药试验和室内分析试验,研究代森锰锌在辣椒及土壤中的消解动态和最终残留,采用气相色谱法进行定量分析.[结果]研究所用残留分析方法,辣椒和土壤中代森锰锌的平均回收率分别为86.59% ~93.03%、92.57% ~95.14%.代森锰锌在辣椒和土壤中消解较快,其半衰期分别为2.29~4.65 d和4.01 ~4.65 d.在辣椒上使用精甲.霜灵·代森锰锌水分散粒剂,按照推荐使用剂量最多施药3次(每次间隔5d),最后一次施药3d后,采收的辣椒中代森锰锌的残留量均小于2 mg/kg.[结论]研究结果为代森锰锌安全使用标准的制定奠定了基础.%[Objective] The paper was to study the residue dynamics of mancozeb in chilli and soil. [ Method ] Field spraying test and indoor analysis were carried out in three places of Changsha, Guangzhou and Beijing City during 2008 -2009 to study the degradation dynamics and the final residue of mancozeb in chilli and soil, and gas chromatography was used for quantitative analysis. [ Result ] The average recovery rates of mancozeb in chilli and soil were 86.59% -93.03% and 92.57% -95.14% .respectively. Mancozeb had rapid digestion in chilli and soil with the half-life of 2.29 -4. 65 and 4. 01 -4. 65 d, respectively. When metalaxyl-M · mancozeb WDG was used in chilli according to the recommend dosage (spraying for three times at most with the spraying interval of 5 d) ,3 d later after the last spraying,the final residue of mancozeb in chilli collected was less than 2 mg/kg. [ Conclusion ] The result provided basis for preparation of safety standards of mancozeb.

  18. Insight into the interactive residues between two domains of human somatic Angiotensin-converting enzyme and Angiotensin II by MM-PBSA calculation and steered molecular dynamics simulation.

    Science.gov (United States)

    Guan, Shan-shan; Han, Wei-wei; Zhang, Hao; Wang, Song; Shan, Ya-ming

    2016-01-01

    Angiotensin-converting enzyme (ACE), a membrane-bound zinc metallopeptidase, catalyzes the formation of Angiotensin-II (AngII) and the deactivation of bradykinin in the renin-angiotensin-aldosterone and kallikrein-kinin systems. As a hydrolysis product of ACE, AngII is regarded as an inhibitor and displays stronger competitive inhibition in the C-domain than the N-domain of ACE. However, the AngII binding differences between the two domains and the mechanisms behind AngII dissociation from the C-domain are rarely explored. In this work, molecular docking, Molecular Mechanics/Poisson-Boltzmann Surface Area calculation, and steered molecular dynamics (SMD) are applied to explore the structures and interactions in the binding or unbinding of AngII with the two domains of human somatic ACE. Calculated free energy values suggest that the C-domain-AngII complex is more stable than the N-domain-AngII complex, consistent with available experimental data. SMD simulation results imply that electrostatic interaction is dominant in the dissociation of AngII from the C-domain. Moreover, Gln106, Asp121, Glu123, and Tyr213 may be the key residues in the unbinding pathway of AngII. The simulation results in our work provide insights into the interactions between the two domains of ACE and its natural peptide inhibitor AngII at a molecular level. Moreover, the results provide theoretical clues for the design of new inhibitors.

  19. Variation of the residual resistivity ratio of the aluminium stabiliser for the Compact Muon Solenoid (CMS) conductor under dynamic stress at 4.2 K

    CERN Document Server

    Seeber, B; Flükiger, R; Horváth, I L; Neuenschwander, J

    2000-01-01

    Superconducting detector magnets are frequently manufactured with aluminium stabilised NbTi cables. Actually there are two new detectors in fabrication, namely the CMS and the ATLAS detector at CERN in Geneva, Switzerland. For the CMS project we have studied the variation of the residual resistivity ratio (RRR) of high purity aluminium (HPA) (99.998%) under dynamic mechanical stress, applied at 4.2 K, and in a transverse magnetic field of up to 6 T. This information is required for the design of the quench protection system. Because of the mechanical weakness of HPA, a high strength aluminium (HSA) alloy reinforces the CMS-conductor. According to the specification for CMS, the conductor at maximum field is strained up to 0.15%. At this strain the HSA is still in the elastic regime, whereas the HPA is already deformed plastically. Applying a full stress cycle (e.g. loading and unloading of the magnet), the HPA is deformed first under tension and then under compression, resulting in a decrease of the RRR. For m...

  20. Extraction and preconcentration of residual solvents in pharmaceuticals using dynamic headspace-liquid phase microextraction and their determination by gas chromatography-flame ionization detection.

    Science.gov (United States)

    Farajzadeh, Mir Ali; Dehghani, Hamideh; Yadeghari, Adeleh; Khoshmaram, Leila

    2017-02-01

    The present study describes a microextraction and determination method for analyzing residual solvents in pharmaceutical products using dynamic headspace-liquid phase microextraction technique followed by gas chromatography-flame ionization detection. In this method dimethyl sulfoxide (μL level) placed into a GC liner-shaped extraction vessel is used as a collection/extraction solvent. Then the liner is exposed to the headspace of a vial containing the sample solution. The effect of different parameters influencing the microextraction procedure including collection/extraction solvent type and its volume, ionic strength, extraction time, extraction temperature and concentration of NaOH solution used in dissolving the studied pharmaceuticals are investigated and optimized. Under the optimum extraction conditions, the method showed wide linear ranges between 0.5 and 5000 mg L(-1) . The other analytical parameters were obtained in the following ranges: enrichment factors 240-327, extraction recoveries 72-98% and limits of detection 0.1-0.8 mg L(-1) in solution and 0.6-3.2 μg g(-1) in solid. Relative standard deviations for the extraction of 100 mg L(-1) of each analyte were obtained in the ranges of 4-7 and 5-8% for intra-day (n = 6) and inter-day (n = 4) respectively. Finally the target analytes were determined in different samples such as erythromycin, azithromycin, cefalexin, amoxicillin and co-amoxiclav by the proposed method.

  1. The importance of large benthic foraminifera to reef island sediment budget and dynamics at Raine Island, northern Great Barrier Reef

    Science.gov (United States)

    Dawson, John L.; Smithers, Scott G.; Hua, Quan

    2014-10-01

    Low-lying reef islands are among the most vulnerable environments on earth to anthropogenic-induced climate change and sea-level rise over the next century because they are low, composed of unconsolidated sediment that is able to be mobilised by waves and currents, and depend on sediments supplied by reef organisms that are particularly sensitive to environmental changes (e.g. ocean temperatures and chemistry). Therefore, the spatial and temporal links between active carbonate production and island formation and dynamics are fundamental to predicting future island resilience, yet remain poorly quantified. In this paper we present results of a detailed geomorphological and sedimentological study of a reef and sand cay on the northern Great Barrier Reef. We provide an empirical investigation of the temporal linkages between sediment production and reef island development using a large collection of single grain AMS 14C dates. Large benthic foraminifera (LBF) are the single most important contributor to contemporary island sand mass (47%; ranging from 36% to 63%) at Raine Island, reflecting rapid rates of sediment production and delivery. Standing stock data reveal extremely high production rates on the reef (1.8 kg m- 2 yr- 1), while AMS 14C dates of single LBF tests indicate rapid rates of sediment transferral across the reef. We also demonstrate that age is statistically related to preservation and taphonomic grade (severely abraded tests > moderately abraded tests > pristine tests). We construct a contemporary reef and island sediment budget model for Raine Island that shows that LBF (Baculogypsina, Marginopora and Amphistegina) contribute 55% of the sediment produced on the reef annually, of which a large proportion (54%) contribute to the net annual accretion of the island. The tight temporal coupling between LBF growth and island sediment supply combined with the sensitivity of LBF to bleaching and ocean acidification suggests that islands dominated by LBF are

  2. Analysis of the residual dynamics of chlorothalonil and myclobutanil in bananas%百菌清、腈菌唑在香蕉上的残留动态

    Institute of Scientific and Technical Information of China (English)

    郭建辉; 蔡恩兴; 陈丽萍; 杨淑娟

    2011-01-01

    The thesis is entitled to make clear the residual dynamic of chlorothalonil and myclobutanil in bananas in hoping to control the likely disease in the fruit trees. As a kind of main tropic and sub-tropic fruit growing in Zhangzhou, Fujian, bananas should be protected from being harmed by the drug-residuals like chlorothalonil and myclobutanil. For this purpose, we have studied the residual dynamics of chlorothalonil and myclobutanil in bananas by using a method of GC and field experiment. Results of our studies indicated that the methods here used were simple and convenient. The analysis of samples can satisfy the actual needs when we determine the residue of chlorothalonil with GB/T 5009.105-2003 and myclobutanil with GB/T 5009.146-2003. The original sediment of chlorothalonil in bananas had been found more than that of myclobutanil, which was closely related to their application dosage for the same pesticide. On the other hand, chlorothalonil proved to be faster dissipated than myclobutanil during the first 14d after application, with their dissipation rate going up to the almost same level 14 d to 21 d later. In addition, the dissipation of chlorothalonil and myclobutanil in bananas proved to be well fitted by the first-order kinetics, with the correlation coefficient standing between 0.942 8 to 0.998 0 (p < 0.01). The experimental results also showed that the degradation coefficient ( | k | ) of chlorothalonil was 0.220 45 ± 0.009 15, with T1/2 being in a range from 3.1 d to 3.3 d, while T0.99 in a range from 20.1 d to 21.7 d. On the contrary, myclobutanil had the | k | , T1/2 and T0.99 parameters of myclobutanil of 0.170 3 ± 0.000 1, 4.1 d and 27.1 d , respectively. Therefore, the chlorothalonil and myclobutanil residues in the banana could hardly be detected 55 - 68 d after the second application.%为了科学、安全地使用百菌清、腈菌唑防治香蕉病害,采用气相色谱法及田间试验方法研究百菌清、腈菌唑在香蕉上的残

  3. Study on properties of residue-residue contacts in protein

    Institute of Scientific and Technical Information of China (English)

    王向红; 柯见洪; 郑亦庄; 陈爱; 徐银香

    2004-01-01

    Residue-residue contacts are very important in forming protein structure. In this work, we calculated the average probability of residue-residue contacts in 470 globular proteins and analyzed the distribution of contacts in the different interval of residues using Contacts of Structural Units (CSU) and Structural Classification (SCOP) software. It was found that the relationship between the average probability PL and the residue distance L for four structural classes of proteins could be expressed as lgPL=a+b×L, where a and b are coefficients. We also discussed the connection between two aspects of proteins which have equal array residue number and found that the distribution probability was stable (or un-stable) if the proteins had the same (or different) comnact (for examnle svnthase) in the same structural class.

  4. Study on properties of residue-residue contacts in protein

    Institute of Scientific and Technical Information of China (English)

    王向红; 柯见洪; 郑亦庄; 陈爱; 徐银香

    2004-01-01

    Residue-residue contacts are very important in forming protein structure. In this work, we calculated theaverage probability of residue-residue contacts in 470 globular proteins and analyzed the distribution of contacts in thedifferent interval of residues using Contacts of Structural Units (CSU) and Structural Classification (SCOP) software. Itwas found that the relationship between the average probability -PL and the residue distance L for four structural classes ofproteins could be expressed as lgPL=a+b×L, where a and b are coefficients. We also discussed the connection between twoaspects of proteins which have equal array residue number and found that the distribution probability was stable (or un-stable) if the proteins had the same (or different) compact (for example synthase) in the same structural class.

  5. The importance of socio-ecological system dynamics in understanding adaptation to global change in the forestry sector.

    Science.gov (United States)

    Blanco, Victor; Brown, Calum; Holzhauer, Sascha; Vulturius, Gregor; Rounsevell, Mark D A

    2017-07-01

    Adaptation is necessary to cope with or take advantage of the effects of climate change on socio-ecological systems. This is especially important in the forestry sector, which is sensitive to the ecological and economic impacts of climate change, and where the adaptive decisions of owners play out over long periods of time. Relatively little is known about how successful these decisions are likely to be in meeting demands for ecosystem services in an uncertain future. We explore adaptation to global change in the forestry sector using CRAFTY-Sweden; an agent-based model that represents large-scale land-use dynamics, based on the demand and supply of ecosystem services. Future impacts and adaptation within the Swedish forestry sector were simulated for scenarios of socio-economic change (Shared Socio-economic Pathways) and climatic change (Representative Concentration Pathways, for three climate models), between 2010 and 2100. Substantial differences were found in the competitiveness and coping ability of land owners implementing different management strategies through time. Generally, multi-objective management was found to provide the best basis for adaptation. Across large regions, however, a combination of management strategies was better at meeting ecosystem service demands. Results also show that adaptive capacity evolves through time in response to external (global) drivers and interactions between individual actors. This suggests that process-based models are more appropriate for the study of autonomous adaptation and future adaptive and coping capacities than models based on indicators, discrete time snapshots or exogenous proxies. Nevertheless, a combination of planned and autonomous adaptation by institutions and forest owners is likely to be more successful than either group acting alone. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Drought and Recovery: Independently Regulated Processes Highlighting the Importance of Protein Turnover Dynamics and Translational Regulation in Medicago truncatula.

    Science.gov (United States)

    Lyon, David; Castillejo, Maria Angeles; Mehmeti-Tershani, Vlora; Staudinger, Christiana; Kleemaier, Christoph; Wienkoop, Stefanie

    2016-06-01

    Climate change in conjunction with population growth necessitates a systems biology approach to characterize plant drought acclimation as well as a more thorough understanding of the molecular mechanisms of stress recovery. Plants are exposed to a continuously changing environment. Extremes such as several weeks of drought are followed by rain. This requires a molecular plasticity of the plant enabling drought acclimation and the necessity of deacclimation processes for recovery and continuous growth.During drought stress and subsequent recovery, the metabolome and proteome are regulated through a sequence of molecular processes including synthesis and degradation and molecular interaction networks are part of this regulatory process. In order to study this complex regulatory network, a comprehensive analysis is presented for the first time, investigating protein turnover and regulatory classes of proteins and metabolites during a stress recovery scenario in the model legume Medicago truncatula The data give novel insights into the molecular capacity and differential processes required for acclimation and deacclimation of severe drought stressed plants.Functional cluster and network analyses unraveled independent regulatory mechanisms for stress and recovery with different dynamic phases that during the course of recovery define the plants deacclimation from stress. The combination of relative abundance levels and turnover analysis revealed an early transition phase that seems key for recovery initiation through water resupply and is independent from renutrition. Thus, a first indication for a metabolite and protein-based load capacity was observed necessary for the recovery from drought, an important but thus far ignored possible feature toward tolerance. The data indicate that apart from the plants molecular stress response mechanisms, plasticity may be related to the nutritional status of the plant prior to stress initiation. A new perspective and possible new

  7. 旱地土壤中残留肥料氮的动向及作物有效性%Dynamics and Availability to Crops of Residual Fertilizer Nitrogen in Upland Soil

    Institute of Scientific and Technical Information of China (English)

    王西娜; 王朝辉; 李华; 王荣辉; 谭军利; 李生秀

    2016-01-01

    Objective]Nitrogen is one of the most important and essential elements for growth of crops. Reasonable application of nitrogen fertilizer may promote crop growth and increase its yield,while excessive N fertilization may not only inhibit crop growth,but also leave a large amount of fertilizer nitrogen(N) in the soil as residue,which disturbs balance of soil nutrients and poses a potential threat to the ecological environment. So,it is necessary to study dynamics and availability to crops of the residual N to provide a theoretical basis for rationalizing N fertilization,improving N use efficiency and reducing fertilizer N loss.[Method]To that end,a 4-year stationary field experiment was carried out on a winter wheat and summer maize rotation system,using15N-tracing technique. During the first cycle of the winter wheat and summer maize rotation,240 kg hm-2 of nitrogen was applied in the form of15N-laballed urea in all the plots before winter wheat was sown,in order to make a background of high N residual,and in the following summer maize season,the plots were divided into two groups applied with 0 and 120 kg hm-2 of ordinary urea,separately, at the prolonging stage of the crop to explore effect of N fertilizer application on fertilizer N residue in the soil. During the following three cycles of the rotation,no N fertilizer was applied for analysis of dynamic and availability to the crops of the residual fertilizer N in the soil.[Result]Results show that residue of the15N-laballed N fertilizer that was applied before sowing of winter wheat during the first cycle of the rotation, was found throughout the whole soil profiles of 0~200 cm,after the crop was harvested,and most of that accumulated in the 0~40 cm soil layers. The residue amounted to 200.9 kg hm-2 in total,accounting for 83.7% of the total N fertilizer applied. In the subsequent summer maize growth season,the amount of residual fertilizer N first dropped rapidly,and then declined slowly with the season going

  8. Microchannel-induced change of chemical wave propagation dynamics: importance of ratio between the inlet and the channel sizes.

    Science.gov (United States)

    Nabika, Hideki; Sato, Mami; Unoura, Kei

    2013-01-07

    The ability to control chemical wave propagation dynamics could stimulate the science and technology of artificial and biological spatiotemporal oscillating phenomena. In contrast to the conventional chemical approaches to control the wave front dynamics, here we report a physical approach to tune the propagation dynamics under the same chemical conditions. By using well-designed microchannels with different channel widths and depths, the propagation velocity was successfully controlled based on two independent effects: (i) a transition in the proton diffusion mode and (ii) the formation of a slanted wave front. Numerical analysis yielded a simple relationship between the propagation velocity and the microchannel configuration, which offers a simple and general way of controlling chemical wave propagation.

  9. [Importance, especially in aeronautics, of color perception tests under dynamic conditions. Study of a suitable experimental apparatus].

    Science.gov (United States)

    Linzi, S; Modugno, G C; Bollini, M

    1977-12-15

    Following a review of the most recent opinion on the physiology of colour vision, a device for examining it in dynamic, i.e. real-life conditions is described. The apparatus consist of two projectors which flash two absolutely identical pictures on to the screen, one of them is upside down. It appears at fixed but adjustable intervals so that the exposure time of the intelligible image can be varied. Subjects were also controlled with Ishihara charts and Nägel anomaloscope. The results are compared and point to the higher sensitivity of the dynamic test to even slight degrees of dyschromatopsia.

  10. Structural and Functional Importance of Transmembrane Domain 3 (TM3) in the Aspartate:Alanine Antiporter AspT: Topology and Function of the Residues of TM3 and Oligomerization of AspT▿

    OpenAIRE

    Nanatani, Kei; Maloney, Peter C.; Abe, Keietsu

    2009-01-01

    AspT, the aspartate:alanine antiporter of Tetragenococcus halophilus, a membrane protein of 543 amino acids with 10 putative transmembrane (TM) helices, is the prototype of the aspartate:alanine exchanger (AAE) family of transporters. Because TM3 (isoleucine 64 to methionine 85) has many amino acid residues that are conserved among members of the AAE family and because TM3 contains two charged residues and four polar residues, it is thought to be located near (or to form part of) the substrat...

  11. Critical analysis of the current approaches to modelling educational effectiveness : The importance of establishing a dynamic model

    NARCIS (Netherlands)

    Creemers, B. P. M.; Kyriakides, L.

    2006-01-01

    Researchers in the area of educational effectiveness should attempt to develop a new theoretical framework. A critical analysis of the current models of educational effectiveness research is provided and reveals that a dynamic model of effectiveness must: (a) be multilevel in nature, (b) be based on

  12. The relative importance of fertilization and soil erosion on C-dynamics in agricultural landscapes of NE Germany

    Science.gov (United States)

    Pohl, Madlen; Hoffmann, Mathias; Hagemann, Ulrike; Jurisch, Nicole; Remus, Rainer; Sommer, Michael; Augustin, Jürgen

    2016-04-01

    The hummocky ground moraine landscape of north-east Germany is characterized by distinct small-scale soil heterogeneity on the one hand, and intensive energy crop cultivation on the other. Both factors are assumed to significantly influence gaseous C exchange, and thus driving the dynamics of soil organic carbon stocks in terrestrial, agricultural ecosystems. However, it is not yet clear to which extent fertilization and soil erosional status influence soil C dynamics and whether one of these factors is more relevant than the other. We present seasonal and dynamic soil C balances of biogas maize for the growing season 2011, recorded at different sites located within the CarboZALF experimental area. The sites differ regarding soils (non-eroded Albic Luvisols (Cutanic), extremely eroded Calcaric Regosol and depositional Endogleyic Colluvic Regosol,) and applied fertilizer (100% mineral N fertilizer, 50% mineral and 50% N organic fertilizer, 100% organic N fertilizer). Fertilization treatments were established on the Albic Luvisol (Cutanic). Net-CO2-exchange (NEE) and ecosystem respiration (Reco) were measured every four weeks using a dynamic flow-through non-steady-state closed manual chamber system. Gap filling was performed based on empirical temperature and PAR dependency functions to derive daily NEE values. At the same time, daily above-ground biomass production (NPP) was estimated based on biomass samples and final harvest, using a sigmoidal growth function. In a next step, dynamic soil C balances were generated as the balance of daily NEE and NPP considering the initial C input due to N fertilizers. The resulted seasonal soil C balances varied from strong C losses at the Endogleyic Colluvic Regosol (602 g C m-2) to C gains at the Calcaric Regosol (-132 g C m-2). In general, soils exerted a stronger impact on seasonal and dynamic C balances compared to differences in applied N fertilizer. There are indications that inter-annual variations in climate conditions

  13. The importance of tides for sediment dynamics in the deep sea—Evidence from the particulate-matter tracer 234Th in deep-sea environments with different tidal forcing

    Science.gov (United States)

    Peine, Florian; Turnewitsch, Robert; Mohn, Christian; Reichelt, Theresa; Springer, Barbara; Kaufmann, Manfred

    2009-07-01

    Key aspects of deep-ocean fluid dynamics such as basin-scale (residual) and tidal flow are believed to have changed over glacial/interglacial cycles, with potential relevance for climatic change. To constrain the mechanistic links, magnitudes and temporal succession of events analyses of sedimentary paleo-records are of great importance. Efforts have been underway for some time to reconstruct residual-flow patterns from sedimentary records. Attempts to reconstruct tidal flow characteristics from deep-sea sediment deposits, however, are at a very early stage and first require a better understanding of the reflection of modern tides in sediment dynamics. In this context internal (baroclinic) tides, which are formed by the surface (barotropic) tide interacting with seafloor obstacles, are believed to play a particularly important role. Here we compare two modern deep-sea environments with respect to the effect of tides on sediment dynamics. Both environments are influenced by kilometre-scale topographic features but with vastly different tidal forcing: (1) two sites in the Northeast Atlantic (NEA) being surrounded by, or located downstream of, fields of short seamounts (maximum barotropic tidal current velocities ˜5 cm s -1); and (2) a site next to the Anaximenes seamount in the Eastern Mediterranean (EMed) (maximum barotropic tidal current velocities ˜0.5 cm s -1). With respect to other key fluid-dynamical parameters both environments are very similar. Signals of sedimentary particle dynamics, as influenced by processes taking place in the bottom boundary layer, were traced by the vertical water-column distribution of radioactive disequilibria (daughter/parent activity ratios≠1) between the naturally occurring, short-lived (half-life: 24.1 d) particulate-matter tracer 234Th relative to its very long-lived and non-particle-reactive parent nuclide 238U. Activity ratios of 234Th/ 238Ucurrent velocities near the seafloor across the critical current velocity threshold

  14. A free-interface component mode synthesis method based on residual dynamic flexibility%实验模型和有限元模型的混合建模方法

    Institute of Scientific and Technical Information of China (English)

    董兴建; 孟光

    2009-01-01

    给出了更容易由实验测量的基于剩余动柔度的剩余惯性释放附着模态的定义式,通过部分忽略高阶截断模态的动态效应,给出了剩余质量和剩余刚度的近似表达式,简化了子结构的实验建模过程.提出了基于自由界面模态综合法的实验模型和有限元分析模型的混合建模方法.数值计算表明,基于剩余动柔度的剩余惯性释放附着模态更容易通过实验获得,而对剩余质量和剩余刚度的近似处理并不影响模态综合的精度.%Based on residual dynamic flexibility, a new definition of the inertia relief attachment mode was pro- posed. The approximated representations of residual mass and residual stiffness were deduced by partly ignoring the dy- namic effects of the truncated modes. A free-interface component mode synthesis method was used to set up the dynamic model of a full structure by coupling the experimental model of component A and the finite element model of component B. Finally, numerical examples demonstrated the validity and efficiency of the proposed method. Furthermore, the results in- dicated that the influence of the residual mass and residual stiffness on the accuracy of the final results could be neglected.

  15. 甲萘威在棉花和土壤中的残留和消解动态%Residue Dynamics of Carbaryl in Cotton and Soil

    Institute of Scientific and Technical Information of China (English)

    马婧玮; 李通; 张军锋; 周玲; 司敬沛; 吴绪金

    2014-01-01

    In order to provide scientific basis for the safe use of carbaryl on cotton, the degradation dynamics of carbaryl in cotton and soil were studied by LC-MS/MS. The sample was extracted with methanol + dichloromethane (volume ratio of 1:99), cleaned up by amino solid phase extraction column, then determined by LC-MS/MS. The results showed that the half-lives of carbaryl in cotton leaf and soil were 1.1-1.9 days and 4.3-6.2 days, respectively. The final residues in cotton seed were all under 0.023 mg/kg. The results suggested that metaldehyde + carbaryl 30% GR could be used in cotton field at most one time and the pre-harvest interval should be 7 days.%采用液相色谱-串联质谱法(LC-MS/MS)研究了甲萘威在棉花和土壤中的残留消解动态,为棉花上甲萘威的安全使用提供科学依据。样品经甲醇+二氯甲烷(体积比1∶99)提取,氨基固相萃取柱净化,后经LC-MS/MS测定其残留量。甲萘威在棉叶上的半衰期为1.1~1.9 d;在土壤中的半衰期为4.3~6.2 d。试验条件下,甲萘威在收获前14 d、收获前7 d、收获期棉籽中的残留量≤0.023 mg/kg。建议30%聚醛·甲萘威颗粒剂在推荐剂量下最多施药1次,采收间隔期为7 d。

  16. 吡虫啉在稻田水环境中的残留动态%Dynamics of Imidacloprid Residue in Paddy-field Water Environment

    Institute of Scientific and Technical Information of China (English)

    郑岚; 王梅; 段劲生; 胡本进; 孙明娜; 张勇; 高同春

    2011-01-01

    [ Objective] The dynamics of imidacloprid residue in paddy-field water environment by HPLC was studied in this paper. [ Method]Imidacloprid in the samples was extracted with dichloromethane and detected by HPLC with UV. [ Result ] The average of recoveries were ranged from 89.69% to 92.06%, the standard deviations were from 3.01% to 3.73%, and the coefficients of variation were from 3.79% to 4.46%. The minmium detectable amount of imidacloprid was 1.0 × 10-9 g, and the minimum detectable concentrations in paddy-field water was 0.005 mg/L. The test in Anhui province indicated that the half-lives of imidacloprid was 4.4 days. [ Conclusion] 10% EC imidacloprid was applied in paddy-field; imidacloprid in water was more quickly degradated%[目的]研究了稻田水环境中吡虫啉的残留动态.[方法]田水样品采用二氯甲烷萃取,HPLC-UV测定不同田水样品中的吡虫啉残留量.[结果]田水中吡虫啉的平均添加回收率为89.69%~92.06%、标准偏差为3.01%~3.73%、变异系数为3.79%~4.46%,吡虫啉的最小检出量为1.0×10g,在田水中最低检测浓度为0.005 mg/L.在安徽的试验结果表明,吡虫啉在碍水中降解半衰期为4.4 d.[结论]10%吡虫啉乳油在稻田使用后,在田水中降解较快.

  17. Importance of polarity of the α4-α5 loop residue-Asn(166) in the pore-forming domain of the Bacillus thuringiensis Cry4Ba toxin: implications for ion permeation and pore opening.

    Science.gov (United States)

    Juntadech, Thanate; Kanintronkul, Yodsoi; Kanchanawarin, Chalermpol; Katzenmeier, Gerd; Angsuthanasombat, Chanan

    2014-01-01

    Bacillus thuringiensis Cry4Ba toxin is lethal to mosquito-larvae by forming ion-permeable pores in the target midgut cell membrane. Previously, the polarity of Asn(166) located within the α4-α5 loop composing the Cry4Ba pore-forming domain was shown to be crucial for larvicidal activity. Here, structurally stable-mutant toxins of both larvicidal-active (N166D) and inactive (N166A and N166I) mutants were FPLC-purified and characterized for their relative activities in liposomal-membrane permeation and single-channel formation. Similar to the 65-kDa trypsin-activated wild-type toxin, the N166D bio-active mutant toxin was still capable of releasing entrapped calcein from lipid vesicles. Conversely, the two other bio-inactive mutants showed a dramatic decrease in causing membrane permeation. When the N166D mutant was incorporated into planar lipid bilayers (under symmetrical conditions at 150mM KCl, pH8.5), it produced single-channel currents with a maximum conductance of about 425pS comparable to the wild-type toxin. However, maximum conductances for single K(+)-channels formed by both bio-inactive mutants (N166I and N166A) were reduced to approximately 165-205pS. Structural dynamics of 60-ns simulations of a trimeric α4-α5 pore model in a fully hydrated-DMPC system revealed that an open-pore structure could be observed only for the simulated pores of the wild type and N166D. Additionally, the number of lipid molecules interacting with both wild-type and N166D pores is relatively higher than those of N166A and N166I pores. Altogether, our results further signify that the polarity at the α4-α5 loop residue-Asn(166) is directly involved in ion permeation through the Cry4Ba toxin-induced ionic pore and pore opening at the membrane-water interface.

  18. Theoretical prediction of the importance of the 3B2 state in the dynamics of sulfur dioxide

    CERN Document Server

    Lévêque, Camille; Köppel, Horst

    2013-01-01

    While, the sulfur dioxide molecule has been extensively studied over the last decades, its photoexcitation dynamics is still unclear, due to its complexity, combining conical intersections and spin-orbit coupling between a manifold of states. We present for the first time a comprehensive ab initio study of the intersystem crossing of the molecule in the low energy domain, based on a wave-packet propagation on the manifold of the lowest singlet and triplet states. Furthermore, spin-orbit couplings are evaluated on a geometry-dependent grid, and diabatized along with the different conical intersections. Our results show for the first time the primordial role of the triplet $^3$B$_2$ state which has not been discussed before, giving new insights into the dynamics of the intersystem crossing in $SO_2$.

  19. Accuracy and importance of projections from a dynamic simulation model of smoking prevalence in the United States.

    Science.gov (United States)

    Warner, Kenneth E; Méndez, David

    2012-11-01

    We compared projections from a dynamic model of US adult smoking prevalence with official estimates of prevalence from the National Health Interview Survey. Ten years after they were made, the model projections closely fit the National Health Interview Survey estimates for 2005 and 2010. We conclude that a verified model of adult smoking prevalence can assist governmental authorities in establishing aspirational but feasible targets for tobacco control. By extension, carefully crafted models can help in goal setting in multiple areas of public health.

  20. Collimator system for the stabilization of the dynamical residual-gas pressure in the heavy-ion synchrotron SIS18; Kollimatorsystem zur Stabilisierung des dynamischen Restgasdruckes im Schwerionensynchrotron SIS18

    Energy Technology Data Exchange (ETDEWEB)

    Omet, Carsten

    2009-01-15

    In order to achieve higher beam intensities of heavy ion beams in ring accelerators, low charge state ions can be used. By lowering the charge state, the space charge limit is shifted to higher particle numbers and stripping losses can be avoided. During test operation of the SIS18 at GSI with high intensity low charge state heavy ion beams, strong intensity dependent beam losses have been observed. It was found that these beam losses are originated to a large extent by the change of charge state of the circulating ions during collisions with residual gas atoms. The resulting deviation of m/q relative to the reference ion leads, in combination with dispersive elements in the ion optic lattice, to a modified trajectory, followed by the loss of the ion on the beam pipe. At the impact position, loosely bound residual gas molecules are released by ion stimulated desorption which increases the residual gas pressure locally. This pressure rise itself enhances the charge exchange rate, which can develop into a self amplifying process of pressure rise and subsequent beam loss. A method for the stabilization of the dynamic residual gas pressure is the use of special catcher systems, which minimize the production of desorption gases and remove them by strong pumping. Therefore, the pressure on the beam axis should remain as stable as possible. Other processes, e.g. Coulomb scattering of the beam ions by residual gas particles and unavoidable systematic beam losses can increase the gas pressure additionally. The pressure in the accelerator is further subjected to ionization of the residual gas atoms themselves, thermal out gassing of the beam pipes, insertions and pumps. In this work, a detailed numerical model of the interplay between the residual gas pressure dynamics in the accelerator, possible stabilization measures, e.g. by catchers and the resulting beam life time has been developed. The forecasted beam life times and pressures are verified by machine experiments, as

  1. Phosphorylation statuses at different residues of lamin B2, B1, and A/C dynamically and independently change throughout the cell cycle

    Energy Technology Data Exchange (ETDEWEB)

    Kuga, Takahisa, E-mail: t-kuga@nibio.go.jp [Laboratory of Proteome Research, National Institute of Biomedical Innovation, Ibaraki, Osaka 567-0085 (Japan); Department of Molecular Diagnosis (F8), Graduate School of Medicine, Chiba University, Chuo-ku, Chiba 260-8670 (Japan); Nozaki, Naohito [Department of Biochemistry and Molecular Biology, Kanagawa Dental College, Yokosuka, Kanagawa 238-8580 (Japan); Matsushita, Kazuyuki; Nomura, Fumio [Department of Molecular Diagnosis (F8), Graduate School of Medicine, Chiba University, Chuo-ku, Chiba 260-8670 (Japan); Tomonaga, Takeshi, E-mail: tomonaga@nibio.go.jp [Laboratory of Proteome Research, National Institute of Biomedical Innovation, Ibaraki, Osaka 567-0085 (Japan); Department of Molecular Diagnosis (F8), Graduate School of Medicine, Chiba University, Chuo-ku, Chiba 260-8670 (Japan)

    2010-08-15

    Lamins, major components of the nuclear lamina, undergo phosphorylation at multiple residues during cell cycle progression, but their detailed phosphorylation kinetics remain largely undetermined. Here, we examined changes in the phosphorylation of major phosphorylation residues (Thr14, Ser17, Ser385, Ser387, and Ser401) of lamin B2 and the homologous residues of lamin B1, A/C during the cell cycle using novel antibodies to the site-specific phosphorylation. The phosphorylation levels of these residues independently changed during the cell cycle. Thr14 and Ser17 were phosphorylated during G{sub 2}/M phase to anaphase/telophase. Ser385 was persistently phosphorylated during mitosis to G{sub 1} phase, whereas Ser387 was phosphorylated discontinuously in prophase and G{sub 1} phase. Ser401 phosphorylation was enhanced in the G{sub 1}/S boundary. Immunoprecipitation using the phospho-antibodies suggested that metaphase-phosphorylation at Thr14, Ser17, and Ser385 of lamins occurred simultaneously, whereas G{sub 1}-phase phosphorylation at Ser385 and Ser387 occurred in distinct pools or with different timings. Additionally, we showed that lamin B2 phosphorylated at Ser17, but not Ser385, Ser387 and Ser401, was exclusively non-ionic detergent soluble, depolymerized forms in growing cells, implicating specific involvement of Ser17 phosphorylation in lamin depolymerization and nuclear envelope breakdown. These results suggest that the phosphorylations at different residues of lamins might play specific roles throughout the cell cycle.

  2. Mechanically induced residual stresses: Modelling and characterisation

    Science.gov (United States)

    Stranart, Jean-Claude E.

    Accurate characterisation of residual stress represents a major challenge to the engineering community. This is because it is difficult to validate the measurement and the accuracy is doubtful. It is with this in mind that the current research program concerning the characterisation of mechanically induced residual stresses was undertaken. Specifically, the cold expansion of fastener holes and the shot peening treatment of aerospace alloys, aluminium 7075 and titanium Ti-6Al-4V, are considered. The objective of this study is to characterise residual stresses resulting from cold working using three powerful techniques. These are: (i) theoretical using three dimensional non-linear finite element modelling, (ii) semi-destructive using a modified incremental hole drilling technique and (iii) nondestructive using a newly developed guided wave method supplemented by traditional C-scan measurements. The three dimensional finite element results of both simultaneous and sequential cold expansion of two fastener holes revealed the importance of the separation distance, the expansion level and the loading history upon the development and growth of the plastic zone and unloading residual stresses. It further showed that the commonly adopted two dimensional finite element models are inaccurate and incapable of predicting these residual stresses. Similarly, the dynamic elasto-plastic finite element studies of shot peening showed that the depth of the compressed layer, surface and sub-surface residual stresses are significantly influenced by the shot characteristics. Furthermore, the results reveal that the separation distance between two simultaneously impacting shots governs the plastic zone development and its growth. In the semi-destructive incremental hole drilling technique, the accuracy of the newly developed calibration coefficients and measurement techniques were verified with a known stress field and the method was used to measure peening residual stresses. Unlike

  3. Dynamic behaviour and residual pattern of thiamethoxam and its metabolite clothianidin in Swiss chard using liquid chromatography-tandem mass spectrometry.

    Science.gov (United States)

    Rahman, Md Musfiqur; Farha, Waziha; Abd El-Aty, A M; Kabir, Md Humayun; Im, So Jeong; Jung, Da-I; Choi, Jeong-Heui; Kim, Sung-Woo; Son, Young Wook; Kwon, Chan-Hyeok; Shin, Ho-Chul; Shim, Jae-Han

    2015-05-01

    A simultaneous method was developed to analyse thiamethoxam and its metabolite clothianidin in Swiss chard using tandem mass spectrometry (in the positive electrospray ionisation mode using multiple reaction monitoring mode) to estimate the dissipation pattern and the pre-harvest residue limit (PHRL). Thiamethoxam (10%, WG) was sprayed on Swiss chard grown in two different areas under greenhouse conditions at the recommended dose rate of 10 g/20 L water. Samples were collected randomly up to 14 days post-application, extracted using quick, easy, cheap, effective, rugged, safe (QuEChERS) acetate-buffered method and purified via a dispersive solid phase extraction (d-SPE) procedure. Matrix matched calibration showed good linearity with determination coefficients (R(2)) ⩾ 0.998. The limits of detection (LOD) and quantification (LOQ) were 0.007 and 0.02 mg/kg. The method was validated in triplicate at two different spiked concentration levels. Good recoveries (n=3) of 87.48-105.61% with relative standard deviations (RSDs) thiamethoxam residues in/on Swiss chard was best described by first-order kinetics with half-lives of 6.3 and 4.2 days. We predicted from the PHRL curves that if the residues were thiamethoxam concentrations would be below the maximum residue limits during harvest.

  4. Constraining the dynamical importance of hot gas and radiation pressure in quasar outflows using emission line ratios

    CERN Document Server

    Stern, Jonathan; Zakamska, Nadia L; Hennawi, Joseph F

    2015-01-01

    Quasar feedback models often predict an expanding hot gas bubble which drives a galaxy-scale outflow. In many circumstances the hot gas is predicted to radiate inefficiently, making the hot bubble hard to observe directly. We present an indirect method to detect the presence of a hot bubble using hydrostatic photoionization models of the cold (10^4 K) line-emitting gas. These models assume that the cold gas is in pressure equilibrium with either the hot gas pressure or with the radiation pressure, whichever is larger. We compare our models with observations of the broad line region (BLR), the inner face of the dusty torus, the narrow line region (NLR), and the extended NLR, and thus constrain the hot gas pressure over a dynamical range of 10^5 in radius, from 0.1 pc to 10 kpc. We find that the emission line ratios observed in the average quasar spectrum are consistent with radiation-pressure-dominated models on all scales. On scales > L_AGN/c inferred for galaxy-scale outflows in luminous quasars. This appare...

  5. Relative Importance of Biotic and Abiotic Forces on the Composition and Dynamics of a Soft-Sediment Intertidal Community.

    Science.gov (United States)

    Gerwing, Travis G; Drolet, David; Hamilton, Diana J; Barbeau, Myriam A

    2016-01-01

    Top-down, bottom-up, middle-out and abiotic factors are usually viewed as main forces structuring biological communities, although assessment of their relative importance, in a single study, is rarely done. We quantified, using multivariate methods, associations between abiotic and biotic (top-down, bottom-up and middle-out) variables and infaunal population/community variation on intertidal mudflats in the Bay of Fundy, Canada, over two years. Our analysis indicated that spatial structural factors like site and plot accounted for most of the community and population variation. Although we observed a significant relationship between the community/populations and the biotic and abiotic variables, most were of minor importance relative to the structural factors. We suggest that community and population structure were relatively uncoupled from the structuring influences of biotic and abiotic factors in this system because of high concentrations of resources that sustain high densities of infauna and limit exploitative competition. Furthermore, we hypothesize that the infaunal community primarily reflects stochastic spatial events, namely a "first come, first served" process.

  6. Relative Importance of Biotic and Abiotic Forces on the Composition and Dynamics of a Soft-Sediment Intertidal Community

    Science.gov (United States)

    Barbeau, Myriam A.

    2016-01-01

    Top-down, bottom-up, middle-out and abiotic factors are usually viewed as main forces structuring biological communities, although assessment of their relative importance, in a single study, is rarely done. We quantified, using multivariate methods, associations between abiotic and biotic (top-down, bottom-up and middle-out) variables and infaunal population/community variation on intertidal mudflats in the Bay of Fundy, Canada, over two years. Our analysis indicated that spatial structural factors like site and plot accounted for most of the community and population variation. Although we observed a significant relationship between the community/populations and the biotic and abiotic variables, most were of minor importance relative to the structural factors. We suggest that community and population structure were relatively uncoupled from the structuring influences of biotic and abiotic factors in this system because of high concentrations of resources that sustain high densities of infauna and limit exploitative competition. Furthermore, we hypothesize that the infaunal community primarily reflects stochastic spatial events, namely a “first come, first served” process. PMID:26790098

  7. Structural and Functional Importance of Transmembrane Domain 3 (TM3) in the Aspartate:Alanine Antiporter AspT: Topology and Function of the Residues of TM3 and Oligomerization of AspT▿

    Science.gov (United States)

    Nanatani, Kei; Maloney, Peter C.; Abe, Keietsu

    2009-01-01

    AspT, the aspartate:alanine antiporter of Tetragenococcus halophilus, a membrane protein of 543 amino acids with 10 putative transmembrane (TM) helices, is the prototype of the aspartate:alanine exchanger (AAE) family of transporters. Because TM3 (isoleucine 64 to methionine 85) has many amino acid residues that are conserved among members of the AAE family and because TM3 contains two charged residues and four polar residues, it is thought to be located near (or to form part of) the substrate translocation pathway that includes the binding site for the substrates. To elucidate the role of TM3 in the transport process, we carried out cysteine-scanning mutagenesis. The substitutions of tyrosine 75 and serine 84 had the strongest inhibitory effects on transport (initial rates of l-aspartate transport were below 15% of the rate for cysteine-less AspT). Considerable but less-marked effects were observed upon the replacement of methionine 70, phenylalanine 71, glycine 74, arginine 76, serine 83, and methionine 85 (initial rates between 15% and 30% of the rate for cysteine-less AspT). Introduced cysteine residues at the cytoplasmic half of TM3 could be labeled with Oregon green maleimide (OGM), whereas cysteines close to the periplasmic half (residues 64 to 75) were not labeled. These results suggest that TM3 has a hydrophobic core on the periplasmic half and that hydrophilic residues on the cytoplasmic half of TM3 participate in the formation of an aqueous cavity in membranes. Furthermore, the presence of l-aspartate protected the cysteine introduced at glycine 62 against a reaction with OGM. In contrast, l-aspartate stimulated the reactivity of the cysteine introduced at proline 79 with OGM. These results demonstrate that TM3 undergoes l-aspartate-induced conformational alterations. In addition, nonreducing sodium dodecyl sulfate-polyacrylamide gel electrophoresis analyses and a glutaraldehyde cross-linking assay suggest that functional AspT forms homo-oligomers as a

  8. Structural and functional importance of transmembrane domain 3 (TM3) in the aspartate:alanine antiporter AspT: topology and function of the residues of TM3 and oligomerization of AspT.

    Science.gov (United States)

    Nanatani, Kei; Maloney, Peter C; Abe, Keietsu

    2009-04-01

    AspT, the aspartate:alanine antiporter of Tetragenococcus halophilus, a membrane protein of 543 amino acids with 10 putative transmembrane (TM) helices, is the prototype of the aspartate:alanine exchanger (AAE) family of transporters. Because TM3 (isoleucine 64 to methionine 85) has many amino acid residues that are conserved among members of the AAE family and because TM3 contains two charged residues and four polar residues, it is thought to be located near (or to form part of) the substrate translocation pathway that includes the binding site for the substrates. To elucidate the role of TM3 in the transport process, we carried out cysteine-scanning mutagenesis. The substitutions of tyrosine 75 and serine 84 had the strongest inhibitory effects on transport (initial rates of l-aspartate transport were below 15% of the rate for cysteine-less AspT). Considerable but less-marked effects were observed upon the replacement of methionine 70, phenylalanine 71, glycine 74, arginine 76, serine 83, and methionine 85 (initial rates between 15% and 30% of the rate for cysteine-less AspT). Introduced cysteine residues at the cytoplasmic half of TM3 could be labeled with Oregon green maleimide (OGM), whereas cysteines close to the periplasmic half (residues 64 to 75) were not labeled. These results suggest that TM3 has a hydrophobic core on the periplasmic half and that hydrophilic residues on the cytoplasmic half of TM3 participate in the formation of an aqueous cavity in membranes. Furthermore, the presence of l-aspartate protected the cysteine introduced at glycine 62 against a reaction with OGM. In contrast, l-aspartate stimulated the reactivity of the cysteine introduced at proline 79 with OGM. These results demonstrate that TM3 undergoes l-aspartate-induced conformational alterations. In addition, nonreducing sodium dodecyl sulfate-polyacrylamide gel electrophoresis analyses and a glutaraldehyde cross-linking assay suggest that functional AspT forms homo-oligomers as a

  9. Galileo Probe Doppler Residuals as the Wave-Dynamical Signature of Weakly Stable, Downward-Increasing Stratification in Jupiter's Deep Wind Layer

    Science.gov (United States)

    Allison, Michael; Atkinson, David H.; Hansen, James E. (Technical Monitor)

    2001-01-01

    Doppler radio tracking of the Galileo probe-to-orbiter relay, previously analyzed for its in situ measure of Jupiter's zonal wind at the equatorial entry site, also shows a record of significant residual fluctuations apparently indicative of varying vertical motions. Regular oscillations over pressure depth in the residual Doppler measurements of roughly 1-8 Hz (increasing upward), as filtered over a 134 sec window, are most plausibly interpreted as gravity waves, and imply a weak, but downward increasing static stability within the 5 - 20 bar region of Jupiter's atmosphere. A matched extension to deeper levels of an independent inertial stability constraint from the measured vertical wind shear at 1 - 4 bars is roughly consistent with a static stability of approximately 0.5 K/km near the 20 bar level, as independently detected by the probe Atmospheric Structure Instrument.

  10. Seven-year follow-up of allogeneic transplant using BCNU, etoposide, cytarabine and melphalan chemotherapy in patients with Hodgkin lymphoma after autograft failure: importance of minimal residual disease.

    Science.gov (United States)

    Sobol, Urszula; Rodriguez, Tulio; Smith, Scott; Go, Aileen; Vimr, Ross; Parthasarathy, Mala; Guo, Rong; Stiff, Patrick

    2014-06-01

    Abstract Allogeneic transplant using reduced intensity conditioning is a therapeutic option for patients with Hodgkin lymphoma (HL) who relapse after an autograft. This was a prospective study of 31 consecutive eligible patients with HL who relapsed after an autograft and underwent an allograft using BEAM (BCNU, etoposide, cytarabine, melphalan) conditioning. At a median follow-up of 7 years the progression-free survival (PFS) was 36% (95% confidence interval [CI] 19-54%) and overall survival (OS) was 42% (95% CI 23-59%). In multivariate analysis only residual disease at the time of transplant predicted outcome, with a 4-year PFS and OS of 62% and 75% for patients with minimal residual disease versus 8% and 8% for patients with gross residual disease, respectively (p = 0.005 and p = 0.001, respectively). This benefit seemed to be irrespective of chemosensitivity, with an OS for patients with chemorefractory yet minimal disease of 71% at 4 years. BEAM allogeneic transplant is effective in producing long-term remissions after autograft failure. Regardless of chemosensitivity, minimizing tumor burden pre-transplant may improve long-term outcome.

  11. Coevolution of amino acid residues in the key photosynthetic enzyme Rubisco

    Directory of Open Access Journals (Sweden)

    Kapralov Maxim V

    2011-09-01

    Full Text Available Abstract Background One of the key forces shaping proteins is coevolution of amino acid residues. Knowing which residues coevolve in a particular protein may facilitate our understanding of protein evolution, structure and function, and help to identify substitutions that may lead to desired changes in enzyme kinetics. Rubisco, the most abundant enzyme in biosphere, plays an essential role in the process of carbon fixation through photosynthesis, thus facilitating life on Earth. This makes Rubisco an important model system for studying the dynamics of protein fitness optimization on the evolutionary landscape. In this study we investigated the selective and coevolutionary forces acting on large subunit of land plants Rubisco using Markov models of codon substitution and clustering approaches applied to amino acid substitution histories. Results We found that both selection and coevolution shape Rubisco, and that positively selected and coevolving residues have their specifically favored amino acid composition and pairing preference. The mapping of these residues on the known Rubisco tertiary structures showed that the coevolving residues tend to be in closer proximity with each other compared to the background, while positively selected residues tend to be further away from each other. This study also reveals that the residues under positive selection or coevolutionary force are located within functionally important regions and that some residues are targets of both positive selection and coevolution at the same time. Conclusion Our results demonstrate that coevolution of residues is common in Rubisco of land plants and that there is an overlap between coevolving and positively selected residues. Knowledge of which Rubisco residues are coevolving and positively selected could be used for further work on structural modeling and identification of substitutions that may be changed in order to improve efficiency of this important enzyme in crops.

  12. Investigating the importance of sediment resuspension in Alexandrium fundyense cyst population dynamics in the Gulf of Maine

    Science.gov (United States)

    Butman, Bradford; Aretxabaleta, Alfredo L.; Dickhudt, Patrick J.; Dalyander, P. Soupy; Sherwood, Christopher R.; Anderson, Donald M.; Keafer, Bruce A.; Signell, Richard P.

    2014-05-01

    . Based on analysis of wave data from offshore buoys from 1996 to 2012, the number of wave events inducing a bottom shear stress large enough to resuspend sediment at 80 m ranged from 0 to 2 in spring (April and May) and 0 to 10 in winter (October through March). Wave-induced resuspension is unlikely in water greater than about 100 m deep. The observations and model results suggest that a millimeter or so of sediment and associated cysts may be mobilized in both winter and spring, and that the frequency of resuspension will vary interannually. Depending on cyst concentration in the sediment and the vertical distribution in the water column, these events could result in a concentration in the water column of at least 104 cysts m-3. In some years, resuspension events could episodically introduce cysts into the water column in spring, where germination is likely to be facilitated at the time of bloom formation. An assessment of the quantitative effects of cyst resuspension on bloom dynamics in any particular year requires more detailed investigation.

  13. Spatiotemporal dynamics and demographic profiles of imported Plasmodium falciparum and Plasmodium vivax infections in Ontario, Canada (1990-2009.

    Directory of Open Access Journals (Sweden)

    Mark P Nelder

    Full Text Available We examined malaria cases reported to Ontario's public health surveillance systems from 1990 through 2009 to determine how temporal scale (longitudinal, seasonal, spatial scale (provincial, health unit, and demography (gender, age contribute to Plasmodium infection in Ontario travellers. Our retrospective study included 4,551 confirmed cases of imported malaria reported throughout Ontario, with additional analysis at the local health unit level (i.e., Ottawa, Peel, and Toronto. During the 20-year period, Plasmodium vivax accounted for 50.6% of all cases, P. falciparum (38.6%, Plasmodium sp. (6.0%, P. ovale (3.1%, and P. malariae (1.8%. During the first ten years of the study (1990-1999, P. vivax (64% of all cases was the dominant agent, followed by P. falciparum (28%; however, during the second ten years (2000-2009 the situation reversed and P. falciparum (55% dominated, followed by P. vivax (30%. The prevalence of P. falciparum and P. vivax cases varied spatially (e.g., P. falciparum more prevalent in Toronto, P. vivax more prevalent in Peel, temporally (e.g. P. falciparum incidence increased during the 20-year study, and demographically (e.g. preponderance of male cases. Infection rates per 100,000 international travellers were estimated: rates of infection were 2× higher in males compared to females; rates associated with travel to Africa were 37× higher compared to travel to Asia and 126× higher compared to travel to the Americas; rates of infection were 2.3-3.5× higher in June and July compared to October through March; and rates of infection were highest in those 65-69 years old. Where exposure country was reported, 71% of P. falciparum cases reported exposure in Ghana or Nigeria and 63% of P. vivax cases reported exposure in India. Our study provides insights toward improving pre-travel programs for Ontarians visiting malaria-endemic regions and underscores the changing epidemiology of imported malaria in the province.

  14. Computational fluid dynamics (CFD) analysis of the combustion process of a leather residuals gasification fuel gas: influence of fuel moisture content

    Energy Technology Data Exchange (ETDEWEB)

    Antonietti, Anderson Jose; Beskow, Arthur Bortolin; Silva, Cristiano Vitorino da [Universidade Regional Integrada do Alto Uruguai e das Missoes (URI), Erechim, RS (Brazil)], E-mails: arthur@uricer.edu.br, mlsperb@unisinos.br; Indrusiak, Maria Luiza Sperb [Universidade do Vale do Rio dos Sinos (UNISINOS), Sao Leopoldo, RS (Brazil)], E-mail: cristiano@uricer.edu.br

    2010-07-01

    This work presents a numerical study of the combustion process of leather residuals gasification gas, aiming the improvement of the process efficiency, considering different concentrations of water on the gas. The heating produced in this combustion process can be used to generation of thermal and/or electrical energy, for use at the leather industrial plant. However, the direct burning of this leather-residual-gas into the chambers is not straightforward. The alternative in development consists in processing this leather residuals by gasification or pyrolysis, separating the volatiles and products of incomplete combustion, for after use as fuel in a boiler. At these processes, different quantities of water can be used, resulting at different levels of moisture content in this fuel gas. This humidity can affect significantly the burning of this fuel, producing unburnt gases, as the carbon monoxide, or toxic gases as NOx, which must have their production minimized on the process, with the purpose of reducing the emission of pollutants to the atmosphere. Other environment-harmful-gases, remaining of the chemical treatment employed at leather manufacture, as cyanide, and hydrocarbons as toluene, must burn too, and the moisture content has influence on it. At this way, to increase understanding of the influence of moisture in the combustion process, it was made a numerical investigation study of reacting flow in the furnace, evaluating the temperature field, the chemical species concentration fields, flow mechanics and heat transfer at the process. The commercial CFD code CFX Ansys Inc. was used. Considering different moisture contents in the fuel used on the combustion process, with this study was possible to achieve the most efficient burning operation parameters, with improvement of combustion efficiency, and reduction of environmental harmful gases emissions. It was verified that the different moisture contents in the fuel gas demand different operation conditions

  15. Residual analysis for spatial point processes

    DEFF Research Database (Denmark)

    Baddeley, A.; Turner, R.; Møller, Jesper

    We define residuals for point process models fitted to spatial point pattern data, and propose diagnostic plots based on these residuals. The techniques apply to any Gibbs point process model, which may exhibit spatial heterogeneity, interpoint interaction and dependence on spatial covariates. Our...... residuals generalise the well-known residuals for point processes in time, used in signal processing and survival analysis. An important difference is that the conditional intensity or hazard rate of the temporal point process must be replaced by the Papangelou conditional intensity $lambda$ of the spatial...... process. Residuals are ascribed to locations in the empty background, as well as to data points of the point pattern. We obtain variance formulae, and study standardised residuals. There is also an analogy between our spatial residuals and the usual residuals for (non-spatial) generalised linear models...

  16. Recurrence and mortality according to Estrogen Receptor status for breast cancer patients undergoing conservative surgery. Ipsilateral breast tumour recurrence dynamics provides clues for tumour biology within the residual breast

    Directory of Open Access Journals (Sweden)

    Ferraris Cristina

    2010-11-01

    Full Text Available Abstract Background the study was designed to determine how tumour hormone receptor status affects the subsequent pattern over time (dynamics of breast cancer recurrence and death following conservative primary breast cancer resection. Methods Time span from primary resection until both first recurrence and death were considered among 2825 patients undergoing conservative surgery with or without breast radiotherapy. The hazard rates for ipsilateral breast tumour recurrence (IBTR, distant metastasis (DM and mortality throughout 10 years of follow-up were assessed. Results DM dynamics displays the same bimodal pattern (first early peak at about 24 months, second late peak at the sixth-seventh year for both estrogen receptor (ER positive (P and negative (N tumours and for all local treatments and metastatic sites. The hazard rates for IBTR maintain the bimodal pattern for ERP and ERN tumours; however, each IBTR recurrence peak for ERP tumours is delayed in comparison to the corresponding timing of recurrence peaks for ERN tumours. Mortality dynamics is markedly different for ERP and ERN tumours with more early deaths among patients with ERN than among patients with ERP primary tumours. Conclusion DM dynamics is not influenced by the extent of conservative primary tumour resection and is similar for both ER phenotypes across different metastatic sites, suggesting similar mechanisms for tumour development at distant sites despite apparently different microenvironments. The IBTR risk peak delay observed in ERP tumours is an exception to the common recurrence risk rhythm. This suggests that the microenvironment within the residual breast tissue may enforce more stringent constraints upon ERP breast tumour cell growth than other tissues, prolonging the latency of IBTR. This local environment is, however, apparently less constraining to ERN cells, as IBTR dynamics is similar to the corresponding recurrence dynamics among other distant tissues.

  17. On the importance of including vegetation dynamics in hydrological simulation under climate change: A case study in the Jing River Basin

    Science.gov (United States)

    Li, Q.; Li, Z.; Ishidaira, H.

    2012-04-01

    The role of catchment vegetation within the hydrological cycle and its impact on hydrological processes has long been a topic of research within hydrology. A key element in quantifying the hydrological impact of climate change is the relationship between catchment vegetation and runoff, which continues to be a productive area of research within hydrology. However, the parameterization of vegetation composition and distribution as a dynamic component is insufficient in stand-alone hydrological modeling studies. Dynamic global vegetation models (DGVMs) are able to simulate transient structural changes in major vegetation types but do not simulate runoff generation reliably. A biosphere hydrological model (LPJH) coupling a prominent DGVM (Lund-Postdam-Jena model referred to as LPJ) with a stand-alone hydrological model (HYMOD) may simulate both vegetation dynamics and runoff generation reasonably. This study applies the LPJH model to the Jing River basin, a tributary of the Yellow River, with the objective of analyzing the role of vegetation in the hydrological processes at this semi-arid basin and evaluating the impact of vegetation change on the hydrological processes under climate change. The results show that the LPJH model gives reasonable hydrological simulation in terms of runoff. It is shown that changing climate conditions in terms of co2, temperature, precipitation, and the combination changes of these variables would result in actual evapotranspiration and runoff changes. Theses changes are mainly attributable to changes in transpiration driven by vegetation dynamics, which are not simulated in stand-alone hydrological models. Therefore, the composition and distribution of vegetation are of fundamental importance for evapotranspiration and runoff generation, especially under climate change. The percent of impact from each climate variable is also explored by using the LPJH model, which gives an overall view of climate change impact on hydrological processes

  18. The Importance of Permafrost Thaw, Fire and Logging Disturbances as Driving Factors of Historical and Projected Carbon Dynamics in Alaskan Ecosystems

    Science.gov (United States)

    Genet, H.; Zhang, Y.; McGuire, A. D.; He, Y.; Johnson, K. D.; D'Amore, D. V.; Zhou, X.; Bennett, A.; Breen, A. L.; Biles, F. E.; Bliss, N. B.; Euskirchen, E. S.; Kurkowski, T. A.; Pastick, N.; Rupp, S. T.; Wylie, B. K.; Zhu, Z.; Zhuang, Q.

    2014-12-01

    Carbon dynamics of natural ecosystems are influenced by disturbance regimes of various frequencies and magnitudes. With global change, these disturbances are projected to increase in frequency and/or magnitude and may have significant effects on future net carbon balance, especially in high latitude ecosystems where carbon stocks are among the largest on Earth and climate change is substantial. In Alaska, permafrost degradation and fire in the boreal and arctic regions and logging in the southern coastal region are the main disturbances that affect ecosystems. Large uncertainties related to the effects of these disturbances on the capacity of these regions to store carbon still exist mainly due to difficulty in representing permafrost degradation in current ecosystem models. We ran the Terrestrial Ecosystem Model (TEM), which explicitly simulates the carbon cycle and permafrost dynamics, coupled with a disturbance model (the Alaska Frame Based Ecosystem Code, ALFRESCO) to assess the relative importance of permafrost thaw, wildfire, and forest management on historical and projected carbon balance and carbon stocks in Alaska, from 1950 to 2100, at a 1-km resolution. Our simulations showed that the increase in plant productivity in response to warming in boreal and arctic regions is offset by soil carbon loss due to permafrost degradation and wildfire combustion during both historical and future simulations. Fire disturbances act as a catalyst accelerating permafrost degradation and associated soil carbon loss. In addition, our preliminary results for south coastal regions of Alaska indicate that logging of second growth forests could influence carbon dynamics in that region. Overall, these results have implications for land management strategies and illustrate the importance of taking into account multiple types of disturbance regimes in ecosystem models for Alaska.

  19. Evaluation of aerobic co-composting of penicillin fermentation fungi residue with pig manure on penicillin degradation, microbial population dynamics and composting maturity.

    Science.gov (United States)

    Zhang, Zhenhua; Zhao, Juan; Yu, Cigang; Dong, Shanshan; Zhang, Dini; Yu, Ran; Wang, Changyong; Liu, Yan

    2015-12-01

    Improper treatment of penicillin fermentation fungi residue (PFFR), one of the by-products of penicillin production process, may result in environmental pollution due to the high concentration of penicillin. Aerobic co-composting of PFFR with pig manure was determined to degrade penicillin in PFFR. Results showed that co-composting of PFFR with pig manure can significantly reduce the concentration of penicillin in PFFR, make the PFFR-compost safer as organic fertilizer for soil application. More than 99% of penicillin in PFFR were removed after 7-day composting. PFFR did not affect the composting process and even promote the activity of the microorganisms in the compost. Quantitative PCR (qPCR) indicated that the bacteria and actinomycetes number in the AC samples were 40-80% higher than that in the pig-manure compost (CK) samples in the same composting phases. This research indicated that the aerobic co-composting was a feasible PFFR treatment method.

  20. Selection bias in dynamically measured supermassive black hole samples: scaling relations and correlations between residuals in semi-analytic galaxy formation models

    Science.gov (United States)

    Barausse, Enrico; Shankar, Francesco; Bernardi, Mariangela; Dubois, Yohan; Sheth, Ravi K.

    2017-07-01

    Recent work has confirmed that the scaling relations between the masses of supermassive black holes and host-galaxy properties such as stellar masses and velocity dispersions may be biased high. Much of this may be caused by the requirement that the black hole sphere of influence must be resolved for the black hole mass to be reliably estimated. We revisit this issue with a comprehensive galaxy evolution semi-analytic model. Once tuned to reproduce the (mean) correlation of black hole mass with velocity dispersion, the model cannot account for the correlation with stellar mass. This is independent of the model's parameters, thus suggesting an internal inconsistency in the data. The predicted distributions, especially at the low-mass end, are also much broader than observed. However, if selection effects are included, the model's predictions tend to align with the observations. We also demonstrate that the correlations between the residuals of the scaling relations are more effective than the relations themselves at constraining models for the feedback of active galactic nuclei (AGNs). In fact, we find that our model, while in apparent broad agreement with the scaling relations when accounting for selection biases, yields very weak correlations between their residuals at fixed stellar mass, in stark contrast with observations. This problem persists when changing the AGN feedback strength, and is also present in the hydrodynamic cosmological simulation Horizon-AGN, which includes state-of-the-art treatments of AGN feedback. This suggests that current AGN feedback models are too weak or simply not capturing the effect of the black hole on the stellar velocity dispersion.

  1. Interactions between beta D372 and gamma subunit N-terminus residues gamma K9 and gamma S12 are important to catalytic activity catalyzed by Escherichia coli F1F0-ATP synthase.

    Science.gov (United States)

    Lowry, David S; Frasch, Wayne D

    2005-05-17

    Substitution of Escherichia coli F(1)F(0) ATP synthase residues betaD372 or gammaS12 with groups that are unable to form a hydrogen bond at this location decreased ATP synthase-dependent cell growth by 2 orders of magnitude, eliminated the ability of F(1)F(0) to catalyze ATPase-dependent proton pumping in inverted E. coli membranes, caused a 15-20% decrease in the coupling efficiency of the membranes as measured by the extent of succinate-dependent acridine orange fluorescence quenching, but increased soluble F(1)-ATPase activity by about 10%. Substitution of gammaK9 to eliminate the ability to form a salt bridge with betaD372 decreased soluble F(1)-ATPase activity and ATPase-driven proton pumping by 2-fold but had no effect on the proton gradient induced by addition of succinate. Mutations to eliminate the potential to form intersubunit hydrogen bonds and salt bridges between other less highly conserved residues on the gamma subunit N-terminus and the beta subunits had little effect on ATPase or ATP synthase activities. These results suggest that the betaD372-gammaK9 salt bridge contributes significantly to the rate-limiting step in ATP hydrolysis of soluble F(1) while the betaD372-gammaS12 hydrogen bond may serve as a component of an escapement mechanism for ATP synthesis in which alphabetagamma intersubunit interactions provide a means to make substrate binding a prerequisite of proton gradient-driven gamma subunit rotation.

  2. 乙酰甲胺磷及其高毒代谢物甲胺磷在白菜中的残留动态%Residue Dynamics of Acephate and Its Metabolite Methamidophos in Pakchoi

    Institute of Scientific and Technical Information of China (English)

    洪文英; 吴燕君; 王道泽; 谢国雄; 周航; 洪奎贤

    2011-01-01

    为明确乙酰甲胺磷在叶菜类蔬菜上使用后的环境安全性,采用气相色谱法比较研究了露地与设施栽培条件下乙酰甲胺磷及其高毒代谢物甲胺磷在白菜中的残留动态规律和最终残留.结果表明,按推荐使用剂量、2倍推荐使用剂量施药1次,乙酰甲胺磷在白菜中降解半衰期为2.060~3.203 d,大棚条件下降解速度慢于露地条件下降解速度;乙酰甲胺磷在降解过程中可代谢产生甲胺磷,作物中甲胺磷的残留量是乙酰甲胺磷代谢生成和甲胺磷本身降解两个过程共同作用的结果,施药几天后,出现一个甲胺磷残留的高峰;乙酰甲胺磷施用在白菜上可能会有较高的甲胺磷残留风险,尤其是大棚栽培方式、施药浓度高的情况下使用乙酰甲胺磷具有更高的甲胺磷残留风险.因此,在白菜等叶菜类蔬菜上应谨慎使用乙酰甲胺磷,露地栽培条件下的安全间隔期应延长为21 d,设施栽培条件下不宜使用.%In order to definitude environmental safety and establish safe application standard, residue dynamics and final residue of acephate and its metabolite methamidophos were comparatively studied by the method of gas chromatography in open field and greenhouse vegetables.Meanwhile a safe application method of the insecticide was developed to provide a guidline for application of acephate in field, and to refine and update the residue data which was helpful to determine the harvest interval. The results showed that when the 30% acephate (EC) was applied one time by the dilution with 1:1 000 and 1:500, the half-lives of acephate in pakchoi were 2.060~3.203 d, respectively. The halflives in greenhouse were longer than that in open field, which implied that acephate in greenhouse was more slowly degraded than that in open field. Aeephate could be metabolized to methamidophos in the process of degradation, and the residue of methamidophos resulted from both degradation and metabolism

  3. 15%腐霉利烟剂在保护地番茄及土壤中的消解动态与残留量%Residue and Degradation Dynamic of Procymidone 15%FU in Tomato and Soil

    Institute of Scientific and Technical Information of China (English)

    陈柏

    2014-01-01

    为评价腐霉利在保护地番茄上使用的安全性,建立其使用规范,2013年在6地进行了15%腐霉利烟剂在番茄和土壤中的残留试验。样品采用乙腈提取,固相萃取柱净化,气相色谱电子捕获检测器进行检测,外标法定量。结果表明:腐霉利在番茄和土壤中的半衰期分别为1.9~3.7 d和1.4~2.7 d。番茄及土壤中腐霉利残留量均低于2 mg/kg。%In order to evaluate the safety and establish the regular use of procymidone in tomato in protected field, the final residue and degradation dynamic of procymidone 15%FU were studied in six provinces in 2013. The samples were extracted with acetonitrile, cleaned up by SPE column, and determined using GC with ECD. The results showed that the half-lives of procymidone in tomato and soil were 1.9-3.7 d and 1.4-2.7 d. The residues were all below 2 mg/kg.

  4. A phosphorylation cluster of five serine and threonine residues in the C-terminus of the follicle-stimulating hormone receptor is important for desensitization but not for beta-arrestin-mediated ERK activation.

    Science.gov (United States)

    Kara, Elodie; Crépieux, Pascale; Gauthier, Christophe; Martinat, Nadine; Piketty, Vincent; Guillou, Florian; Reiter, Eric

    2006-11-01

    Classically, the FSH receptor (FSH-R) mediates its effects through coupling to guanine nucleotide-binding protein alpha S subunit (Galpha(s)) and activation of the cAMP/protein kinase A (PKA) signaling pathway. beta-Arrestins are rapidly recruited to the FSH-activated receptor and play key roles in its desensitization and internalization. Here, we show that the FSH-R expressed in HEK 293 cells activated ERK by two temporally distinct pathways dependent, respectively, on Galpha(s)/PKA and beta-arrestins. Galpha(s)/PKA-dependent ERK activation was rapid, transient, and blocked by H89 (a PKA inhibitor), but it was insensitive to small interfering RNA-mediated depletion of beta-arrestins. beta-Arrestin-dependent ERK activation was slower but more sustained and was insensitive to H89. We identified five Ser/Thr residues in the C terminus of the receptor (638-644) as a major phosphorylation site. Mutation of these residues into Ala (5A FSH-R) significantly reduced the stability of FSH-induced beta-arrestin 1 and 2 interaction when compared with the wild-type receptor. As expected, the 5A FSH-R-mediated cAMP accumulation was enhanced, and its internalization was reduced. In striking contrast, the ability of the 5A FSH-R to activate ERK via the beta-arrestin-dependent pathway was increased. G protein-coupled receptor kinase 5 (GRK5) and GRK6 were required for beta-arrestin-dependent ERK activation by both the wild-type and 5A FSH-R. By contrast, GRK2 depletion enhanced ERK activation by the wild-type FSH-R but not by the 5A FSH-R. In conclusion, we demonstrate the existence of a beta-arrestin-dependent, GRK-regulated mechanism for ERK activation by the FSH-R. A phosphorylation cluster in the C terminus of the FSH-R, identified as a site of beta-arrestin recruitment, positively regulated both desensitization and internalization but negatively regulated beta-arrestin-dependent ERK activation.

  5. Resíduos de anabolizantes na produção animal: importância e métodos de detecção Anabolic residues in livestock prodution: relevancy and detection methods

    Directory of Open Access Journals (Sweden)

    Keila Maria Roncato Duarte

    2002-08-01

    Full Text Available Com o desenvolvimento da indústria farmacêutica e o conseqüente surgimento de novas substâncias promotoras do crescimento animal, o setor agropecuário necessita de tecnologias cada vez mais eficientes e sensíveis para detectar possíveis resíduos deixados por este vasto número de substâncias anabolizantes, principalmente esteróides com atividades estrogênicas, androgênicas e progestogênicas. Tais substâncias, quando presentes na carne, gordura, ovos, entre outros, podem ser detectadas e quantificadas por uma série de métodos, dentre os quais, descrevemos os cromatográficos, baseados principalmente em cromatografia gasosa acoplada à espectrometria de massa (CG-EM, cromatografia líquida de alta eficiência (CLAE, cromatografia em camada delgada de alta eficiência (CCDAE e os métodos imunológicos, como radioomunoensaio (RIA e ensaio imunoenzimático (ELISA. Estes métodos têm como vantagens o elevado número de amostras que podem ser analisadas por período de tempo, aliadas à alta sensibilidade na detecção de resíduos.With the development of the pharmaceutical industry, and consequently appearance of new substances which promote animal growth, the agricultural sector needs technologies more and more efficient and sensitive to detect possible residues left by this vast number of anabolic substances, mainly steroids with estrogenic, androgenic and progesterogenics activities. Such substances, when present in meat, fat, and eggs among others, can be detected and quantified by a series of methods, among the ones which we described the chromatographic methods, based mainly on gaseous chromatography coupled to the mass espectrometry (CG-MS, high performance liquid chromatography (HPLC, thin layer chromatography (HPTLC and the immunological methods, as radioimmunoassay (RIA and enzyme linked immunosorbent assay (ELISA. These methods have as advantages the high number of samples that can be analyzed by period of time, toghether

  6. Analysis of flashing and swelling phenomena in tanks of nuclear power plants; the importance of bubble growth dynamics and bubble transport models with size tracking

    Energy Technology Data Exchange (ETDEWEB)

    Cerezo A, E. [University of Caribe, Department of Basics Sciences and Engineering, Lote 1, Manzana 1, Region 78, esq. Fracc. Tabachines, 77500 Cancun, Quintana Roo (Mexico)]. E-mail: ecerezo@unicaribe.edu.mx; Munoz C, J.L. [Department of Chemical and Nuclear Engineering, Polytechnic University of Valencia, Camino de Vera 14, 46022 Valencia (Spain)

    2004-07-01

    This paper presents a non-equilibrium model to describe flashing phenomena in tanks and cooling pools. The present model is based on Watanabe's work that we have extended by developing a realistic model for the growth of bubbles. We have made the corresponding venting model, continuity equation, gas and liquid phase energy conservation equations for the model. This model takes into account both drag and virtual mass force. The dynamics of bubble growth plays an important role in two-phase phenomena such as flashing. In our model the growth rate is assumed to be limited by the heat conduction in the liquid. The results of the analytic model were compared with the experimental data of Watanabe [1]. The results have shown that the present model evaluates fairly accurately the pressure evolution, the void fraction and the swelling level of a tank.

  7. Deep dynamical processes in the central-southern Qinghai-Tibet Plateau—Receiver functions and travel-time residuals analysis of north Hi-Climb

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Teleseismic receiver functions and travel-time residuals along the north Hi-Climb broadband seismic array in the central-southern Qinghai-Tibet Plateau show that the lithosphere structures in the central and western Qinghai-Tibet Plateau are different. In the central Qinghai-Tibet Plateau, the Indian Plate is northward subducted beneath the Qiangtang block and arrives at the greatest depth beneath the central-southern Qiangtang block. The delaminated Indian lithospheric slab remains beneath the central Lhasa block to a depth possibly greater than that of the upper interface of the mantle transform zone. In the western Qinghai-Tibet Plateau, the Indian lithospheric plate is gently northward subducted and may have arrived to the south of Tarim plate. Due to the resistance from the gently northward subduction of the Indian mantle lithosphere in the western Qinghai-Tibet Plateau, the upwelling mantle material be-neath the Qiangtang block moves mostly toward the east to bring about the lateral eastward flow of the deep mantle hot material in the central Qinghai-Tibet Plateau.

  8. Deep dynamical processes in the central-southern Qinghai-Tibet Plateau——Receiver functions and travel-time residuals analysis of north Hi-Climb

    Institute of Scientific and Technical Information of China (English)

    LI HaiOu; XU XiWei; JIANG Mei

    2008-01-01

    Teleseismic receiver functions and travel-time residuals along the north Hi-Climb broadband seismic array in the central-southern Qinghai-Tibet Plateau show that the lithosphere structures in the central and western Qinghai-Tibet Plateau are different.In the central Qinghai-Tibet Plateau, the Indian Plate is northward subducted beneath the Qiangtang block and arrives at the greatest depth beneath the central-southern Qiangtang block.The delaminated Indian lithospheric slab remains beneath the central Lhasa block to a depth possibly greater than that of the upper interface of the mantle transform zone.In the western Qinghai-Tibet Plateau, the Indian lithospheric plate is gently northward subducted and may have arrived to the south of Tarim plate.Due to the resistance from the gently northward subduction of the Indian mantle lithosphere in the western Qinghai-Tibet Plateau, the upwelling mantle material beneath the Qiangtang block moves mostly toward the east to bring about the lateral eastward flow of the deep mantle hot material in the central Qinghai-Tibet Plateau.

  9. Order through disorder: hyper-mobile C-terminal residues stabilize the folded state of a helical peptide. a molecular dynamics study.

    Directory of Open Access Journals (Sweden)

    Kalliopi K Patapati

    Full Text Available Conventional wisdom has it that the presence of disordered regions in the three-dimensional structures of polypeptides not only does not contribute significantly to the thermodynamic stability of their folded state, but, on the contrary, that the presence of disorder leads to a decrease of the corresponding proteins' stability. We have performed extensive 3.4 µs long folding simulations (in explicit solvent and with full electrostatics of an undecamer peptide of experimentally known helical structure, both with and without its disordered (four residue long C-terminal tail. Our simulations clearly indicate that the presence of the apparently disordered (in structural terms C-terminal tail, increases the thermodynamic stability of the peptide's folded (helical state. These results show that at least for the case of relatively short peptides, the interplay between thermodynamic stability and the apparent structural stability can be rather subtle, with even disordered regions contributing significantly to the stability of the folded state. Our results have clear implications for the understanding of peptide energetics and the design of foldable peptides.

  10. Deep wastewater: internal dynamics and efficiency during the regeneration waste water process; Lagunaje profundo: dinamica interna y rendimientos en el proceso de autorregeneracion del agua residual

    Energy Technology Data Exchange (ETDEWEB)

    Arauzo Sanchez, M.

    2001-07-01

    In order to look for solutions for the increasing water demand, the improvement of the conservation of our river basins and the reutilization of regenerated wastewater in the best quality conditions, a deep wastewater self-regeneration pond, supplied with secondary effluent produced at a conventional purifying plant, has been started up. Research Project 07/0060/1998 (Comunidad Autonoma de Madrid) has allowed us to explain in detail the system dynamics in order to obtain the maximum yield in self-regeneration process. (Author) 25 refs.

  11. Effect of texture and grain size on the residual stress of nanocrystalline thin films

    Science.gov (United States)

    Cao, Lei; Sengupta, Arkaprabha; Pantuso, Daniel; Koslowski, Marisol

    2017-10-01

    Residual stresses develop in thin film interconnects mainly as a result of deposition conditions and multiple thermal loading cycles during the manufacturing flow. Understanding the relation between the distribution of residual stress and the interconnect microstructure is of key importance to manage the nucleation and growth of defects that can lead to failure under reliability testing and use conditions. Dislocation dynamics simulations are performed in nanocrystalline copper subjected to cyclic loading to quantify the distribution of residual stresses as a function of grain misorientation and grain size distribution. The outcomes of this work help to evaluate the effect of microstructure in thin films failure by identifying potential voiding sites. Furthermore, the simulations show how dislocation structures are influenced by texture and grain size distribution that affect the residual stress. For example, when dislocation loops reach the opposite grain boundary during loading, these dislocations remain locked during unloading.

  12. The functional importance of a pair of conserved glutamic acid residues and of Ca2+ binding in the cbb3–type oxygen reductases from Rhodobacter sphaeroides and Vibrio cholerae

    Science.gov (United States)

    Ouyang, Hanlin; Han, Huazhi; Roh, Jung H.; Hemp, James; Hosler, Jonathan P.; Gennis, Robert B.

    2012-01-01

    The cbb3-type cytochrome c oxidases are members of the heme-copper proton pumping respiratory oxygen reductases. The structure of the cbb3-type oxidase from Pseudomonas stutzeri reveals that, in addition to the six redox-active metal centers (two hemes b, three hemes c and CuB), the enzyme also contains at least one Ca2+. The calcium bridges two propionate carboxyls at the interface between the low-spin heme b and the active-site heme b3 and, in addition, is ligated to a serine in subunit CcoO and by a glutamate in CcoN. The glutamate that is ligated to Ca2+ is one of a pair of glutamic acid residues that has previously been suggested to be part of a proton exit pathway for pumped protons. In the current work, mutants in these glutamates are investigated in the cbb3-type oxidases from Vibrio cholerae and from Rhodobacter sphaeroides. Metal analysis shows that each of these wild type enzymes contains Ca2+. Mutations of the glutamate expected to ligate the Ca2+ in each of these enzymes (E126 in V. cholerae; E180 in R. sphaeroides) result in the loss of activity as well as loss of Ca2+. Mutations in the nearby glutamate (E129 in V. cholerae; E183 in R. sphaeroides) also resulted in loss of oxidase activity and loss of Ca2+. It is concluded that the Ca2+ is essential for assembly of the fully functional enzyme and that neither of the glutamates is likely to be part of a pathway for pumped protons within the cbb3-type oxygen reductases. A more likely role for these glutamates is the maintenance of the structural integrity of the active conformation of the enzyme. PMID:22913716

  13. 三唑酮在设施栽培土壤及大白菜中的消解动态及残留%Degradation Dynamics and Residues of Triadimefon in Protected Cultivation Soil and Chinese cabbage

    Institute of Scientific and Technical Information of China (English)

    邵金良; 佴注; 刘宏程; 杨东顺; 邹艳虹; 杜丽娟; 王志飞; 樊建麟

    2012-01-01

    为评价三唑酮在大白菜施用后的环境安全性,建立了GC测定蔬菜及土壤中三唑酮残留的方法,进行露地与设施栽培条件三唑酮在大白莱和土壤中的消解动态和最终残留研究.在大白菜和土壤中的最低检测质量分数均为0.001 mg/kg,三唑酮的平均加标回收率为81.5%~110.6%,变异系数为1.32%~6.04%.消解动态试验为2倍推荐使用剂量施药1次,三唑酮在设施栽培大白菜的半衰期分别为2.72~3.30 d和3.21~3.35 d;露地栽培为2.35~2.87 d和2.30~3.12 d.设施栽培大白菜中三唑酮残留量与用药量正相关,随着施药量的增加,消解速度减慢,残留量相应增大.研究可为制定三唑酮设施栽培大白菜上最大残留限量和合理使用准则以及风险评估提供科学依据.%In order to definitude environmental safety and establish safe application standard, residue dynamics and final residue of Iriadimefon were comparatively studied by the method of GC in soil and Chinese cabbage in open field and greenhouse. The results showed that the limit of quantification in Chinese cabbage and soil were 0.001 mg/kg for Iriadimefon. Average fortified recovery of the method varied from 81.5% to 110.6% with the relative standard deviation ranging from 1.32% to 6.04%. The half-lives of triadimefon in greenhouse Chinese cabbage were 2.72 to 3.30 and 3.21 to 3.35 d, respectively, and those in open field were 2.35 to 2.87 d and 2.30 to 3.12 d. A positive correlation was found between pesticide residue in Chinese cabbage and pesticide dose. With the pesticide dose increased, the digestion rale of pesticide residue lowed down and the residual quantity increased. The scientific basis could be provided in the study for the establishment on the maximum residue limit of triadiraefon in greenhouse Chinese cabbage, setting up reasonable application rule, and risk assessment.

  14. Long-term stability of FeSO{sub 4} and H{sub 2}SO{sub 4} treated chromite ore processing residue (COPR): Importance of H{sup +} and SO{sub 4}{sup 2−}

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Xin [School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074 (China); School of Environmental Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074 (China); Zhang, Jingdong [School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074 (China); Wang, Linling, E-mail: wanglinling@mail.hust.edu.cn [School of Environmental Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074 (China); Chen, Jing, E-mail: chenjing@mail.hust.edu.cn [School of Environmental Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074 (China); Hou, Huijie; Yang, Jiakuan [School of Environmental Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074 (China); Lu, Xiaohua [School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074 (China)

    2017-01-05

    Highlights: • The long-term stability of the FeSO{sub 4}-H{sub 2}SO{sub 4} treated COPR was evaluated. • Reliable long-term stability for samples curing 400 days was achieved. • H{sub 2}SO{sub 4} significantly enhanced the stabilization efficiency of COPR using FeSO{sub 4}. • H{sup +} and SO{sub 4}{sup 2−} both reinforced Cr(VI) release from COPR core to react with Fe(II). - Abstract: In this study, the long-term stability of Cr(VI) in the FeSO{sub 4} and H{sub 2}SO{sub 4} (FeSO{sub 4}-H{sub 2}SO{sub 4}) treated chromite ore processing residue (COPR) after 400 curing days and the stabilization mechanisms were investigated. FeSO{sub 4}-H{sub 2}SO{sub 4} treatment significantly reduced toxicity characteristic leaching procedure (TCLP) and synthetic precipitation leaching procedure (SPLP) Cr(VI) concentrations to lower than the regulatory limit of 1.5 mg L{sup −1} (HJ/T 301-2007, China EPA) even for the samples curing 400 days, achieving an outstanding long-term stability. Our independent leaching tests revealed that H{sup +} and SO{sub 4}{sup 2−} have synergistic effect on promoting the release of Cr(VI), which would make Cr(VI) easier accessed by Fe(II) during stabilization. The contributions of H{sup +} and SO{sub 4}{sup 2−} to Cr(VI) release ratio were 25%–44% and 19%–38%, respectively, as 5 mol H{sub 2}SO{sub 4} per kg COPR was used. X-ray powder diffraction (XRD), X-ray photoelectron spectroscopy (XPS) and alkaline digestion analyses were also employed to interpret the possible stabilization mechanism. Cr(VI) released from COPR solid was reduced to Cr(III) by Fe(II), and then formed stable Fe{sub x}Cr{sub (1−x)}(OH){sub 3} precipitate. This study provides a facile and reliable scheme for COPR stabilization, and verifies the excellent long-term stability of the FeSO{sub 4}-H{sub 2}SO{sub 4} treated COPR.

  15. Ser⁄ Thr residues at α3⁄β5 loop of Gαs are important in morphine-induced adenylyl cyclase sensitization but not mitogen-activated protein kinase phosphorylation

    Science.gov (United States)

    Seyedabadi, Mohammad; Ostad, Seyed Nasser; Albert, Paul R.; Dehpour, Ahmad R.; Rahimian, Reza; Ghazi-Khansari, Mahmoud; Ghahremani, Mohammad H.

    2015-01-01

    The signaling switch of β2-adrenergic and μ1-opioid receptors from stimulatory G-protein (Gαs) to inhibitory G-protein (Gαi) (and vice versa) influences adenylyl cyclase (AC) and extracellular-regulated kinase (ERK)1 ⁄ 2 activation. Post-translational modifications, including dephosphorylation of Gαs, enhance opioid receptor coupling to Gαs. In the present study, we substituted the Ser ⁄ Thr residues of Gαs at the α3 ⁄ β5 and α4 ⁄ β6 loops aiming to study the role of Gαs lacking Ser ⁄ Thr phosphorylation with respect to AC sensitization and mitogen-activated protein kinase activation. Isoproterenol increased the cAMP concentration (EC50 = 22.8 ± 3.4 μM) in Gαs-transfected S49 cyc– cells but not in nontransfected cells. However, there was no significant difference between the Gαs-wild-type (wt) and mutants. Morphine (10 μM) inhibited AC activity more efficiently in cyc– compared to Gαs-wt introduced cells (P < 0.05); however, we did not find a notable difference between Gαs-wt and mutants. Interestingly, Gαs-wt transfected cells showed more sensitization with respect to AC after chronic morphine compared to nontransfected cells (101 ± 12% versus 34 ± 6%; P < 0.001); μ1-opioid receptor interacted with Gαs, and both co-immunoprecipitated after chronic morphine exposure. Furthermore, mutation of T270A and S272A (P < 0.01), as well as T270A, S272A and S261A (P < 0.05), in α3 ⁄ β5, resulted in a higher level of AC supersensitization. ERK1⁄ 2 phosphorylation was rapidly induced by isoproterenol (by 9.5 ± 2.4-fold) and morphine (22 ± 2.2-fold) in Gαs-transfected cells; mutations of α3 ⁄ β5 and α4 ⁄ β6 did not affect the pattern or extent of mitogen-activated protein kinase activation. The findings of the present study show that Gαs interacts with the μ1-opioid receptor, and the Ser ⁄ Thr mutation to Ala at the α3 ⁄ β5 loop of Gαs enhances morphine-induced AC sensitization. In addition, Gαs was required for

  16. Behavior of peptides combining 1 alanine residue and 8 glycine residues on papain associated with structural fluctuations

    Science.gov (United States)

    Nishiyama, Katsuhiko

    2011-12-01

    I investigated the behavior of the peptides combining 1 ALA residue and 8 GLY residues on papain associated with structural fluctuations via molecular dynamics and docking simulations. Although the chance of binding to sites near the active center of papain was reduced by replacing the GLY residue in 9GLY with ALA residue, binding stability was improved by the replacement. Furthermore, both the chance and binding stability were greatly affected by positioning of ALA residue in the peptides. Residue in peptides should be replaced in view of the balance between chance of binding to sites near active center and binding stability.

  17. Residual stresses in welded plates

    Science.gov (United States)

    Bernstein, Edward L.

    1994-01-01

    The purpose of this project was to develop a simple model which could be used to study residual stress. The mechanism that results in residual stresses in the welding process starts with the deposition of molten weld metal which heats the immediately adjacent material. After solidification of weld material, normal thermal shrinkage is resisted by the adjacent, cooler material. When the thermal strain exceeds the elastic strain corresponding to the yield point stress, the stress level is limited by this value, which decreases with increasing temperature. Cooling then causes elastic unloading which is restrained by the adjoining material. Permanent plastic strain occurs, and tension is caused in the region immediately adjacent to the weld material. Compression arises in the metal farther from the weld in order to maintain overall static equilibrium. Subsequent repair welds may add to the level of residual stresses. The level of residual stress is related to the onset of fracture during welding. Thus, it is of great importance to be able to predict the level of residual stresses remaining after a weld procedure, and to determine the factors, such as weld speed, temperature, direction, and number of passes, which may affect the magnitude of remaining residual stress. It was hoped to use traditional analytical modeling techniques so that it would be easier to comprehend the effect of these variables on the resulting stress. This approach was chosen in place of finite element methods so as to facilitate the understanding of the physical processes. The accuracy of the results was checked with some existing experimental studies giving residual stress levels found from x-ray diffraction measurements.

  18. 敌敌畏、 溴氰菊酯、三氟氯氰菊酯在香蕉上的残留动态%Residual Dynamics of Dichlorvos, Deltamethrin and Cyhalothrin in Bananas

    Institute of Scientific and Technical Information of China (English)

    郭建辉; 杨淑娟; 陈丽萍; 蔡恩兴

    2011-01-01

    The residual dynamics of dichlorvos, deltamethrin and cyhalothrin in bananas were studied by the methods of the GC and the field experiment. Results indicated that the original sediment of the pesticides in bananas followed the order of dichlorvos >deltamethrin> cyhalothrin, which were closely related to their application dosage about the same pesticide. Dichlorvos could be dissipated rapidly, and the dissipation rate seemed all above 80% after applying 1 d and the residual contents were less than 0.005 mg/kg after applying 3 d. The residual degradation dynamics of deltamethrin and cyhalothrin in bananas could be followed first order kinetic equation. The equations of deltamethrin residual dynamics of the decommended and double dosage were C=0.1298×e-0.1201, and C=0.2489×e-0.11451, respectively, with T1/2 and T0.99 ranged from 5.8 d to 6.1 d, from 38.4 d to 40.3 d, respectively; and the equations of cyhalothrin residual dynamics of the decommended and double dosage were C =0.0339×e-0.07001, and C=0.0707×e-0.06951 respectively, with T1/2 and T0.99 ranged from 9.9 d to 10.0 d, from 65.8 d to 66.3 d respectively. The final residue of dichlorvos, deltamethrin and cyhalothrin was below 0.005 mg/kg, 0.01 mg/kg and 0.008 mg/kg separately 60-70 d after the second application. If dichlorvos, deltamethrin and cyhalothrin were applied scientifically and safely during banana production, the products quality was safe.%采用气相色谱法及田间试验方法,研究敌敌畏、溴氰菊酯、三氟氯氰菊酯在香蕉上的残留动态.结果表明,在香蕉上的原始沉积量,敌敌畏>溴氰菊酯>三氟氯氰菊酯,同一农药的原始沉积量与施用量密切相关.敌敌畏在香蕉上消解迅速,在施药1d后消解率均在80%以上,施药后3d的残留量≤0.005 mg/kg.溴氰菊酯、三氟氯氰菊酯在香蕉上的残留消解动态符合一级动力学方程,溴氰菊酯推荐剂量为C=0.129 8xe-0.120 1t,加倍剂量为C=0.248 9×e-0.114 5t

  19. Evaluation and optimization of nutritional and environmental impact of biogas residues; Bewertung und Optimierung der Naehrstoff- und Umweltwirkung von Gaerrueckstaenden aus der Biogasgewinnung

    Energy Technology Data Exchange (ETDEWEB)

    Lichti, Fabian Heribert

    2013-04-29

    On the basis of the dynamic growth of biogas plants in Germany the fertilization with biogas residues has obtained an important role for recirculation of plant nutrients, particularly with regard to nitrogen. In this work the effect of N nutrition with biogas residues was assessed in a 3-year on-field trial conducted at four sites throughout Bavaria. The fertilizing effects were tested by varying rate and time of biogas residues application, using different application techniques and the addition of nitrification inhibitors on several crops. The biogas residues achieved mineral fertilizer equivalents of 30 - 45 %. Overall, the untreated biogas residues showed a slightly increased N efficiency compared to cattle manure, whereas particularly site-dependent differences resulted in large differences in N efficiency of biogas residues.

  20. Dynamical Mapping of Anopheles darlingi Densities in a Residual Malaria Transmission Area of French Guiana by Using Remote Sensing and Meteorological Data

    Science.gov (United States)

    Adde, Antoine; Roux, Emmanuel; Mangeas, Morgan; Dessay, Nadine; Nacher, Mathieu; Dusfour, Isabelle; Girod, Romain; Briolant, Sébastien

    2016-01-01

    Local variation in the density of Anopheles mosquitoes and the risk of exposure to bites are essential to explain the spatial and temporal heterogeneities in the transmission of malaria. Vector distribution is driven by environmental factors. Based on variables derived from satellite imagery and meteorological observations, this study aimed to dynamically model and map the densities of Anopheles darlingi in the municipality of Saint-Georges de l’Oyapock (French Guiana). Longitudinal sampling sessions of An. darlingi densities were conducted between September 2012 and October 2014. Landscape and meteorological data were collected and processed to extract a panel of variables that were potentially related to An. darlingi ecology. Based on these data, a robust methodology was formed to estimate a statistical predictive model of the spatial-temporal variations in the densities of An. darlingi in Saint-Georges de l’Oyapock. The final cross-validated model integrated two landscape variables—dense forest surface and built surface—together with four meteorological variables related to rainfall, evapotranspiration, and the minimal and maximal temperatures. Extrapolation of the model allowed the generation of predictive weekly maps of An. darlingi densities at a resolution of 10-m. Our results supported the use of satellite imagery and meteorological data to predict malaria vector densities. Such fine-scale modeling approach might be a useful tool for health authorities to plan control strategies and social communication in a cost-effective, targeted, and timely manner. PMID:27749938

  1. 咪鲜胺在人参和土壤中的残留动态及安全性评价%Residual dynamics and safety evaluation of prochloraz in ginseng and soil

    Institute of Scientific and Technical Information of China (English)

    王燕; 王春伟; 高洁; 崔丽丽; 吕雁斌

    2014-01-01

    To determine the residual dynamics and environmental safety of prochloraz 25% EC and ensure the quality safety of ginseng products, a high performance liquid chromatography coupled with electrospray mass spectrometry (HPLC-MS/MS) method was developed for determining residual dynamics and final residues of prochloraz in ginseng root, stem, leaf and soil. The samples were extracted with acetonitrile, cleaned-up with PSA solid phase extraction cartridge, separated by liquid chromatography and analyzed with the multiple reaction monitoring (MRM) in positive ion mode by employing the external standard method, using electron spray ionization source (ESI). The results show-ed that the recoveries of prochloraz were 86.8%-90.8%, and the relative standard deviations were 3.95%-7.15%in ginseng root, stem, leaf and soil. The half-lives of prochloraz were from 8.39 to 13.20 d at spraying dosage of 1 000 g·hm-2. Final residues of prochloraz were less 0.0417 mg·kg-1 in ginseng root, stem, leaf and soil, below the MRLs of Japan (0.05 mg·kg-1), EU (0.20 mg·kg-1) and Korea (0.30 mg·kg-1) over 60 d, which at spraying dosage range from 500 to 1 000 g·hm-2. Therefore, it is safe to apply prochloraz to ginseng at the recommended dosage.%为明确人参中咪鲜胺的残留量及环境安全性,确保人参产品质量安全,采用高效液相色谱-串联质谱法测定25%咪鲜胺乳油在人参根、茎、叶及土壤中的残留动态及最终残留量。样品经乙腈提取,PSA固相萃取柱净化后以液相色谱分离,采用电喷雾电离源,以质谱正离子扫描多反应监测模式进行定量分析,外标法定量。结果表明,咪鲜胺在人参根、茎、叶及土壤中的回收率为86.8%~90.8%,相对标准偏差为3.95%~7.15%。施药剂量为1000 g·hm-2(以有效成分计)时,咪鲜胺在人参根、茎、叶和土壤中的降解半衰期为8.39~13.20 d。施药剂量为500~1000 g·hm-2时,施药后60 d咪鲜胺在人参根、茎、

  2. Residual Dynamics of Dry 50% Kresoxim-methyl Suspending Agent in Strawberry and Soil%醚菌酯50%干悬浮剂在草莓及土壤中的残留动态研究

    Institute of Scientific and Technical Information of China (English)

    李辉; 张玉婷; 郭永泽; 邵辉; 刘磊; 宋淑荣

    2009-01-01

    [Objective]The research aimed to make clear the residual dynamics of kresoxim-methyl in strawberry and soil.[Method] Two dosages of solution diluted at 3 000 times and 2 000 times were applied in Tianjin,Jilin,Nanjing and Kunming in 2007~2008,the degradation dynamics and final residue of dry 50% kresoxim-methyl suspending agent in strawberry and soil were tested.[Result] The half-life of kresoxim-methyl was 6.4 d in strawberry and 12.6 d in soil in Tianjin area; the half-life of kresoxim-methyl was 8.3 d in strawberry and 16.2 d in soil in Jilin; the half-life of kresoxim-methyl was 5.2 d in strawberry and 8.3 d in soil in Nanjing; the half-life of kresoxim-methyl in Kunming was 6.3 d in strawberry and 12.3 d in soil.The kresoxim-methyl residues in strawberry were all lower than 1 mg/kg for interval of 3,5,7 and 14 d after pesticide application.[Conclusion] The rule of reasonable use of 50% kresoxim-methyl DF in strawberry was:spraying on strawberry for 3 times by the drug solution diluted at 3 000 times and the safety interval time was 3 d.The recommended value of the highest residue limit was 1 mg/kg.%[目的]明确醚菌酯在草莓和土壤中的残留动态情况. [方法] 于2007~2008年,在天津、吉林、南京和昆明,设3 000倍液和2 000倍液2个剂量,对醚菌酯50%干悬浮剂在草莓及土壤中的消解动态和最终残留量进行了试验.[结果] 在天津地区,醚菌酯在草莓和土壤中的半衰期分别为6.4 和12.6 d;在吉林地区,醚菌酯在草莓和土壤中的半衰期分别为8.3 和16.2 d;在南京地区,醚菌酯在草莓和土壤中的半衰期分别为5.2 和8.3 d;在昆明地区,醚菌酯在草莓和土壤中的半衰期分别为6.3和12.3 d.施药后间隔3、5、7 和14 d的草莓中醚菌酯的残留量均低于1 mg/kg.[结论] 醚菌酯50%干悬浮剂在草莓中合理使用的准则为:按3 000倍液在草莓上喷雾使用3次,安全间隔期为3 d,最高残留限量推荐值为1 mg/kg.

  3. Decreasing residual aluminum level in drinking water

    Institute of Scientific and Technical Information of China (English)

    王志红; 崔福义

    2004-01-01

    The relativity of coagulant dosage, residual turbidity, temperature, pH etc. with residual aluminum concentration were investigated, and several important conclusions were achieved. Firstly, dosage of alum-coagulant or PAC1 influences residual aluminum concentration greatly. There is an optimal-dosage-to-aluminum, a bit less than the optimal-dosage-to-turbidity. Secondly, it proposes that decreasing residual aluminum concentration can be theoretically divided into two methods, either decreasing (even removing) the concentration of particulate aluminum component, or decreasing dissolved aluminum. In these tests there is an optimal value of residual turbidity of postprecipitation at 7.0 NTU. Thirdly, residual aluminum level will increase while water temperature goes higher. At the last, optimal pH value corresponds a minimum dissolved aluminum at a given turbidity. Data shows the optimal pH value decreases with water temperature's increasing.

  4. Dynamics

    CERN Document Server

    Goodman, Lawrence E

    2001-01-01

    Beginning text presents complete theoretical treatment of mechanical model systems and deals with technological applications. Topics include introduction to calculus of vectors, particle motion, dynamics of particle systems and plane rigid bodies, technical applications in plane motions, theory of mechanical vibrations, and more. Exercises and answers appear in each chapter.

  5. Histidine at Residue 99 and the Transmembrane Region of the Precursor Membrane prM Protein Are Important for the prM-E Heterodimeric Complex Formation of Japanese Encephalitis Virus

    OpenAIRE

    Lin, Ying-Ju; Wu, Suh-Chin

    2005-01-01

    The formation of the flavivirus prM-E complex is an important step for the biogenesis of immature virions, which is followed by a subsequent cleavage of prM to M protein through cellular protease to result in the production and release of mature virions. In this study, the intracellular formation of the prM-E complex of Japanese encephalitis virus was investigated by baculovirus coexpression of prM and E in trans in Sf9 insect cells as analyzed by anti-E antibody immunoprecipitation and sucro...

  6. The Lysine Residues within the Human Ribosomal Protein S17 Sequence Naturally Inserted into the Viral Nonstructural Protein of a Unique Strain of Hepatitis E Virus Are Important for Enhanced Virus Replication

    OpenAIRE

    Kenney, Scott P.; Meng, Xiang-Jin

    2015-01-01

    Hepatitis E virus (HEV) is an important but extremely understudied human pathogen. Due largely to the lack of an efficient cell culture system for HEV, the molecular mechanisms of HEV replication and pathogenesis are poorly understood. Recently, a unique genotype 3 strain of HEV recovered from a chronically infected patient was adapted for growth in HepG2C3A human hepatoma cells. The adaptation of the Kernow C-1 P6 HEV to propagate in HepG2C3A cells selected for a rare virus recombinant that ...

  7. Two arginine residues suppress the flexibility of nucleosomal DNA in the canonical nucleosome core.

    Science.gov (United States)

    Kono, Hidetoshi; Shirayama, Kazuyoshi; Arimura, Yasuhiro; Tachiwana, Hiroaki; Kurumizaka, Hitoshi

    2015-01-01

    The dynamics of nucleosomes containing either canonical H3 or its centromere-specific variant CENP-A were investigated using molecular dynamics simulations. The simulations showed that the histone cores were structurally stable during simulation periods of 100 ns and 50 ns, while DNA was highly flexible at the entry and exit regions and partially dissociated from the histone core. In particular, approximately 20-25 bp of DNA at the entry and exit regions of the CENP-A nucleosome exhibited larger fluctuations than DNA at the entry and exit regions of the H3 nucleosome. Our detailed analysis clarified that this difference in dynamics was attributable to a difference in two basic amino acids in the αN helix; two arginine (Arg) residues in H3 were substituted by lysine (Lys) residues at the corresponding sites in CENP-A. The difference in the ability to form hydrogen bonds with DNA of these two residues regulated the flexibility of nucleosomal DNA at the entry and exit regions. Our exonuclease III assay consistently revealed that replacement of these two Arg residues in the H3 nucleosome by Lys enhanced endonuclease susceptibility, suggesting that the DNA ends of the CENP-A nucleosome are more flexible than those of the H3 nucleosome. This difference in the dynamics between the two types of nucleosomes may be important for forming higher order structures in different phases.

  8. Outdoor dynamic subject-specific evaluation of internal stresses in the residual limb: hydraulic energy-stored prosthetic foot compared to conventional energy-stored prosthetic feet.

    Science.gov (United States)

    Portnoy, Sigal; Kristal, Anat; Gefen, Amit; Siev-Ner, Itzhak

    2012-01-01

    The prosthetic foot plays an important role in propelling, breaking, balancing and supporting body loads while the amputee ambulates on different grounds. It is therefore important to quantify the effect of the prosthetic foot mechanism on biomechanical parameters, in order to prevent pressure ulcers and deep tissue injury. Our aim was to monitor the internal stresses in the residuum of transtibial amputation (TTA) prosthetic-users ambulating on different terrains, which the amputees encounter during their daily activities, i.e. paved floor, grass, ascending and descending stairs and slope. We specifically aimed to compare between the internal stresses in the TTA residuum of amputees ambulating with a novel hydraulic prosthetic foot compared to conventional energy storage and return (ESR) prosthetic feet. Monitoring of internal stresses was accomplished using a portable subject-specific real-time internal stress monitor. We found significant decrease (phydraulic foot, compared to walking with ESR feet. The loading rate calculated while ambulating with the hydraulic foot was at least three times lower than the loading rate calculated while ambulating with the ESR foot. Although the average decrease in internal stresses was ≈ 2-fold larger when replacing single-toe ESR feet with the hydraulic foot than when replacing split-toed ESR feet with the hydraulic foot, the differences were statistically insignificant. Our findings suggest that using a hydraulic prosthetic foot may protect the distal tibial end of the TTA residuum from high stresses, therefore preventing pressure-related injury and pain.

  9. The Importance of the Strictly Conserved, C-terminal Glycine Residue in Phosphoenolpyruvate Carboxylase for Overall Catalysis: Mutagenesis and Truncation of GLY-961 in the Sorghum C4 Leaf Isoform

    Energy Technology Data Exchange (ETDEWEB)

    Xu,W.; Ahmed, S.; Moriyama, H.; Chollet, R.

    2006-01-01

    Phosphoenolpyruvate carboxylase (PEPC) is a 'multifaceted', allosteric enzyme involved in C4 acid metabolism in green plants/microalgae and prokaryotes. Before the elucidation of the three-dimensional structures of maize C4 leaf and Escherichia coli PEPC, our truncation analysis of the sorghum C4 homologue revealed important roles for the enzyme's C-terminal {alpha}-helix and its appended QNTG{sup 961} tetrapeptide in polypeptide stability and overall catalysis, respectively. Collectively, these functional and structural observations implicate the importance of the PEPC C-terminal tetrapeptide for both catalysis and negative allosteric regulation. We have now more finely dissected this element of PEPC structure-function by modification of the absolutely conserved C-terminal glycine of the sorghum C4 isoform by site-specific mutagenesis (G961(A/V/D)) and truncation ({Delta}C1/C4). Although the C4 polypeptide failed to accumulate in a PEPC{sup -} strain (XH11) of E. coli transformed with the Asp mutant, the other variants were produced at wild-type levels. Although neither of these four mutants displayed an apparent destabilization of the purified PEPC homotetramer, all were compromised catalytically in vivo and in vitro. Functional complementation of XH11 cells under selective growth conditions was restricted progressively by the Ala, {Delta}C1 and Val, and {Delta}C4 modifications. Likewise, steady-state kinetic analysis of the purified mutant enzymes revealed corresponding negative trends in k{sub cat} and k{sub cat}/K0.5 (phosphoenolpyruvate) but not in K{sub 0.5} or the Hill coefficient. Homology modeling of these sorghum C-terminal variants against the structure of the closely related maize C4 isoform predicted perturbations in active-site molecular cavities and/or ion-pairing with essential, invariant Arg-638. These collective observations reveal that even a modest, neutral alteration of the PEPC C-terminal hydrogen atom side chain is detrimental

  10. Seasonal structure and dynamics of sarcosaprophagous fauna on pig carrion in a rural area of Cordoba (Argentina): their importance in forensic science.

    Science.gov (United States)

    Battán Horenstein, Moira; Rosso, Beatriz; García, M Dolores

    2012-04-10

    Four experiments, one in each season, were carried out during 2004 in a rural area of Córdoba, central Argentina. Two pigs (Sus scrofa L.), weighing approximately 8 kg each, were used in each of the four experiments. The animals were killed by a sharp blow to the head and immediately placed in an appropriate arthropod trap. One pig was placed in the shade and the other under direct sunlight. This research was conducted to determine the seasonal structure and dynamics of arthropods that constitute the sarcosaprophagous community in a given area of the central region of Argentina. The decomposition process was divided into five stages: fresh, bloated, decay, advanced decay and dry. The duration of each stage varied in different seasons, showing that the temperature and humidity are the most important variables that influence this process. A total of 51,500 adults and 36,909 immature were collected. More than 80% of the specimens collected belong to Insecta, and within this, Diptera were the most abundant order. The flies were mainly represented by adults and immature of the following species: Chrysomya albiceps (Wiedemann) (Calliphoridae), Musca domestica Linnaeus (Muscidae) and Fannia femoralis (Stein) (Fanniidae). Coleoptera were mainly represented by adults and immature of the species Creophilus maxillosus (Linnaeus) (Staphylinidae) and Dermestes maculatus (Geer) (Dermestidae). More than 50% of hymenopteran fauna collected belong to Formicidae. The trophic levels associated with the decomposition of the remains included five categories: necrophagous, parasites and predators of the necrophagous species, omnivores, opportunists and adventives. During faunal succession a strong dominance of the necrophagous species of the family Calliphoridae and Muscidae was observed, mainly during the early stages of decay process in all seasons.

  11. 阿特拉津和乙草胺在玉米和土壤中残留动态研究%Study on the Residue Dynamics of Atrazine and Acetochlor in Maize and Soil

    Institute of Scientific and Technical Information of China (English)

    王姗姗; 王颜红; 王万红; 谢娟; 王世成

    2011-01-01

    采用田间试验和气相色谱-质谱(GC-MS)联用的检测方法研究了阿特拉津和乙草胺在玉米和土壤中的消解动态及最终残留规律。结果表明,该方法阿特拉津最低检出浓度为0.08 ng g-1,添加浓度在10~250 ng g-1范围内,回收率在85%~97%之间,相对标准偏差(RSD)在10.0%~14.4%之间;乙草胺最低检出浓度为0.40 ng g-1,添加浓度在10~250 ng g-1范围内,回收率在102%~109%之间,相对标准偏差(RSD)在9.7%~14.0%之间。阿特拉津和乙草胺在土壤中的消解动态方程分别为C=1942.7e-0.0492T和C=916.53e-0.0343T,降解半衰期分别为14.1 d和20.2 d。38%阿特拉津水悬浮液、900 g L-1乙草胺乳油剂用于玉米田除草,施药剂量分别为5.25~10.50 g hm-2、2.25~4.50 g hm-2,在玉米播种后出苗前施药,施药1次,收获期玉米籽粒中阿特拉津残留量低于0.08 ng g-1、乙草胺残留量低于0.40 ng g-1,土壤中阿特拉津残留量低于3.3 ng g-1、乙草胺残留量低于12.4 ng g-1,均满足相应的限量标准。%Field trials and Gas Chromatography-Mass Spectrum(GC-MS) were conducted to study the residual dynamics and final residues of atrazine and acetochlor which were widely used as herbicides in maize and soil.The results showed that,the limits of determination for the atrazine and acetochlor were 0.08 ng g-1 and 0.40 ng g-1,respectively.When the added concentration of atrazine and acetochlor ranged from 10 ng g-1 to 250 ng g-1,the recoveries changed individually from 85% to 97% and from 102% to 109%,and their respective relative standard deviations varied from 10.0% to 14.4% and from 9.7% to 14.0%,respectively.The kinetic equations of atrazine and acetochlor degradation in soil were C=1942.7e-0.0492T and C=916.53e-0.0343T and the half lives were 14.1 d and 20.2 d,respectively.According to the research,if atrazine and acetochlor were sprayed between maize sowing and seedling emergence,and when atrazine 38% aqueous suspension concentrate

  12. Mass Losses and Nitrogen and Phosphorous Dynamics during the Decomposition of Different Organic Residues of Triploid Populus tomentosa%三倍体毛白杨不同有机残体分解及氮磷释放特征

    Institute of Scientific and Technical Information of China (English)

    宋曰钦; 谢宗强; 翟明普; 贾黎明

    2014-01-01

    采用网袋法研究三倍体毛白杨落叶、小枝(直径小于0.5 cm)、细根(直径小于2mm)和皮的分解速率以及 N,P动态。结果表明:4种有机残体在357天中分解速率存在显著性差异,到试验结束时(2008年11月)细根的分解率最大(42.5%),其次是落叶(30.5%)和皮(26.0%),小枝的分解率最低(20.9%); Olson指数方程对4种有机残体的分解拟合效果较好,相关系数 R2为0.96~0.98,由此计算得到4种有机残体的年分解率分别为42.88%,31.74%,26.25%和20.54%;不同有机残体分解初期存在 N,P元素富集现象,但富集程度与富集持续的时间存在差异,细根、叶、皮、小枝中 N 的富集度分别为11.6%,127.2%,122.6%和126.7%,P 的富集度分别为105.9%,172.9%,123.0%和163.9%,因此N,P的富集度均以叶最高,以细根最低;从富集持续的时间来看,细根、叶、皮、小枝中的 N富集持续时间分别为205,239,297和265天,以皮持续的时间最长,P 富集持续的时间分别是205,205,265和239天,以小枝持续的时间最长;从不同有机残体释放的N,P量来看,细根释放量最多,其次是叶,皮和小枝释放量较少。三倍体毛白杨纸浆林中不同有机残体在养分归还上存在不同特点,尤其是皮和小枝分解率低,养分富集持续时间长,今后应采取针对性措施加快其分解,以不断提高林地生产力。%In order to understand the decomposition rate and nutrient dynamic of different organic residues of triploid Populus tomentoza,and to find out feasible ways for maintaining and improving long - term soil productivity,litterbag method was used to investigate the decomposition rate and macro nutrients( N,P) release of leaf litter,fine branch litter (≤5 mm) ,fine root litter(≤2 mm) and bark litter for 357 days. By the end of experiment,decomposition rates of fine root litter,leaf litter,bark litter and fine branch

  13. Effect of Residue Nitrogen Concentration and Time Duration on Carbon Mineralization Rate of Alfalfa Residues in Regions with Different Climatic Conditions

    Directory of Open Access Journals (Sweden)

    saeid shafiei

    2017-01-01

    Full Text Available Introduction Various factors like climatic conditions, vegetation, soil properties, topography, time, plant residue quality and crop management strategies affect the decomposition rate of organic carbon (OC and its residence time in soil. Plant residue management concerns nutrients recycling, carbon recycling in ecosystems and the increasing CO2 concentration in the atmosphere. Plant residue decomposition is a fundamental process in recycling of organic matter and elements in most ecosystems. Soil management, particularly plant residue management, changes soil organic matter both qualitatively and quantitatively. Soil respiration and carbon loss are affected by soil temperature, soil moisture, air temperature, solar radiation and precipitation. In natural agro-ecosystems, residue contains different concentrations of nitrogen. It is important to understand the rate and processes involved in plant residue decomposition, as these residues continue to be added to the soil under different weather conditions, especially in arid and semi-arid climates. Material and methods Organic carbon mineralization of alfalfa residue with different nitrogen concentrations was assessed in different climatic conditions using split-plot experiments over time and the effects of climate was determined using composite analysis. The climatic conditions were classified as warm-arid (Jiroft, temperate arid (Narab and cold semi-arid (Sardouiyeh using cluster analysis and the nitrogen (N concentrations of alfalfa residue were low, medium and high. The alfalfa residue incubated for four different time periods (2, 4, 6 and 8 months. The dynamics of organic carbon in different regions measured using litter bags (20×10 cm containing 20 g alfalfa residue of 2-10 mm length which were placed on the soil surface. Results and discussion The results of this study showed that in a warm-arid (Jiroft, carbon loss and the carbon decomposition rate constant were low in a cold semi

  14. Dinâmica do potássio nos resíduos vegetais de plantas de cobertura no Cerrado Potassium dynamics in crop residues of cover plants in Cerrado

    Directory of Open Access Journals (Sweden)

    José Luiz Rodrigues Torres

    2008-08-01

    Full Text Available A produção de biomassa, a manutenção dos resíduos vegetais sobre o solo e sua posterior decomposição são fatores de grande importância no estudo da ciclagem de nutrientes. Este estudo foi desenvolvido na área experimental do CEFET-Uberaba-MG, onde foram avaliados oito tipos de coberturas vegetais: milheto (Pennisetum americanum sin. tiphoydes, braquiária (Brachiaria brizantha, sorgo-forrageiro (Sorghum bicolor L. Moench, guandu (Cajanus cajan (L. Mill sp., crotalária (Crotalarea juncea, aveia-preta (Avena strigosa Schreb, pousio e área em preparo convencional de solo (testemunha em área de Cerrado, na região do Triângulo Mineiro. Avaliaram-se a fitomassa seca (FS, a decomposição dos resíduos em bolsas de decomposição, e a liberação de K. Utilizou-se um modelo matemático para descrever a decomposição dos resíduos e a liberação de K, e calcularam-se a constante de decomposição (k e o tempo de meia-vida (T½. O milheto, o sorgo e a crotalária foram as coberturas que apresentaram maiores produções de matéria seca. O maior acúmulo de K ocorreu em gramíneas e a maior liberação de K ocorreu no milheto, aveia, braquiária e crotalária nos primeiros 42 dias após manejo, nos dois períodos avaliados. A braquiária apresentou o menor T½ vida e a maior taxa de liberação de K.Crop residue production, plant residue maintenance and their decomposition are important factors in the understanding of nutrient recycling process. To evaluate K accumulation and release a study with eight cover crops types was developed: pearl millet (Pennisetum americanum sin. tiphoydes, brachiaria grass (Brachiaria brizantha, sorghum (Sorghum bicolor L. Moench, pigeonpea (Cajanus cajan (L. Millsp, sunn hemp (Crotalarea juncea and black oats (Avena strigosa Schreb, fallow land and conventional culture (control in the experimental area of CEFET-Uberaba-MG, in a Cerrado area. The dry mass production, crop residue decomposition in litter bags

  15. On Line Current Monitoring and Application of a Residual Method for Eccentricity Fault Detection

    Directory of Open Access Journals (Sweden)

    METATLA, A.

    2011-02-01

    Full Text Available This work concerns the monitoring and diagnosis of faults in induction motors. We develop an approach based on residual analysis of stator currents to detect and diagnose faults eccentricity static, dynamic and mixed in three phase induction motor. To simulate the behavior of motor failure, a model is proposed based on the approach of magnetically coupled coils. The simulation results show the importance of the approach applied for the detection and diagnosis of fault in three phase induction motor.

  16. The Research of Welding Residual Stress Based Finite Element Method

    Directory of Open Access Journals (Sweden)

    Qinghua Bai

    2013-06-01

    Full Text Available Welding residual stress was caused by local heating during the welding process, tensile residual stress reduce fatigue strength and corrosion resistance, Compressive residual stress decreases stability limit. So it will produce brittle fracture, reduce working life and strength of workpiece; Based on the simulation of welding process with finite element method, calculate the welding temperature field and residual stress, and then measure residual stress in experiments, So as to get the best welding technology and welding parameters, to reduce welding residual stress effective, it has very important significance.

  17. The role of basic residues in the adsorption of blood proteins onto the graphene surface

    Science.gov (United States)

    Gu, Zonglin; Yang, Zaixing; Wang, Lingle; Zhou, Hong; Jimenez-Cruz, Camilo A.; Zhou, Ruhong

    2015-06-01

    With its many unique properties, graphene has shown great potential in various biomedical applications, while its biocompatibility has also attracted growing concerns. Previous studies have shown that the formation of protein-graphene corona could effectively reduce its cytotoxicity; however, the underlying molecular mechanism remains not well-understood. Herein, we use extensive molecular dynamics simulations to demonstrate that blood proteins such as bovine fibrinogen (BFG) can absorb onto the graphene surface quickly and tightly to form a corona complex. Aromatic residues contributed significantly during this adsorption process due to the strong π-π stacking interactions between their aromatic rings and the graphene sp2-carbons. Somewhat surprisingly, basic residues like arginine, also played an equally or even stronger role during this process. The strong dispersion interactions between the sidechains of these solvent-exposed basic residues and the graphene surface provide the driving force for a tight binding of these basic residues. To the best of our knowledge, this is the first study with blood proteins to show that, in addition to the aromatic residues, the basic residues also play an important role in the formation of protein-graphene corona complexes.

  18. Residual perception of biological motion in cortical blindness.

    Science.gov (United States)

    Ruffieux, Nicolas; Ramon, Meike; Lao, Junpeng; Colombo, Françoise; Stacchi, Lisa; Borruat, François-Xavier; Accolla, Ettore; Annoni, Jean-Marie; Caldara, Roberto

    2016-12-01

    From birth, the human visual system shows a remarkable sensitivity for perceiving biological motion. This visual ability relies on a distributed network of brain regions and can be preserved even after damage of high-level ventral visual areas. However, it remains unknown whether this critical biological skill can withstand the loss of vision following bilateral striate damage. To address this question, we tested the categorization of human and animal biological motion in BC, a rare case of cortical blindness after anoxia-induced bilateral striate damage. The severity of his impairment, encompassing various aspects of vision (i.e., color, shape, face, and object recognition) and causing blind-like behavior, contrasts with a residual ability to process motion. We presented BC with static or dynamic point-light displays (PLDs) of human or animal walkers. These stimuli were presented either individually, or in pairs in two alternative forced choice (2AFC) tasks. When confronted with individual PLDs, the patient was unable to categorize the stimuli, irrespective of whether they were static or dynamic. In the 2AFC task, BC exhibited appropriate eye movements towards diagnostic information, but performed at chance level with static PLDs, in stark contrast to his ability to efficiently categorize dynamic biological agents. This striking ability to categorize biological motion provided top-down information is important for at least two reasons. Firstly, it emphasizes the importance of assessing patients' (visual) abilities across a range of task constraints, which can reveal potential residual abilities that may in turn represent a key feature for patient rehabilitation. Finally, our findings reinforce the view that the neural network processing biological motion can efficiently operate despite severely impaired low-level vision, positing our natural predisposition for processing dynamicity in biological agents as a robust feature of human vision.

  19. Optimization of Conformational Dynamics in an Epistatic Evolutionary Trajectory.

    Science.gov (United States)

    González, Mariano M; Abriata, Luciano A; Tomatis, Pablo E; Vila, Alejandro J

    2016-07-01

    The understanding of protein evolution depends on the ability to relate the impact of mutations on molecular traits to organismal fitness. Biological activity and robustness have been regarded as important features in shaping protein evolutionary landscapes. Conformational dynamics, which is essential for protein function, has received little attention in the context of evolutionary analyses. Here we employ NMR spectroscopy, the chief experimental tool to describe protein dynamics at atomic level in solution at room temperature, to study the intrinsic dynamic features of a metallo- Β: -lactamase enzyme and three variants identified during a directed evolution experiment that led to an expanded substrate profile. We show that conformational dynamics in the catalytically relevant microsecond to millisecond timescale is optimized along the favored evolutionary trajectory. In addition, we observe that the effects of mutations on dynamics are epistatic. Mutation Gly262Ser introduces slow dynamics on several residues that surround the active site when introduced in the wild-type enzyme. Mutation Asn70Ser removes the slow dynamics observed for few residues of the wild-type enzyme, but increases the number of residues that undergo slow dynamics when introduced in the Gly262Ser mutant. These effects on dynamics correlate with the epistatic interaction between these two mutations on the bacterial phenotype. These findings indicate that conformational dynamics is an evolvable trait, and that proteins endowed with more dynamic active sites also display a larger potential for promoting evolution.

  20. Optimized Combination of Residue Hydrodesulfurization and Residue Fluid Catalytic Cracking

    Institute of Scientific and Technical Information of China (English)

    Chen Junwu

    2003-01-01

    @@1 Introduction Combination of residue hydrodesulfurization (HDS) and resi-due fluid catalytic cracking (RFCC) is a unique technologyfor processing high-sulfur residue. This paper discusses theoptimized combination of these two processes.

  1. Residual residential space as commons

    Directory of Open Access Journals (Sweden)

    Dan Rabinowitz

    2012-08-01

    Full Text Available Research on common pool resources (CPR, which began with a focus on rural communities and their defining agricultural practices, shifted recently also to the urban context, looking at community gardens, city parks and other recreational facilities. This article extends the use of CPR theory to residential complexes. Courtyards, lawns, lobbies, cellars, stairwells and other parts that fall outside individual apartments are aggregated as a new sub-set of CPR, defined herewith as Residual Residential Space (RRS. Based on findings from three main types of RRS in Israel, the article evaluates some of the mechanisms designed to regulate such space. In line with earlier work on CPR, the article suggests that legal instruments, important as they are for general guidance, do not suffice. To be effective they need to echo popular framings of Residual Residential Space, to be congruent with local sensibilities regarding micro-history, and to concur with expectations stake-holders might have from their own community.

  2. Analysis on Residue Dynamics of Thiamethoxam Seed Coating on Potato by High Performance Liquid Chromatography%HPLC检测分析噻虫嗪种衣剂在马铃薯中的残留动态变化

    Institute of Scientific and Technical Information of China (English)

    胡梅; 刘永刚; 张海英; 郭建国; 吕和平; 李晓蓉

    2012-01-01

    To study the residue dynamic, make an assessment on the security of thiamethoxam in seed coating potato and establish the detection method of potato plant and tuber. The samples were extracted with methanol, concentrated and cleaned up, determined using HPLC equipped with UVD and external standard method. The results showed that, this method was characterized by that recovery rates of plant and tuber were 86.73%-92.58% and 86.03%-93.35%, relative standard deviation were 3.46%-8.19%and 3.65%-6.22%, respectively. LOD at l.0x10-9g and sensitivity of 0.001 mg/kg. The decline rules of thiamethoxam seed coating in plant of potato followed the first order chemical reactions dynamics equation, 60 days after planting, residual quantity of Tthiamethoxam was 33.975 mg/kg which was the primitive quantities of sediment. Accordingly, its half-lives were 12.4 days. Thiamethoxam were not detected in tubers under the condition of this study.%为明确马铃薯种薯包衣播种后活性成分噻虫嗪在植株和薯块上的残留动态,评价噻虫嗪种衣剂 的使用安全性,建立其在马铃薯植株和薯块上的残留检测方法.采用田间试验和高效液相色谱法,样品 经甲醇超声提取,浓缩净化后,通过HPLC-UVD检测,外标法定量.添加回收率实验结果表明:该方法 在马铃薯植株及薯块上添加回收率分别为86.73%~92.58%、86.03%~93.35%,相对标准偏差(RSD)分别 为3.46%~8.19%、3.65%~6.22%,最低检出量为1.0×10-9g,最低检测浓度为0.001 mg/kg,符合农药残留检 测要求.残留动态实验结果表明:噻虫嗪种衣剂在马铃薯植株中的残留动态符合一级动力学方程,包衣 播种后60天,噻虫嗪在马铃薯植株中的残留量高,为33.975 mg/kg,以此为原始沉积量得到半衰期为 12.4天.在马铃薯块茎中未检测到噻虫嗪.

  3. 氰戊菊酯在香蕉及蕉园土壤中的残留动态与安全性评价%Residual Dynamics and Safe Evaluation of Fenvalerate in Bananas and Its Orchard Soil

    Institute of Scientific and Technical Information of China (English)

    陈丽萍

    2014-01-01

    采用气相色谱(GC-ECD)及田间试验方法,研究氰戊菊酯在香蕉及蕉园土壤中的残留降解动态。结果表明,氰戊菊酯在香蕉上的原始残留沉积量因不同施药处理有所差异,香蕉及蕉园土壤上的降解速度较缓慢,降解规律符合“C=C0·e-kt”一级动力学关系。在香蕉上,相关系数r=0.9722~0.9980(P<0.01),降解系数k =0.0703~0.0767,半衰期T1/2=9.1~9.9 d,降解99%所需要时间T0.99=60.1~65.6 d;在土壤中,k =0.0821,T1/2=8.5 d,T0.99=56.1 d。距第2次施药后62~68 d,最终香蕉的残留量<0.01 mg·kg-1,土壤中为0.015~0.020 mg·kg-1。在福建蕉区,氰戊菊酯的常规施药方法是间隔期7 d连续2次施用有效剂量112.50 g·hm-2,采样前安全间隔期可推荐为>13.6 d,产品质量最终可符合GB/T 2763-2012、NY/T 750-2011的要求。%The residue dynamics of fenvalerate in bananas and the soil were studied by using the methods of GC and field experiments. The results showed that the original sediment of fenvalerate in bananas was significant differences among different treatments. Fenvalerate was degrading at a slow rate in bananas and its soil. The residual degradation dynamics of fenvalerate degradation in bananas and its orchard soil could be followed first order kinetic equation ‘C=C0·e-kt’. In bananas, the correlation coefficient (r) ranged from 0.9722 to 0.9980 (P 13.6 d can be recommended as pre-harvest time. The quality safety of their products was fulfilled quality requirements of GB/T 2763-2012 and NY/T 750-2011.

  4. TENORM: Coal Combustion Residuals

    Science.gov (United States)

    Burning coal in boilers to create steam for power generation and industrial applications produces a number of combustion residuals. Naturally radioactive materials that were in the coal mostly end up in fly ash, bottom ash and boiler slag.

  5. Modelling pesticides residues

    OpenAIRE

    2004-01-01

    This work is a contribution to the development of a specific method to assess the presence of residues in agricultural commodities. The following objectives are formulated: to identify and describe main processes in environment — plant exchanges, to build of a model to assess the residue concentration at harvest in agricultural commodities, to understand the functioning of the modelled system, to characterise pesticides used in field crops and identify optimisation potentials in phytosanitary...

  6. Effects of dynamic luminance modulation on visually induced self-motion perception: observers' perception of illumination is important in perceiving self-motion.

    Science.gov (United States)

    Nakamura, Shinji; Seno, Takeharu; Ito, Hiroyuki; Sunaga, Shoji

    2013-01-01

    Coherent luminance modulation of visual objects affects visually induced perception of self-motion (vection). The perceptual mechanism underlying the effects of dynamic luminance modulation were investigated with a visual stimulus simulating an external environment illuminated by a moving spotlight (the normal spotlight condition) or an inverted luminance version of it (the inverted luminance condition). Two psychophysical experiments indicated that vection was generally weakened in the inverted luminance condition. The results cannot be fully explained by the undesirable differences of luminosity within the experimental environment, and suggest that the contrast polarity of the visual stimulus has a significant impact on vection. Furthermore, the results show that the dynamic luminance variations weaken vection in the normal spotlight condition in which the observers perceived illumination modulations. In contrast, in the inverted luminance condition, in which the observers cannot perceive the illumination manipulation, the dynamic luminance variations may not impair vection, and may even be expected to strengthen vection, even though they shared similar global and systematic luminance variation with the normal spotlight condition. These experiments suggest that the observer's perception of illumination is a key factor in considering the effects of dynamic luminance modulation of the visual stimulus.

  7. The importance of plant-soil interactions and plant life history traits for the population dynamics of Jacobaea vulgaris during old-field succession

    NARCIS (Netherlands)

    Voorde, van de T.F.J.; Putten, van der W.H.; Bezemer, T.M.

    2012-01-01

    We examined to what extent temporal dynamics of Jacobaea vulgaris cover in old-fields were related to plant–soil feedback, soil nutrients, seed availability and performance, and seedling establishment. Long-term measurements at an experimental field and in ten old-fields representing a chronosequenc

  8. The importance of plant-soil interactions and plant life history traits for the population dynamics of Jacobaea vulgaris during old-field succession

    NARCIS (Netherlands)

    Voorde, van de T.F.J.; Putten, van der W.H.; Bezemer, T.M.

    2012-01-01

    We examined to what extent temporal dynamics of Jacobaea vulgaris cover in old-fields were related to plant–soil feedback, soil nutrients, seed availability and performance, and seedling establishment. Long-term measurements at an experimental field and in ten old-fields representing a

  9. Depth Effects on Plant Residue Decay in Diverse Soils

    Science.gov (United States)

    Gregorich, Edward; Ellert, Benjamin; Janzen, Henry; Helgason, Bobbi; Beare, Michael; Curtin, Denis

    2017-04-01

    Decay of plant residues is tied to many ecosystem functions, affecting atmospheric CO2, plant-available nutrients, microbial diversity, soil organic matter quality, among others. The rate of decay, in turn, is governed by soil type and management, location in the soil profile, and environmental variables, some of which may be changing in coming decades. Our objective in this study was to elucidate the decomposition dynamics of plant-derived C and N at different soil depths. To describe mathematically the importance of these variables across a broad scale, we established a long-term study at two sites in Canada and one site in New Zealand. At each site, labelled barley straw (13C = 10.2 atom%, 15N = 8.3 atom %; C = 37.9%; N = 0.95%; C:N = 40) was installed at 3 depths (5-10, 20-25 and 40-45 cm). Soil temperature was logged at each depth. Samples were collected at different times over 5-6 year after application of the residues. Data on recovery and kinetics of residue C and N over the experimental period will be discussed as well as 13C- PLFA results.

  10. IMPORTANT NOTIFICATION

    CERN Multimedia

    HR Department

    2009-01-01

    Green plates, removals and importation of personal effects Please note that, as from 1 April 2009, formalities relating to K and CD special series French vehicle plates (green plates), removals and importation of personal effects into France and Switzerland will be dealt with by GS Department (Building 73/3-014, tel. 73683/74407). Importation and purchase of tax-free vehicles in Switzerland, as well as diplomatic privileges, will continue to be dealt with by the Installation Service of HR Department (Building 33/1-011, tel. 73962). HR and GS Departments

  11. Molecular interactions and residues involved in force generation in the T4 viral DNA packaging motor.

    Science.gov (United States)

    Migliori, Amy D; Smith, Douglas E; Arya, Gaurav

    2014-12-12

    Many viruses utilize molecular motors to package their genomes into preformed capsids. A striking feature of these motors is their ability to generate large forces to drive DNA translocation against entropic, electrostatic, and bending forces resisting DNA confinement. A model based on recently resolved structures of the bacteriophage T4 motor protein gp17 suggests that this motor generates large forces by undergoing a conformational change from an extended to a compact state. This transition is proposed to be driven by electrostatic interactions between complementarily charged residues across the interface between the N- and C-terminal domains of gp17. Here we use atomistic molecular dynamics simulations to investigate in detail the molecular interactions and residues involved in such a compaction transition of gp17. We find that although electrostatic interactions between charged residues contribute significantly to the overall free energy change of compaction, interactions mediated by the uncharged residues are equally if not more important. We identify five charged residues and six uncharged residues at the interface that play a dominant role in the compaction transition and also reveal salt bridging, van der Waals, and solvent hydrogen-bonding interactions mediated by these residues in stabilizing the compact form of gp17. The formation of a salt bridge between Glu309 and Arg494 is found to be particularly crucial, consistent with experiments showing complete abrogation in packaging upon Glu309Lys mutation. The computed contributions of several other residues are also found to correlate well with single-molecule measurements of impairments in DNA translocation activity caused by site-directed mutations.

  12. The importance of accurately modelling human interactions. Comment on "Coupled disease-behavior dynamics on complex networks: A review" by Z. Wang et al.

    Science.gov (United States)

    Rosati, Dora P.; Molina, Chai; Earn, David J. D.

    2015-12-01

    Human behaviour and disease dynamics can greatly influence each other. In particular, people often engage in self-protective behaviours that affect epidemic patterns (e.g., vaccination, use of barrier precautions, isolation, etc.). Self-protective measures usually have a mitigating effect on an epidemic [16], but can in principle have negative impacts at the population level [12,15,18]. The structure of underlying social and biological contact networks can significantly influence the specific ways in which population-level effects are manifested. Using a different contact network in a disease dynamics model-keeping all else equal-can yield very different epidemic patterns. For example, it has been shown that when individuals imitate their neighbours' vaccination decisions with some probability, this can lead to herd immunity in some networks [9], yet for other networks it can preserve clusters of susceptible individuals that can drive further outbreaks of infectious disease [12].

  13. Calibration and validation of models for short-term decomposition and N mineralization of plant residues in the tropics

    Directory of Open Access Journals (Sweden)

    Alexandre Ferreira do Nascimento

    2012-12-01

    Full Text Available Insight of nutrient release patterns associated with the decomposition of plant residues is important for their effective use as a green manure in food production systems. Thus, this study aimed to evaluate the ability of the Century, APSIM and NDICEA simulation models for predicting the decomposition and N mineralization of crop residues in the tropical Atlantic forest biome, Brazil. The simulation models were calibrated based on actual decomposition and N mineralization rates of three types of crop residues with different chemical and biochemical composition. The models were also validated for different pedo-climatic conditions and crop residues conditions. In general, the accuracy of decomposition and N mineralization improved after calibration. Overall RMSE values for the decomposition and N mineralization of the crop materials varied from 7.4 to 64.6% before models calibration compared to 3.7 to 16.3 % after calibration. Therefore, adequate calibration of the models is indispensable for use them under humid tropical conditions. The NDICEA model generally outperformed the other models. However, the decomposition and N mineralization was not very accurate during the first 30 days of incubation, especially for easily decomposable crop residues. An additional model variable may be required to capture initial microbiological growth as affected by the moisture dynamics of the residues, as is the case in surface residues decomposition models.

  14. At your own risk : The importance of group dynamics and peer processes in adolescent peer groups for adolescents’ involvement in risk behaviors

    NARCIS (Netherlands)

    Pattiselanno, Kim Lianne

    2016-01-01

    During adolescence peers become increasingly important to the social and emotional development of adolescents. Peer groups form one of the most important settings where adolescents socialize, find social support, and feel connected and accepted. However, these groups also form a context where

  15. Covariant Residual Entropy

    CERN Document Server

    Hubeny, Veronika E

    2014-01-01

    A recently explored interesting quantity in AdS/CFT, dubbed 'residual entropy', characterizes the amount of collective ignorance associated with either boundary observers restricted to finite time duration, or bulk observers who lack access to a certain spacetime region. However, the previously-proposed expression for this quantity involving variation of boundary entanglement entropy (subsequently renamed to 'differential entropy') works only in a severely restrictive context. We explain the key limitations, arguing that in general, differential entropy does not correspond to residual entropy. Given that the concept of residual entropy as collective ignorance transcends these limitations, we identify two correspondingly robust, covariantly-defined constructs: a 'strip wedge' associated with boundary observers and a 'rim wedge' associated with bulk observers. These causal sets are well-defined in arbitrary time-dependent asymptotically AdS spacetimes in any number of dimensions. We discuss their relation, spec...

  16. Structural dynamics flexibility informs function and evolution at a proteome scale

    Science.gov (United States)

    Nevin Gerek, Zeynep; Kumar, Sudhir; Banu Ozkan, Sefika

    2013-01-01

    Protein structures are dynamic entities with a myriad of atomic fluctuations, side-chain rotations, and collective domain movements. Although the importance of these dynamics to proper functioning of proteins is emerging in the studies of many protein families, there is a lack of broad evidence for the critical role of protein dynamics in shaping the biological functions of a substantial fraction of residues for a large number of proteins in the human proteome. Here, we propose a novel dynamic flexibility index (dfi) to quantify the dynamic properties of individual residues in any protein and use it to assess the importance of protein dynamics in 100 human proteins. Our analyses involving functionally critical positions, disease-associated and putatively neutral population variations, and the rate of interspecific substitutions per residue produce concordant patterns at a proteome scale. They establish that the preservation of dynamic properties of residues in a protein structure is critical for maintaining the protein/biological function. Therefore, structural dynamics needs to become a major component of the analysis of protein function and evolution. Such analyses will be facilitated by the dfi, which will also enable the integrative use of structural dynamics with evolutionary conservation in genomic medicine as well as functional genomics investigations. PMID:23745135

  17. Towards improved estimation of the dynamic topography and ocean circulation in the high latitude and arctic ocean: The importance of GOCE

    DEFF Research Database (Denmark)

    Johannessen, J. A.; Raj, R. P.; Nilsen, J. E. Ø.

    2013-01-01

    The Arctic plays a fundamental role in the climate system and shows significant sensitivity to anthropogenic climate forcing and the ongoing climate change. Evidently changes in the Arctic and surrounding seas have far reaching influences on regional and global environment and climate variability...... dynamic topography for studies of the ocean circulation and transport estimates in the Nordic Seas and Arctic Ocean........ In this respect this study combines in-situ hydrographical data, surface drifter data and direct current meter measurements, with coupled sea ice - ocean models, radar altimeter data and the latest GOCE-based geoid in order to estimate and assess the quality, usefulness and validity of the new GOCE derived mean...

  18. Residual-stress measurements

    Energy Technology Data Exchange (ETDEWEB)

    Ezeilo, A.N.; Webster, G.A. [Imperial College, London (United Kingdom); Webster, P.J. [Salford Univ. (United Kingdom)

    1997-04-01

    Because neutrons can penetrate distances of up to 50 mm in most engineering materials, this makes them unique for establishing residual-stress distributions non-destructively. D1A is particularly suited for through-surface measurements as it does not suffer from instrumental surface aberrations commonly found on multidetector instruments, while D20 is best for fast internal-strain scanning. Two examples for residual-stress measurements in a shot-peened material, and in a weld are presented to demonstrate the attractive features of both instruments. (author).

  19. Decomposition of residue currents

    OpenAIRE

    Andersson, Mats; Wulcan, Elizabeth

    2007-01-01

    Given a submodule $J\\subset \\mathcal O_0^{\\oplus r}$ and a free resolution of $J$ one can define a certain vector valued residue current whose annihilator is $J$. We make a decomposition of the current with respect to Ass$(J)$ that correspond to a primary decomposition of $J$. As a tool we introduce a class of currents that includes usual residue and principal value currents; in particular these currents admit a certain type of restriction to analytic varieties and more generally to construct...

  20. Sharing Residual Liability

    DEFF Research Database (Denmark)

    Carbonara, Emanuela; Guerra, Alice; Parisi, Francesco

    2016-01-01

    Economic models of tort law evaluate the efficiency of liability rules in terms of care and activity levels. A liability regime is optimal when it creates incentives to maximize the value of risky activities net of accident and precaution costs. The allocation of primary and residual liability...... allows policy makers to induce parties to undertake socially desirable care and activity levels. Traditionally, tort law systems have assigned residual liability either entirely on the tortfeasor or entirely on the victim. In this paper, we unpack the cheapest-cost-avoider principle to consider...

  1. Role of the N-terminal seven residues of surfactant protein B (SP-B.

    Directory of Open Access Journals (Sweden)

    Mahzad Sharifahmadian

    Full Text Available Breathing is enabled by lung surfactant, a mixture of proteins and lipids that forms a surface-active layer and reduces surface tension at the air-water interface in lungs. Surfactant protein B (SP-B is an essential component of lung surfactant. In this study we probe the mechanism underlying the important functional contributions made by the N-terminal 7 residues of SP-B, a region sometimes called the "insertion sequence". These studies employed a construct of SP-B, SP-B (1-25,63-78, also called Super Mini-B, which is a 41-residue peptide with internal disulfide bonds comprising the N-terminal 7-residue insertion sequence and the N- and C-terminal helices of SP-B. Circular dichroism, solution NMR, and solid state (2H NMR were used to study the structure of SP-B (1-25,63-78 and its interactions with phospholipid bilayers. Comparison of results for SP-B (8-25,63-78 and SP-B (1-25,63-78 demonstrates that the presence of the 7-residue insertion sequence induces substantial disorder near the centre of the lipid bilayer, but without a major disruption of the overall mechanical orientation of the bilayers. This observation suggests the insertion sequence is unlikely to penetrate deeply into the bilayer. The 7-residue insertion sequence substantially increases the solution NMR linewidths, most likely due to an increase in global dynamics.

  2. Designing with residual materials

    NARCIS (Netherlands)

    Walhout, W.; Wever, R.; Blom, E.; Addink-Dölle, L.; Tempelman, E.

    2013-01-01

    Many entrepreneurial businesses have attempted to create value based on the residual material streams of third parties. Based on ‘waste’ materials they designed products, around which they built their company. Such activities have the potential to yield sustainable products. Many of such companies

  3. Sharing Residual Liability

    DEFF Research Database (Denmark)

    Carbonara, Emanuela; Guerra, Alice; Parisi, Francesco

    2016-01-01

    allows policy makers to induce parties to undertake socially desirable care and activity levels. Traditionally, tort law systems have assigned residual liability either entirely on the tortfeasor or entirely on the victim. In this paper, we unpack the cheapest-cost-avoider principle to consider...

  4. DMPD: Lipopolysaccharide sensing an important factor in the innate immune response toGram-negative bacterial infections: benefits and hazards of LPShypersensitivity. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available portant factor in the innate immune response toGram-negative bacterial infections: benefits and hazards of L...une response toGram-negative bacterial infections: benefits and hazards of LPShyp...18406367 Lipopolysaccharide sensing an important factor in the innate immune response toGram-negative bacter...ial infections: benefits and hazards of LPShypersensitivity. Freudenberg MA, Tchapt

  5. [Imported histoplasmosis].

    Science.gov (United States)

    Stete, Katarina; Kern, Winfried V; Rieg, Siegbert; Serr, Annerose; Maurer, Christian; Tintelnot, Kathrin; Wagner, Dirk

    2015-06-01

    Infections with Histoplasma capsulatum are rare in Germany, and mostly imported from endemic areas. Infections can present as localized or disseminated diseases in immunocompromised as well as immunocompetent hosts. A travel history may be a major clue for diagnosing histoplasmosis. Diagnostic tools include histology, cultural and molecular detection as well as serology. Here we present four cases of patients diagnosed and treated in Freiburg between 2004 and 2013 that demonstrate the broad range of clinical manifestations of histoplasmosis: an immunocompetent patient with chronic basal meningitis; a patient with HIV infection and fatal disseminated disease; a patient with pulmonary and cutaneous disease and mediastinal and cervical lymphadenopathy; and an immunosuppressed patient with disseminated involvement of lung, bone marrow and adrenal glands.

  6. Theory for cross effect dynamic nuclear polarization under magic-angle spinning in solid state nuclear magnetic resonance: the importance of level crossings.

    Science.gov (United States)

    Thurber, Kent R; Tycko, Robert

    2012-08-28

    We present theoretical calculations of dynamic nuclear polarization (DNP) due to the cross effect in nuclear magnetic resonance under magic-angle spinning (MAS). Using a three-spin model (two electrons and one nucleus), cross effect DNP with MAS for electron spins with a large g-anisotropy can be seen as a series of spin transitions at avoided crossings of the energy levels, with varying degrees of adiabaticity. If the electron spin-lattice relaxation time T(1e) is large relative to the MAS rotation period, the cross effect can happen as two separate events: (i) partial saturation of one electron spin by the applied microwaves as one electron spin resonance (ESR) frequency crosses the microwave frequency and (ii) flip of all three spins, when the difference of the two ESR frequencies crosses the nuclear frequency, which transfers polarization to the nuclear spin if the two electron spins have different polarizations. In addition, adiabatic level crossings at which the two ESR frequencies become equal serve to maintain non-uniform saturation across the ESR line. We present analytical results based on the Landau-Zener theory of adiabatic transitions, as well as numerical quantum mechanical calculations for the evolution of the time-dependent three-spin system. These calculations provide insight into the dependence of cross effect DNP on various experimental parameters, including MAS frequency, microwave field strength, spin relaxation rates, hyperfine and electron-electron dipole coupling strengths, and the nature of the biradical dopants.

  7. Choosing the appropriate configuration and cannulation strategies for extracorporeal membrane oxygenation: the potential dynamic process of organ support and importance of hybrid modes.

    Science.gov (United States)

    Sorokin, Vitaly; MacLaren, Graeme; Vidanapathirana, Puwalani C; Delnoij, Thijs; Lorusso, Roberto

    2017-05-01

    Extracorporeal membrane oxygenation (ECMO) is becoming a common procedure to support patients with severe cardio-circulatory or respiratory failure as well as in case of combined compromise of the two systems. Deciding which ECMO configuration and proceeding with an uneventful implantation, however, may present minor or major shortcomings. Cannulation techniques should be tailored to specific patient conditions to provide sufficient regional and systemic perfusion, both of which must be comprehensively monitored. Changes in the patient's status or suboptimal ECMO-related support, however, may occur and should trigger re-appraisal of the cannulation strategy and circuit configuration. This dynamic management, based around the adequacy of end organ perfusion and patient requirements, may dictate ECMO configuration and cannulation changes. In these circumstances, adjunct of a cannula in the venous or arterial vasculature may represent a mandatory procedure to solve unfavorable hemodynamic status or enhance ECMO efficiency. These type of ECMO configurations, different from basic one, and called hybrid configurations, may represent, therefore, a critical aspect of optimal ECMO management towards optimized and successful temporary support. The aim of this review is to critically appraise and summarize the existing literature on adult ECMO configuration including cannulation strategies and circuit arrangement, and highlighting more complex pattern required in some specific clinical settings. © 2017 The Authors. European Journal of Heart Failure © 2017 European Society of Cardiology.

  8. Swift J1644+57 gone MAD: the case for dynamically-important magnetic flux threading the black hole in a jetted tidal disruption event

    CERN Document Server

    Tchekhovskoy, Alexander; Giannios, Dimitrios; Kelley, Luke Zoltan

    2013-01-01

    The unusual transient Swift J1644+57 likely resulted from a collimated relativistic jet powered by accretion onto a massive black hole (BH) following the tidal disruption (TD) of a star. Several mysteries cloud the interpretation of this event: (1) extreme flaring and `plateau' shape of the X-ray/gamma-ray light curve during the first 10 days after the gamma-ray trigger; (2) unexpected rebrightening of the forward shock radio emission months after trigger; (3) no obvious evidence for jet precession, despite misalignment typically expected between the angular momentum of the accretion disk and BH; (4) recent abrupt shut-off in jet X-ray emission after 1.5 years. Here we show that all of these seemingly disparate mysteries are naturally resolved by one assumption: the presence of strong magnetic flux Phi threading the BH. Initially, Phi is weak relative to high fall-back mass accretion rate, Mdot, and the disk and jets precess about the BH axis = our line of sight. As Mdot drops, Phi becomes dynamically importa...

  9. Stomatal proxy record of CO2 concentrations during the Last Termination demonstrates dynamic climate behaviour and an important role for CO2.

    Science.gov (United States)

    Steinthorsdottir, Margret; Wohlfarth, Barbara; Kylander, Malin E.; Blaauw, Maarten; Reimer, Paula J.

    2013-04-01

    We present a new stomatal proxy-based record of CO2 concentrations spanning Greenland Interstadial 1 (Allerød pollen zone, GI-1a to 1c), Greenland Stadial 1 (Younger Dryas pollen zone, GS-1) and the first part of the Holocene (Preboreal pollen zone). The calibrated atmospheric CO2 concentrations are based on Betula nana (dwarf birch) leaves from a fossil lake sedimentary sequence in south-eastern Sweden. The stomatal proxy method relies on the inverse relationship between stomatal density on plant leaves and atmospheric CO2 concentrations to reconstruct variations in past CO2 concentrations. The record presented here demonstrates that the overall pattern of CO2 evolution during this period was dynamic, with significant abrupt fluctuations in CO2 concentration when the climate moved from interstadial to stadial state and vice versa. The cooling at the GI-1/GS-1 transition was preceded by an abrupt warming, and the warming at the GS-1/Holocene transition was preceded by an abrupt cooling. This scenario is in contrast to CO2 records reconstructed from air bubbles trapped in ice, which indicate a gradual increase in concentrations, but largely in alignment with previously published stomatal proxy-based CO2 records. A new loss-on-ignition chemical record (used here as a proxy for temperature), from the same locality, lends independent support to the CO2 record.

  10. Ensemble Kalman filtering with residual nudging

    CERN Document Server

    Luo, Xiaodong; 10.3402/tellusa.v64i0.17130

    2012-01-01

    Covariance inflation and localization are two important techniques that are used to improve the performance of the ensemble Kalman filter (EnKF) by (in effect) adjusting the sample covariances of the estimates in the state space. In this work an additional auxiliary technique, called residual nudging, is proposed to monitor and, if necessary, adjust the residual norms of state estimates in the observation space. In an EnKF with residual nudging, if the residual norm of an analysis is larger than a pre-specified value, then the analysis is replaced by a new one whose residual norm is no larger than a pre-specified value. Otherwise the analysis is considered as a reasonable estimate and no change is made. A rule for choosing the pre-specified value is suggested. Based on this rule, the corresponding new state estimates are explicitly derived in case of linear observations. Numerical experiments in the 40-dimensional Lorenz 96 model show that introducing residual nudging to an EnKF may improve its accuracy and/o...

  11. Ensemble Kalman filtering with residual nudging

    Directory of Open Access Journals (Sweden)

    Xiaodong Luo

    2012-10-01

    Full Text Available Covariance inflation and localisation are two important techniques that are used to improve the performance of the ensemble Kalman filter (EnKF by (in effect adjusting the sample covariances of the estimates in the state space. In this work, an additional auxiliary technique, called residual nudging, is proposed to monitor and, if necessary, adjust the residual norms of state estimates in the observation space. In an EnKF with residual nudging, if the residual norm of an analysis is larger than a pre-specified value, then the analysis is replaced by a new one whose residual norm is no larger than a pre-specified value. Otherwise, the analysis is considered as a reasonable estimate and no change is made. A rule for choosing the pre-specified value is suggested. Based on this rule, the corresponding new state estimates are explicitly derived in case of linear observations. Numerical experiments in the 40-dimensional Lorenz 96 model show that introducing residual nudging to an EnKF may improve its accuracy and/or enhance its stability against filter divergence, especially in the small ensemble scenario.

  12. Ensemble Kalman filtering with residual nudging

    KAUST Repository

    Luo, X.

    2012-10-03

    Covariance inflation and localisation are two important techniques that are used to improve the performance of the ensemble Kalman filter (EnKF) by (in effect) adjusting the sample covariances of the estimates in the state space. In this work, an additional auxiliary technique, called residual nudging, is proposed to monitor and, if necessary, adjust the residual norms of state estimates in the observation space. In an EnKF with residual nudging, if the residual norm of an analysis is larger than a pre-specified value, then the analysis is replaced by a new one whose residual norm is no larger than a pre-specified value. Otherwise, the analysis is considered as a reasonable estimate and no change is made. A rule for choosing the pre-specified value is suggested. Based on this rule, the corresponding new state estimates are explicitly derived in case of linear observations. Numerical experiments in the 40-dimensional Lorenz 96 model show that introducing residual nudging to an EnKF may improve its accuracy and/or enhance its stability against filter divergence, especially in the small ensemble scenario.

  13. Observer's observables. Residual diffeomorphisms

    CERN Document Server

    Duch, Paweł; Świeżewski, Jedrzej

    2016-01-01

    We investigate the fate of diffeomorphisms when the radial gauge is imposed in canonical general relativity. As shown elsewhere, the radial gauge is closely related to the observer's observables. These observables are invariant under a large subgroup of diffeomorphisms which results in their usefulness for canonical general relativity. There are, however, some diffeomorphisms, called residual diffeomorphisms, which might be "observed" by the observer as they do not preserve her observables. The present paper is devoted to the analysis of these diffeomorphisms in the case of the spatial and spacetime radial gauges. Although the residual diffeomorphisms do not form a subgroup of all diffeomorphisms, we show that their induced action in the phase space does form a group. We find the generators of the induced transformations and compute the structure functions of the algebras they form. The obtained algebras are deformations of the algebra of the Euclidean group and the algebra of the Poincar\\'e group in the spat...

  14. Natural radioactivity in petroleum residues

    Energy Technology Data Exchange (ETDEWEB)

    Gazineu, M.H.P. [UNICAP, Dept. de Quimica, Recife (Brazil); Gazineu, M.H.P.; Hazin, C.A. [UFPE, Dept. de Energia Nuclear, Recife (Brazil); Hazin, C.A. [Centro Regional de Ciencias Nucleares/ CNEN, Recife (Brazil)

    2006-07-01

    The oil extraction and production industry generates several types of solid and liquid wastes. Scales, sludge and water are typical residues that can be found in such facilities and that can be contaminated with Naturally Occurring Radioactive Material (N.O.R.M.). As a result of oil processing, the natural radionuclides can be concentrated in such residues, forming the so called Technologically Enhanced Naturally Occurring Radioactive Material, or T.E.N.O.R.M.. Most of the radionuclides that appear in oil and gas streams belong to the {sup 238}U and {sup 232}Th natural series, besides 40 K. The present work was developed to determine the radionuclide content of scales and sludge generated during oil extraction and production operations. Emphasis was given to the quantification of {sup 226}Ra, {sup 228}Ra and 40 K since these radionuclides,are responsible for most of the external exposure in such facilities. Samples were taken from the P.E.T.R.O.B.R.A.S. unity in the State of Sergipe, in Northeastern Brazil. They were collected directly from the inner surface of water pipes and storage tanks, or from barrels stored in the waste storage area of the E and P unit. The activity concentrations for {sup 226}Ra, {sup 228}Ra and 40 K were determined by using an HP Ge gamma spectrometric system. The results showed concentrations ranging from 42.7 to 2,110.0 kBq/kg for {sup 226}Ra, 40.5 to 1,550.0 kBq/kg for {sup 228}Ra, and 20.6 to 186.6 kBq/kg for 40 K. The results highlight the importance of determining the activity concentration of those radionuclides in oil residues before deciding whether they should be stored or discarded to the environment. (authors)

  15. Relative importance of nutrient inputs from streams and the sea entrance for phytoplankton dynamics in a shallow estuary - insights from 3D model simulations

    DEFF Research Database (Denmark)

    Timmermann, Karen; Gustafsson, Karin; Markager, Svend Stiig

    Danish estuaries are highly eutrophic due to high N and P inputs from local streams and a general increase in nutrient concentrations in the Baltic Sea region. Recovery plans have been implemented to reduce local loadings. A key issue for these plans is the relative importance of local sources...... (streams and open sea inputs) on phytoplankton growth and biomass. Model simulations revealed that local streams accounted for about 40% of the phytoplankton nitrogen content and that changes in local discharges and open sea nutrient concentrations almost had similar impact on phytoplankton biomass....

  16. Importance of vector-borne infections in different production systems: bovine trypanosomosis and the innovation dynamics of livestock producers in Senegal.

    Science.gov (United States)

    Bouyer, F; Bouyer, J; Seck, M T; Sall, B; Dicko, A H; Lancelot, R; Chia, E

    2015-04-01

    In Senegal, a project has been undertaken to eradicate a population of tsetse flies (Glossina palpalis gambiensis) from a prime area for intensifying livestock production--the coastal region of Niayes. The project is intended to remove the constraint of trypanosomosis and allow the ecological intensification of cattle production. A cross-sectional analysis of ten case studies was the inductive phase of an assessment to gauge the impact of removing trypanosomosis on livestock production strategies. The methodology used was comprehensive analysis, with participatory epidemiology tools to understand farmers' rationales. The authors analysed the strategies of three main types of livestock producer (agro-pastoralists, mixed crop/livestock farmers and intensive dairy farmers). The strategies were in line with the farmers' goals and their ability to mobilise the socio-technical network. The risk management of trypanosomosis has been incorporated into livestock management practices through the use of trypanotolerant breeds, medical prophylaxis or placing livestock in low-risk areas. Removing the risk of disease would therefore have a major impact on decisions about the composition and strategic direction of herds. This change in the animal health environment would steer livestock production along different routes of intensification in a highly competitive environment. The indicators of innovation capacity revealed by this study will be used to quantitatively monitor various change scenarios, taking livestock producers' reasoning into account, in order to assess the socio-economic impact of eradicating the tsetse fly population in this area. The methodology presented in the study can be used to understand the impact of controlling other vector-borne infections on the innovation dynamics of livestock producers.

  17. Phylogeography of the Mekong mud snake (Enhydris subtaeniata): the biogeographic importance of dynamic river drainages and fluctuating sea levels for semiaquatic taxa in Indochina.

    Science.gov (United States)

    Lukoschek, Vimoksalehi; Osterhage, Jennifer L; Karns, Daryl R; Murphy, John C; Voris, Harold K

    2011-11-01

    During the Cenozoic, Southeast Asia was profoundly affected by plate tectonic events, dynamic river systems, fluctuating sea levels, shifting coastlines, and climatic variation, which have influenced the ecological and evolutionary trajectories of the Southeast Asian flora and fauna. We examined the role of these paleogeographic factors on shaping phylogeographic patterns focusing on a species of semiaquatic snake, Enhydris subtaeniata (Serpentes: Homalopsidae) using sequence data from three mitochondrial fragments (cytochrome b, ND4, and ATPase-2785 bp). We sampled E. subtaeniata from seven locations in three river drainage basins that encompassed most of this species' range. Genetic diversities were typically low within locations but high across locations. Moreover, each location had a unique suite of haplotypes not shared among locations, and pairwise φ(ST) values (0.713-0.998) were highly significant between all location pairs. Relationships among phylogroups were well resolved and analysis of molecular variance (AMOVA) revealed strong geographical partitioning of genetic variance among the three river drainage basins surveyed. The genetic differences observed among the populations of E. subtaeniata were likely shaped by the Quaternary landscapes of Indochina and the Sunda Shelf. Historically, the middle and lower Mekong consisted of strongly dissected river valleys separated by low mountain ranges and much of the Sunda Shelf consisted of lowland river valleys that served to connect faunas associated with major regional rivers. It is thus likely that the contemporary genetic patterns observed among populations of E. subtaeniata are the result of their histories in a complex terrain that created abundant opportunities for genetic isolation and divergence yet also provided lowland connections across now drowned river valleys.

  18. Residual contaminants in milk

    Directory of Open Access Journals (Sweden)

    Nevijo Zdolec

    2006-07-01

    Full Text Available Various chemical agents are used during the whole production chain of milk and dairy products. Production of feedingstuffs is accompanied with pesticide usage, which may remain in environment, thus are transported through feeding into animals, animal products and finally in human organism. Preparation procedure and storage conditions of feed also influence on milk safety in the sense of mycotoxins entering into the food chain. Chemical agents are, on daily basis, used on dairy farms either as detergents or disinfections. The residuals of cleaning agents might remain in milk if the cleaning agents and its dosage are not performed adequately. Besides already mentioned agents, a great influence in milk production can bee seen through veterinary drugs usage, particularly antibacterial drugs (mastitis. Proper application of drugs and by following legal recommendation, a by-reactions can be avoided such as allergic reaction in humans, development of resisting bacteria or even undesirable influence on starter cultures in dairy products manufacture. The maximum residue limits, monitoring plan as well as sampling procedures are set up within the harmonization of Croatian and European legislation, in order to provide official control of residues in foodstuffs of animal origin.

  19. Desempenho dinâmico de um trator agrícola utilizando biodiesel destilado de óleo residual Dynamic performance of an agricultural tractor utilizing distilled biodiesel from spent oil

    Directory of Open Access Journals (Sweden)

    Ana M. Soranso

    2008-10-01

    Full Text Available Propôs-se, com este trabalho, avaliar o desempenho dinâmico de um trator agrícola funcionando com biodiesel destilado (50% etílico + 50% metílico em função das proporções de biodiesel e diesel de petróleo (0 e 100%, 5 e 95%, 15 e 85%, 25 e 75%, 50 e 50%, 75 e 25% e 100 e 0% respectivamente. O experimento foi realizado na área do Departamento de Engenharia Rural da Universidade Estadual Paulista - UNESP, Campus de Jaboticabal, SP, localizado na latitude 21º 14' 28" S e longitude 48º 17'12" W. Utilizou-se um trator 4 x 2 TDA com potência de 73,6 kW (100 cv no motor e um trator de lastro. O biodiesel utilizado foi produzido à base de óleo residual de fritura de alimentos, o delineamento experimental foi inteiramente casualizado (DIC, com 7 tratamentos e 5 repetições, totalizando 35 observações, e os resultados evidenciaram que a mistura biodiesel e diesel de petróleo influenciou significativamente as variáveis consumo horário volumétrico, consumo horário mássico, consumo de combustível por área trabalhada e consumo específico. Quando o trator operou com 100% de biodiesel (B100 o consumo específico aumentou em média 18% em relação ao diesel (B0.The objective of this study was to evaluate the dynamic performance of an agricultural tractor utilizing distilled biodiesel (50% ethylic + 50% methylic as a function of the proportion of biodiesel and diesel of petroleum (0 and 100%, 5 and 95%, 15 and 85%, 25 and 75%, 50 and 50%, 75 and 25% and 100 and 0%, respectively. This research was done in the area of the Department of Rural Engineering of the Paulista State University (UNESP, Jaboticabal Campus, SP, located in the latitude 21º 14' 28" S and longitude 48º 17'12" W. A tractor 4 x 2 FWA was used, with a 73.6 kW (100 HP motor and a ballast tractor. The biodiesel used was produced from spent oil from food frying. The experimental design was entirely randomized, with 7 treatments and 5 repetitions, totaling 35 observations

  20. 氯氰菊酯在香蕉、土壤上的残留动态及安全性评价%The Residual Dynamics and Safety Evaluation of Cypermethrin on Bananas and the Orchard Soil

    Institute of Scientific and Technical Information of China (English)

    张奇泓; 郭建辉; 蔡恩兴; 陈丽萍

    2013-01-01

    The degradation dynamics of cypermethrin in bananas and its orchard were studied by using GC and field experiment. The results showed that the original sediment of cypermethrin in bananas was relatively lower. The rule of cypermethrin degradation in bananas and the soil were well-fitted with first-order kinetics. On one hand, two different application doses share the same degradation coefficient, T1/2 ranged from 12.1 d to 12.88 d and T0.99 ranged from 80.3 d to 85.1 d in bananas. On the other hand, in the soil T1/2 and T0.99 were 8.0 d, 52.9 d respectively. Furthermore, after applying for 62~70 d, the residue of cypermethrin in banana orchard was less than 0.01 mg/kg. The application of cypermethrin into bananas according to the regular method in Fujian, which is an effective dose of 56.25 g/hm2, was applied continually with an interval of 7 d. So it meaned that more than 7 d can be recommended as pre-harvest time. The quality safety of their products was fulfill quality requirements of NY/T 750-2011.%采用气相色谱法及田间试验法研究氯氰菊酯在香蕉及蕉园土壤上的残留降解动态。结果表明,氯氰菊酯在香蕉上的原始沉积量较低,不同施药剂量有明显的差异。氯氰菊酯在香蕉及蕉园土壤上降解速度较缓慢,残留降解规律均符合一级动力学关系,在香蕉上两种施药剂量的降解速率相接近,半衰(T1/2)为12.1~12.8 d、降解99%需时(T0.99)为80.3~85.1 d;在蕉园土壤上T1/2、T0.99分别为8.0 d、52.9 d。在香蕉上距第2次施药后62~70 d最终产品残留量<0.01 mg/kg。在福建蕉区氯氰菊酯按常规施药方法,间隔期7 d连续施用有效剂量56.25 g/hm2两次,施药安全间隔期可推荐为>7 d,最终产品质量符合NY/T 750-2011规定的MRL要求。

  1. Relative importance of nutrient inputs from streams and the sea entrance for phytoplankton dynamics in a shallow estuary - insights from 3D model simulations

    DEFF Research Database (Denmark)

    Timmermann, Karen; Gustafsson, Karin; Markager, Svend Stiig

    the relative contribution to phytoplankton growth from nutrients originating from local sources and from the Baltic Sea outflow, respectively, which constituted the open boundary. Nutrient reduction scenarios were performed to asses the potential effects of reducing nutrient loadings from different sources...... (streams and open sea inputs) on phytoplankton growth and biomass. Model simulations revealed that local streams accounted for about 40% of the phytoplankton nitrogen content and that changes in local discharges and open sea nutrient concentrations almost had similar impact on phytoplankton biomass.......Danish estuaries are highly eutrophic due to high N and P inputs from local streams and a general increase in nutrient concentrations in the Baltic Sea region. Recovery plans have been implemented to reduce local loadings. A key issue for these plans is the relative importance of local sources...

  2. eCOMPAGT integrates mtDNA: import, validation and export of mitochondrial DNA profiles for population genetics, tumour dynamics and genotype-phenotype association studies

    Directory of Open Access Journals (Sweden)

    Specht Günther

    2010-03-01

    Full Text Available Abstract Background Mitochondrial DNA (mtDNA is widely being used for population genetics, forensic DNA fingerprinting and clinical disease association studies. The recent past has uncovered severe problems with mtDNA genotyping, not only due to the genotyping method itself, but mainly to the post-lab transcription, storage and report of mtDNA genotypes. Description eCOMPAGT, a system to store, administer and connect phenotype data to all kinds of genotype data is now enhanced by the possibility of storing mtDNA profiles and allowing their validation, linking to phenotypes and export as numerous formats. mtDNA profiles can be imported from different sequence evaluation programs, compared between evaluations and their haplogroup affiliations stored. Furthermore, eCOMPAGT has been improved in its sophisticated transparency (support of MySQL and Oracle, security aspects (by using database technology and the option to import, manage and store genotypes derived from various genotyping methods (SNPlex, TaqMan, and STRs. It is a software solution designed for project management, laboratory work and the evaluation process all-in-one. Conclusions The extended mtDNA version of eCOMPAGT was designed to enable error-free post-laboratory data handling of human mtDNA profiles. This software is suited for small to medium-sized human genetic, forensic and clinical genetic laboratories. The direct support of MySQL and the improved database security options render eCOMPAGT a powerful tool to build an automated workflow architecture for several genotyping methods. eCOMPAGT is freely available at http://dbis-informatik.uibk.ac.at/ecompagt.

  3. Measurement of residual stresses using fracture mechanics weight functions

    Energy Technology Data Exchange (ETDEWEB)

    Fan, Y. [Bettis Atomic Power Laboratory, West Mifflin, PA (United States)

    2001-07-01

    A residual stress measurement method has been developed to quantify through-the-thickness residual stresses. Accurate measurement of residual stresses is crucial for many engineering structures. Fabrication processes such as welding and machining generate residual stresses that are difficult to predict. Residual stresses affect the integrity of structures through promoting failures due to brittle fracture, fatigue, stress corrosion cracking, and wear. In this work, the weight function theory of fracture mechanics is used to measure residual stresses. The weight function theory is an important development in computational fracture mechanics. Stress intensity factors for arbitrary stress distribution on the crack faces can be accurately and efficiently computed for predicting crack growth. This paper demonstrates that the weight functions are equally useful in measuring residual stresses. In this method, an artificial crack is created by a thin cut in a structure containing residual stresses. The cut relieves the residual stresses normal to the crack-face and allows the relieved residual stresses to deform the structure. Strain gages placed adjacent to the cut measure the relieved strains corresponding to incrementally increasing depths of the cut. The weight functions of the cracked body relate the measured strains to the residual stresses normal to the cut within the structure. The procedure details, such as numerical integration of the singular functions in applying the weight function method, will be discussed. (author)

  4. Reduction of residual limb volume in people with transtibial amputation

    Directory of Open Access Journals (Sweden)

    Audrey T. Tantua, MD

    2014-11-01

    Full Text Available The early postoperative phase after transtibial amputation is characterized by rapid residual limb volume reduction. Accurate measurement of residual limb volume is important for the timing of fitting a prosthesis. The aim of this study was to analyze the reduction of residual limb volume in people with transtibial amputation and to correlate residual limb volume with residual limb circumference. In a longitudinal cohort study of 21 people who had a transtibial amputation, residual limb volume was measured using a laser scanner and circumference was measured using a tape measure 1 wk postamputation and every 3 wk thereafter until 24 wk postamputation. A linear mixed model analysis was performed with weeks postamputation transformed according to the natural logarithm as predictor. Residual limb volume decreased significantly over time, with a large variation between patients. Residual limb volume did not correlate well with circumference. On average, residual limb volume decreased 200.5 mL (9.7% of the initial volume per natural logarithm of the weeks postamputation. The decrease in residual limb volume following a transtibial amputation was substantial in the early postamputation phase, followed by a leveling off. It was not possible to determine the specific moment at which the residual limb volume stabilized.

  5. Spallation Fragment Investigation on Nb, Au and Pb by Using Many Stage Dynamical Model

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The formation cross section of the nuclides production of proton-induced nuclear reactions withintermediate energy is of importance for a variety of applications. For instance, the mass and chargedistribution of residual products produced in the spallation reactions needs to be studied, because it canprovide useful information for the disposal of nuclear waste and residual radioactivity generated by thespallation neutron target system. At present work, we developed the many stage dynamical model

  6. L-Fuzzy Rough Set Based on Complete Residuated Lattice

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Residuated lattice is an important non-classical logic algebra, and L-fuzzy rough set based on residuated lattice can describe the information with incompleteness, fuzziness and uncomparativity in information systems. In this paper, the representation theorems of L-fuzzy rough sets based on residuated lattice are given. The properties and axiomatic definition of the lower and upper approximation operators in L-fuzzy rough sets are discussed.

  7. Quadratic residues and non-residues selected topics

    CERN Document Server

    Wright, Steve

    2016-01-01

    This book offers an account of the classical theory of quadratic residues and non-residues with the goal of using that theory as a lens through which to view the development of some of the fundamental methods employed in modern elementary, algebraic, and analytic number theory. The first three chapters present some basic facts and the history of quadratic residues and non-residues and discuss various proofs of the Law of Quadratic Reciprosity in depth, with an emphasis on the six proofs that Gauss published. The remaining seven chapters explore some interesting applications of the Law of Quadratic Reciprocity, prove some results concerning the distribution and arithmetic structure of quadratic residues and non-residues, provide a detailed proof of Dirichlet’s Class-Number Formula, and discuss the question of whether quadratic residues are randomly distributed. The text is a valuable resource for graduate and advanced undergraduate students as well as for mathematicians interested in number theory.

  8. Dynamics of a Highly Flexible Protein

    DEFF Research Database (Denmark)

    Andersen, Lisbeth

    Protein dynamics are important for protein function. Especially, dynamics plays an important role in ligand-binding where the induced fit and conformational selection binding mechanisms represent the extremes in a continuum of dynamic mechanisms. The difference between the mechanisms lies...... in the sequence of events; either the protein changes it conformation after initial binding of the ligand (induced fit) or before binding of the ligand (conformational selection). The nuclear co-activator binding domain (NCBD) interacts with many different binding partners to control gene transcription. High...... malleability are the subject of this defense. Using nuclear magnetic resonance (NMR) spectroscopy, the dynamics of NCBD have been investigated on timescales ranging from picoseconds to milliseconds using relaxation dispersion experiments, residual dipolar couplings and methyl group deuterium relaxation. From...

  9. THE IMPORTANCE OF SCHOOL GUIDANCE ACTIVITIES IN THE CONTEXT OF THE NECESSITY OF KNOWING THE VOCATIONAL INTERESTS IN A DYNAMIC EUROPE

    Directory of Open Access Journals (Sweden)

    Maria-Elena, GHEORDUNESCU

    2014-11-01

    Full Text Available Strategy Europe 2020 aims to ensure an economic growth: smart, more efficient throught investment in education, reseatch and innovation; durable, by decisive orientation to a new economy with low-emisions of carbon dioxide and favorable to inclusion, by focusing on creating jobs and redcuing poverty. The priorites of the strategy will be achieved through five objectives, one which is linked to emplyment, namely: employment rate of 75% for population aged between 20 and 64 years. Providing such rate of occupancy implies policies at microeconomical level, but we consider also at individual level. So the young, future employees must be properly trained, and have the right to be able to handle a job. Current realities show that employers are interested in having by their side in accomplishing their goals, employees who are proactive, who improvise, who can cope with various demands in which they are involved, and respond positively to companies. They require a career choice to meet the vocational interests. Based on these issues, this paper aims to analyze the importance of knowing the vocational interests in school orientation by highlighting the correlation between the selected profile and personality of each. However, in this paper we try to show that school guidance is an early process and that if they knew their vocational interests, young people would be more decisive in the choice of future profession. We believe that, if the counseling activites and school oriantation would be conducted in a professiona way, youth might focus on those occupations which best define them and also could access appropriate university programs with favorable effects on employment levels.

  10. Exposure from residual radiation after synchrotron shutdown

    Energy Technology Data Exchange (ETDEWEB)

    Moyers, M.F. [Proton Therapy, Inc., Colton, CA 92324 (United States)], E-mail: mfmoyers@roadrunner.com; Lesyna, D.A. [Optivus Proton Therapy, San Bernardino, CA 92408 (United States)

    2009-02-15

    Personnel exposure from residual radiation present after an accelerator is shutdown for preventative or corrective maintenance is an important aspect that governs the manner in which a light ion facility can be used. This radiation is not only a safety issue for maintenance personnel but also can affect the patient throughput of the facility. Measurements were made with survey instruments around the synchrotron accelerator at the Loma Linda University Proton Treatment Facility and personnel dosimetry records of maintenance staff were reviewed. Results showed that the residual radiation in this facility design is very low, does not significantly impact maintenance staff safety, and has placed no restrictions on patient throughput.

  11. Residual Representations of Spacetime

    CERN Document Server

    Saller, H

    2001-01-01

    Spacetime is modelled by binary relations - by the classes of the automorphisms $\\GL(\\C^2)$ of a complex 2-dimensional vector space with respect to the definite unitary subgroup $\\U(2)$. In extension of Feynman propagators for particle quantum fields representing only the tangent spacetime structure, global spacetime representations are given, formulated as residues using energy-momentum distributions with the invariants as singularities. The associatated quantum fields are characterized by two invariant masses - for time and position - supplementing the one mass for the definite unitary particle sector with another mass for the indefinite unitary interaction sector without asymptotic particle interpretation.

  12. Finite Element Residual Stress Analysis of Planetary Gear Tooth

    Directory of Open Access Journals (Sweden)

    Jungang Wang

    2013-01-01

    Full Text Available A method to simulate residual stress field of planetary gear is proposed. In this method, the finite element model of planetary gear is established and divided to tooth zone and profile zone, whose different temperature field is set. The gear's residual stress simulation is realized by the thermal compression stress generated by the temperature difference. Based on the simulation, the finite element model of planetary gear train is established, the dynamic meshing process is simulated, and influence of residual stress on equivalent stress of addendum, pitch circle, and dedendum of internal and external meshing planetary gear tooth profile is analyzed, according to non-linear contact theory, thermodynamic theory, and finite element theory. The results show that the equivalent stresses of planetary gear at both meshing and nonmeshing surface are significantly and differently reduced by residual stress. The study benefits fatigue cracking analysis and dynamic optimization design of planetary gear train.

  13. Do the ticks of birds at an important migratory hotspot reflect the seasonal dynamics of Ixodes ricinus at the migration initiation site? A case study in the Danube Delta.

    Directory of Open Access Journals (Sweden)

    Attila D Sándor

    Full Text Available Migratory birds play important roles as distributors of ticks within and between continents. In the Old World, the most important migratory route of birds links Asia, Europe and Africa. During their migration, birds use various stopover sites, where they feed and rest and where ticks may attach or detach, creating new natural foci for vector-borne diseases. Danube Delta is one of the most important migration hotspots and so far no studies were focused on ticks of migratory birds herein. The aim of the present study was to assess the species diversity and seasonal dynamics of ticks parasitizing migratory birds in Danube Delta Biosphere Reserve. Migratory birds were trapped on Grindul Lupilor (44°41'N; 28°56'E using mist nets during 4 migratory seasons (2 spring and 2 autumn in 2011 and 2012. From each bird, all the ticks were collected and identified based on morphological features. Epidemiological parameters (prevalence, mean abundance, mean intensity were calculated and all data were analysed statistically based on the season (spring and autumn, regional status of birds (migrants and breeding and foraging behaviour (ground feeders, reed-bed feeders, foliage feeders. A total of 1434 birds (46 species were captured. Ticks were found on 94 birds (10 species. Significantly more migratory birds hosted ticks, compared to resident birds. The 400 collected ticks belonged to four species: Ixodes ricinus (92.25%, I. arboricola (6.25%, I. redikorzevi (1.00% and Haemaphysalis punctata (0.50%. A higher prevalence was found for I. ricinus in spring, with higher prevalence of nymphs in this season, while larvae occurred with the same prevalence in both seasons. Larval intensity was higher during spring and nymphs were more abundant during autumn. The seasonal differences in our study may be related not to the local seasonal dynamics of ticks, but on the seasonal dynamics at the site of migration initiation.

  14. Residual stress simulation of circumferential welded joints

    Directory of Open Access Journals (Sweden)

    Melicher R.

    2007-11-01

    Full Text Available Residual stresses are an important consideration in the component integrity and life assessment of welded structure. The welding process is very complex time dependent physical phenomenon with material nonlinearity. The welding is a thermal process with convection between fluid flow and welding body, between welding bodyand environment. Next type of boundary conditions is radiation and thermo-mechanical contact on the outer surface of gas pipe in the near of weld. The temperature variation so obtained is utilised to find the distribution of the stress field.In this paper, a brief review of weld simulation and residual stress modelling using the finite element method (FEM by commercial software ANSYS is presented. Thermo-elastic-plastic formulations using a von Mises yield criterion with nonlinear kinematics hardening has been employed. Residual axial and hoop stresses obtained from the analysis have been shown. The commercial FEM code ANSYS was used for coupled thermalmechanical analysis.

  15. Microstructure and Residual Stress of Shot Coating

    Science.gov (United States)

    Itoh, Yoshiyasu; Suyama, Shoko; Fuse, Toshiaki

    A shot coating process for metalizing at the surface of ceramics has been newly developed as the shot peening treatment. However, microstructure and residual stress of shot coatings, which have an important effect on the adherent strength of coatings and the strength of ceramic substrates, have not always been clarified. An experimental investigation on the microstructure and residual stress was carried out for the shot coating of aluminum on zinc-oxide substrate by comparison with the atmospheric plasma sprayed aluminum coatings. As a result, low porosity, low oxide content and flat surface could be obtained from the aluminum coatings formed by shot coating process in comparison with the atmospheric plasma sprayed aluminum coatings. Also, it was confirmed by the X-ray diffraction technique that the residual stress of shot coated aluminum over zinc-oxide substrate was high compressive in comparison with the atmospheric plasma spraying process.

  16. Bioenergy from sisal residues

    Energy Technology Data Exchange (ETDEWEB)

    Jungersen, G. [Dansk Teknologisk Inst. (Denmark); Kivaisi, A.; Rubindamayugi, M. [Univ. of Dar es Salaam (Tanzania, United Republic of)

    1998-05-01

    The main objectives of this report are: To analyse the bioenergy potential of the Tanzanian agro-industries, with special emphasis on the Sisal industry, the largest producer of agro-industrial residues in Tanzania; and to upgrade the human capacity and research potential of the Applied Microbiology Unit at the University of Dar es Salaam, in order to ensure a scientific and technological support for future operation and implementation of biogas facilities and anaerobic water treatment systems. The experimental work on sisal residues contains the following issues: Optimal reactor set-up and performance; Pre-treatment methods for treatment of fibre fraction in order to increase the methane yield; Evaluation of the requirement for nutrient addition; Evaluation of the potential for bioethanol production from sisal bulbs. The processing of sisal leaves into dry fibres (decortication) has traditionally been done by the wet processing method, which consumes considerable quantities of water and produces large quantities of waste water. The Tanzania Sisal Authority (TSA) is now developing a dry decortication method, which consumes less water and produces a waste product with 12-15% TS, which is feasible for treatment in CSTR systems (Continously Stirred Tank Reactors). (EG)

  17. Binding stability of peptides derived from 1ALA residue and 7GLY residues to sites near active center of fluctuating papain

    Science.gov (United States)

    Nishiyama, Katsuhiko

    2012-05-01

    We investigated the binding stability of peptides derived from 1ALA residue and 7GLY residues to sites near active center of fluctuating papain via molecular dynamics and docking simulations. Replacing GLY residue in 8GLY with ALA residue had a positive effect on binding stability to the sites in some cases although the replacing had a negative effect on it in other cases. Furthermore the replacing had a negative effect on the chance of binding to the sites. Residue in peptide should be replaced on the basis of systematic exploration of its position.

  18. Effect of Solder Flux Residues on Corrosion of Electronics

    DEFF Research Database (Denmark)

    Hansen, Kirsten Stentoft; Jellesen, Morten Stendahl; Møller, Per

    2009-01-01

    Flux from ‘No Clean’ solder processes can cause reliability problems in the field due to aggressive residues, which may be electrical conducting or corrosive in humid environments. The solder temperature during a wave solder process is of great importance to the amount of residues left on a PCBA[...

  19. Analytical electron microscopy of LDEF impactor residues

    Science.gov (United States)

    Bernhard, Ronald P.; Barrett, Ruth A.; Zolensky, Michael E.

    1995-01-01

    The LDEF contained 57 individual experiment trays or tray portions specifically designed to characterize critical aspects of meteoroid and debris environment in low-Earth orbit (LEO). However, it was realized from the beginning that the most efficient use of the satellite would be to characterize impact features from the entire surface of the LDEF. With this in mind particular interest has focused on common materials facing in all 26 LDEF facing directions; among the most important of these materials has been the tray clamps. Therefore, in an effort to better understand the nature and flux of particulates in LEO, and their effects on spacecraft hardware, we are analyzing residues found in impact features on LDEF tray clamp surfaces. This paper summarizes all data from 79 clamps located on Bay A & B of the LDEF. We also describe current efforts to characterize impactor residues recovered from the impact craters, and we have found that a low, but significant, fraction of these residues have survived in a largely unmelted state. These residues can be characterized sufficiently to permit resolution of the impactor origin. We have concentrated on the residue from chondritic interplanetary dust particles (micrometeoroids), as these represent the harshest test of our analytical capabilities.

  20. Insight into the mechanism of galactokinase: Role of a critical glutamate residue and helix/coil transitions.

    Science.gov (United States)

    McAuley, Margaret; Huang, Meilan; Timson, David J

    2017-03-01

    Galactokinase, the enzyme which catalyses the first committed step in the Leloir pathway, has attracted interest due to its potential as a biocatalyst and as a possible drug target in the treatment of type I galactosemia. The mechanism of the enzyme is not fully elucidated. Molecular dynamics (MD) simulations of galactokinase with the active site residues Arg-37 and Asp-186 altered predicted that two regions (residues 174-179 and 231-240) had different dynamics as a consequence. Interestingly, the same two regions were also affected by alterations in Arg-105, Glu-174 and Arg-228. These three residues were identified as important in catalysis in previous computational studies on human galactokinase. Alteration of Arg-105 to methionine resulted in a modest reduction in activity with little change in stability. When Arg-228 was changed to methionine, the enzyme's interaction with both ATP and galactose was affected. This variant was significantly less stable than the wild-type protein. Changing Glu-174 to glutamine (but not to aspartate) resulted in no detectable activity and a less stable enzyme. Overall, these combined in silico and in vitro studies demonstrate the importance of a negative charge at position 174 and highlight the critical role of the dynamics in to key regions of the protein. We postulate that these regions may be critical for mediating the enzyme's structure and function.

  1. Nitrogen deposition promotes the production of new fungal residues but retards the decomposition of old residues in forest soil fractions.

    Science.gov (United States)

    Griepentrog, Marco; Bodé, Samuel; Boeckx, Pascal; Hagedorn, Frank; Heim, Alexander; Schmidt, Michael W I

    2014-01-01

    Atmospheric nitrogen (N) deposition has frequently been observed to increase soil carbon (C) storage in forests, but the underlying mechanisms still remain unclear. Changes in microbial community composition and substrate use are hypothesized to be one of the key mechanisms affected by N inputs. Here, we investigated the effects of N deposition on amino sugars, which are used as biomarkers for fungal- and bacterial-derived microbial residues in soil. We made use of a 4-year combined CO2 enrichment and N deposition experiment in model forest ecosystems, providing a distinct (13) C signal for 'new' and 'old' C in soil organic matter and microbial residues measured in density and particle-size fractions of soils. Our hypothesis was that N deposition decreases the amount of fungal residues in soils, with the new microbial residues being more strongly affected than old residues. The soil fractionation showed that organic matter and microbial residues are mainly stabilized by association with soil minerals in the heavy and fine fractions. Moreover, the bacterial residues are relatively enriched at mineral surfaces compared to fungal residues. The (13) C tracing indicated a greater formation of fungal residues compared to bacterial residues after 4 years of experiment. In contradiction to our hypotheses, N deposition significantly increased the amount of new fungal residues in bulk soil and decreased the decomposition of old microbial residues associated with soil minerals. The preservation of old microbial residues could be due to decreased N limitation of microorganisms and therefore a reduced dependence on organic N sources. This mechanism might be especially important in fine heavy fractions with low C/N ratios, where microbial residues are effectively protected from decomposition by association with soil minerals.

  2. Extracting sea level residual in tidally dominated estuarine environments

    Science.gov (United States)

    Brown, Jennifer M.; Bolaños, Rodolfo; Howarth, Michael J.; Souza, Alejandro J.

    2012-07-01

    Sea level comprises a mean level, tidal elevation and a residual elevation. Knowledge of what causes maximum water levels is often key in coastal management. However, different methods to extract deviations in water level (residuals) from modelled and observed elevation can give different results. The Dee Estuary, northwest England is a macrotidal estuary that undergoes periodic stratification. It is used here to demonstrate methods to extract the residual water level in response to the following interactive processes: tidal, river-induced stratification and flow, meteorology and waves. Using modelling techniques, the interaction and contribution of different physical processes are investigated. Classical harmonic tidal analysis, model simulations and filtering techniques have been used to "de-tide" the total elevation for short-term (approximately month long) records. Each technique gives a different result highlighting the need to select the correct method for a required study. Analysis of the residual components demonstrates that all processes inducing residuals interact with the tide generating a semi-diurnal residual component. It is suggested that modelling methods enable the full effect of tidal interaction to remain in the residual, whilst harmonic tidal analysis (partly) modify and filtering methods (fully) remove this component of the residual. The analysis methods presented and their influences on the resultant residual are applicable to other study sites. However, when applied specifically to the mouth of the Dee Estuary, the external surge is found to be the main contributor to the total residual, whilst local wind and stratification effects are of secondary importance.

  3. American coal imports 2015

    Energy Technology Data Exchange (ETDEWEB)

    Frank Kolojeski [TransGlobal Ventures Corp. (United States)

    2007-09-15

    As 2007 ends, the US coal industry passes two major milestones - the ending of the Synfuel tax break, affecting over 100M st annually, and the imposition of tighter and much more expensive safety measures, particularly in deep mines. Both of these issues, arriving at a time of wretched steam coal price levels, promise to result in a major shake up in the Central Appalachian mining sector. The report utilizes a microeconomic regional approach to determine whether either of these two schools of thought have any validity. Transport, infrastructure, competing fuels and regional issues are examined in detail and this forecasts estimates coal demand and imports on a region by region basis for the years 2010 and 2015. Some of the major highlights of the forecast are: Import growth will be driven by steam coal demand in the eastern and southern US; Transport will continue to be the key driver - we believe that inland rail rates will deter imports from being railed far inland and that the great majority of imports will be delivered directly by vessel, barge or truck to end users; Colombian coal will be the overwhelmingly dominant supply source and possesses a costs structure to enable it to compete with US-produced coal in any market conditions; Most of the growth will come from existing power plants - increasing capacity utilization at existing import facilities and other plants making investments to add imports to the supply portfolio - the growth is not dependent upon a lot of new coal fired capacity being built. Contents of the report are: Key US market dynamics; International supply dynamics; Structure of the US coal import market; and Geographic analysis.

  4. residue and shunting pinholes

    Science.gov (United States)

    Gorji, Nima E.

    2014-09-01

    The present work considers two observable phenomena through the experimental fabrication and electrical characterization of the rf-sputtered CdS/CdTe thin film solar cells that extremely reduce the overall conversion efficiency of the device: CdCl2 residue on the surface of the semiconductor and shunting pinholes. The former happens through nonuniform treatment of the As-deposited solar cells before annealing at high temperature and the latter occurs by shunting pinholes when the cell surface is shunted by defects, wire-like pathways or scratches on the metallic back contact caused from the external contacts. Such physical problems may be quite common in the experimental activities and reduce the performance down to 4-5 % which leads to dismantle the device despite its precise fabrication. We present our electrical characterization on the samples that received wet CdCl2 surface treatment (uniform or nonuniform) and are damaged by the pinholes.

  5. Hierarchically deflated conjugate residual

    CERN Document Server

    Yamaguchi, Azusa

    2016-01-01

    We present a progress report on a new class of multigrid solver algorithm suitable for the solution of 5d chiral fermions such as Domain Wall fermions and the Continued Fraction overlap. Unlike HDCG \\cite{Boyle:2014rwa}, the algorithm works directly on a nearest neighbour fine operator. The fine operator used is Hermitian indefinite, for example $\\Gamma_5 D_{dwf}$, and convergence is achieved with an indefinite matrix solver such as outer iteration based on conjugate residual. As a result coarse space representations of the operator remain nearest neighbour, giving an 8 point stencil rather than the 81 point stencil used in HDCG. It is hoped this may make it viable to recalculate the matrix elements of the little Dirac operator in an HMC evolution.

  6. Residual stress around the cortical surface in bovine femoral diaphysis.

    Science.gov (United States)

    Yamada, Satoshi; Tadano, Shigeru

    2010-04-01

    Residual stress in living tissue plays an important role in mechanical strength. We have reported that residual stress exists in the bone tissue of a rabbit's tibiofibula. The purpose of this study is to measure the residual stress around the outer cortical region of bovine femoral diaphysis and to discuss the distribution of the stress. This work proposed the sin(2) psi method of X-ray diffraction to the measurement of residual stresses in bone tissue. In this method, residual stress can be estimated from the variation in the interplanar spacings orientated to a number of directions without the lattice strain in the stress direction. Four-point bending tests of strip specimens taken from bovine femoral diaphysis were carried out during X-ray irradiation in advance. In the proximal, middle, and distal sections of bovine femoral diaphyses, the residual stresses at the cortical surface were measured using characteristic Mo-Kalpha X-rays. The bending tests of strip specimens with X-ray irradiation showed that the method could reliably estimate residual stresses in the bone tissue. The residual stress of the bone axial direction was larger than that of the circumferential direction. The stresses in the middle part of five diaphyses along the bone axial direction were tensile. The maximum stress was 162 MPa at the lateral position and the minimum was 78 MPa at the posterior position. The residual stress in the bone axial direction varies around the circumferential region. In addition, the bone axial distributions of residual stresses were different in the proximal, middle, and distal sections of the individual femur. Furthermore, it was confirmed that residual stress in the bone tissue was released by the cutting out of the specimen. The residual stresses in bone tissue could be measured by this method. The results show that residual stress in the bone axial direction at the cortical surface in bovine femoral diaphysis is tensile and varies around the circumferential

  7. Experimental determination of residual stress

    Science.gov (United States)

    Ferguson, Milton W.

    1991-01-01

    Residual stresses in finished parts have often been regarded as factors contributing to premature part failure and geometric distortions. Currently, residual stresses in welded structures and railroad components are being investigated. High residual stresses formed in welded structures due primarily to the differential contractions of the weld material as it cools and solidifies can have a profound effect on the surface performance of the structure. In railroad wheels, repeated use of the brakes causes high residual stresses in the rims which may lead to wheel failure and possible derailment. The goals of the study were: (1) to develop strategies for using x-ray diffraction to measure residual stress; (2) to subject samples of Inconel 718 to various mechanical and heat treatments and to measure the resulting stress using x-ray diffraction; and (3) to measure residual stresses in ferromagnetic alloys using magnetoacoustics.

  8. Prediction of interface residue based on the features of residue interaction network.

    Science.gov (United States)

    Jiao, Xiong; Ranganathan, Shoba

    2017-11-07

    Protein-protein interaction plays a crucial role in the cellular biological processes. Interface prediction can improve our understanding of the molecular mechanisms of the related processes and functions. In this work, we propose a classification method to recognize the interface residue based on the features of a weighted residue interaction network. The random forest algorithm is used for the prediction and 16 network parameters and the B-factor are acting as the element of the input feature vector. Compared with other similar work, the method is feasible and effective. The relative importance of these features also be analyzed to identify the key feature for the prediction. Some biological meaning of the important feature is explained. The results of this work can be used for the related work about the structure-function relationship analysis via a residue interaction network model. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Variation in one residue associated with the metal ion-dependent adhesion site regulates αIIbβ3 integrin ligand binding affinity.

    Directory of Open Access Journals (Sweden)

    Joel Raborn

    Full Text Available The Asp of the RGD motif of the ligand coordinates with the β I domain metal ion dependent adhesion site (MIDAS divalent cation, emphasizing the importance of the MIDAS in ligand binding. There appears to be two distinct groups of integrins that differ in their ligand binding affinity and adhesion ability. These differences may be due to a specific residue associated with the MIDAS, particularly the β3 residue Ala(252 and corresponding Ala in the β1 integrin compared to the analogous Asp residue in the β2 and β7 integrins. Interestingly, mutations in the adjacent to MIDAS (ADMIDAS of integrins α4β7 and αLβ2 increased the binding and adhesion abilities compared to the wild-type, while the same mutations in the α2β1, α5β1, αVβ3, and αIIbβ3 integrins demonstrated decreased ligand binding and adhesion. We introduced a mutation in the αIIbβ3 to convert this MIDAS associated Ala(252 to Asp. By combination of this mutant with mutations of one or two ADMIDAS residues, we studied the effects of this residue on ligand binding and adhesion. Then, we performed molecular dynamics simulations on the wild-type and mutant αIIbβ3 integrin β I domains, and investigated the dynamics of metal ion binding sites in different integrin-RGD complexes. We found that the tendency of calculated binding free energies was in excellent agreement with the experimental results, suggesting that the variation in this MIDAS associated residue accounts for the differences in ligand binding and adhesion among different integrins, and it accounts for the conflicting results of ADMIDAS mutations within different integrins. This study sheds more light on the role of the MIDAS associated residue pertaining to ligand binding and adhesion and suggests that this residue may play a pivotal role in integrin-mediated cell rolling and firm adhesion.

  10. Materials recovery from shredder residues

    Energy Technology Data Exchange (ETDEWEB)

    Daniels, E. J.; Jody, B. J.; Pomykala, J., Jr.

    2000-07-24

    Each year, about five (5) million ton of shredder residues are landfilled in the US. Similar quantities are landfilled in Europe and the Pacific Rim. Landfilling of these residues results in a cost to the existing recycling industry and also represents a loss of material resources that are otherwise recyclable. In this paper, the authors outline the resources recoverable from typical shredder residues and describe technology that they have developed to recover these resources.

  11. Residual entropy and simulated annealing

    OpenAIRE

    Ettelaie, R.; Moore, M. A.

    1985-01-01

    Determining the residual entropy in the simulated annealing approach to optimization is shown to provide useful information on the true ground state energy. The one-dimensional Ising spin glass is studied to exemplify the procedure and in this case the residual entropy is related to the number of one-spin flip stable metastable states. The residual entropy decreases to zero only logarithmically slowly with the inverse cooling rate.

  12. Employing the fluorescence anisotropy and quenching kinetics of tryptophan to hunt for residual structures in denatured proteins

    Indian Academy of Sciences (India)

    Satish Kumar; Rajaram Swaminathan

    2007-03-01

    Residual structures in denatured proteins have acquired importance in recent years owing to their role as protein-folding initiation sites. Locating these structures in proteins has proved quite formidable, requiring techniques like NMR. Here in this report, we take advantage of the ubiquitous presence of tryptophan residues in residual structures to hunt for their presence using steady-state fluorescence spectroscopy. The surface accessibility and rotational dynamics of tryptophan in putative residual structures among ten different proteins, namely glucagon, melittin, subtilisin carlsberg, myelin basic protein, ribonuclease T1, human serum albumin, barstar mutant, bovine serum albumin, lysozyme and Trp-Met-Asp-Phe-NH2 peptide, was studied using steady state fluorescence quenching and anisotropy, respectively. Five proteins, namely ribonuclease T1, bovine serum albumin, melittin, barstar and hen egg white lysozyme appear likely to possess tryptophan(s) in hydrophobic clusters based on their reduced bimolecular quenching rates and higher steady-state anisotropy in proportion to their chain length. We also show that the fluorescence emission maximum of tryptophan is insensitive to the presence of residual structures.

  13. Dynamic Allostery Mediated by a Conserved Tryptophan in the Tec Family Kinases.

    Directory of Open Access Journals (Sweden)

    Nikita Chopra

    2016-03-01

    Full Text Available Bruton's tyrosine kinase (Btk is a Tec family non-receptor tyrosine kinase that plays a critical role in immune signaling and is associated with the immunological disorder X-linked agammaglobulinemia (XLA. Our previous findings showed that the Tec kinases are allosterically activated by the adjacent N-terminal linker. A single tryptophan residue in the N-terminal 17-residue linker mediates allosteric activation, and its mutation to alanine leads to the complete loss of activity. Guided by hydrogen/deuterium exchange mass spectrometry results, we have employed Molecular Dynamics simulations, Principal Component Analysis, Community Analysis and measures of node centrality to understand the details of how a single tryptophan mediates allostery in Btk. A specific tryptophan side chain rotamer promotes the functional dynamic allostery by inducing coordinated motions that spread across the kinase domain. Either a shift in the rotamer population, or a loss of the tryptophan side chain by mutation, drastically changes the coordinated motions and dynamically isolates catalytically important regions of the kinase domain. This work also identifies a new set of residues in the Btk kinase domain with high node centrality values indicating their importance in transmission of dynamics essential for kinase activation. Structurally, these node residues appear in both lobes of the kinase domain. In the N-lobe, high centrality residues wrap around the ATP binding pocket connecting previously described Catalytic-spine residues. In the C-lobe, two high centrality node residues connect the base of the R- and C-spines on the αF-helix. We suggest that the bridging residues that connect the catalytic and regulatory architecture within the kinase domain may be a crucial element in transmitting information about regulatory spine assembly to the catalytic machinery of the catalytic spine and active site.

  14. Evaluation of residue-residue contact predictions in CASP9

    KAUST Repository

    Monastyrskyy, Bohdan

    2011-01-01

    This work presents the results of the assessment of the intramolecular residue-residue contact predictions submitted to CASP9. The methodology for the assessment does not differ from that used in previous CASPs, with two basic evaluation measures being the precision in recognizing contacts and the difference between the distribution of distances in the subset of predicted contact pairs versus all pairs of residues in the structure. The emphasis is placed on the prediction of long-range contacts (i.e., contacts between residues separated by at least 24 residues along sequence) in target proteins that cannot be easily modeled by homology. Although there is considerable activity in the field, the current analysis reports no discernable progress since CASP8.

  15. Homogeneity of Residual Layer thickness in UV Nanoimprint Lithography

    Science.gov (United States)

    Hiroshima, Hiroshi; Atobe, Hidemasa

    2009-06-01

    In nanoimprint lithography, control of residual layer thickness is a very important issue. Pattern density variation is inconvenient for nanoimprint lithography but UV nanoimprint is considered more adaptive to pattern density variation thanks to the higher fluidity of UV-curable resin. Despite this consideration, methods to overcome pattern density problems have been developed and adopted in UV nanoimprint lithography. These methods work well; however, it is still remains there a question of whether residual layer thickness uniformity is improved without such methods. In this study, UV nanoimprint is carried out using a conformable contact mechanism, and the impact of pattern density variation and pressing time of nanoimprint on the residual layer profile is investigated for an initially thin UV-curable resin. After recess filling, UV-curable resin moves very locally so as to make the residual layer smoothly change, but does not move sufficiently for the residual layer to be modified across the entire imprint field. For a longer pressing time, the residual layer thickness is decreased only at the edges. A small amount of the UV-curable resin was expelled from the mold, but most was retained between the mold and wafer, and the UV-curable resin moved inward. For realization of a thin and uniform residual layer, the residual layer must be thin throughout the imprint field from the beginning of the pressing process; otherwise the resulting residual layer that is thick only at peripheral regions must be thinned by a long pressing time.

  16. 77 FR 24671 - Compliance Guide for Residue Prevention and Agency Testing Policy for Residues

    Science.gov (United States)

    2012-04-25

    ... administered by FSIS to collect data on chemical residues in domestic and imported meat, poultry, and egg... collects samples of meat, poultry, and egg products at federally inspected establishments and analyzes the... contaminants. With the implementation of the Hazard Analysis and Critical Control Points (HACCP)...

  17. 莠去津在沈阳地区土壤中的残留动态分析%Analysis of Atrazine Residue Dynamic in the Soil in Shenyang

    Institute of Scientific and Technical Information of China (English)

    王素娜; 高增贵; 孙艳秋; 刘限; 李婉莹

    2014-01-01

    采用高效液相色谱法对莠去津在沈阳市和新民市土壤中的消解动态进行了研究。结果表明:在添加浓度为0.05~0.5 mg/kg时,莠去津在土壤中的回收率为87.35%~120.12%,相对标准偏差为3.32%~7.03%,满足农药残留分析要求。莠去津在沈阳市和新民市土壤中的消解动态均符合一级降解动力学方程。莠去津在沈阳市土壤中的半衰期为15.61~16.27 d,在新民市土壤中的半衰期为14.65~15.34 d,两者消解速率相近。莠去津在土壤中的最终残留量为未检出,说明该农药为低残留、易消解农药。建议田间使用38%莠去津悬浮剂防治玉米田杂草时,有效成分用量不高于3377 g/hm2,于玉米播后苗前施药1次。%A HPLC method was established for determining the residue and the degradation of atrazine in Shenyang and Xinmin. The results showed that the fortified recoveries of atrazine were 87.35%-120.12%at the spiking levels of 0.05-0.5 mg/kg with the relative standard deviations of 3.32%-7.03%. The method met the requirements of residue analysis. The degradation of atrazine in soil conformed to the first-order kinetic equation, and the half-lives of atrazine were 15.61-16.27 d and 14.65-15.34 d in Shenyang and Xinmin, respectively. The rates of degradation in soil in Shenyang and Xinmin were similar. The final residues of atrazine in soil were not detected. Atrazine 38%SC could be used to control weed in corn field with the maximum active ingredient dosages of 3 377 g/hm2.

  18. Local fluctuation control of papain by changing a highly fluctuating residue

    Science.gov (United States)

    Nishiyama, Katsuhiko

    2013-01-01

    To control the local fluctuation of the amino acid residues of papain, ARG59, a highly fluctuating residue in papain, has been changed to GLY. We investigated the binding properties of 2-10GLY (peptides with between 2 and 10 glycine residues) to the modified papain structure via molecular dynamics and docking simulations. The change of the ARG59 residue to GLY alters the binding sites for some peptides, and changed its substrate specificity. Furthermore, the modification alters the binding stability of some peptides. Thus, control of the local fluctuations of residues in proteins has the potential to alter the protein's function.

  19. Residual number processing in dyscalculia.

    OpenAIRE

    Cappelletti, M.; Price, C.J.

    2014-01-01

    Developmental dyscalculia - a congenital learning disability in understanding numerical concepts - is typically associated with parietal lobe abnormality. However, people with dyscalculia often retain some residual numerical abilities, reported in studies that otherwise focused on abnormalities in the dyscalculic brain. Here we took a different perspective by focusing on brain regions that support residual number processing in dyscalculia. All participants accurately performed semantic and ca...

  20. Selenium speciation in flue desulfurization residues.

    Science.gov (United States)

    Zhong, Liping; Cao, Yan; Li, Wenying; Xie, Kechang; Pan, Wei-Ping

    2011-01-01

    Flue gas from coal combustion contains significant amounts of volatile selenium (Se). The capture of Se in the flue gas desulfurization (FGD) scrubber unit has resulted in a generation of metal-laden residues. It is important to determine Se speciation to understand the environmental impact of its disposal. A simple method has been developed for selective inorganic Se(IV), Se(VI) and organic Se determination in the liquid-phase FGD residues by hydride generation atomic fluorescence spectrometry (AFS). It has been determined that Se(IV), Se(VI) and organic Se can be accurately determined with detection limits (DL) of 0.05, 0.06 and 0.06 microg/L, respectively. The accuracy of the proposed method was evaluated by analyzing the certified reference material, NIST CRM 1632c, and also by analyzing spiked tap-water samples. Analysis indicates that the concentration of Se is high in FGD liquid residues and primarily exists in a reduced state as selenite (Se(IV)). The toxicity of Se(IV) is the strongest of all Se species. Flue gas desulfurization residues pose a serious environmental risk.

  1. Selenium speciation in flue desulfurization residues

    Institute of Scientific and Technical Information of China (English)

    Liping Zhong; Yan Cao; Wenying Li; Kechang Xie; Wei-Ping Pan

    2011-01-01

    Flue gas from coal combustion contains significant amounts of volatile selenium (Se).The capture of Se in the flue gas desulfurization (FGD) scrubber unit has resulted in a generation of metal-laden residues.It is important to determine Se speciation to understand the environmental impact of its disposal.A simple method has been developed for selective inorganic Se(Ⅳ), Se(Ⅵ) and organic Se determination in the liquid-phase FGD residues by hydride generation atomic fluorescence spectrometry (AFS).It has been determined that Se(Ⅳ), Se(Ⅵ) and organic Se can be accurately determined with detection limits (DL) of 0.05, 0.06 and 0.06 μg/L, respectively.The accuracy of the proposed method was evaluated by analyzing the certified reference material, NIST CRM 1632c, and also by analyzing spiked tap-water samples.Analysis indicates that the concentration of Se is nigh in FGD liquid residues and primarily exists in a reduced state as selenite (Se(Ⅳ)).The toxicity of Se(Ⅳ) is the strongest of all Se species.Flue gas desulfurization residues pose a serious environmental risk.

  2. Recovery of silver residues from dental amalgam

    Directory of Open Access Journals (Sweden)

    Heloísa Aparecida Barbosa da Silva Pereira

    2010-04-01

    Full Text Available Dental amalgam residues are probably the most important chemical residues generated from clinical dental practice because of the presence of heavy metals among its constituents, mainly mercury and silver. OBJECTIVE: The purpose of this study was to develop an alternative method for the recovery of silver residues from dental amalgam. MATERIAL AND METHODS: The residue generated after vacuum distillation of dental amalgam for the separation of mercury was initially diluted with 32.5% HNO3, followed by precipitation with 20% NaCl. Sequentially, under constant heating and agitation with NaOH and sucrose, the sample was reduced to metallic silver. However, the processing time was too long, which turned this procedure not viable. In another sequence of experiments, the dilution was accomplished with concentrated HNO3 at 90ºC, followed by precipitation with 20% NaCl. After washing, the pellet was diluted with concentrated NH4OH, water and more NaCl in order to facilitate the reaction with the reducer. RESULTS: Ascorbic acid was efficiently used as reducer, allowing a fast reduction, thus making the procedure viable. CONCLUSIONS: The proposed methodology is of easy application and does not require sophisticated equipment or expensive reagents.

  3. Torrefaction process for agriculture and forest residues

    Energy Technology Data Exchange (ETDEWEB)

    Dutta, A. [Nova Scotia Agricultural College, Truro, NS (Canada). Dept. of Engineering; Pimchuai, A. [Burapha Univ., Chonburi (Thailand). Dept. of Mechanical Engineering

    2009-07-01

    This paper reported on a study in which 2 energy crops, notably agriculture and forest residues, were torrefied with subsequent analysis of the solid residues. The purpose of the study was to remove some disadvantages of agriculture residues as a fuel and to enhance their solid fuel qualities. The 5 agriculture residues studied were rice husk, sawdust, peanut husk, bagasse and water hyacinth. Temperature and residence time for the process was varied at 250, 270, 300 degrees C and 1, 1.5, 2 hours respectively. The torrefied products were then characterized in terms of yield, proximate analysis, heating value and hydrophobic properties. The optimum condition based on mass and energy balance for the torrefaction process was determined. The torrefied products were found to be more brown in colour and had lower moisture content and volatile matter. The fixed carbon content and energy density of the ash increased. The bagasse that was torrefied at 300 degrees C and 1.5 hours had the highest HHV content, comparable to that of lignite. Depending on the severity of the torrefaction conditions, the torrefied fuel can contain up to 98 per cent of the original energy content on a mass basis. It was concluded that the operating temperature is the most important parameter for producing a better torrefied product.

  4. Statistical inference on residual life

    CERN Document Server

    Jeong, Jong-Hyeon

    2014-01-01

    This is a monograph on the concept of residual life, which is an alternative summary measure of time-to-event data, or survival data. The mean residual life has been used for many years under the name of life expectancy, so it is a natural concept for summarizing survival or reliability data. It is also more interpretable than the popular hazard function, especially for communications between patients and physicians regarding the efficacy of a new drug in the medical field. This book reviews existing statistical methods to infer the residual life distribution. The review and comparison includes existing inference methods for mean and median, or quantile, residual life analysis through medical data examples. The concept of the residual life is also extended to competing risks analysis. The targeted audience includes biostatisticians, graduate students, and PhD (bio)statisticians. Knowledge in survival analysis at an introductory graduate level is advisable prior to reading this book.

  5. Residual strains in conduit arteries.

    Science.gov (United States)

    Rachev, A; Greenwald, S E

    2003-05-01

    Residual strains and stresses are those that exist in a body when all external loads are removed. Residual strains in arteries can be characterized by the opening angle of the sector-like cross-section which arises when an unloaded ring segment is radially cut. A review of experimental methods for measuring residual strains and the main results about the variation of the opening angle with arterial localization, age, smooth muscle activity, mechanical environment and certain vascular pathologies are presented and discussed. It is shown that, in addition to their well-established ability to homogenize the stress field in the arterial wall, residual strains make arteries more compliant and thereby improve their performance as elastic reservoirs and ensure more effective local control of the arterial lumen by smooth muscle cells. Finally, evidence that, in some cases, residual strains remain in arteries even after they have been cut radially is discussed.

  6. 代森锰锌、乙撑硫脲在大棚、露地黄瓜上的残留动态对比研究%Comparison of Residual Dynamics of Mancozeb and Ethylenethioureaon Cucumbers Grown in Plastic House and Open Field

    Institute of Scientific and Technical Information of China (English)

    范志先; 叶志强; 许允成; 初丽伟

    2001-01-01

    The residual dynamics of mancozeb and ethylenethio urea on cucumbers grown in plastic house and open field were compared. After application, the dynamics of mancozeb residues on cucumbers grown in plastic house and field could be described, respectively, as Ct=1.058e-0.1282t,Ct=0.751 e-0.4689t, with a half-life of 5.4 and 1.4 days, respectively. The degradation of mancozeb on cucumbers grown in the plastic house was slower than that of cucumbers grown in open field. The dynamics of ethylenethiourea residues on cucumbers grown in plastic house and field could be described, respectively, as Ct=0.152e-0.1794t ,Ct=0.059e-0.1366t, and respectively with a half-life of 3.9 and 5.4 days. The degradation of eth ylenethiourea on cucumbers grown in the plastic house was faster than that of cucumbers grown in open field.%对代森锰锌、乙撑硫脲在大棚、露地黄瓜上的残留动态进行了对比研究。喷药后,代森锰锌在大棚黄瓜上的降解动态方程为Ct=1.058e-0. 1282t,露地为Ct=0.751e-0.4689t。半衰期分别为5.4 d和1.4 d。代森锰锌在大棚黄瓜上的降解速度要慢于露地黄瓜。乙撑硫脲在大棚黄瓜上的降解动态方程为Ct=0.152e-0.1794t,露地为Ct=0 .059e-0.1366t 。半衰期分别为3.9 d和5.4 d。乙撑硫脲在大棚黄瓜上的降解速度要稍快于露地黄瓜。

  7. Observations of the field-aligned residual flow inside magnetic cloud structure

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    In this paper,we report two MC events observed by WIND spacecraft with good examples of fieldaligned residual flow inside the MC structure. For both events,the co-moving frames are determined through the deHoffman-Teller (HT) analysis and the axial orientations are inferred by the newly developed minimal residue (MR) method. The nature coordinate system for both events are constructed with velocity of the HT frame and the inferred MC axis,the field and flow remaining in the HT frame are analyzed at this coordinate system. As a result,we find that the residual flows in the co-moving HT frame of the two MC events are almost anti-parallel to the helical magnetic field. We speculate that the field-aligned residual flows are large scale coherent hydrodynamic vortices co-moving with the MCs at the supersonic speed near 1 AU. Data analyses show that the event in slow ambient solar wind is expanding at 1 AU and another one in fast solar wind does not show apparent expansion. Proton behaviors for both events are quasi-isothermal. Accelerated HT analysis shows that both events have no suitable HT frame with constant accelerations,which suggests that both events may be moving at the constant speed near 1 AU under the assumptions of the HT analysis. For both events,the ratio of the dynamic pressure to the magnetic pressure is larger than that of the thermal pressure to magnetic pressure,which suggests that the dynamic effects due to the plasma flows remaining in the co-moving HT frame are more important than the thermal effects in the study of MC evolution and propagation.

  8. Observations of the field-aligned residual flow inside magnetic cloud structure

    Institute of Scientific and Technical Information of China (English)

    LI HuiJun; FENG XueShang; ZUO PingBing; XIE YanQiong

    2009-01-01

    In this paper, we report two MC events observed by WIND spacecraft with good examples of field-aligned residual flow inside the MC structure. For both events, the co-moving frames are determined through the deHoffman-Teller (HT) analysis and the axial orientations are inferred by the newly devel-oped minimal residue (MR) method. The nature coordinate system for both events are constructed with velocity of the HT frame and the inferred MC axis, the field and flow remaining in the HT frame are analyzed st this coordinate system. As a result, we find that the residual flows in the co-moving HT frame of the two MC events are almost anti-parallel to the helical magnetic field. We speculate that the field-aligned residual flows are large scale coherent hydrodynamic vortices co-moving with the MCs at the supersonic speed near 1 AU. Data analyses show that the event in slow ambient solar wind is ex- panding at 1 AU and another one in fast solar wind does not show apparent expansion. Proton behav-iors for both events are quasi-isothermal. Accelerated HT analysis shows that both events have no suitable HT frame with constant accelerations, which suggests that both events may be moving at the constant speed near 1 AU under the assumptions of the HT analysis. For both events, the ratio of the dynamic pressure to the magnetic pressure is larger than that of the thermal pressure to magnetic pressure, which suggests that the dynamic effects due to the plasma flows remaining in the co-moving HT frame are more important than the thermal effects in the study of MC evolution and propagation.

  9. Identification of catalytic residues using a novel feature that integrates the microenvironment and geometrical location properties of residues.

    Directory of Open Access Journals (Sweden)

    Lei Han

    Full Text Available Enzymes play a fundamental role in almost all biological processes and identification of catalytic residues is a crucial step for deciphering the biological functions and understanding the underlying catalytic mechanisms. In this work, we developed a novel structural feature called MEDscore to identify catalytic residues, which integrated the microenvironment (ME and geometrical properties of amino acid residues. Firstly, we converted a residue's ME into a series of spatially neighboring residue pairs, whose likelihood of being located in a catalytic ME was deduced from a benchmark enzyme dataset. We then calculated an ME-based score, termed as MEscore, by summing up the likelihood of all residue pairs. Secondly, we defined a parameter called Dscore to measure the relative distance of a residue to the center of the protein, provided that catalytic residues are typically located in the center of the protein structure. Finally, we defined the MEDscore feature based on an effective nonlinear integration of MEscore and Dscore. When evaluated on a well-prepared benchmark dataset using five-fold cross-validation tests, MEDscore achieved a robust performance in identifying catalytic residues with an AUC1.0 of 0.889. At a ≤ 10% false positive rate control, MEDscore correctly identified approximately 70% of the catalytic residues. Remarkably, MEDscore achieved a competitive performance compared with the residue conservation score (e.g. CONscore, the most informative singular feature predominantly employed to identify catalytic residues. To the best of our knowledge, MEDscore is the first singular structural feature exhibiting such an advantage. More importantly, we found that MEDscore is complementary with CONscore and a significantly improved performance can be achieved by combining CONscore with MEDscore in a linear manner. As an implementation of this work, MEDscore has been made freely accessible at http://protein.cau.edu.cn/mepi/.

  10. Evaluation of pesticide residues in fruits and vegetables from Algeria.

    Science.gov (United States)

    Mebdoua, Samira; Lazali, Mohamed; Ounane, Sidi Mohamed; Tellah, Sihem; Nabi, Fahima; Ounane, Ghania

    2017-01-17

    A total of 160 samples of 13 types of fresh fruits and vegetables from domestic production and import were analysed to detect the presence of pesticide residues. Analysis was performed by multi-residual extraction followed by gas chromatography-mass spectrometry. In 42.5% of the tested samples, no residues were found and 12.5% of samples contained pesticide residues above maximum residue limits. Risk assessment for long-term exposure was done for all pesticides detected in this study. Except chlorpyrifos and lambda-cyhalothrin, exposure to pesticides from vegetables and fruits was below 1% of the acceptable daily intake. Short-term exposure assessment revealed that in seven pesticide/commodity combinations, including three pesticides (chlorpyrifos, deltamethrin and lambda-cyhalothrin), the acute reference dose had been exceeded.

  11. Landfilling of waste incineration residues

    DEFF Research Database (Denmark)

    Christensen, Thomas Højlund; Astrup, Thomas; Cai, Zuansi

    2002-01-01

    Residues from waste incineration are bottom ashes and air-pollution-control (APC) residues including fly ashes. The leaching of heavy metals and salts from the ashes is substantial and a wide spectrum of leaching tests and corresponding criteria have been introduced to regulate the landfilling...... of the ashes. Leaching test, however, must be selected carefully to provide information relevant for the actual disposal scenario and for evaluating the benefits of pre-treating the residues prior to landfilling. This paper describes research at the Technical University of Denmark addressing some...

  12. RESIDUAL RISK ASSESSMENT: ETHYLENE OXIDE ...

    Science.gov (United States)

    This document describes the residual risk assessment for the Ethylene Oxide Commercial Sterilization source category. For stationary sources, section 112 (f) of the Clean Air Act requires EPA to assess risks to human health and the environment following implementation of technology-based control standards. If these technology-based control standards do not provide an ample margin of safety, then EPA is required to promulgate addtional standards. This document describes the methodology and results of the residual risk assessment performed for the Ethylene Oxide Commercial Sterilization source category. The results of this analyiss will assist EPA in determining whether a residual risk rule for this source category is appropriate.

  13. Corn Residue Use by Livestock in the United States

    Directory of Open Access Journals (Sweden)

    Marty R. Schmer

    2017-01-01

    Full Text Available Corn ( L. residue grazing or harvest provides a simple and economical practice to integrate crops and livestock, but limited information is available on how widespread corn residue utilization is practiced by US producers. In 2010, the USDA Economic Research Service surveyed producers from 19 states on corn grain and residue management practices. Total corn residue grazed or harvested was 4.87 million ha. Approximately 4.06 million ha was grazed by 11.7 million livestock (primarily cattle in 2010. The majority of grazed corn residue occurred in Nebraska (1.91 million ha, Iowa (385,000 ha, South Dakota (361,000 ha, and Kansas (344,000 ha. Average grazing days ranged from 10 to 73 d (mean = 40 d. Corn residue harvests predominantly occurred in the central and northern Corn Belt, with an estimated 2.9 Tg of corn residue harvested across the 19 states. This survey highlights the importance of corn residue for US livestock, particularly in the western Corn Belt.

  14. What governs the presence of residual vegetation in boreal wildfires?

    Science.gov (United States)

    Araya, Yikalo H.; Remmel, Tarmo K.; Perera, Ajith H.

    2016-04-01

    Wildfires are frequent boreal forest disturbances in Canada, and emulating their patterns with forest harvesting has emerged as a common forest management goal. Wildfires contain many patches of residual vegetation of various size, shape, and composition; understanding their characteristics provides insights for improved emulation criteria. We studied the occurrence of residual vegetation within eleven boreal wildfire events in a natural setting; fires ignited by lightning, no suppression efforts, and no prior anthropogenic disturbances. Relative importance of the measurable geo-environmental factors and their marginal effects on residual presence are studied using Random Forests. These factors included distance from natural firebreaks (wetland, bedrock and non-vegetated areas, and water), land cover, and topographic variables (elevation, slope, and ruggedness index). We present results at spatial resolutions ranging from four to 64 m while emphasizing four and 32 m since they mimic IKONOS- and Landsat-type images. Natural firebreak features, especially the proximity to wetlands, are among the most important variables that explain the likelihood residual occurrence. The majority of residual vegetation areas are concentrated within 100 m of wetlands. Topographic variables, typically important in rugged terrain, are less important in explaining the presence of residuals within our study fires.

  15. Nitrogen availability of biogas residues

    Energy Technology Data Exchange (ETDEWEB)

    El-Sayed Fouda, Sara

    2011-09-07

    The objectives of this study were to characterize biogas residues either unseparated or separated into a liquid and a solid phase from the fermentation of different substrates with respect to their N and C content. In addition, short and long term effects of the application of these biogas residues on the N availability and N utilization by ryegrass was investigated. It is concluded that unseparated or liquid separated biogas residues provide N at least corresponding to their ammonium content and that after the first fertilizer application the C{sub org}:N{sub org} ratio of the biogas residues was a crucial factor for the N availability. After long term application, the organic N accumulated in the soil leads to an increased release of N.

  16. OECD Maximum Residue Limit Calculator

    Science.gov (United States)

    With the goal of harmonizing the calculation of maximum residue limits (MRLs) across the Organisation for Economic Cooperation and Development, the OECD has developed an MRL Calculator. View the calculator.

  17. Landfilling of waste incineration residues

    DEFF Research Database (Denmark)

    Christensen, Thomas Højlund; Astrup, Thomas; Cai, Zuansi

    2002-01-01

    Residues from waste incineration are bottom ashes and air-pollution-control (APC) residues including fly ashes. The leaching of heavy metals and salts from the ashes is substantial and a wide spectrum of leaching tests and corresponding criteria have been introduced to regulate the landfilling...... of the ashes. Leaching test, however, must be selected carefully to provide information relevant for the actual disposal scenario and for evaluating the benefits of pre-treating the residues prior to landfilling. This paper describes research at the Technical University of Denmark addressing some...... of these issues focusing on pH-development in landfilled residues, effects of leaching test conditions on Cr leaching and effects of pre-treatment with FeSO4....

  18. Perturbation-based Markovian transmission model for probing allosteric dynamics of large macromolecular assembling: a study of GroEL-GroES.

    Directory of Open Access Journals (Sweden)

    Hsiao-Mei Lu

    2009-10-01

    Full Text Available Large macromolecular assemblies are often important for biological processes in cells. Allosteric communications between different parts of these molecular machines play critical roles in cellular signaling. Although studies of the topology and fluctuation dynamics of coarse-grained residue networks can yield important insights, they do not provide characterization of the time-dependent dynamic behavior of these macromolecular assemblies. Here we develop a novel approach called Perturbation-based Markovian Transmission (PMT model to study globally the dynamic responses of the macromolecular assemblies. By monitoring simultaneous responses of all residues (>8,000 across many (>6 decades of time spanning from the initial perturbation until reaching equilibrium using a Krylov subspace projection method, we show that this approach can yield rich information. With criteria based on quantitative measurements of relaxation half-time, flow amplitude change, and oscillation dynamics, this approach can identify pivot residues that are important for macromolecular movement, messenger residues that are key to signal mediating, and anchor residues important for binding interactions. Based on a detailed analysis of the GroEL-GroES chaperone system, we found that our predictions have an accuracy of 71-84% judged by independent experimental studies reported in the literature. This approach is general and can be applied to other large macromolecular machineries such as the virus capsid and ribosomal complex.

  19. Residue arithmetic in binary systems

    OpenAIRE

    Barsi, Ferruccio

    1988-01-01

    A natural approach to the problem of performing mod m computations in a binary system is presented and a solution is suggested which is based upon a straightforward relation between the residues of a same integer X with respect to different moduli. The proposed solution proves fruitful in various applications, such as converting binary integers to residue notation and mod m addition or multiplication. Even if the most usual implementation approach for mod m processors is based on look-up tabl...

  20. Marine Tar Residues: a Review.

    Science.gov (United States)

    Warnock, April M; Hagen, Scott C; Passeri, Davina L

    Marine tar residues originate from natural and anthropogenic oil releases into the ocean environment and are formed after liquid petroleum is transformed by weathering, sedimentation, and other processes. Tar balls, tar mats, and tar patties are common examples of marine tar residues and can range in size from millimeters in diameter (tar balls) to several meters in length and width (tar mats). These residues can remain in the ocean environment indefinitely, decomposing or becoming buried in the sea floor. However, in many cases, they are transported ashore via currents and waves where they pose a concern to coastal recreation activities, the seafood industry and may have negative effects on wildlife. This review summarizes the current state of knowledge on marine tar residue formation, transport, degradation, and distribution. Methods of detection and removal of marine tar residues and their possible ecological effects are discussed, in addition to topics of marine tar research that warrant further investigation. Emphasis is placed on benthic tar residues, with a focus on the remnants of the Deepwater Horizon oil spill in particular, which are still affecting the northern Gulf of Mexico shores years after the leaking submarine well was capped.

  1. Residue Analysis and Degradation Dynamics of Tebuconazole in Rice%戊唑醇在水稻中的残留分析方法及消解动态

    Institute of Scientific and Technical Information of China (English)

    张昌朋; 赵华; 蔡晓明; 何红梅; 朱亚红; 李振

    2012-01-01

    [Aims] The method for the determination of tebuconazole residues in rice plant, rice hull, rice and soil were estimated for evaluating the safety of tebuconazole in paddy field. [Methods] The samples were extracted with acetonitrile, clean-up using a Florisil solid phase extraction cartridge, and subsequent determination by GC-NPD. And the field experiments were investigated in Zhejiang, Shandong and Hunan, [Results] Average recoveries of tebuconazole in rice plant and rice hull were found in the range of 88.80-103,86% at the three spiking levels from 0.05 to 5.0 mg/kg with relative standard deviations of 4.25-1436%. Average recoveries of tebuconazole in rice and soil were found in the range of 89.19-102.27% at the three spiking levels from 0.02 to 2.0 mg/kg with relative standard deviations of 2,26-8.58%. The limits of quantification (LOQ) in rice plant and rice hull were 0.05 mg/kg. The limits of quantification (LOQ) in rice and soil were 0.02 mg/kg. The field experiments demonstrated that the decline curves of tebuconazole in rice plant were accorded with the first-order kinetics equation, and the half-lives were 0.60 d in Zhejiang, 11.48 d in Shandong, and 3.14 d in Hunan, respectively. The residue of tebuconazole was 0.30 mg/kg in rice plant, 0,22 mg/kg in rice hull, <0,02 mg/kg in rice and <0.02 mg/kg in soil, respectively, after 21 d of spray. [Conclusions] The method was suitable for the determination of tebuconazole residues in rice. Tebuconazole was easily degradable pesticides in rice plant, and the half-lives were 0.60-11.48 d.%[目的]为检测水稻中戊唑醇残留及评价其在水稻上使用的安全性,建立了戊唑醇在水稻植株、稻壳、糙米和土壤中的残留分析方法.[方法]水稻样品采用乙腈提取,Florisil小柱净化,GC-NPD测定.同时,于浙江、山东和湖南3地进行了田间试验.[结果]戊唑醇在水稻植株和稻壳中的添加质量分数为0.05~5.0 mg/kg时,平均回收率为88.80%~103.86

  2. Predicting transmembrane helix packing arrangements using residue contacts and a force-directed algorithm.

    Science.gov (United States)

    Nugent, Timothy; Jones, David T

    2010-03-19

    Alpha-helical transmembrane proteins constitute roughly 30% of a typical genome and are involved in a wide variety of important biological processes including cell signalling, transport of membrane-impermeable molecules and cell recognition. Despite significant efforts to predict transmembrane protein topology, comparatively little attention has been directed toward developing a method to pack the helices together. Here, we present a novel approach to predict lipid exposure, residue contacts, helix-helix interactions and finally the optimal helical packing arrangement of transmembrane proteins. Using molecular dynamics data, we have trained and cross-validated a support vector machine (SVM) classifier to predict per residue lipid exposure with 69% accuracy. This information is combined with additional features to train a second SVM to predict residue contacts which are then used to determine helix-helix interaction with up to 65% accuracy under stringent cross-validation on a non-redundant test set. Our method is also able to discriminate native from decoy helical packing arrangements with up to 70% accuracy. Finally, we employ a force-directed algorithm to construct the optimal helical packing arrangement which demonstrates success for proteins containing up to 13 transmembrane helices. This software is freely available as source code from http://bioinf.cs.ucl.ac.uk/memsat/mempack/.

  3. Predicting transmembrane helix packing arrangements using residue contacts and a force-directed algorithm.

    Directory of Open Access Journals (Sweden)

    Timothy Nugent

    2010-03-01

    Full Text Available Alpha-helical transmembrane proteins constitute roughly 30% of a typical genome and are involved in a wide variety of important biological processes including cell signalling, transport of membrane-impermeable molecules and cell recognition. Despite significant efforts to predict transmembrane protein topology, comparatively little attention has been directed toward developing a method to pack the helices together. Here, we present a novel approach to predict lipid exposure, residue contacts, helix-helix interactions and finally the optimal helical packing arrangement of transmembrane proteins. Using molecular dynamics data, we have trained and cross-validated a support vector machine (SVM classifier to predict per residue lipid exposure with 69% accuracy. This information is combined with additional features to train a second SVM to predict residue contacts which are then used to determine helix-helix interaction with up to 65% accuracy under stringent cross-validation on a non-redundant test set. Our method is also able to discriminate native from decoy helical packing arrangements with up to 70% accuracy. Finally, we employ a force-directed algorithm to construct the optimal helical packing arrangement which demonstrates success for proteins containing up to 13 transmembrane helices. This software is freely available as source code from http://bioinf.cs.ucl.ac.uk/memsat/mempack/.

  4. Earthworms and Plant Residues Modify Nematodes in Tropical Cropping Soils (Madagascar: A Mesocosm Experiment

    Directory of Open Access Journals (Sweden)

    Cécile Villenave

    2010-01-01

    Full Text Available Free-living nematodes present several characteristics that have led to their use as bioindicators of soil quality. Analyzing the structure of nematofauna is a pertinent way to understand soil biological processes. Earthworms play an important role in soil biological functioning and organic matter dynamics. Their effects on soil nematofauna have seldom been studied. We studied the effect of the tropical endogeic earthworm, Pontoscolex corethrurus, on nematode community structure in a 5-month field mesocosm experiment conducted in Madagascar. Ten different treatments with or without earthworms and with or without organic residues (rice, soybean were compared. Organic residues were applied on the soil surface or mixed with the soil. The abundance of nematodes (bacterial and fungal feeders was higher in presence of P. corethrurus than in their absence. The type of plant residues as well as their localisation had significant effects on the abundance and composition of soil nematodes. The analysis of nematode community structure showed that earthworm activity led to an overall activation of the microbial compartment without specific stimulation of the bacterial or fungal compartment.

  5. Structures, Mixed Types - Residual Waste Operations

    Data.gov (United States)

    NSGIC GIS Inventory (aka Ramona) — A Residual Waste Operation is a DEP primary facility type related to the Waste Management Residual Waste Program. Residual waste is waste generated at an industrial,...

  6. Improved Interaction Potentials for Charged Residues in Proteins

    DEFF Research Database (Denmark)

    Kepp, Kasper Planeta

    2008-01-01

    Electrostatic interactions dominate the structure and free energy of biomolecules. To obtain accurate free energies involving charged groups from molecular simulations, OPLS-AA parameters have been reoptimized using Monte Carlo free energy perturbation. New parameters fit a self-consistent, exper...... directly in molecular simulations with no modification of neutral residues needed and are envisioned to be particular important in simulations where charged residues change environment....

  7. Evaluation of residue-residue contact prediction in CASP10

    KAUST Repository

    Monastyrskyy, Bohdan

    2013-08-31

    We present the results of the assessment of the intramolecular residue-residue contact predictions from 26 prediction groups participating in the 10th round of the CASP experiment. The most recently developed direct coupling analysis methods did not take part in the experiment likely because they require a very deep sequence alignment not available for any of the 114 CASP10 targets. The performance of contact prediction methods was evaluated with the measures used in previous CASPs (i.e., prediction accuracy and the difference between the distribution of the predicted contacts and that of all pairs of residues in the target protein), as well as new measures, such as the Matthews correlation coefficient, the area under the precision-recall curve and the ranks of the first correctly and incorrectly predicted contact. We also evaluated the ability to detect interdomain contacts and tested whether the difficulty of predicting contacts depends upon the protein length and the depth of the family sequence alignment. The analyses were carried out on the target domains for which structural homologs did not exist or were difficult to identify. The evaluation was performed for all types of contacts (short, medium, and long-range), with emphasis placed on long-range contacts, i.e. those involving residues separated by at least 24 residues along the sequence. The assessment suggests that the best CASP10 contact prediction methods perform at approximately the same level, and comparably to those participating in CASP9.

  8. DISSOLUTION OF NEPTUNIUM OXIDE RESIDUES

    Energy Technology Data Exchange (ETDEWEB)

    Kyser, E

    2009-01-12

    This report describes the development of a dissolution flowsheet for neptunium (Np) oxide (NpO{sub 2}) residues (i.e., various NpO{sub 2} sources, HB-Line glovebox sweepings, and Savannah River National Laboratory (SRNL) thermogravimetric analysis samples). Samples of each type of materials proposed for processing were dissolved in a closed laboratory apparatus and the rate and total quantity of off-gas were measured. Samples of the off-gas were also analyzed. The quantity and type of solids remaining (when visible) were determined after post-dissolution filtration of the solution. Recommended conditions for dissolution of the NpO{sub 2} residues are: Solution Matrix and Loading: {approx}50 g Np/L (750 g Np in 15 L of dissolver solution), using 8 M nitric acid (HNO{sub 3}), 0.025 M potassium fluoride (KF) at greater than 100 C for at least 3 hours. Off-gas: Analysis of the off-gas indicated nitric oxide (NO), nitrogen dioxide (NO{sub 2}) and nitrous oxide (N{sub 2}O) as the only identified components. No hydrogen (H{sub 2}) was detected. The molar ratio of off-gas produced per mole of Np dissolved ranged from 0.25 to 0.4 moles of gas per mole of Np dissolved. A peak off-gas rate of {approx}0.1 scfm/kg bulk oxide was observed. Residual Solids: Pure NpO{sub 2} dissolved with little or no residue with the proposed flowsheet but the NpCo and both sweepings samples left visible solid residue after dissolution. For the NpCo and Part II Sweepings samples the residue amounted to {approx}1% of the initial material, but for the Part I Sweepings sample, the residue amounted to {approx}8 % of the initial material. These residues contained primarily aluminum (Al) and silicon (Si) compounds that did not completely dissolve under the flowsheet conditions. The residues from both sweepings samples contained minor amounts of plutonium (Pu) particles. Overall, the undissolved Np and Pu particles in the residues were a very small fraction of the total solids.

  9. Characterization of the residual structure in the unfolded state of the Delta 131 Delta fragment of staphylococcal nuclease

    DEFF Research Database (Denmark)

    Francis, C. J.; Lindorff-Larsen, Kresten; Best, R. B.;

    2006-01-01

    The determination of the conformational preferences in unfolded states of proteins constitutes an important challenge in structural biology. We use inter-residue distances estimated from site-directed spin-labeling NMR experimental measurements as ensemble-averaged restraints in all-atom molecular...... dynamics simulations to characterise the residual structure of the 131 fragment of staphylococcal nuclease under physiological conditions. Our findings indicate that 131 under these conditions shows a tendency to form transiently hydrophobic clusters similar to those present in the native state of wild......-type staphylococcal nuclease. Only rarely, however, all these interactions are simultaneously realized to generate conformations with an overall native topology. Proteins 2006. © 2006 Wiley-Liss, Inc....

  10. 非线性结构动力学系统的首次穿越%An important sampling procedure for estimating failure probabilities of non-linear dynamic systems

    Institute of Scientific and Technical Information of China (English)

    任丽梅; 徐伟; 李战国

    2013-01-01

    The failure probability is one of the most important reliability measures in structural reliability assessment of dynamical systems. Here, a procedure for estimating failure probabilities of non-linear systems based on the important sampling technique was presented. Firstly ,by using Rice formula,the equivalent linear version of the non-linear systems was derived. Using the equivalent linear equation, the design point of the equivalent linear systems was used to construct control function. Secondly, an important sampling technique was used to estimate the first excursion probabilities for the non-linear system. Finally, a Duffing oscillator was taken for example. The simulation results showed that the proposed method is correct and effective; the number of samples and the computational time are reduced significantly compared with those of direct Monte Carlo simulations.%在结构动力学系统的可靠性分析中,动力学系统的首次穿越失效一直是研究重点问题之一.基于重要抽样法基础上研究了非线性结构动力学系统的首次穿越.首先根据Rice公式,得到与非线性系统方程具有相同平均上穿率的等效线性化系统方程,利用此等效方程得到设计点的解析表达式,并用此解析式来构造控制函数,最后将此控制函数运用到非线性系统中,利用重要抽样法估计非线性系统的首穿失效概率.以Duffing振子为例,模拟结果显示了方法的正确性与有效性,与原始蒙特卡罗模拟方法相比较,样本数量、计算所需时间都有明显减小.

  11. Oscillations and residual displacements of buildings of varying heights and widths, constructed on elastic-plastic base

    Directory of Open Access Journals (Sweden)

    Ter-Martirosyan Zaven

    2016-01-01

    Full Text Available Modern regulations in the field of design and construction of buildings in seismically dangerous areas provide for stability calculation of bases, foundations and underground structures, i.e. calculations for the first group of limited states. At the same time, calculations for the second group of limited states, like deformations (yields, relative difference in yields, as a rule, are not fulfilled. This state of affairs is due to insufficient knowledge of the issues of appearance and development of additional stress and strain in ground arrays during seismic influences, that ultimately leads to residual yields and rolls of foundations of industrial and civil buildings. Essentially, residual displacements depend on the type and intensity of dynamic effects, as well as on the model foundation soils. At the same time, the most important factor is the compulsory registration of collaboration between the subgrade and the structure. Therefore, quantification of additional residual displacements of foundations of industrial buildings and structures under dynamic loads, is an actual problem of the modern earthquake-resistant construction.

  12. Conformational flexibility of β-secretase:molecular dynamics simulation and essential dynamics analysis

    Institute of Scientific and Technical Information of China (English)

    Bing XIONG; Xiao-qin HUANG; Ling-ling SHEN; Jian-hua SHEN; Xiao-min LUO; Xu SHEN; Hua-liang JIANG; Kai-xian CHEN

    2004-01-01

    AIM: Based on the structural analysis to reveal the mechanism of ligand binding to β-secretase and the specificity of each binding sub-site. METHODS: Molecular dynamics was used to simulate on the ligand free β-secretase and ligand bound β-secretase. The trajectories were analyzed using the essential dynamics, and the significant conformational change was illustrated employing the DynDom program. RESULTS: The essential dynamics and DynDom analyses clearly showed that the β-secretase experienced a large conformational change upon the substrate or inhibitor binding. The flap structure adopted a swing motion, gradually covering the active site to facilitate the ligand binding process. Residues Ser86 and Ile87 served as the hinge point. Inhibitor-enzyme interaction analysis revealed that residues at P2, Pl, and P1' positions of the inhibitor were very important for the binding, and residues at P2' and P3' positions may be modified to improve the binding specificity. S3 subsite of the enzyme still had space to modify the inhibitors in increasing the binding affinity. CONCLUSION: The information presented here is valuable and could be used to identify small molecular inhibitors of β-secretase.

  13. Reactivity of Athabasca residue and of its SARA fractions during residue hydroconversion

    Energy Technology Data Exchange (ETDEWEB)

    Verstraete, J.; Danial-Fortain, P.; Gauthier, T.; Merdrignac, I. [IFP-Lyon, Vermaison (France); Budzinski, H. [Bordeaux Univ. (France). ISM-LPTC, UMR CNRS

    2009-07-01

    Residue conversion processes are becoming increasingly important because of the declining market for residual fuel oil and a greater demand for middle distillates. Ebullated-bed hydroconversion is a commercially proven technology for converting heavy feedstocks with high amounts of impurities. The process enables the conversion of atmospheric or vacuum residues at temperatures up to 440 degrees C, and at liquid hourly space velocity (LHSV) conditions in the range of 0.15 to 0.5 per hour. A 540 degrees C conversion of up to 80 weight per cent can be achieved under these conditions. This paper reported on a research study conducted at IFP Lyon in which the residue hydroconversion in a large-scale ebullated bed bench unit was investigated to determine the impact of operating conditions and feed properties on yield and product qualities. Hydrogen was added to the feed in the bench units to keep a high hydrogen partial pressure and favour the catalytic hydroconversion reactions. In a typical test, the reactor was fed with 50 g of feedstock and 0.45 g of crushed equilibrium industrial NiMo catalyst, pressurized hydrogen and quickly heated at the reaction temperature. This paper also discussed the conversion of Athabasca bitumen residue in the large-scale pilot plant and also in the small scale batch reactor. The effect of operating temperature and space velocity was examined. The reactivity of the saturates, aromatics, resins and asphaltenes (SARA) fractions of the bitumen was studied separately in order to better understand the conversion mechanisms and reactivities. The Athabasca bitumen feed and SARA fractions were also analyzed in terms of standard petroleum analysis, SARA fractionation, elemental analysis, size exclusion chromatography (SEC) and 13C NMR. Hydroconversion experiments were conducted in the batch unit at different reaction temperatures and reaction times. A comparison of small-scale batch results with those obtained with the continuous large-scale bench

  14. Residues from waste incineration. Final report. Rev. ed.

    Energy Technology Data Exchange (ETDEWEB)

    Astrup, T.; Juul Pedersen, A.; Hyks, J.; Frandsen, F.J.

    2010-04-15

    The overall objective of the project was to improve the understanding of the formation and characteristics of residues from waste incineration. This was done focusing on the importance of the waste input and the operational conditions of the furnace. Data and results obtained from the project have been discussed in this report according to the following three overall parts: i) mass flows and element distribution, ii) flue gas/particle partitioning and corrosion/deposition aspects, and iii) residue leaching. This has been done with the intent of structuring the discussion while tacitly acknowledging that these aspects are interrelated and cannot be separated. Overall, it was found that the waste input composition had significant impact of the characteristics of the generated residues. A similar correlation between operational conditions and residue characteristics could not be observed. Consequently, the project recommend that optimization of residue quality should focus on controlling the waste input composition. The project results showed that including specific waste materials (and thereby also excluding the same materials) may have significant effects on the residue composition, residue leaching, aerosol and deposit formation.It is specifically recommended to minimize Cl in the input waste. Based on the project results, it was found that a significant potential for optimization of waste incineration exist. (Author)

  15. Agricultural Residues and Biomass Energy Crops

    Energy Technology Data Exchange (ETDEWEB)

    None

    2016-06-01

    There are many opportunities to leverage agricultural resources on existing lands without interfering with production of food, feed, fiber, or forest products. In the recently developed advanced biomass feedstock commercialization vision, estimates of potentially available biomass supply from agriculture are built upon the U.S. Department of Agriculture’s (USDA’s) Long-Term Forecast, ensuring that existing product demands are met before biomass crops are planted. Dedicated biomass energy crops and agricultural crop residues are abundant, diverse, and widely distributed across the United States. These potential biomass supplies can play an important role in a national biofuels commercialization strategy.

  16. Dry fermentation of agricultural residues

    Science.gov (United States)

    Jewell, W. J.; Chandler, J. A.; Dellorto, S.; Fanfoni, K. J.; Fast, S.; Jackson, D.; Kabrick, R. M.

    1981-09-01

    A dry fermentation process is discussed which converts agricultural residues to methane, using the residues in their as produced state. The process appears to simplify and enhance the possibilities for using crop residues as an energy source. The major process variables investigated include temperature, the amount and type of inoculum, buffer requirements, compaction, and pretreatment to control the initial available organic components that create pH problems. A pilot-scale reactor operation on corn stover at a temperature of 550 C, with 25 percent initial total solids, a seed-to-feed ratio of 2.5 percent, and a buffer-to-feed ratio of 8 percent achieved 33 percent total volatile solids destruction in 60 days. Volumetric biogas yields from this unit were greater than 1 vol/vol day for 12 days, and greater than 0.5 vol/vol day for 32 days, at a substrate density of 169 kg/m (3).

  17. Morphing of geometric composites via residual swelling.

    Science.gov (United States)

    Pezzulla, Matteo; Shillig, Steven A; Nardinocchi, Paola; Holmes, Douglas P

    2015-08-07

    Understanding and controlling the shape of thin, soft objects has been the focus of significant research efforts among physicists, biologists, and engineers in the last decade. These studies aim to utilize advanced materials in novel, adaptive ways such as fabricating smart actuators or mimicking living tissues. Here, we present the controlled growth-like morphing of 2D sheets into 3D shapes by preparing geometric composite structures that deform by residual swelling. The morphing of these geometric composites is dictated by both swelling and geometry, with diffusion controlling the swelling-induced actuation, and geometric confinement dictating the structure's deformed shape. Building on a simple mechanical analog, we present an analytical model that quantitatively describes how the Gaussian and mean curvatures of a thin disk are affected by the interplay among geometry, mechanics, and swelling. This model is in excellent agreement with our experiments and numerics. We show that the dynamics of residual swelling is dictated by a competition between two characteristic diffusive length scales governed by geometry. Our results provide the first 2D analog of Timoshenko's classical formula for the thermal bending of bimetallic beams - our generalization explains how the Gaussian curvature of a 2D geometric composite is affected by geometry and elasticity. The understanding conferred by these results suggests that the controlled shaping of geometric composites may provide a simple complement to traditional manufacturing techniques.

  18. REDCAT: a residual dipolar coupling analysis tool.

    Science.gov (United States)

    Valafar, Homayoun; Prestegard, James H

    2004-04-01

    Recent advancements in the utilization of residual dipolar couplings (RDCs) as a means of structure validation and elucidation have demonstrated the need for, not only a more user friendly, but also a more powerful RDC analysis tool. In this paper, we introduce a software package named REsidual Dipolar Coupling Analysis Tool (REDCAT) designed to address the above issues. REDCAT is a user-friendly program with its graphical-user-interface developed in Tcl/Tk, which is highly portable. Furthermore, the computational engine behind this GUI is written in C/C++ and its computational performance is therefore excellent. The modular implementation of REDCAT's algorithms, with separation of the computational engine from the graphical engine allows for flexible and easy command line interaction. This feature can be utilized for the design of automated data analysis sessions. Furthermore, this software package is portable to Linux clusters for high throughput applications. In addition to basic utilities to solve for order tensors and back calculate couplings from a given order tensor and proposed structure, a number of improved algorithms have been incorporated. These include the proper sampling of the Null-space (when the system of linear equations is under-determined), more sophisticated filters for invalid order-tensor identification, error analysis for the identification of the problematic measurements and simulation of the effects of dynamic averaging processes.

  19. Residual contact restraints in cryogenics

    Science.gov (United States)

    Cretegny, J. F.; Demonicault, J. M.

    The use of residual stress measurements to evaluate the state of cryogenic turbomachines, whose surfaces are worn by the working conductions in dry contact, is addressed. Their contribution to the understanding of the reasons of possible ruptures is considered. It is stated that residual stress measurements should be used as a complementary tool rather than as input data for models. It is shown, thanks to two examples concerning the ball bearings and splines of the liquid hydrogen turbopump of the Vulcain engine, what can be expected from such techniques. Total exploitation of the results has still to be done, but preliminary results are quite encouraging.

  20. Interferometric Measurement Of Residual Stress

    Science.gov (United States)

    Danyluk, Steven; Andonian, A. T.

    1990-01-01

    Stress averaged through thickness of plate measured nondestructively. Theory of elasticity combined with laser interferometric technique into technique for measurement of residual stresses in solid objects - usually in thin, nominally-flat plates. Measurements particularly useful in inspection of wafers of single-crystal silicon for making solar cells or integrated circuits, because stresses remaining after crystal-growing process cause buckling or fracture. Used to predict deflections of plates caused by known applied loads under specified boundary condition, or to infer applied loads that cause known deflections. Also used to relate known deflections to residual stresses equivalent to stresses produced by fictitious applied loads.

  1. Leaching From Biomass Gasification Residues

    DEFF Research Database (Denmark)

    Allegrini, Elisa; Boldrin, Alessio; Polletini, A.

    2011-01-01

    The aim of the present work is to attain an overall characterization of solid residues from biomass gasification. Besides the determination of chemical and physical properties, the work was focused on the study of leaching behaviour. Compliance and pH-dependence leaching tests coupled...... with geochemical modelling were carried out both on fresh and aged samples. The results showed that the material is comparable to residues from wood combustion and the leaching behaviour was dominated by Ca-containing minerals and solid solutions. Heavy metals were detected in very low concentrations in the bulk...

  2. Leaching From Biomass Gasification Residues

    DEFF Research Database (Denmark)

    Allegrini, Elisa; Boldrin, Alessio; Polletini, A.

    2011-01-01

    The aim of the present work is to attain an overall characterization of solid residues from biomass gasification. Besides the determination of chemical and physical properties, the work was focused on the study of leaching behaviour. Compliance and pH-dependence leaching tests coupled with geoche......The aim of the present work is to attain an overall characterization of solid residues from biomass gasification. Besides the determination of chemical and physical properties, the work was focused on the study of leaching behaviour. Compliance and pH-dependence leaching tests coupled...

  3. Mutual positional preference of IPMDH proteins for binding studied by coarse-grained molecular dynamics simulation

    Science.gov (United States)

    Ishioka, T.; Yamada, H.; Miyakawa, T.; Morikawa, R.; Akanuma, S.; Yamagishi, A.; Takasu, M.

    2016-12-01

    Proteins, which incorporate charged and hydrophobic amino acid residues, are useful as a material of nanotechnology. Among these proteins, IPMDH (3-isopropylmalate dehydrogenase), which has thermal stability, has potential as a material of nanofiber. In this study, we performed coarse-grained molecular dynamics simulation of IPMDH using MARTINI force fields, and we investigated the orientation for the binding of IPMDH. In simulation, we analyzed wild type of IPMDH and the mutated IPMDH proteins, where 13, 20, 27, 332, 335 and 338th amino acid residues are replaced by lysine residues which have positive charge and by glutamic acid residues which have negative charge. Since the binding of mutated IPMDH is advantageous compared with the binding of wild type for one orientation, we suggest that the Coulomb interaction for the binding of IPMDH is important.

  4. 新烟碱类杀虫剂拌种对麦蚜田间防效及药剂残留动态分析%Effectiveness of imidacloprid and thiamethoxam in controlling wheat aphids and the dynamics of pesticide residues in wheat leaves

    Institute of Scientific and Technical Information of China (English)

    都振宝; 苗进; 武予清; 陈锡岭; 李广领; 巩中军; 段云; 蒋月丽

    2011-01-01

    为了分析两代新烟碱类杀虫剂吡虫啉和噻虫嗪拌种对麦蚜的防治效果的差异以及2种药剂在小麦叶片内的残留动态,采用呲虫啉和噻虫嗪有效剂量0.5、1.0、2.0和4.0 g/kg小麦种子在播种前进行1次性拌种处理,随后调查了不同处理下田间麦蚜的种群密度,并对不同时期小麦叶片内的药剂残留进行了监测.结果表明:吡虫啉有效剂量2.0和4.0 g/kg,噻虫嗪有效剂量1.0、2.0和4.0 g/kg小麦种子播前拌种能有效的降低田间麦蚜的种群数量.在4月10日前,吡虫啉在小麦叶片内的含量明显高于噻虫嗪,4月28日后两者差异不明显.与吡虫啉相比,噻虫嗪对麦蚜具有更高的生物活性和控制效果.%The relative effectiveness of two second generation neonicotinoid insecticides, thiamethoxam and imidacloprid, in controlling wheat aphids and the dynamics of their residues in wheat leaves was investigated. Wheat seeds were treated with 0. 5, 1,2 and 4 a. I. G/kg of either thiamethoxam or imidacloprid before sowing and the population density of wheat aphids and the amount of pesticide residue in wheat leaves was determined at different points in time. The results show that both pesticides were effective in reducing populations of wheat aphids and the damage these cause to wheat crops. The best results were achieved by spraying wheat seeds with 2 and 4 a. I. G/ kg of 25% imidacloprid and 1, 2 and 4 a. I. G/ kg of 70% thiamethoxam. The concentration of thiamethoxam in wheat leaves before 10-Apr. Was significantly lower than that of imidacloprid, but there was no difference in the amount of residue of either pesticide after 28 - Apr. In conclusion, thiamethoxam is a better choice for controlling wheat aphids than imidacloprid.

  5. Development of residual stress prediction model in pipe weldment

    Energy Technology Data Exchange (ETDEWEB)

    Eom, Yun Yong; Lim, Se Young; Choi, Kang Hyeuk; Cho, Young Sam; Lim, Jae Hyuk [Korea Advanced Institute of Science and Technology, Taejon (Korea, Republic of)

    2002-03-15

    When Leak Before Break(LBB) concepts is applied to high energy piping of nuclear power plants, residual weld stresses is a important variable. The main purpose of his research is to develop the numerical model which can predict residual weld stresses. Firstly, basic theories were described which need to numerical analysis of welding parts. Before the analysis of pipe, welding of a flat plate was analyzed and compared. Appling the data of used pipes, thermal/mechanical analysis were accomplished and computed temperature gradient and residual stress distribution. For thermal analysis, proper heat flux was regarded as the heat source and convection/radiation heat transfer were considered at surfaces. The residual stresses were counted from the computed temperature gradient and they were compared and verified with a result of another research.

  6. Solution oxygen-17 NMR application for observing a peroxidized cysteine residue in oxidized human SOD1

    Science.gov (United States)

    Fujiwara, Noriko; Yoshihara, Daisaku; Sakiyama, Haruhiko; Eguchi, Hironobu; Suzuki, Keiichiro

    2016-12-01

    NMR active nuclei, 1H, 13C and 15N, are usually used for determination of protein structure. However, solution 17O-NMR application to proteins is extremely limited although oxygen is an essential element in biomolecules. Proteins are oxidized through cysteine residues by two types of oxidation. One is reversible oxidation such as disulphide bonding (Cys-S-S-Cys) and the other is irreversible oxidation to cysteine sulfinic acid (Cys-SO 2H) and cysteine sulfonic acid (Cys-SO 3H). Copper,Zinc-superoxide dismutase (SOD1) is a key enzyme in the protection of cells from the superoxide anion radical. The SH group at Cys 111 residue in human SOD1 is selectively oxidized to -SO 2H and -SO 3H with atmospheric oxygen, and this oxidized human SOD1 is also suggested to play an important role in the pathophysiology of various neurodegenerative diseases, probably mainly via protein aggregation. Therefore, information on the structural and the dynamics of the oxidized cysteine residue would be crucial for the understanding of protein aggregation mechanism. Although the -SO 3H group on proteins cannot be directly detected by conventional NMR techniques, we successfully performed the site-specific 17O-labeling of Cys 111 in SOD1 using ^{17}it {O}2 gas and the 17O-NMR analysis for the first time. We observed clear 17O signal derived from a protein molecule and show that 17O-NMR is a sensitive probe for studying the structure and dynamics of the 17O-labeled protein molecule. This novel and unique strategy can have great impact on many research fields in biology and chemistry.

  7. Assessment of residual body weight gain and residual intake and body weight gain as feed efficiency traits in the turkey (Meleagris gallopavo)

    OpenAIRE

    Willems, Owen W; Miller, Stephen P.; Wood, Benjamin J

    2013-01-01

    Background Since feed represents 70% of the total cost in poultry production systems, an animal’s ability to convert feed is an important trait. In this study, residual feed intake (RFI) and residual body weight gain (RG), and their linear combination into residual feed intake and body weight gain (RIG) were studied to estimate their genetic parameters and analyze the potential differences in feed intake between the top ranked birds based on the criteria for each trait. Methods Phenotypic and...

  8. Assessment of residual body weight gain and residual intake and body weight gain as feed efficiency traits in the turkey (Meleagris gallopavo)

    OpenAIRE

    Willems, Owen W; Miller, Stephen P.; Wood, Benjamin J

    2013-01-01

    Background Since feed represents 70% of the total cost in poultry production systems, an animal’s ability to convert feed is an important trait. In this study, residual feed intake (RFI) and residual body weight gain (RG), and their linear combination into residual feed intake and body weight gain (RIG) were studied to estimate their genetic parameters and analyze the potential differences in feed intake between the top ranked birds based on the criteria for each trait. Methods Phenotypic and...

  9. COMPARISON OF THE EULERIAN AND LAGRANGIAN TIDAL RESIDUALS IN THE BOHAI SEA

    Institute of Scientific and Technical Information of China (English)

    魏皓; 赵亮; 冯士笮

    2001-01-01

    Tidal residual is very important to the transport of water particles, nutrients, plank-ton, etc. in the coastal sea. Eulerian scheme and Lagrangian scheme are two different ways to get the time averaged residual. Solution of the Bohai Sea's hydrodynamic system using a semi-implicit layer aver-aged numerical model yielded different direction Eulerian and Lagrangian tidal residuals. The latter were stronger than the former in most sea areas. Their different directions produced different ciretdation pattern in some areas. Compared with the Eulerian residual, the Lagranglan residual seemed to be more in accord with the observation.

  10. COMPARISON OF THE EULERIAN AND LAGRANGIAN TIDAL RESIDUALS IN THE BOHAI SEA

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Tidal residual is very important to the transport of water particles, nutrients, plankton, etc. in the coastal sea. Eulerian scheme and Lagrangian scheme are two different ways to get the time averaged residual. Solution of the Bohai Sea's hydrodynamic system using a semi-implicit layer averaged numerical model yielded different direction Eulerian and Lagrangian tidal residuals. The latter were stronger than the former in most sea areas. Their different directions produced different circulation pattern in some areas. Compared with the Eulerian residual, the Lagrangian residual seemed to be more in accord with the observation.

  11. Analytical methods for residual solvents determination in pharmaceutical products.

    Science.gov (United States)

    Grodowska, Katarzyna; Parczewski, Andrzej

    2010-01-01

    Residual solvents (RS) are not desirable substances in the final pharmaceutical product and their acceptable limits have been published in pharmacopoeias and ICH guidelines. The intension of this paper was to review and discuss some of the current analytical procedures including gas chromatographic (GC) and other alternative techniques which are used for residual solvents determination. GC methods have been developed to monitor this kind of impurities routinely. The most popular techniques of sample introduction into the gas chromatograph include direct injection, static or dynamic headspace, solid-phase microextraction and single drop microextraction. Different separation techniques like two dimensional chromatography or multicapillary chromatography were compared with classical separation mode with use of single capillary column. Also alternative methodologies for residual solvents testing were discussed in this review. In conclusions, gas chromatography-based procedures were described as the most appropriate because of the lowest detection limits, ease of sample preparation and specificity.

  12. Toxicological evaluation of organic residues

    Directory of Open Access Journals (Sweden)

    Eduardo de la Peña de Torres

    2005-12-01

    Full Text Available It is pointed out the importance of short term assays for the characterization of organic residues, specially some methods for toxicological, mutagenic, genotoxic and cytotoxic evaluation (Vibrio fischeri, Salmonella typhimurium and Allium cepa, used in the characterization of environmental complex mixtures lixiviates. These methods take part together with other bioassays in the evaluation by toxicological identification (VIT, which allows the evaluation of other ecotoxicological effects: a bioluminescence inhibition of Vibrio fischeri; b germination and root length of Lepidum sativum; c root length of Allium cepa and Tradescantia sp.; d inhibition of the mobility of Daphnia magna; and e abnormalities in the development of Oryzias latipes, or medaka fish. All these assays take part in the EU battery of bioassays, applied to discriminate and select between those environmental matrixes which must be subject to more complex and specific chemical characterizations.We make a review of the methods for toxicological evaluation, used for the characterization of chemical compounds or complex mixtures, as well as the use of its results for the human and environmental risk assessment. This evaluation consists, in short, of the identification of dangers, evaluation of dose-response ratio, evaluation of exposure and risk characterization, resulting in the analysis, use and communication of this risk. It is emphasized the high predictive value for carcinogenicity of some of these bioassays.It is shown the utility of short term assays for the evaluation of substances, products and complex mixtures, which would contribute to improve the toxicological knowledge of a greater number substances. This is a vital need in the EU, due to the lack of complete toxicological information of about the 70% of the 106.000 existing and used substances.It is emphasized the great value that mutagenicity assays represent inside the toxicological tests in the basic level, which

  13. Landfill Mining of Shredder Residues

    DEFF Research Database (Denmark)

    Hansen, Jette Bjerre; Hyks, Jiri; Shabeer Ahmed, Nassera

    In Denmark, shredder residues (SR) are classified as hazardous waste and until January 2012 the all SR were landfilled. It is estimated that more than 1.8 million tons of SR have been landfilled in mono cells. This paper describes investigations conducted at two Danish landfills. SR were excavated...

  14. Leptogenesis and residual CP symmetry

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Peng; Ding, Gui-Jun [Department of Modern Physics, University of Science and Technology of China,Hefei, Anhui 230026 (China); King, Stephen F. [Physics and Astronomy, University of Southampton,Southampton, SO17 1BJ (United Kingdom)

    2016-03-31

    We discuss flavour dependent leptogenesis in the framework of lepton flavour models based on discrete flavour and CP symmetries applied to the type-I seesaw model. Working in the flavour basis, we analyse the case of two general residual CP symmetries in the neutrino sector, which corresponds to all possible semi-direct models based on a preserved Z{sub 2} in the neutrino sector, together with a CP symmetry, which constrains the PMNS matrix up to a single free parameter which may be fixed by the reactor angle. We systematically study and classify this case for all possible residual CP symmetries, and show that the R-matrix is tightly constrained up to a single free parameter, with only certain forms being consistent with successful leptogenesis, leading to possible connections between leptogenesis and PMNS parameters. The formalism is completely general in the sense that the two residual CP symmetries could result from any high energy discrete flavour theory which respects any CP symmetry. As a simple example, we apply the formalism to a high energy S{sub 4} flavour symmetry with a generalized CP symmetry, broken to two residual CP symmetries in the neutrino sector, recovering familiar results for PMNS predictions, together with new results for flavour dependent leptogenesis.

  15. Temperature dependent dynamics of DegP-trimer: A molecular dynamics study.

    Science.gov (United States)

    Rai, Nivedita; Ramaswamy, Amutha

    2015-01-01

    DegP is a heat shock protein from high temperature requirement protease A family, which reacts to the environmental stress conditions in an ATP independent way. The objective of the present analysis emerged from the temperature dependent functional diversity of DegP between chaperonic and protease activities at temperatures below and above 28 °C, respectively. DegP is a multimeric protein and the minimal functional unit, DegP-trimer, is of great importance in understanding the DegP pathway. The structural aspects of DegP-trimer with respect to temperature variation have been studied using molecular dynamics simulations (for 100 ns) and principal component analysis to highlight the temperature dependent dynamics facilitating its functional diversity. The DegP-trimer revealed a pronounced dynamics at both 280 and 320 K, when compared to the dynamics observed at 300 K. The LA loop is identified as the highly flexible region during dynamics and at extreme temperatures, the residues 46-80 of LA loop express a flip towards right (at 280) and left ( at 320 K) with respect to the fixed β-sheet connecting the LA loop of protease for which Phe46 acts as one of the key residues. Such dynamics of LA loop facilitates inter-monomeric interaction with the PDZ1 domain of the neighbouring monomer and explains its active participation when DegP exists as trimer. Hence, the LA loop mediated dynamics of DegP-trimer is expected to provide further insight into the temperature dependent dynamics of DegP towards the understanding of its assembly and functional diversity in the presence of substrate.

  16. Temperature dependent dynamics of DegP-trimer: A molecular dynamics study

    Directory of Open Access Journals (Sweden)

    Nivedita Rai

    2015-01-01

    Full Text Available DegP is a heat shock protein from high temperature requirement protease A family, which reacts to the environmental stress conditions in an ATP independent way. The objective of the present analysis emerged from the temperature dependent functional diversity of DegP between chaperonic and protease activities at temperatures below and above 28 °C, respectively. DegP is a multimeric protein and the minimal functional unit, DegP-trimer, is of great importance in understanding the DegP pathway. The structural aspects of DegP-trimer with respect to temperature variation have been studied using molecular dynamics simulations (for 100 ns and principal component analysis to highlight the temperature dependent dynamics facilitating its functional diversity. The DegP-trimer revealed a pronounced dynamics at both 280 and 320 K, when compared to the dynamics observed at 300 K. The LA loop is identified as the highly flexible region during dynamics and at extreme temperatures, the residues 46–80 of LA loop express a flip towards right (at 280 and left ( at 320 K with respect to the fixed β-sheet connecting the LA loop of protease for which Phe46 acts as one of the key residues. Such dynamics of LA loop facilitates inter-monomeric interaction with the PDZ1 domain of the neighbouring monomer and explains its active participation when DegP exists as trimer. Hence, the LA loop mediated dynamics of DegP-trimer is expected to provide further insight into the temperature dependent dynamics of DegP towards the understanding of its assembly and functional diversity in the presence of substrate.

  17. A computational investigation on the connection between dynamics properties of ribosomal proteins and ribosome assembly.

    Directory of Open Access Journals (Sweden)

    Brittany Burton

    Full Text Available Assembly of the ribosome from its protein and RNA constituents has been studied extensively over the past 50 years, and experimental evidence suggests that prokaryotic ribosomal proteins undergo conformational changes during assembly. However, to date, no studies have attempted to elucidate these conformational changes. The present work utilizes computational methods to analyze protein dynamics and to investigate the linkage between dynamics and binding of these proteins during the assembly of the ribosome. Ribosomal proteins are known to be positively charged and we find the percentage of positive residues in r-proteins to be about twice that of the average protein: Lys+Arg is 18.7% for E. coli and 21.2% for T. thermophilus. Also, positive residues constitute a large proportion of RNA contacting residues: 39% for E. coli and 46% for T. thermophilus. This affirms the known importance of charge-charge interactions in the assembly of the ribosome. We studied the dynamics of three primary proteins from E. coli and T. thermophilus 30S subunits that bind early in the assembly (S15, S17, and S20 with atomic molecular dynamic simulations, followed by a study of all r-proteins using elastic network models. Molecular dynamics simulations show that solvent-exposed proteins (S15 and S17 tend to adopt more stable solution conformations than an RNA-embedded protein (S20. We also find protein residues that contact the 16S rRNA are generally more mobile in comparison with the other residues. This is because there is a larger proportion of contacting residues located in flexible loop regions. By the use of elastic network models, which are computationally more efficient, we show that this trend holds for most of the 30S r-proteins.

  18. Impact of diverse soil microbial communities on crop residues decomposition

    Science.gov (United States)

    Mrad, Fida; Bennegadi-Laurent, Nadia; Ailhas, Jérôme; Leblanc, Nathalie; Trinsoutrot-Gattin, Isabelle; Laval, Karine; Gattin, Richard

    2017-04-01

    Soils provide many basic ecosystem services for our society and most of these services are carried out by the soil communities, thus influencing soils quality. Soil organic matter (SOM) can be considered as one of the most important soil quality indices for it plays a determinant role in many physical, chemical and biological processes, such as soil structure and erosion resistance, cation exchange capacity, nutrient cycling and biological activity (Andrews et al., 2004). Since a long time, exogenous organic inputs are largely used for improving agricultural soils, affecting highly soil fertility and productivity. The use of organic amendments such as crop residues influences the soil microbial populations' diversity and abundance. In the meantime, soil microbial communities play a major role in the organic matter degradation, and the effect of different microbial communities on the decomposition of crop residues is not well documented. In this context, studying the impact of crop residues on soil microbial ecology and the processes controlling the fate of plant residues in different management practices is essential for understanding the long-term environmental and agronomic effects on soil and organic matters. Our purpose in the present work was to investigate the decomposition by two contrasting microbial communities of three crop residues, and compare the effect of different residues amendments on the abundance and function of each soil microbial communities. Among the main crops which produce large amounts of residues, we focused on three different plants: wheat (Triticum aestivum L.), rape (Brassica napus) and sunflower (Helianthus annuus). The residues degradation in two soils of different management practices and the microbial activity were evaluated by: microbial abundance (microbial carbon, culturable bacteria, total DNA, qPCR), in combination with functional indicators (enzymatic assays and Biolog substrate utilization), kinetics of C and N

  19. Tidal residual current and its role in the mean flow on the Changjiang Bank

    Energy Technology Data Exchange (ETDEWEB)

    Xuan, Jiliang; Yang, Zhaoqing; Huang, Daji; Wang, Taiping; Zhou, Feng

    2016-02-01

    Tidal residual current may play an important role in the mean flow in the Changjiang Bank region, in addition to other residual currents, such as the Taiwan Warm Current, the Yellow Sea Coastal Current, and the Yellow Sea Warm Current. In this paper, a detailed structure of the tidal residual current, in particular the meso-scale eddies, in the Changjiang Bank region is observed from model simulations, and its role in the mean flow is quantified using the well-validated Finite Volume Coastal Ocean Model). The tidal residual current in the Changjiang Bank region consists of two components: an anticyclonic regional-scale tidal residual circulation around the edge of the Changjiang Bank and some cyclonic meso-scale tidal residual eddies across the Changjiang Bank. The meso-scale tidal residual eddies occur across the Changjiang Bank and contribute to the regional-scale tidal residual circulation offshore at the northwest boundary and at the northeast edge of the Changjiang Bank, southeastward along the 50 m isobath. Tidal rectification is the major mechanism causing the tidal residual current to flow along the isobaths. Both components of the tidal residual current have significant effects on the mean flow. A comparison between the tidal residual current and the mean flow indicates that the contribution of the tidal residual current to the mean flow is greater than 50%.

  20. Impact of Residual Inducer on Titratable Expression Systems.

    Directory of Open Access Journals (Sweden)

    Taliman Afroz

    Full Text Available Inducible expression systems are widely employed for the titratable control of gene expression, yet molecules inadvertently present in the growth medium or synthesized by the host cells can alter the response profile of some of these systems. Here, we explored the quantitative impact of these residual inducers on the apparent response properties of inducible systems. Using a simple mathematical model, we found that the presence of residual inducer shrinks the apparent dynamic range and causes the apparent Hill coefficient to converge to one. We also found that activating systems were more sensitive than repressing systems to the presence of residual inducer and the response parameters were most heavily dependent on the original Hill coefficient. Experimental interrogation of common titratable systems based on an L-arabinose inducible promoter or a thiamine pyrophosphate-repressing riboswitch in Escherichia coli confirmed the predicted trends. We finally found that residual inducer had a distinct effect on "all-or-none" systems, which exhibited increased sensitivity to the added inducer until becoming fully induced. Our findings indicate that residual inducer or repressor alters the quantitative response properties of titratable systems, impacting their utility for scientific discovery and pathway engineering.

  1. Exploring the Use of Non-Image-Based Ultrasound to Detect the Position of the Residual Femur within a Stump

    Science.gov (United States)

    Chong, Sook-Yee; Röhrle, Oliver

    2016-01-01

    A satisfactorily fitted socket interacts dynamically with the stump in order to support body weight, transmit load effectively, enhance dynamic stability, and enable the control and stabilization of the residual limb. The internal dynamics occurring within a socket is important in determining optimal fit. Many measurement and imaging techniques, such as X-rays, have been utilized to investigate the movement of the residual femur within the stump during gait. However, due to associated health risks and costs, none of the current techniques have been extended to clinical prosthetics. The use of B-mode ultrasound has been suggested as a safe and cheap alternative, and has been utilized in previous studies to monitor the motion of the femur. However, the need to create a duplicate socket and time-consuming analysis of the images were obstacles to the system being applied clinically. This study aims to gauge the effectiveness of a non-image based ultrasound system. Here, we determined errors expected from the measurements. Accuracy errors of 2.9 mm to 8.4 mm and reproducibility measurements within a standard deviation of 3.9 mm are reported. We also estimated errors up to 14.4 mm in in-vivo measurements. We think there is potential in developing this technique, and we hope to reduce some technical difficulties such that it can, one day, be easily incorporated into prosthetic fitting. PMID:27764120

  2. NbIT--a new information theory-based analysis of allosteric mechanisms reveals residues that underlie function in the leucine transporter LeuT.

    Directory of Open Access Journals (Sweden)

    Michael V LeVine

    2014-05-01

    Full Text Available Complex networks of interacting residues and microdomains in the structures of biomolecular systems underlie the reliable propagation of information from an input signal, such as the concentration of a ligand, to sites that generate the appropriate output signal, such as enzymatic activity. This information transduction often carries the signal across relatively large distances at the molecular scale in a form of allostery that is essential for the physiological functions performed by biomolecules. While allosteric behaviors have been documented from experiments and computation, the mechanism of this form of allostery proved difficult to identify at the molecular level. Here, we introduce a novel analysis framework, called N-body Information Theory (NbIT analysis, which is based on information theory and uses measures of configurational entropy in a biomolecular system to identify microdomains and individual residues that act as (i-channels for long-distance information sharing between functional sites, and (ii-coordinators that organize dynamics within functional sites. Application of the new method to molecular dynamics (MD trajectories of the occluded state of the bacterial leucine transporter LeuT identifies a channel of allosteric coupling between the functionally important intracellular gate and the substrate binding sites known to modulate it. NbIT analysis is shown also to differentiate residues involved primarily in stabilizing the functional sites, from those that contribute to allosteric couplings between sites. NbIT analysis of MD data thus reveals rigorous mechanistic elements of allostery underlying the dynamics of biomolecular systems.

  3. NbIT--a new information theory-based analysis of allosteric mechanisms reveals residues that underlie function in the leucine transporter LeuT.

    Science.gov (United States)

    LeVine, Michael V; Weinstein, Harel

    2014-05-01

    Complex networks of interacting residues and microdomains in the structures of biomolecular systems underlie the reliable propagation of information from an input signal, such as the concentration of a ligand, to sites that generate the appropriate output signal, such as enzymatic activity. This information transduction often carries the signal across relatively large distances at the molecular scale in a form of allostery that is essential for the physiological functions performed by biomolecules. While allosteric behaviors have been documented from experiments and computation, the mechanism of this form of allostery proved difficult to identify at the molecular level. Here, we introduce a novel analysis framework, called N-body Information Theory (NbIT) analysis, which is based on information theory and uses measures of configurational entropy in a biomolecular system to identify microdomains and individual residues that act as (i)-channels for long-distance information sharing between functional sites, and (ii)-coordinators that organize dynamics within functional sites. Application of the new method to molecular dynamics (MD) trajectories of the occluded state of the bacterial leucine transporter LeuT identifies a channel of allosteric coupling between the functionally important intracellular gate and the substrate binding sites known to modulate it. NbIT analysis is shown also to differentiate residues involved primarily in stabilizing the functional sites, from those that contribute to allosteric couplings between sites. NbIT analysis of MD data thus reveals rigorous mechanistic elements of allostery underlying the dynamics of biomolecular systems.

  4. NbIT - A New Information Theory-Based Analysis of Allosteric Mechanisms Reveals Residues that Underlie Function in the Leucine Transporter LeuT

    Science.gov (United States)

    LeVine, Michael V.; Weinstein, Harel

    2014-01-01

    Complex networks of interacting residues and microdomains in the structures of biomolecular systems underlie the reliable propagation of information from an input signal, such as the concentration of a ligand, to sites that generate the appropriate output signal, such as enzymatic activity. This information transduction often carries the signal across relatively large distances at the molecular scale in a form of allostery that is essential for the physiological functions performed by biomolecules. While allosteric behaviors have been documented from experiments and computation, the mechanism of this form of allostery proved difficult to identify at the molecular level. Here, we introduce a novel analysis framework, called N-body Information Theory (NbIT) analysis, which is based on information theory and uses measures of configurational entropy in a biomolecular system to identify microdomains and individual residues that act as (i)-channels for long-distance information sharing between functional sites, and (ii)-coordinators that organize dynamics within functional sites. Application of the new method to molecular dynamics (MD) trajectories of the occluded state of the bacterial leucine transporter LeuT identifies a channel of allosteric coupling between the functionally important intracellular gate and the substrate binding sites known to modulate it. NbIT analysis is shown also to differentiate residues involved primarily in stabilizing the functional sites, from those that contribute to allosteric couplings between sites. NbIT analysis of MD data thus reveals rigorous mechanistic elements of allostery underlying the dynamics of biomolecular systems. PMID:24785005

  5. 基于重要样本法的结构动力学系统的首次穿越%FIRST EXCURSION PROBABILITIES OF DYNAMICAL SYSTEMS BY IMPORTANCE SAMPLING

    Institute of Scientific and Technical Information of China (English)

    任丽梅; 徐伟; 肖玉柱; 王文杰

    2012-01-01

    基于Gisranov定理,提出一种估计稳态高斯白噪声激励的结构动力学系统首穿失效概率的重要样本法.文章重点是构造控制函数,控制函数促使随机响应尽量集中在样本空间中最易导致首次穿越发生的部分.利用设计点构造控制函数,在线性系统场合,结合时不变系统的结构可靠性理论,通过解有约束的优化问题得到设计点;在非线性系统场合,利用Heonsang Koo提出的设计点激励,通过镜像法得到设计点.最后给出例子,将所提方法与原始蒙特卡罗法相比较,模拟结果显示方法的正确性与有效性.%Based on the Girsanov transformation, this paper develops a method for estimating the first excursion probability of dynamical systems with stationary gauss white noise. The focus is to construct control function that concentrates on the samples paths in the "most important part" of the sample space, to achieve the purpose of variance reduction. The paper uses design point to construct control function. For linear systems, the present approach combines with the time-invariant structure reliability theory to get design points by solving the problem of the optimization. For non-linear systems, the paper uses mirror-images method to get design points. Finally the paper gives two examples. The results show the method of this paper to be correct and effective by comparing with the primitive Monte Carlo method.

  6. Investigation of Manufacturing Residual Stresses in Cold Formed Truck Frame Rail Sections

    Directory of Open Access Journals (Sweden)

    Dr. Chinnaraj K.

    2014-04-01

    Full Text Available Series of manufacturing processes such as coiling-uncoiling, cold forming and hole cutting processes involved in the making of truck frame rail sections leave certain amount of manufacturing imperfections into the frame rail. As the manufacturing imperfections in the form of residual stresses play a significant role in determining the dynamic structural behavior of truck frame rail members, a careful assessment of residual stresses resulting from coiling-uncoiling and cold forming processes is needed. In the present investigation, non-linear Finite Element (FE simulation of coiling-uncoiling and cold forming processes were carried out and the resulting residual stresses in frame rail corner, flat web and flange sections were compared with the experimentally measured residual stress values using X-ray diffraction technique. It is observed that in corner sections, the numerically predicted residual stresses are in close agreement with the experimentally measured residual stresses in forming (transverse direction. In the direction perpendicular to forming (longitudinal direction, while the trends of numerical and experimental residual stresses are observed to follow the same pattern, some deviation in stress values are observed in the inner half of the corner sections. As the coiling-uncoiling process is the main cause for the residual stress presence in flat web and flange sections, the computed coiling-uncoiling residual stresses in longitudinal directions are compared with experimentally measured residual stresses in frame web sections and the trends are observed to be in good agreement.

  7. Residual gallbladder stones after cholecystectomy: A literature review

    Science.gov (United States)

    Chowbey, Pradeep; Sharma, Anil; Goswami, Amit; Afaque, Yusuf; Najma, Khoobsurat; Baijal, Manish; Soni, Vandana; Khullar, Rajesh

    2015-01-01

    BACKGROUND: Incomplete gallbladder removal following open and laparoscopic techniques leads to residual gallbladder stones. The commonest presentation is abdominal pain, dyspepsia and jaundice. We reviewed the literature to report diagnostic modalities, management options and outcomes in patients with residual gallbladder stones after cholecystectomy. MATERIALS AND METHODS: Medline, Google and Cochrane library between 1993 and 2013 were reviewed using search terms residual gallstones, post-cholecystectomy syndrome, retained gallbladder stones, gallbladder remnant, cystic duct remnant and subtotal cholecystectomy. Bibliographical references from selected articles were also analyzed. The parameters that were assessed include demographics, time of detection, clinical presentation, mode of diagnosis, nature of intervention, site of stone, surgical findings, procedure performed, complete stone clearance, sequelae and follow-up. RESULTS: Out of 83 articles that were retrieved between 1993 and 2013, 22 met the inclusion criteria. In most series, primary diagnosis was established by ultrasound/computed tomography scan. Localization of calculi and delineation of biliary tract was performed using magnetic resonance imaging/magnetic resonance cholangiopancreatography and endoscopic retrograde cholangiopancreatography. In few series, diagnosis was established by endoscopic ultrasound, intraoperative cholangiogram and percutaneous transhepatic cholangiography. Laparoscopic surgery, endoscopic techniques and open surgery were the most common treatment modalities. The most common sites of residual gallstones were gallbladder remnant, cystic duct remnant and common bile duct. CONCLUSION: Residual gallbladder stones following incomplete gallbladder removal is an important sequelae after cholecystectomy. Completion cholecystectomy (open or laparoscopic) is the most common treatment modality reported in the literature for the management of residual gallbladder stones. PMID:26622110

  8. Residual gallbladder stones after cholecystectomy: A literature review

    Directory of Open Access Journals (Sweden)

    Pradeep Chowbey

    2015-01-01

    Full Text Available Background: Incomplete gallbladder removal following open and laparoscopic techniques leads to residual gallbladder stones. The commonest presentation is abdominal pain, dyspepsia and jaundice. We reviewed the literature to report diagnostic modalities, management options and outcomes in patients with residual gallbladder stones after cholecystectomy. Materials And Methods: Medline, Google and Cochrane library between 1993 and 2013 were reviewed using search terms residual gallstones, post-cholecystectomy syndrome, retained gallbladder stones, gallbladder remnant, cystic duct remnant and subtotal cholecystectomy. Bibliographical references from selected articles were also analyzed. The parameters that were assessed include demographics, time of detection, clinical presentation, mode of diagnosis, nature of intervention, site of stone, surgical findings, procedure performed, complete stone clearance, sequelae and follow-up. Results: Out of 83 articles that were retrieved between 1993 and 2013, 22 met the inclusion criteria. In most series, primary diagnosis was established by ultrasound/computed tomography scan. Localization of calculi and delineation of biliary tract was performed using magnetic resonance imaging/magnetic resonance cholangiopancreatography and endoscopic retrograde cholangiopancreatography. In few series, diagnosis was established by endoscopic ultrasound, intraoperative cholangiogram and percutaneous transhepatic cholangiography. Laparoscopic surgery, endoscopic techniques and open surgery were the most common treatment modalities. The most common sites of residual gallstones were gallbladder remnant, cystic duct remnant and common bile duct. Conclusion: Residual gallbladder stones following incomplete gallbladder removal is an important sequelae after cholecystectomy. Completion cholecystectomy (open or laparoscopic is the most common treatment modality reported in the literature for the management of residual gallbladder

  9. Biogas systems for sisal and other agro-industrial residues

    Energy Technology Data Exchange (ETDEWEB)

    Jungersen, G. [Danish Technological Inst., Section for Biotechnology, Taastrup (Denmark)

    1997-12-31

    Most of the East-African agro-industries are generating very large quantities of organic residues from production and processing of different crops. In the East-African Region the most important of these crops are: Sisal, Sugar, Coffee, Cashew nuts and Pineapple. In other 3. world countries, Palm oil and Cassava (Tapioca starch) processing are main producers of organic waste products. Moreover, large quantities of organic residues are generated from other food processing activities like breweries, consumption of bananas etc. The following pages give examples of setups and system designs of anaerobic treatment systems for some of the residues mentioned above. When considering anaerobic treatment of sisal residues, which constitutes the main agro-industrial biomass resource in Tanzania, two major issues should be considered: Optimal reactor set-up and performance; And optionally, potential methods for pre-treatment of fibre fraction in order to increase the methane yield. The sisal liquid residues are degraded very fast and efficiently in UASB systems. At COD loading rates less than 11 kg COD/m{sup 3} x day, the reduction in organic matter is more than 90% and methane yields obtained are between 373 and 377 ml CH{sub 4}/g COD reduced. The treatment of sisal solid residues in CSTR systems has been examined both at mesophilic (37 deg. C) and thermophilic temperatures (55 deg. C.). (EG)

  10. The Cauchy method of residues

    CERN Document Server

    Mitrinović, Dragoslav S

    1993-01-01

    Volume 1, i. e. the monograph The Cauchy Method of Residues - Theory and Applications published by D. Reidel Publishing Company in 1984 is the only book that covers all known applications of the calculus of residues. They range from the theory of equations, theory of numbers, matrix analysis, evaluation of real definite integrals, summation of finite and infinite series, expansions of functions into infinite series and products, ordinary and partial differential equations, mathematical and theoretical physics, to the calculus of finite differences and difference equations. The appearance of Volume 1 was acknowledged by the mathematical community. Favourable reviews and many private communications encouraged the authors to continue their work, the result being the present book, Volume 2, a sequel to Volume 1. We mention that Volume 1 is a revised, extended and updated translation of the book Cauchyjev raeun ostataka sa primenama published in Serbian by Nau~na knjiga, Belgrade in 1978, whereas the greater part ...

  11. Effect of O horizon and Forest Harvest Residue Manipulations on Soil Organic Matter Content and Composition of a Loblolly Pine Plantation in the Southeastern United States

    Science.gov (United States)

    Hatten, J.; Mack, J.; Dewey, J.; Sucre, E.; Leggett, Z.

    2012-04-01

    Forest harvest residues and forest floor materials are significant sources of mineral soil organic matter and nutrients for regenerating and establishing forests. Harvest residues in particular are occasionally removed, piled, or burned following harvesting. While the forest floor is never purposely removed during operational harvesting and site preparation, they could become in high demand as bioenergy markets develop. Weyerhaeuser Company established an experimental study to evaluate the effect of forest-floor manipulation on site productivity and soil carbon. This study was installed in a loblolly pine plantation near Millport, Alabama, USA on the Upper Gulf Coastal Plain to test both extremes from complete removal of harvest residues and forest floor to doubling of these materials. This study has been continuously monitored since its establishment in 1994. We have examined the effects of varying forest floor levels on the biomass, soil carbon content, and soil carbon composition in the context of these management activities. Above- and below-ground productivity, soil moisture, soil temperature, and nutrient dynamics have been related to soil organ