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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. Salt dynamics in well-mixed estuaries: importance of advection by tides

    OpenAIRE

    Wei, X.; Schramkowski, G.P.; Schuttelaars, H.M.

    2016-01-01

    Understanding salt dynamics is important to adequately model salt intrusion, baroclinic forcing, and sediment transport. In this paper, the importance of the residual salt transport due to tidal advection in well-mixed tidal estuaries is studied. The water motion is resolved in a consistent way with a width-averaged analytical model, coupled to an advection–diffusion equation describing the salt dynamics. The residual salt balance obtained from the coupled model shows that the seaward salt tr...

  3. Water dynamics clue to key residues in protein folding

    International Nuclear Information System (INIS)

    Gao, Meng; Zhu, Huaiqiu; Yao, Xin-Qiu; She, Zhen-Su

    2010-01-01

    A computational method independent of experimental protein structure information is proposed to recognize key residues in protein folding, from the study of hydration water dynamics. Based on all-atom molecular dynamics simulation, two key residues are recognized with distinct water dynamical behavior in a folding process of the Trp-cage protein. The identified key residues are shown to play an essential role in both 3D structure and hydrophobic-induced collapse. With observations on hydration water dynamics around key residues, a dynamical pathway of folding can be interpreted.

  4. Independent alignment of RNA for dynamic studies using residual dipolar couplings

    Energy Technology Data Exchange (ETDEWEB)

    Bardaro, Michael F.; Varani, Gabriele, E-mail: varani@chem.washington.edu [University of Washington, Department of Chemistry (United States)

    2012-09-15

    Molecular motion and dynamics play an essential role in the biological function of many RNAs. An important source of information on biomolecular motion can be found in residual dipolar couplings which contain dynamics information over the entire ms-ps timescale. However, these methods are not fully applicable to RNA because nucleic acid molecules tend to align in a highly collinear manner in different alignment media. As a consequence, information on dynamics that can be obtained with this method is limited. In order to overcome this limitation, we have generated a chimeric RNA containing both the wild type TAR RNA, the target of our investigation of dynamics, as well as the binding site for U1A protein. When U1A protein was bound to the portion of the chimeric RNA containing its binding site, we obtained independent alignment of TAR by exploiting the physical chemical characteristics of this protein. This technique can allow the extraction of new information on RNA dynamics, which is particularly important for time scales not covered by relaxation methods where important RNA motions occur.

  5. Global warming impact assessment of a crop residue gasification project—A dynamic LCA perspective

    International Nuclear Information System (INIS)

    Yang, Jin; Chen, Bin

    2014-01-01

    Highlights: • A dynamic LCA is proposed considering time-varying factors. • Dynamic LCA is used to highlight GHG emission hotspots of gasification projects. • Indicators are proposed to reflect GHG emission performance. • Dynamic LCA alters the static LCA results. • Crop residue gasification project has high GHG abatement potential. - Abstract: Bioenergy from crop residues is one of the prevailing sustainable energy sources owing to the abundant reserves worldwide. Amongst a wide variety of energy conversion technologies, crop residue gasification has been regarded as promising owing to its higher energy efficiency than that of direct combustion. However, prior to large-scale application of crop residue gasification, the lifetime environmental performance should be investigated to shed light on sustainable strategies. As traditional static life cycle assessment (LCA) does not include temporal information for dynamic processes, we proposed a dynamic life cycle assessment approach, which improves the static LCA approach by considering time-varying factors, e.g., greenhouse gas characterization factors and energy intensity. As the gasification project can reduce greenhouse gas (GHG) discharge compared with traditional direct fuel combustion, trade-offs between the benefits of global warming mitigation and the impact on global warming of crop residue gasification should be considered. Therefore, indicators of net global warming mitigation benefit and global warming impact mitigation period are put forward to justify the feasibility of the crop residue gasification project. The proposed dynamic LCA and indicators were then applied to estimate the life cycle global warming impact of a crop residue gasification system in China. Results show that the crop residue gasification project has high net global warming mitigation benefit and a short global warming impact mitigation period, indicating its prominent potential in alleviating global warming impact. During

  6. The importance of antibiotic residues presence detection in milk

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    Dubravka Samaržija

    2002-01-01

    Full Text Available Antibiotic residues are the most present inhibitory substances in milkhaving undesirable effect on human health, technological characteristics and the quality of milk and dairy products. In order to protect consumer's health and to ensure high quality milk production, European Union (EU regulation 2377/90 sets a maximum permitted levels for antibiotic residues in milk. Although the presence of antibiotic residues in milk can be due to animal diseases treatment, and in the case of milking animals, they are mostly present after mastitis treatment. The aim of this work is to stress the importance of the continuous control on antibiotic residues presence in milk, due to the role that milk and dairy products have in human nutrition. In this paper, different groups of antibiotics, mechanisms of theirs action, mistakes occurring in dairy products manufacture as well as the methods for theirs detection are described.

  7. Effectiveness of dynamic MRI for diagnosing pericicatricial minimal residual breast cancer following excisional biopsy

    International Nuclear Information System (INIS)

    Kawashima, Hiroko; Tawara, Mari; Suzuki, Masayuki; Matsui, Osamu; Kadoya, Masumi

    2001-01-01

    The purpose of this study was to investigate the effectiveness of dynamic MRI for diagnosing pericicatricial minimal residual breast cancer following excisional biopsy. Twenty-six patients who underwent excisional biopsy of a tumor or calcified lesion of the breast underwent gadolinium-enhanced dynamic MRI by the fat-saturated 2D fast spoiled gradient echo (SPGR) sequence (group 1), 24 patients by the spectral IR enhanced 3D fast gradient echo (Efgre3d) sequence (group 2). Pericicatricial residual cancer was confirmed histologically in 29 of the 50 patients. The overall sensitivity, specificity, accuracy, positive predictive value, and negative predictive value of MRI for residual cancer diagnosis was 66, 81, 72, 83 and 63%. A nodular, thick and discontinuous enhanced rim around the scar is indicative of a residual tumor. However, false-positive findings due to granulation or proliferative fibrocystic change remain limitations

  8. Effectiveness of dynamic MRI for diagnosing pericicatricial minimal residual breast cancer following excisional biopsy

    Energy Technology Data Exchange (ETDEWEB)

    Kawashima, Hiroko E-mail: hirokok@med.kanazawa-u.ac.jp; Tawara, Mari; Suzuki, Masayuki; Matsui, Osamu; Kadoya, Masumi

    2001-10-01

    The purpose of this study was to investigate the effectiveness of dynamic MRI for diagnosing pericicatricial minimal residual breast cancer following excisional biopsy. Twenty-six patients who underwent excisional biopsy of a tumor or calcified lesion of the breast underwent gadolinium-enhanced dynamic MRI by the fat-saturated 2D fast spoiled gradient echo (SPGR) sequence (group 1), 24 patients by the spectral IR enhanced 3D fast gradient echo (Efgre3d) sequence (group 2). Pericicatricial residual cancer was confirmed histologically in 29 of the 50 patients. The overall sensitivity, specificity, accuracy, positive predictive value, and negative predictive value of MRI for residual cancer diagnosis was 66, 81, 72, 83 and 63%. A nodular, thick and discontinuous enhanced rim around the scar is indicative of a residual tumor. However, false-positive findings due to granulation or proliferative fibrocystic change remain limitations.

  9. Temperature-dependent dynamical transitions of different classes of amino acid residue in a globular protein.

    Science.gov (United States)

    Miao, Yinglong; Yi, Zheng; Glass, Dennis C; Hong, Liang; Tyagi, Madhusudan; Baudry, Jerome; Jain, Nitin; Smith, Jeremy C

    2012-12-05

    The temperature dependences of the nanosecond dynamics of different chemical classes of amino acid residue have been analyzed by combining elastic incoherent neutron scattering experiments with molecular dynamics simulations on cytochrome P450cam. At T = 100-160 K, anharmonic motion in hydrophobic and aromatic residues is activated, whereas hydrophilic residue motions are suppressed because of hydrogen-bonding interactions. In contrast, at T = 180-220 K, water-activated jumps of hydrophilic side chains, which are strongly coupled to the relaxation rates of the hydrogen bonds they form with hydration water, become apparent. Thus, with increasing temperature, first the hydrophobic core awakens, followed by the hydrophilic surface.

  10. Research on Formation Mechanism of Dynamic Response and Residual Stress of Sheet Metal Induced by Laser Shock Wave

    Science.gov (United States)

    Feng, Aixin; Cao, Yupeng; Wang, Heng; Zhang, Zhengang

    2018-01-01

    In order to reveal the quantitative control of the residual stress on the surface of metal materials, the relevant theoretical and experimental studies were carried out to investigate the dynamic response of metal thin plates and the formation mechanism of residual stress induced by laser shock wave. In this paper, the latest research trends on the surface residual stress of laser shock processing technology were elaborated. The main progress of laser shock wave propagation mechanism and dynamic response, laser shock, and surface residual stress were discussed. It is pointed out that the multi-scale characterization of laser and material, surface residual stress and microstructure change is a new hotspot in laser shock strengthening technology.

  11. Dynamically consistent oil import tariffs

    International Nuclear Information System (INIS)

    Karp, L.; Newbery, D.M.

    1992-01-01

    The standard theory of optimal tariffs considers tariffs on perishable goods produced abroad under static conditions, in which tariffs affect prices only in that period. Oil and other exhaustable resources do not fit this model, for current tariffs affect the amount of oil imported, which will affect the remaining stock and hence its future price. The problem of choosing a dynamically consistent oil import tariff when suppliers are competitive but importers have market power is considered. The open-loop Nash tariff is solved for the standard competitive case in which the oil price is arbitraged, and it was found that the resulting tariff rises at the rate of interest. This tariff was found to have an equilibrium that in general is dynamically inconsistent. Nevertheless, it is shown that necessary and sufficient conditions exist under which the tariff satisfies the weaker condition of time consistency. A dynamically consistent tariff is obtained by assuming that all agents condition their current decisions on the remaining stock of the resource, in contrast to open-loop strategies. For the natural case in which all agents choose their actions simultaneously in each period, the dynamically consistent tariff was characterized, and found to differ markedly from the time-inconsistent open-loop tariff. It was shown that if importers do not have overwhelming market power, then the time path of the world price is insensitive to the ability to commit, as is the level of wealth achieved by the importer. 26 refs., 4 figs

  12. Risk importance measures in the dynamic flowgraph methodology

    International Nuclear Information System (INIS)

    Tyrväinen, T.

    2013-01-01

    This paper presents new risk importance measures applicable to a dynamic reliability analysis approach with multi-state components. Dynamic reliability analysis methods are needed because traditional methods, such as fault tree analysis, can describe system's dynamical behaviour only in limited manner. Dynamic flowgraph methodology (DFM) is an approach used for analysing systems with time dependencies and feedback loops. The aim of DFM is to identify root causes of a top event, usually representing the system's failure. Components of DFM models are analysed at discrete time points and they can have multiple states. Traditional risk importance measures developed for static and binary logic are not applicable to DFM as such. Some importance measures have previously been developed for DFM but their ability to describe how components contribute to the top event is fairly limited. The paper formulates dynamic risk importance measures that measure the importances of states of components and take the time-aspect of DFM into account in a logical way that supports the interpretation of results. Dynamic risk importance measures are developed as generalisations of the Fussell-Vesely importance and the risk increase factor. -- Highlights: • New risk importance measures are developed for the dynamic flowgraph methodology. • Dynamic risk importance measures are formulated for states of components. • An approach to handle failure modes of a component in DFM is presented. • Dynamic risk importance measures take failure times into account. • Component's influence on the system's reliability can be analysed in detail

  13. Evaluation of Some Pesticide Residues in Fruits import by High Performance Liquid Chromatography

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    Lamees Munef Abdul-Latef

    2017-02-01

    Full Text Available Pesticide residues have been found in various fruits and vegetables.  This studycollected 24 samples and reported a method based on High Performance Liquid Chromatography (HPLC. For determination of pesticide residues used in Some fruits which were collected from different markets of Baghdad city to make 24 samples from (peel , core, mixture for each type of fruits markets as:  Oranges( Egypt , Africa, Pomegranate ( Egypt, Mango ( Kenya , Pears (China,  Plum fruits ( Africa , Kiwi (Turkey .That detective of ( 5 different  pesticides (diazinon,  malathion, chlorpyrifos ,parathion  and cypermethrin. The results were detected of multi-residues of  pesticides on the fruit in ( peel , core , mixture may be in the limit of Maximum residue limits(MRL or higher of it   . The pesticides detected that exceeding the limits are: cypermethrin  in Kiwi (peel, core and mixtureat(0.204,0.038, 0.537, in pomegranate detected in (peel and mixture at (0.509,0.189 mg/kg , Diazinondetccted in Egyptian orange in (peel ,core and mixture at (0.031,0.207, 0.099 mg/kg . Malathion and Parathion was not detected at any type of fruits and  that results was compared with codex of FAO/WHO(2013. That data is important to monitor residues in food and to fill gaps in current knowledge would be helpful in assessing human exposure risks from ingestion of contaminated Fruits Imported to our country .

  14. Mapping allostery through computational glycine scanning and correlation analysis of residue-residue contacts.

    Science.gov (United States)

    Johnson, Quentin R; Lindsay, Richard J; Nellas, Ricky B; Fernandez, Elias J; Shen, Tongye

    2015-02-24

    Understanding allosteric mechanisms is essential for the physical control of molecular switches and downstream cellular responses. However, it is difficult to decode essential allosteric motions in a high-throughput scheme. A general two-pronged approach to performing automatic data reduction of simulation trajectories is presented here. The first step involves coarse-graining and identifying the most dynamic residue-residue contacts. The second step is performing principal component analysis of these contacts and extracting the large-scale collective motions expressed via these residue-residue contacts. We demonstrated the method using a protein complex of nuclear receptors. Using atomistic modeling and simulation, we examined the protein complex and a set of 18 glycine point mutations of residues that constitute the binding pocket of the ligand effector. The important motions that are responsible for the allostery are reported. In contrast to conventional induced-fit and lock-and-key binding mechanisms, a novel "frustrated-fit" binding mechanism of RXR for allosteric control was revealed.

  15. Dynamically Coupled Residues within the SH2 Domain of FYN Are Key to Unlocking Its Activity.

    Science.gov (United States)

    Huculeci, Radu; Cilia, Elisa; Lyczek, Agatha; Buts, Lieven; Houben, Klaartje; Seeliger, Markus A; van Nuland, Nico; Lenaerts, Tom

    2016-11-01

    Src kinase activity is controlled by various mechanisms involving a coordinated movement of kinase and regulatory domains. Notwithstanding the extensive knowledge related to the backbone dynamics, little is known about the more subtle side-chain dynamics within the regulatory domains and their role in the activation process. Here, we show through experimental methyl dynamic results and predicted changes in side-chain conformational couplings that the SH2 structure of Fyn contains a dynamic network capable of propagating binding information. We reveal that binding the phosphorylated tail of Fyn perturbs a residue cluster near the linker connecting the SH2 and SH3 domains of Fyn, which is known to be relevant in the regulation of the activity of Fyn. Biochemical perturbation experiments validate that those residues are essential for inhibition of Fyn, leading to a gain of function upon mutation. These findings reveal how side-chain dynamics may facilitate the allosteric regulation of the different members of the Src kinase family. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. 77 FR 3653 - Import Tolerances for Residues of Unapproved New Animal Drugs in Food

    Science.gov (United States)

    2012-01-25

    ... find a safe import tolerance. It could look at toxicity and residue data and build in a conservative... drugs covered by import tolerances are manufactured under good manufacturing practices (GMP)-like... resistant bacteria in or on the target animal and the potential impact on human health. C. International...

  17. Dynamics of Linker Residues Modulate the Nucleic Acid Binding Properties of the HIV-1 Nucleocapsid Protein Zinc Fingers

    Science.gov (United States)

    Zargarian, Loussiné; Tisné, Carine; Barraud, Pierre; Xu, Xiaoqian; Morellet, Nelly; René, Brigitte; Mély, Yves; Fossé, Philippe; Mauffret, Olivier

    2014-01-01

    The HIV-1 nucleocapsid protein (NC) is a small basic protein containing two zinc fingers (ZF) separated by a short linker. It is involved in several steps of the replication cycle and acts as a nucleic acid chaperone protein in facilitating nucleic acid strand transfers occurring during reverse transcription. Recent analysis of three-dimensional structures of NC-nucleic acids complexes established a new property: the unpaired guanines targeted by NC are more often inserted in the C-terminal zinc finger (ZF2) than in the N-terminal zinc finger (ZF1). Although previous NMR dynamic studies were performed with NC, the dynamic behavior of the linker residues connecting the two ZF domains remains unclear. This prompted us to investigate the dynamic behavior of the linker residues. Here, we collected 15N NMR relaxation data and used for the first time data at several fields to probe the protein dynamics. The analysis at two fields allows us to detect a slow motion occurring between the two domains around a hinge located in the linker at the G35 position. However, the amplitude of motion appears limited in our conditions. In addition, we showed that the neighboring linker residues R29, A30, P31, R32, K33 displayed restricted motion and numerous contacts with residues of ZF1. Our results are fully consistent with a model in which the ZF1-linker contacts prevent the ZF1 domain to interact with unpaired guanines, whereas the ZF2 domain is more accessible and competent to interact with unpaired guanines. In contrast, ZF1 with its large hydrophobic plateau is able to destabilize the double-stranded regions adjacent to the guanines bound by ZF2. The linker residues and the internal dynamics of NC regulate therefore the different functions of the two zinc fingers that are required for an optimal chaperone activity. PMID:25029439

  18. gRINN: a tool for calculation of residue interaction energies and protein energy network analysis of molecular dynamics simulations.

    Science.gov (United States)

    Serçinoglu, Onur; Ozbek, Pemra

    2018-05-25

    Atomistic molecular dynamics (MD) simulations generate a wealth of information related to the dynamics of proteins. If properly analyzed, this information can lead to new insights regarding protein function and assist wet-lab experiments. Aiming to identify interactions between individual amino acid residues and the role played by each in the context of MD simulations, we present a stand-alone software called gRINN (get Residue Interaction eNergies and Networks). gRINN features graphical user interfaces (GUIs) and a command-line interface for generating and analyzing pairwise residue interaction energies and energy correlations from protein MD simulation trajectories. gRINN utilizes the features of NAMD or GROMACS MD simulation packages and automatizes the steps necessary to extract residue-residue interaction energies from user-supplied simulation trajectories, greatly simplifying the analysis for the end-user. A GUI, including an embedded molecular viewer, is provided for visualization of interaction energy time-series, distributions, an interaction energy matrix, interaction energy correlations and a residue correlation matrix. gRINN additionally offers construction and analysis of Protein Energy Networks, providing residue-based metrics such as degrees, betweenness-centralities, closeness centralities as well as shortest path analysis. gRINN is free and open to all users without login requirement at http://grinn.readthedocs.io.

  19. 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.

  20. Rigid Residue Scan Simulations Systematically Reveal Residue Entropic Roles in Protein Allostery.

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    Robert Kalescky

    2016-04-01

    Full Text Available Intra-protein information is transmitted over distances via allosteric processes. This ubiquitous protein process allows for protein function changes due to ligand binding events. Understanding protein allostery is essential to understanding protein functions. In this study, allostery in the second PDZ domain (PDZ2 in the human PTP1E protein is examined as model system to advance a recently developed rigid residue scan method combining with configurational entropy calculation and principal component analysis. The contributions from individual residues to whole-protein dynamics and allostery were systematically assessed via rigid body simulations of both unbound and ligand-bound states of the protein. The entropic contributions of individual residues to whole-protein dynamics were evaluated based on covariance-based correlation analysis of all simulations. The changes of overall protein entropy when individual residues being held rigid support that the rigidity/flexibility equilibrium in protein structure is governed by the La Châtelier's principle of chemical equilibrium. Key residues of PDZ2 allostery were identified with good agreement with NMR studies of the same protein bound to the same peptide. On the other hand, the change of entropic contribution from each residue upon perturbation revealed intrinsic differences among all the residues. The quasi-harmonic and principal component analyses of simulations without rigid residue perturbation showed a coherent allosteric mode from unbound and bound states, respectively. The projection of simulations with rigid residue perturbation onto coherent allosteric modes demonstrated the intrinsic shifting of ensemble distributions supporting the population-shift theory of protein allostery. Overall, the study presented here provides a robust and systematic approach to estimate the contribution of individual residue internal motion to overall protein dynamics and allostery.

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

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    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

  2. Coevolving residues of (beta/alpha)(8)-barrel proteins play roles in stabilizing active site architecture and coordinating protein dynamics.

    Science.gov (United States)

    Shen, Hongbo; Xu, Feng; Hu, Hairong; Wang, Feifei; Wu, Qi; Huang, Qiang; Wang, Honghai

    2008-12-01

    Indole-3-glycerol phosphate synthase (IGPS) is a representative of (beta/alpha)(8)-barrel proteins-the most common enzyme fold in nature. To better understand how the constituent amino-acids work together to define the structure and to facilitate the function, we investigated the evolutionary and dynamical coupling of IGPS residues by combining statistical coupling analysis (SCA) and molecular dynamics (MD) simulations. The coevolving residues identified by the SCA were found to form a network which encloses the active site completely. The MD simulations showed that these coevolving residues are involved in the correlated and anti-correlated motions. The correlated residues are within van der Waals contact and appear to maintain the active site architecture; the anti-correlated residues are mainly distributed on opposite sides of the catalytic cavity and coordinate the motions likely required for the substrate entry and product release. Our findings might have broad implications for proteins with the highly conserved (betaalpha)(8)-barrel in assessing the roles of amino-acids that are moderately conserved and not directly involved in the active site of the (beta/alpha)(8)-barrel. The results of this study could also provide useful information for further exploring the specific residue motions for the catalysis and protein design based on the (beta/alpha)(8)-barrel scaffold.

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

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    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.

  4. Generation and importance of linked and irreducible moment diagrams in the recursive residue generation method

    International Nuclear Information System (INIS)

    Schek, I.; Wyatt, R.E.

    1986-01-01

    Molecular multiphoton processes are treated in the Recursive Residue Generation Method (A. Nauts and R.E. Wyatt, Phys. Rev. Lett 51, 2238 (1983)) by converting the molecular-field Hamiltonian matrix into tridiagonal form, using the Lanczos equations. In this study, the self-energies (diagonal) and linking (off-diagaonal) terms in the tridiagonal matrix are obtained by comparing linked moment diagrams in both representations. The dynamics of the source state is introduced and computed in terms of the linked and the irreducible moments

  5. The Dynamic of the N-Turnover of Plant Residues in The soil using nuclear technique

    International Nuclear Information System (INIS)

    Ismail, M.M.A.

    2004-01-01

    Laboratory and greenhouse experiments were carried out to study the dynamic of the N-turnover of leguminous and non-leguminous plant residues in sandy soil using N-15 . tracer technique. Also, the availability of N from labelled or unlabelled ammonium sulfate was included. using 15 N-technique, data obtained generally indicated that 15 N-mineralization percent for soybean (narrow C/N ratio) increased with time, being more effective and superior over wheat residue-N (wide C/N ratio) on the net 15 N-mineralization through out the time of incubation (10 weeks).Data obtained generally indicated that the N-mineralization significantly decreased due to the application of soybean, wheat, wheat + soybean and / or ammonium sulfate along with the time of vegetative growth stage until harvesting period under with or without wheat stands . In general at any period of growth plant stages of wheat, the amount of microbial biomass-N under wheat residue and/or ammonium sulfate treated and untreated soil significantly decreased rapidly from an initial of vegetative stage until harvesting time. the positive effect of plant residues on the amount of biomass-N was arranged as follows : soybean>wheat + soybean> wheat residues

  6. firestar--advances in the prediction of functionally important residues.

    Science.gov (United States)

    Lopez, Gonzalo; Maietta, Paolo; Rodriguez, Jose Manuel; Valencia, Alfonso; Tress, Michael L

    2011-07-01

    firestar is a server for predicting catalytic and ligand-binding residues in protein sequences. Here, we present the important developments since the first release of firestar. Previous versions of the server required human interpretation of the results; the server is now fully automatized. firestar has been implemented as a web service and can now be run in high-throughput mode. Prediction coverage has been greatly improved with the extension of the FireDB database and the addition of alignments generated by HHsearch. Ligands in FireDB are now classified for biological relevance. Many of the changes have been motivated by the critical assessment of techniques for protein structure prediction (CASP) ligand-binding prediction experiment, which provided us with a framework to test the performance of firestar. URL: http://firedb.bioinfo.cnio.es/Php/FireStar.php.

  7. Evaluation and optimization of nutritional and environmental impact of biogas residues

    International Nuclear Information System (INIS)

    Lichti, Fabian Heribert

    2013-01-01

    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.

  8. 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)

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

    International Nuclear Information System (INIS)

    Almond, Andrew; Duus, Jens O.

    2001-01-01

    A method is described for quantitatively investigating the dynamic conformation of small oligosaccharides containing an α(1 → 6) linkage. It was applied to the oligosaccharide Man-α(1 → 3) {Man-α (1 → 6)}Man-α-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 α(1 → 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 α(1 → 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 α(1 → 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

  10. The Signal Importance of Noise

    Science.gov (United States)

    Macy, Michael; Tsvetkova, Milena

    2015-01-01

    Noise is widely regarded as a residual category--the unexplained variance in a linear model or the random disturbance of a predictable pattern. Accordingly, formal models often impose the simplifying assumption that the world is noise-free and social dynamics are deterministic. Where noise is assigned causal importance, it is often assumed to be a…

  11. 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...

  12. Dynamic integrated assessment of bioenergy technologies for energy production utilizing agricultural residues: An input–output approach

    International Nuclear Information System (INIS)

    Song, Junnian; Yang, Wei; Higano, Yoshiro; Wang, Xian’en

    2015-01-01

    Highlights: • A dynamic input–output model is developed with bioenergy technologies complemented. • Availability of agricultural residues for bioenergy technologies is evaluated. • Trends in electricity and biofuel production are simulated dynamically. • Net profit and GHG mitigation contribution of bioenergy technologies are assessed. • Combustion power generation and briquette fuel are more advantageous. - Abstract: In order to facilitate regional agricultural residue utilization for energy production through bioenergy technologies, a dynamic input–output model is developed to estimate and assess the energy, economic and environmental performances of industrialization of five bioenergy technologies within a 15-year time horizon. Electricity and solid, gaseous and liquid biofuels are energy products of bioenergy technologies. Bioenergy technologies are complemented into regional input–output framework and combined with socioeconomic activities aided by their bottom-up economic and energy parameters. The simulation results for the target area indicate that the agricultural residues available for bioenergy technologies could amount to 55.16 million t, facilitating to 8.38 million t coal-equivalent bioenergy production by 2025. A 3.1% net reduction in accumulative greenhouse gas emission compared with the “business as usual” case could be achieved owing to substitution of fossil energy with electricity and biofuels produced by bioenergy technologies. From energy production, economic benefits and greenhouse gas mitigation three aspects integratedly, direct-combustion power generation and briquette fuel are more advantageous in the target area. The quantified energy, economic and environmental performances of bioenergy technologies are expected to give recommendations for their industrial development.

  13. 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...

  14. Research on the optimal dynamical systems of three-dimensional Navier-Stokes equations based on weighted residual

    Science.gov (United States)

    Peng, NaiFu; Guan, Hui; Wu, ChuiJie

    2016-04-01

    In this paper, the theory of constructing optimal dynamical systems based on weighted residual presented by Wu & Sha is applied to three-dimensional Navier-Stokes equations, and the optimal dynamical system modeling equations are derived. Then the multiscale global optimization method based on coarse graining analysis is presented, by which a set of approximate global optimal bases is directly obtained from Navier-Stokes equations and the construction of optimal dynamical systems is realized. The optimal bases show good properties, such as showing the physical properties of complex flows and the turbulent vortex structures, being intrinsic to real physical problem and dynamical systems, and having scaling symmetry in mathematics, etc.. In conclusion, using fewer terms of optimal bases will approach the exact solutions of Navier-Stokes equations, and the dynamical systems based on them show the most optimal behavior.

  15. Residue Geometry Networks: A Rigidity-Based Approach to the Amino Acid Network and Evolutionary Rate Analysis

    Science.gov (United States)

    Fokas, Alexander S.; Cole, Daniel J.; Ahnert, Sebastian E.; Chin, Alex W.

    2016-01-01

    Amino acid networks (AANs) abstract the protein structure by recording the amino acid contacts and can provide insight into protein function. Herein, we describe a novel AAN construction technique that employs the rigidity analysis tool, FIRST, to build the AAN, which we refer to as the residue geometry network (RGN). We show that this new construction can be combined with network theory methods to include the effects of allowed conformal motions and local chemical environments. Importantly, this is done without costly molecular dynamics simulations required by other AAN-related methods, which allows us to analyse large proteins and/or data sets. We have calculated the centrality of the residues belonging to 795 proteins. The results display a strong, negative correlation between residue centrality and the evolutionary rate. Furthermore, among residues with high closeness, those with low degree were particularly strongly conserved. Random walk simulations using the RGN were also successful in identifying allosteric residues in proteins involved in GPCR signalling. The dynamic function of these residues largely remain hidden in the traditional distance-cutoff construction technique. Despite being constructed from only the crystal structure, the results in this paper suggests that the RGN can identify residues that fulfil a dynamical function. PMID:27623708

  16. Combined cycle power plants: A comparison between two different dynamic models to evaluate transient behaviour and residual life

    International Nuclear Information System (INIS)

    Benato, Alberto; Stoppato, Anna; Bracco, Stefano

    2014-01-01

    Highlights: • Two procedures aimed at simulating the dynamic behaviour of power plants are compared. • They both are aimed at predicting the residual life of plant devices. • A single pressure gas-steam combined plant has been modelled. • A good correspondence has been found despite the different approaches used. - Abstract: The deregulated energy market and the increasing quota of electrical capacity covered by non-predictable renewable sources require strongly irregular and discontinuous operation of thermoelectric plants to satisfy users demand and compensate the variability of renewable sources. As a consequence, due to thermo-mechanical fatigue, creep and corrosion, a lifetime reduction of the most critical components occurs. The availability of a procedure able to predict the residual life of plant devices is necessary to assist the management decisions about power plants’ operation and maintenance scheduling. The first step of this procedure is the capability of simulating the plant behaviour versus time by evaluating the trends of the main thermodynamic parameters that describe the plant operation during different transient periods. In this context, the main contribution of the present paper is to propose a complete procedure able to simulate the plant dynamic behaviour and estimate the residual life reduction of some components. Indeed, two different models, developed by two different research groups, of the same single pressure heat recovery steam generator unit are presented and utilized to characterize the dynamic behaviour of the above mentioned power plant. The main thermodynamic variables during different transient operation conditions are predicted and good correspondence between the two methods is obtained. It can be also noted that, when the geometry and size of the devices are considered, the thermal inertia related to heat exchangers tubes, pipes and other physical masses causes a delay in the system response. Moreover, a residual life

  17. Considering human exposure to pesticides in food products: Importance of dissipation dynamics

    DEFF Research Database (Denmark)

    Fantke, Peter; Juraske, Ronnie; Jolliet, Olivier

    2014-01-01

    The general public is continuously concerned about effects from pesticide exposure via residues in food crops. However, impacts from pesticide exposure are mostly neglected in food product-related LCAs. Time-to-harvest and dissipation from crops mainly drive residue dynamics with dissipation...... as most uncertain aspect in characterization modeling. We analyzed measured half-lives (n=4513) with 95% falling between 0.6 and 29 days. With ~500 pesticides authorized alone in the EU for several hundred crops, however, experimental stud-ies only cover few possible pesticide-crop combinations. Therefore......, we estimated dissipation from measured data and provide reference half-lives for 333 pesticides applied at 20°C under field conditions. Our framework allows for detailed explorations of dietary choices in LCA with respect to human health impacts from pesticide exposure via crop consumption. The next...

  18. Carbon balance and crop residue management in dynamic equilibrium under a no-till system in Campos Gerais

    Directory of Open Access Journals (Sweden)

    Ademir de Oliveira Ferreira

    2012-11-01

    Full Text Available The adoption of no-tillage systems (NT and the maintenance of crop residues on the soil surface result in the long-term increase of carbon (C in the system, promoting C sequestration and reducing C-CO2 emissions to the atmosphere. The purpose of this study was to evaluate the C sequestration rate and the minimum amount of crop residues required to maintain the dynamic C equilibrium (dC/dt = 0 of two soils (Typic Hapludox with different textural classes. The experiment was arranged in a 2 x 2 x 2 randomized block factorial design. The following factors were analyzed: (a two soil types: Typic Hapludox (Oxisol with medium texture (LVTM and Oxisol with clay texture (LVTA, (b two sampling layers (0-5 and 5-20 cm, and (c two sampling periods (P1 - October 2007; P2 - September 2008. Samples were collected from fields under a long-term (20 years NT system with the following crop rotations: wheat/soybean/black oat + vetch/maize (LVTM and wheat/maize/black oat + vetch/soybean (LVTA. The annual C sequestration rates were 0.83 and 0.76 Mg ha-1 for LVTM and LVTA, respectively. The estimates of the minimum amount of crop residues required to maintain a dynamic equilibrium (dC/dt = 0 were 7.13 and 6.53 Mg ha-1 year-1 for LVTM and LVTA, respectively. The C conversion rate in both studied soils was lower than that reported in other studies in the region, resulting in a greater amount of crop residues left on the soil surface.

  19. Three-Dimensional Sediment Dynamics in Well-Mixed Estuaries: Importance of the Internally Generated Overtide, Spatial Settling Lag, and Gravitational Circulation

    Science.gov (United States)

    Wei, Xiaoyan; Kumar, Mohit; Schuttelaars, Henk M.

    2018-02-01

    To investigate the dominant sediment transport and trapping mechanisms, a semi-analytical three-dimensional model is developed resolving the dynamic effects of salt intrusion on sediment in well-mixed estuaries in morphodynamic equilibrium. As a study case, a schematized estuary with a converging width and a channel-shoal structure representative for the Delaware estuary is considered. When neglecting Coriolis effects, sediment downstream of the estuarine turbidity maximum (ETM) is imported into the estuary through the deeper channel and exported over the shoals. Within the ETM region, sediment is transported seaward through the deeper channel and transported landward over the shoals. The largest contribution to the cross-sectionally integrated seaward residual sediment transport is attributed to the advection of tidally averaged sediment concentrations by river-induced flow and tidal return flow. This contribution is mainly balanced by the residual landward sediment transport due to temporal correlations between the suspended sediment concentrations and velocities at the M2 tidal frequency. The M2 sediment concentration mainly results from spatial settling lag effects and asymmetric bed shear stresses due to interactions of M2 bottom velocities and the internally generated M4 tidal velocities, as well as the salinity-induced residual currents. Residual advection of tidally averaged sediment concentrations also plays an important role in the landward sediment transport. Including Coriolis effects hardly changes the cross-sectionally integrated sediment balance, but results in a landward (seaward) sediment transport on the right (left) side of the estuary looking seaward, consistent with observations from literature. The sediment transport/trapping mechanisms change significantly when varying the settling velocity and river discharge.

  20. Dependence of the residual surface resistance of superconducting radio frequency cavities on the cooling dynamics around Tc

    Science.gov (United States)

    Romanenko, A.; Grassellino, A.; Melnychuk, O.; Sergatskov, D. A.

    2014-05-01

    We report a strong effect of the cooling dynamics through Tc on the amount of trapped external magnetic flux in superconducting niobium cavities. The effect is similar for fine grain and single crystal niobium and all surface treatments including electropolishing with and without 120 °C baking and nitrogen doping. Direct magnetic field measurements on the cavity walls show that the effect stems from changes in the flux trapping efficiency: slow cooling leads to almost complete flux trapping and higher residual resistance, while fast cooling leads to the much more efficient flux expulsion and lower residual resistance.

  1. 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.

  2. Identification of residues in the insulin molecule important for binding to insulin-degrading enzyme.

    Science.gov (United States)

    Affholter, J A; Cascieri, M A; Bayne, M L; Brange, J; Casaretto, M; Roth, R A

    1990-08-21

    Insulin-degrading enzyme (IDE) hydrolyzes insulin at a limited number of sites. Although the positions of these cleavages are known, the residues of insulin important in its binding to IDE have not been defined. To this end, we have studied the binding of a variety of insulin analogues to the protease in a solid-phase binding assay using immunoimmobilized IDE. Since IDE binds insulin with 600-fold greater affinity than it does insulin-like growth factor I (25 nM and approximately 16,000 nM, respectively), the first set of analogues studied were hybrid molecules of insulin and IGF I. IGF I mutants [insB1-17,17-70]IGF I, [Tyr55,Gln56]IGF I, and [Phe23,Phe24,Tyr25]IGF I have been synthesized and share the property of having insulin-like amino acids at positions corresponding to primary sites of cleavage of insulin by IDE. Whereas the first two exhibit affinities for IDE similar to that of wild type IGF I, the [Phe23,Phe24,Tyr25]IGF I analogue has a 32-fold greater affinity for the immobilized enzyme. Replacement of Phe-23 by Ser eliminates this increase. Removal of the eight amino acid D-chain region of IGF I (which has been predicted to interfere with binding to the 23-25 region) results in a 25-fold increase in affinity for IDE, confirming the importance of residues 23-25 in the high-affinity recognition of IDE. A similar role for the corresponding (B24-26) residues of insulin is supported by the use of site-directed mutant and semisynthetic insulin analogues. Insulin mutants [B25-Asp]insulin and [B25-His]insulin display 16- and 20-fold decreases in IDE affinity versus wild-type insulin.(ABSTRACT TRUNCATED AT 250 WORDS)

  3. Resilient modulus prediction of soft low-plasticity Piedmont residual soil using dynamic cone penetrometer

    Directory of Open Access Journals (Sweden)

    S. Hamed Mousavi

    2018-04-01

    Full Text Available Dynamic cone penetrometer (DCP has been used for decades to estimate the shear strength and stiffness properties of the subgrade soils. There are several empirical correlations in the literature to predict the resilient modulus values at only a specific stress state from DCP data, corresponding to the predefined thicknesses of pavement layers (a 50 mm asphalt wearing course, a 100 mm asphalt binder course and a 200 mm aggregate base course. In this study, field-measured DCP data were utilized to estimate the resilient modulus of low-plasticity subgrade Piedmont residual soil. Piedmont residual soils are in-place weathered soils from igneous and metamorphic rocks, as opposed to transported or compacted soils. Hence the existing empirical correlations might not be applicable for these soils. An experimental program was conducted incorporating field DCP and laboratory resilient modulus tests on “undisturbed” soil specimens. The DCP tests were carried out at various locations in four test sections to evaluate subgrade stiffness variation laterally and with depth. Laboratory resilient modulus test results were analyzed in the context of the mechanistic-empirical pavement design guide (MEPDG recommended universal constitutive model. A new approach for predicting the resilient modulus from DCP by estimating MEPDG constitutive model coefficients (k1, k2 and k3 was developed through statistical analyses. The new model is capable of not only taking into account the in situ soil condition on the basis of field measurements, but also representing the resilient modulus at any stress state which addresses a limitation with existing empirical DCP models and its applicability for a specific case. Validation of the model is demonstrated by using data that were not used for model development, as well as data reported in the literature. Keywords: Dynamic cone penetrometer (DCP, Resilient modulus, Mechanistic-empirical pavement design guide (MEPDG, Residual

  4. Longitudinal and transverse dynamics of ions from residual gas in an electron accelerator

    Science.gov (United States)

    Gamelin, A.; Bruni, C.; Radevych, D.

    2018-05-01

    The ion cloud produced from residual gas in an electron accelerator can degrade machine performances and produce instabilities. The ion dynamics in an accelerator is governed by the beam-ion interaction, magnetic fields and eventual mitigation strategies. Due to the fact that the beam has a nonuniform transverse size along its orbit, the ions move longitudinally and accumulate naturally at some points in the accelerator. In order to design effective mitigation strategies it is necessary to understand the ion dynamics not only in the transverse plane but also in the longitudinal direction. After introducing the physics behind the beam-ion interaction, we show how to get accumulation points for a realistic electron storage ring lattice. Simulations of the ion cloud dynamics, including the effect of magnetic fields on the ions, clearing electrodes and clearing gaps are shown. Longitudinal ion trapping due to the magnetic mirror effect in the dipole fringe fields is also detailed. Finally, the effectiveness of clearing electrode using longitudinal clearing fields is discussed and compared to clearing electrodes producing transverse field only.

  5. Identification of the hot spot residues for pyridine derivative inhibitor CCT251455 and ATP substrate binding on monopolar spindle 1 (MPS1) kinase by molecular dynamic simulation.

    Science.gov (United States)

    Chen, Kai; Duan, Wenxiu; Han, Qianqian; Sun, Xuan; Li, Wenqian; Hu, Shuangyun; Wan, Jiajia; Wu, Jiang; Ge, Yushu; Liu, Dan

    2018-03-08

    Protein kinase monopolar spindle 1 plays an important role in spindle assembly checkpoint at the onset of mitosis. Over expression of MPS1 correlated with a wide range of human tumors makes it an attractive target for finding an effective and specific inhibitor. In this work, we performed molecular dynamics simulations of protein MPS1 itself as well as protein bound systems with the inhibitor and natural substrate based on crystal structures. The reported orally bioavailable 1 h-pyrrolo [3,2-c] pyridine inhibitors of MPS1 maintained stable binding in the catalytic site, while natural substrate ATP could not stay. Comparative study of stability and flexibility of three systems reveals position shifting of β-sheet region within the catalytic site, which indicates inhibition mechanism was through stabilizing the β-sheet region. Binding free energies calculated with MM-GB/PBSA method shows different binding affinity for inhibitor and ATP. Finally, interactions between protein and inhibitor during molecular dynamic simulations were measured and counted. Residue Gly605 and Leu654 were suggested as important hot spots for stable binding of inhibitor by molecular dynamic simulation. Our results reveal an important position shifting within catalytic site for non-inhibited proteins. Together with hot spots found by molecular dynamic simulation, the results provide important information of inhibition mechanism and will be referenced for designing novel inhibitors.

  6. NMR investigations of molecular dynamics

    Science.gov (United States)

    Palmer, Arthur

    2011-03-01

    NMR spectroscopy is a powerful experimental approach for characterizing protein conformational dynamics on multiple time scales. The insights obtained from NMR studies are complemented and by molecular dynamics (MD) simulations, which provide full atomistic details of protein dynamics. Homologous mesophilic (E. coli) and thermophilic (T. thermophilus) ribonuclease H (RNase H) enzymes serve to illustrate how changes in protein sequence and structure that affect conformational dynamic processes can be monitored and characterized by joint analysis of NMR spectroscopy and MD simulations. A Gly residue inserted within a putative hinge between helices B and C is conserved among thermophilic RNases H, but absent in mesophilic RNases H. Experimental spin relaxation measurements show that the dynamic properties of T. thermophilus RNase H are recapitulated in E. coli RNase H by insertion of a Gly residue between helices B and C. Additional specific intramolecular interactions that modulate backbone and sidechain dynamical properties of the Gly-rich loop and of the conserved Trp residue flanking the Gly insertion site have been identified using MD simulations and subsequently confirmed by NMR spin relaxation measurements. These results emphasize the importance of hydrogen bonds and local steric interactions in restricting conformational fluctuations, and the absence of such interactions in allowing conformational adaptation to substrate binding.

  7. Identification of residues in the insulin molecule important for binding to insulin-degrading enzyme

    Energy Technology Data Exchange (ETDEWEB)

    Affholter, J.A.; Roth, R.A. (Stanford Univ. School of Medicine, CA (USA)); Cascieri, M.A.; Bayne, M.L. (Merck Sharp and Dohme Research Labs., Rahway, NJ (USA)); Brange, J. (Novo Research Institute, Bagsvaerd (Denmark)); Casaretto, M. (Deutsches Wollforschungsinstitut an der Technischen, Aachen (West Germany))

    1990-08-21

    Insulin-degrading enzyme (IDE) hydrolyzes insulin at a limited number of sites. Although the positions of these cleavages are known, the residues of insulin important in its binding to IDE have not been defined. To this end, the authors have studied the binding of a variety of insulin analogues to the protease in a solid-phase binding assay using immunoimmobilized IDE. Since IDE binds insulin with 600-fold greater affinity than it does insulin-like growth factor, the first set of analogues studied were hybrid molecules of insulin and IGF I. Removal of the eight amino acid D-chain region of IGF I (which has been predicted to interfere with binding to the 23-25 region) results in a 25-fold increase in affinity for IDE, confirming the importance of residues 23-25 in the high-affinity recognition of IDE. A similar role for the corresponding (B24-26) residues of insulin is supported by the use of site-directed mutant and semisynthetic insulin analogues. Insulin mutants (B25-Asp)insulin and (B25-His)insulin display 16- and 20-fold decreases in IDE affinity versus wild-type insulin. Similar decreases in affinity are observed with the C-terminal truncation mutants (B1-24-His{sup 25}-NH{sub 2})insulin and (B1-24-Leu{sup 25}-NH{sub 2})insulin, but not (B1-24-Trp{sup 25}-NH{sub 2})insulin and (B1-24-Tyr{sup 25}-NH{sub 2})insulin. The truncated analogue with the lowest affinity for IDE ((B1-24-His{sup 25}-NH{sub 2})insulin) has one of the highest affinities for the insulin receptor. Therefore, they have identified a region of the insulin molecule responsible for its high-affinity interaction with IDE. Although the same region has been implicated in the binding of insulin to its receptor, the data suggest that the structural determinants required for binding to receptor and IDE differ.

  8. Identification of residues in the insulin molecule important for binding to insulin-degrading enzyme

    International Nuclear Information System (INIS)

    Affholter, J.A.; Roth, R.A.; Cascieri, M.A.; Bayne, M.L.; Brange, J.; Casaretto, M.

    1990-01-01

    Insulin-degrading enzyme (IDE) hydrolyzes insulin at a limited number of sites. Although the positions of these cleavages are known, the residues of insulin important in its binding to IDE have not been defined. To this end, the authors have studied the binding of a variety of insulin analogues to the protease in a solid-phase binding assay using immunoimmobilized IDE. Since IDE binds insulin with 600-fold greater affinity than it does insulin-like growth factor, the first set of analogues studied were hybrid molecules of insulin and IGF I. Removal of the eight amino acid D-chain region of IGF I (which has been predicted to interfere with binding to the 23-25 region) results in a 25-fold increase in affinity for IDE, confirming the importance of residues 23-25 in the high-affinity recognition of IDE. A similar role for the corresponding (B24-26) residues of insulin is supported by the use of site-directed mutant and semisynthetic insulin analogues. Insulin mutants [B25-Asp]insulin and [B25-His]insulin display 16- and 20-fold decreases in IDE affinity versus wild-type insulin. Similar decreases in affinity are observed with the C-terminal truncation mutants [B1-24-His 25 -NH 2 ]insulin and [B1-24-Leu 25 -NH 2 ]insulin, but not [B1-24-Trp 25 -NH 2 ]insulin and [B1-24-Tyr 25 -NH 2 ]insulin. The truncated analogue with the lowest affinity for IDE ([B1-24-His 25 -NH 2 ]insulin) has one of the highest affinities for the insulin receptor. Therefore, they have identified a region of the insulin molecule responsible for its high-affinity interaction with IDE. Although the same region has been implicated in the binding of insulin to its receptor, the data suggest that the structural determinants required for binding to receptor and IDE differ

  9. Use of a dynamic grid adaptation in the asymmetric weighted residual method

    International Nuclear Information System (INIS)

    Graf, V.; Romstedt, P.; Werner, W.

    1986-01-01

    A dynamic grid adaptive method has been developed for use with the asymmetric weighted residual method. The method automatically adapts the number and position of the spatial mesh points as the solution of hyperbolic or parabolic vector partial differential equations progresses in time. The mesh selection algorithm is based on the minimization of the L 2 norm of the spatial discretization error. The method permits the accurate calculation of the evolution of inhomogeneities, like wave fronts, shock layers, and other sharp transitions, while generally using a coarse computational grid. The number of required mesh points is significantly reduced, relative to a fixed Eulerian grid. Since the mesh selection algorithm is computationally inexpensive, a corresponding reduction of computing time results

  10. Time-dependent climate benefits of using forest residues to substitute fossil fuels

    International Nuclear Information System (INIS)

    Sathre, Roger; Gustavsson, Leif

    2011-01-01

    In this study we analyze and compare the climate impacts from the recovery, transport and combustion of forest residues (harvest slash and stumps), versus the climate impacts that would have occurred if the residues were left in the forest and fossil fuels used instead. We use cumulative radiative forcing (CRF) as an indicator of climate impacts, and we explicitly consider the temporal dynamics of atmospheric carbon dioxide and biomass decomposition. Over a 240-year period, we find that CRF is significantly reduced when forest residues are used instead of fossil fuels. The type of fossil fuel replaced is important, with coal replacement giving the greatest CRF reduction. Replacing oil and fossil gas also gives long-term CRF reduction, although CRF is positive during the first 10-25 years when these fuels are replaced. Biomass productivity is also important, with more productive forests giving greater CRF reduction per hectare. The decay rate for biomass left in the forest is found to be less significant. Fossil energy inputs for biomass recovery and transport have very little impact on CRF. -- Highlights: → Cumulative radiative forcing (CRF) can measure climate impacts of dynamic systems. → Climate impact is reduced when forest slash and stumps are used to replace fossil fuels. → Forest biofuels may cause short-term climate impact, followed by long-term climate benefit. → Forest residues should replace coal to avoid short-term climate impact. → Fossil energy used for biofuel recovery and transport has very little climate impact.

  11. Structure-Activity Relationship in TLR4 Mutations: Atomistic Molecular Dynamics Simulations and Residue Interaction Network Analysis

    Science.gov (United States)

    Anwar, Muhammad Ayaz; Choi, Sangdun

    2017-03-01

    Toll-like receptor 4 (TLR4), a vital innate immune receptor present on cell surfaces, initiates a signaling cascade during danger and bacterial intrusion. TLR4 needs to form a stable hexamer complex, which is necessary to dimerize the cytoplasmic domain. However, D299G and T399I polymorphism may abrogate the stability of the complex, leading to compromised TLR4 signaling. Crystallography provides valuable insights into the structural aspects of the TLR4 ectodomain; however, the dynamic behavior of polymorphic TLR4 is still unclear. Here, we employed molecular dynamics simulations (MDS), as well as principal component and residue network analyses, to decipher the structural aspects and signaling propagation associated with mutations in TLR4. The mutated complexes were less cohesive, displayed local and global variation in the secondary structure, and anomalous decay in rotational correlation function. Principal component analysis indicated that the mutated complexes also exhibited distinct low-frequency motions, which may be correlated to the differential behaviors of these TLR4 variants. Moreover, residue interaction networks (RIN) revealed that the mutated TLR4/myeloid differentiation factor (MD) 2 complex may perpetuate abnormal signaling pathways. Cumulatively, the MDS and RIN analyses elucidated the mutant-specific conformational alterations, which may help in deciphering the mechanism of loss-of-function mutations.

  12. Dependence of the residual surface resistance of superconducting radio frequency cavities on the cooling dynamics around T{sub c}

    Energy Technology Data Exchange (ETDEWEB)

    Romanenko, A., E-mail: aroman@fnal.gov; Grassellino, A., E-mail: annag@fnal.gov; Melnychuk, O.; Sergatskov, D. A. [Fermi National Accelerator Laboratory, Batavia, Illinois 60510 (United States)

    2014-05-14

    We report a strong effect of the cooling dynamics through T{sub c} on the amount of trapped external magnetic flux in superconducting niobium cavities. The effect is similar for fine grain and single crystal niobium and all surface treatments including electropolishing with and without 120 °C baking and nitrogen doping. Direct magnetic field measurements on the cavity walls show that the effect stems from changes in the flux trapping efficiency: slow cooling leads to almost complete flux trapping and higher residual resistance, while fast cooling leads to the much more efficient flux expulsion and lower residual resistance.

  13. 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...... 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...... mutants displayed an increased apparent K+ affinity at the external binding sites in measurements of ATPase activity: for Phe318Trp, Arg882Leu, and Asp886Ala 2.2-, 5.1-, and 1.8-fold increases compared to the wild type, respectively. Similarly the three mutants exhibited 10-, 6.4-, and 4.1-fold decreases...

  14. Anion induced conformational preference of Cα NN motif residues in functional proteins.

    Science.gov (United States)

    Patra, Piya; Ghosh, Mahua; Banerjee, Raja; Chakrabarti, Jaydeb

    2017-12-01

    Among different ligand binding motifs, anion binding C α NN motif consisting of peptide backbone atoms of three consecutive residues are observed to be important for recognition of free anions, like sulphate or biphosphate and participate in different key functions. Here we study the interaction of sulphate and biphosphate with C α NN motif present in different proteins. Instead of total protein, a peptide fragment has been studied keeping C α NN motif flanked in between other residues. We use classical force field based molecular dynamics simulations to understand the stability of this motif. Our data indicate fluctuations in conformational preferences of the motif residues in absence of the anion. The anion gives stability to one of these conformations. However, the anion induced conformational preferences are highly sequence dependent and specific to the type of anion. In particular, the polar residues are more favourable compared to the other residues for recognising the anion. © 2017 Wiley Periodicals, Inc.

  15. Residue dynamics of pyraclostrobin in peanut and field soil by QuEChERS and LC-MS/MS.

    Science.gov (United States)

    Zhang, Fengzu; Wang, Lei; Zhou, Li; Wu, Di; Pan, Hongji; Pan, Canping

    2012-04-01

    A modified QuEChERS-LC-MS/MS (acronym of quick, easy, cheap, effective, rugged and safe-liquid chromatography tandem mass spectrometry) method for the analysis of pyraclostrobin residue in peanut and soil was developed and validated. Pyraclostrobin residue dynamics and final residues in supervised field trials at Good Agricultural Practice (GAP) conditions in peanut and soil were studied. The limits of quantitation (LOQs) for pyraclostrobin in soil, plant, shell and peanut samples were 0.00057, 0.00026, 0.003 and 0.0037 mg kg(-1), respectively. At fortification levels of 0.005, 0.05 and 0.5 mg kg(-1) in all samples, it was shown that recoveries ranged from 80.3% to 109.4% with relative standard deviations of 1.1-8.2% (n=5). The dissipation experiments showed the half-lives (T(1/2)) of pyraclostrobin in soil and plants were 13.1-16.5 days and 10.3-11.2 days, respectively. At pre-harvest intervals (PHI) of 14, 21 and 28 days, pyraclostrobin residue were 0.005-0.20 mg kg(-1) in soil, 0.006-0.27 mg kg(-1) in plants, below 0.053 mg kg(-1) in shells and not detectable in peanuts. Crown Copyright © 2011. Published by Elsevier Inc. All rights reserved.

  16. Protein-protein docking with dynamic residue protonation states.

    Directory of Open Access Journals (Sweden)

    Krishna Praneeth Kilambi

    2014-12-01

    Full Text Available Protein-protein interactions depend on a host of environmental factors. Local pH conditions influence the interactions through the protonation states of the ionizable residues that can change upon binding. In this work, we present a pH-sensitive docking approach, pHDock, that can sample side-chain protonation states of five ionizable residues (Asp, Glu, His, Tyr, Lys on-the-fly during the docking simulation. pHDock produces successful local docking funnels in approximately half (79/161 the protein complexes, including 19 cases where standard RosettaDock fails. pHDock also performs better than the two control cases comprising docking at pH 7.0 or using fixed, predetermined protonation states. On average, the top-ranked pHDock structures have lower interface RMSDs and recover more native interface residue-residue contacts and hydrogen bonds compared to RosettaDock. Addition of backbone flexibility using a computationally-generated conformational ensemble further improves native contact and hydrogen bond recovery in the top-ranked structures. Although pHDock is designed to improve docking, it also successfully predicts a large pH-dependent binding affinity change in the Fc-FcRn complex, suggesting that it can be exploited to improve affinity predictions. The approaches in the study contribute to the goal of structural simulations of whole-cell protein-protein interactions including all the environmental factors, and they can be further expanded for pH-sensitive protein design.

  17. 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

    1990-12-31

    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.

  18. 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.

  19. 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.

  20. Dynamic Response and Residual Helmet Liner Crush Using Cadaver Heads and Standard Headforms.

    Science.gov (United States)

    Bonin, S J; Luck, J F; Bass, C R; Gardiner, J C; Onar-Thomas, A; Asfour, S S; Siegmund, G P

    2017-03-01

    Biomechanical headforms are used for helmet certification testing and reconstructing helmeted head impacts; however, their biofidelity and direct applicability to human head and helmet responses remain unclear. Dynamic responses of cadaver heads and three headforms and residual foam liner deformations were compared during motorcycle helmet impacts. Instrumented, helmeted heads/headforms were dropped onto the forehead region against an instrumented flat anvil at 75, 150, and 195 J. Helmets were CT scanned to quantify maximum liner crush depth and crush volume. General linear models were used to quantify the effect of head type and impact energy on linear acceleration, head injury criterion (HIC), force, maximum liner crush depth, and liner crush volume and regression models were used to quantify the relationship between acceleration and both maximum crush depth and crush volume. The cadaver heads generated larger peak accelerations than all three headforms, larger HICs than the International Organization for Standardization (ISO), larger forces than the Hybrid III and ISO, larger maximum crush depth than the ISO, and larger crush volumes than the DOT. These significant differences between the cadaver heads and headforms need to be accounted for when attempting to estimate an impact exposure using a helmet's residual crush depth or volume.

  1. Probing the importance of hydrogen bonds in the active site of the subtilisin nattokinase by site-directed mutagenesis and molecular dynamics simulation.

    Science.gov (United States)

    Zheng, Zhong-liang; Ye, Mao-qing; Zuo, Zhen-yu; Liu, Zhi-gang; Tai, Keng-chang; Zou, Guo-lin

    2006-05-01

    Hydrogen bonds occurring in the catalytic triad (Asp32, His64 and Ser221) and the oxyanion hole (Asn155) are very important to the catalysis of peptide bond hydrolysis by serine proteases. For the subtilisin NK (nattokinase), a bacterial serine protease, construction and analysis of a three-dimensional structural model suggested that several hydrogen bonds formed by four residues function to stabilize the transition state of the hydrolysis reaction. These four residues are Ser33, Asp60, Ser62 and Thr220. In order to remove the effect of these hydrogen bonds, four mutants (Ser33-->Ala33, Asp60-->Ala60, Ser62-->Ala62, and Thr220-->Ala220) were constructed by site-directed mutagenesis. The results of enzyme kinetics indicated that removal of these hydrogen bonds increases the free-energy of the transition state (DeltaDeltaG(T)). We concluded that these hydrogen bonds are more important for catalysis than for binding the substrate, because removal of these bonds mainly affects the kcat but not the K(m) values. A substrate, SUB1 (succinyl-Ala-Ala-Pro-Phe-p-nitroanilide), was used during enzyme kinetics experiments. In the present study we have also shown the results of FEP (free-energy perturbation) calculations with regard to the binding and catalysis reactions for these mutant subtilisins. The calculated difference in FEP also suggested that these four residues are more important for catalysis than binding of the substrate, and the simulated values compared well with the experimental values from enzyme kinetics. The results of MD (molecular dynamics) simulations further demonstrated that removal of these hydrogen bonds partially releases Asp32, His64 and Asn155 so that the stability of the transition state decreases. Another substrate, SUB2 (H-D-Val-Leu-Lys-p-nitroanilide), was used for FEP calculations and MD simulations.

  2. Residual stresses

    International Nuclear Information System (INIS)

    Macherauch, E.

    1978-01-01

    Residual stresses are stresses which exist in a material without the influence of external powers and moments. They come into existence when the volume of a material constantly changes its form as a consequence of mechanical, thermal, and/or chemical processes and is hindered by neighbouring volumes. Bodies with residual stress are in mechanical balance. These residual stresses can be manifested by means of all mechanical interventions disturbing this balance. Acoustical, optical, radiological, and magnetical methods involving material changes caused by residual stress can also serve for determining residual stress. Residual stresses have an ambivalent character. In technical practice, they are feared and liked at the same time. They cause trouble because they can be the cause for unexpected behaviour of construction elements. They are feared since they can cause failure, in the worst case with catastrophical consequences. They are appreciated, on the other hand, because, in many cases, they can contribute to improvements of the material behaviour under certain circumstances. But they are especially liked for their giving convenient and (this is most important) mostly uncontrollable explanations. For only in very few cases we have enough knowledge and possibilities for the objective evaluation of residual stresses. (orig.) [de

  3. Polynomic nonlinear dynamical systems - A residual sensitivity method for model reduction

    Science.gov (United States)

    Yurkovich, S.; Bugajski, D.; Sain, M.

    1985-01-01

    The motivation for using polynomic combinations of system states and inputs to model nonlinear dynamics systems is founded upon the classical theories of analysis and function representation. A feature of such representations is the need to make available all possible monomials in these variables, up to the degree specified, so as to provide for the description of widely varying functions within a broad class. For a particular application, however, certain monomials may be quite superfluous. This paper examines the possibility of removing monomials from the model in accordance with the level of sensitivity displayed by the residuals to their absence. Critical in these studies is the effect of system input excitation, and the effect of discarding monomial terms, upon the model parameter set. Therefore, model reduction is approached iteratively, with inputs redesigned at each iteration to ensure sufficient excitation of remaining monomials for parameter approximation. Examples are reported to illustrate the performance of such model reduction approaches.

  4. Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamics

    International Nuclear Information System (INIS)

    Lakomek, Nils-Alexander; Walter, Korvin F. A.; Fares, Christophe; Lange, Oliver F.; Groot, Bert L. de; Grubmueller, Helmut; Brueschweiler, Rafael; Munk, Axel; Becker, Stefan; Meiler, Jens; Griesinger, Christian

    2008-01-01

    Residual dipolar couplings (RDCs) provide information about the dynamic average orientation of inter-nuclear vectors and amplitudes of motion up to milliseconds. They complement relaxation methods, especially on a time-scale window that we have called supra-τ c (τ c c rdc > = 0.72 ± 0.02 compared to LS 2 > = 0.778 ± 0.003 for the Lipari-Szabo order parameters, indicating that the inclusion of the supra-τ c window increases the averaged amplitude of mobility observed in the sub-τ c window by about 34%. For the β-strand spanned by residues Lys48 to Leu50, an alternating pattern of backbone NH RDC order parameter S rdc 2 (NH) = (0.59, 0.72, 0.59) was extracted. The backbone of Lys48, whose side chain is known to be involved in the poly-ubiquitylation process that leads to protein degradation, is very mobile on the supra-τ c time scale (S rdc 2 (NH) = 0.59 ± 0.03), while it is inconspicuous (S LS 2 (NH) = 0.82) on the sub-τ c as well as on μs-ms relaxation dispersion time scales. The results of this work differ from previous RDC dynamics studies of ubiquitin in the sense that the results are essentially independent of structural noise providing a much more robust assessment of dynamic effects that underlie the RDC data

  5. DYNAMIC CAPABILITIES AND CREATING ORGANIZATIONAL KNOWLEDGE: IMPORTANT LINKAGE FOR BUILDING COMPETITIVE ADVANTAGE

    Directory of Open Access Journals (Sweden)

    Sugiono A.

    2017-08-01

    Full Text Available As a concept derived from the resource-based view, dynamic capabilities essentially have an important linkage with activities related to the creation of organizational knowledge. Using literature study method, this paper aims to discuss the linkage between the creation of dynamic knowledge capabilities and the creation of knowledge company. The study shows that the discussion of dynamic capabilities creation finally puts both learning and knowledge in an important position. Correspondingly, the relationship between a growth strategy that is generally chosen by the organization brings a consequence that the creation of organizational knowledge becomes something that can not be ignored. In order to make the process of knowledge creation in line with dynamic capabilities creation within a growth strategy creation framework, we need a dynamic process of knowledge creation. Among the various models of knowledge creation, SECI model still becomes a relevant model within organizational knowledge creation framework. In general, this study is still theoretical, therefore, more empirical subsequent discussions are expected.

  6. Identification of C-terminal hydrophobic residues important for dimerization and all known functions of ParB of Pseudomonas aeruginosa.

    NARCIS (Netherlands)

    Mierzejewska, J.; Bartosik, A.A.; Macioszek, M.; Plochocka, D.; Thomas, C.M.G.; Jagura-Burdzy, G.

    2012-01-01

    The ParB protein of Pseudomonas aeruginosa is important for growth, cell division, nucleoid segregation and different types of motility. To further understand its function we have demonstrated a vital role of the hydrophobic residues in the C terminus of ParB(P.a.). By in silico modelling of the

  7. 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.

  8. The residual zonal dynamics in a toroidally rotating tokamak

    International Nuclear Information System (INIS)

    Zhou Deng

    2015-01-01

    Zonal flows, initially driven by ion-temperature-gradient turbulence, may evolve due to the neoclassic polarization in a collisionless tokamak plasma. In this presentation, the form of the residual zonal flow is presented for tokamak plasmas rotating toroidally at arbitrary velocity. The gyro-kinetic equation is analytically solved to give the expression of residual zonal flows with arbitrary rotating velocity. The zonal flow level decreases as the rotating velocity increases. The numerical evaluation is in good agreement with the previous simulation result for high aspect ratio tokamaks. (author)

  9. 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.

  10. 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.

  11. 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

    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......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...

  12. Identification of residues important for the activity of aldehyde-deformylating oxygenase through investigation into the structure-activity relationship.

    Science.gov (United States)

    Wang, Qing; Bao, Luyao; Jia, Chenjun; Li, Mei; Li, Jian-Jun; Lu, Xuefeng

    2017-03-16

    Aldehyde-deformylating oxygenase (ADO) is a key enzyme involved in the biosynthetic pathway of fatty alk(a/e)nes in cyanobacteria. However, cADO (cyanobacterial ADO) showed extreme low activity with the k cat value below 1 min -1 , which would limit its application in biofuel production. To identify the activity related key residues of cADO is urgently required. The amino acid residues which might affect cADO activity were identified based on the crystal structures and sequence alignment of cADOs, including the residues close to the di-iron center (Tyr39, Arg62, Gln110, Tyr122, Asp143 of cADO-1593), the protein surface (Trp 178 of cADO-1593), and those involved in two important hydrogen bonds (Gln49, Asn123 of cADO-1593, and Asp49, Asn123 of cADO-sll0208) and in the oligopeptide whose conformation changed in the absence of the di-iron center (Leu146, Asn149, Phe150 of cADO-1593, and Thr146, Leu148, Tyr150 of cADO-sll0208). The variants of cADO-1593 from Synechococcus elongatus PCC7942 and cADO-sll0208 from Synechocystis sp. PCC6803 were constructed, overexpressed, purified and kinetically characterized. The k cat values of L146T, Q49H/N123H/F150Y and W178R of cADO-1593 and L148R of cADO-sll0208 were increased by more than two-fold, whereas that of R62A dropped by 91.1%. N123H, Y39F and D143A of cADO-1593, and Y150F of cADO-sll0208 reduced activities by ≤ 20%. Some important amino acids, which exerted some effects on cADO activity, were identified. Several enzyme variants exhibited greatly reduced activity, while the k cat values of several mutants are more than two-fold higher than the wild type. This study presents the report on the relationship between amino acid residues and enzyme activity of cADOs, and the information will provide a guide for enhancement of cADO activity through protein engineering.

  13. Residual entanglement and sudden death: A direct connection

    International Nuclear Information System (INIS)

    Oliveira, J.G.G. de; Peixoto de Faria, J.G.; Nemes, M.C.

    2011-01-01

    We explore the results of [V. Coffman, et al., Phys. Rev. A 61 (2000) 052306] derived for general tripartite states in a dynamical context. We study a class of physically motivated tripartite systems. We show that whenever entanglement sudden death occurs in one of the partitions residual entanglement will appear. For fourpartite systems however, the appearance of residual entanglement is not conditioned by sudden death of entanglement. We can only say that if sudden death of entanglement occurs in some partition there will certainly be residual entanglement. -- Highlights: ► For tripartite systems we show there exists residual entanglement if sudden death occurs. ► For fourpartite systems, the residual entanglement is not conditioned by sudden death. ► If sudden death of entanglement occurs there will certainly be residual entanglement.

  14. The Relationship Between Low-Frequency Motions and Community Structure of Residue Network in Protein Molecules.

    Science.gov (United States)

    Sun, Weitao

    2018-01-01

    The global shape of a protein molecule is believed to be dominant in determining low-frequency deformational motions. However, how structure dynamics relies on residue interactions remains largely unknown. The global residue community structure and the local residue interactions are two important coexisting factors imposing significant effects on low-frequency normal modes. In this work, an algorithm for community structure partition is proposed by integrating Miyazawa-Jernigan empirical potential energy as edge weight. A sensitivity parameter is defined to measure the effect of local residue interaction on low-frequency movement. We show that community structure is a more fundamental feature of residue contact networks. Moreover, we surprisingly find that low-frequency normal mode eigenvectors are sensitive to some local critical residue interaction pairs (CRIPs). A fair amount of CRIPs act as bridges and hold distributed structure components into a unified tertiary structure by bonding nearby communities. Community structure analysis and CRIP detection of 116 catalytic proteins reveal that breaking up of a CRIP can cause low-frequency allosteric movement of a residue at the far side of protein structure. The results imply that community structure and CRIP may be the structural basis for low-frequency motions.

  15. Mutational properties of amino acid residues: implications for evolvability of phosphorylatable residues

    DEFF Research Database (Denmark)

    Creixell, Pau; Schoof, Erwin M.; Tan, Chris Soon Heng

    2012-01-01

    in terms of their mutational activity. Moreover, we highlight the importance of the genetic code and physico-chemical properties of the amino acid residues as likely causes of these inequalities and uncover serine as a mutational hot spot. Finally, we explore the consequences that these different......; it is typically assumed that all amino acid residues are equally likely to mutate or to result from a mutation. Here, by reconstructing ancestral sequences and computing mutational probabilities for all the amino acid residues, we refute this assumption and show extensive inequalities between different residues...... mutational properties have on phosphorylation site evolution, showing that a higher degree of evolvability exists for phosphorylated threonine and, to a lesser extent, serine in comparison with tyrosine residues. As exemplified by the suppression of serine's mutational activity in phosphorylation sites, our...

  16. 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.

  17. 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.

  18. Identification of functionally important amino acid residues in the mitochondria targeting sequence of Hepatitis B virus X protein

    International Nuclear Information System (INIS)

    Li, Sai Kam; Ho, Sai Fan; Tsui, Kwok Wing; Fung, Kwok Pui; Waye, M.Y. Mary

    2008-01-01

    Chronic hepatitis B virus (HBV) infection has been strongly associated with hepatocellular carcinoma (HCC) and the X protein (HBx) is thought to mediate the cellular changes associated with carcinogenesis. Recently, isolation of the hepatitis B virus integrants from HCC tissue by others have established the fact that the X gene is often truncated at its C-terminus. Expression of the GFP fusion proteins of HBx and its truncation mutants with a GFP tag in human liver cell-lines in this study revealed that the C-terminus of HBx is indispensable for its specific localization in the mitochondria. A crucial region of seven amino acids at the C-terminus has been mapped out in which the cysteine residue at position 115 serves as the most important residue for the subcellular localization. When cysteine 115 of HBx is mutated to alanine the mitochondria targeting property of HBx is abrogated

  19. 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.

  20. 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.

  1. Evaluation of pesticide residue dynamics in Chinese cabbage, head cabbage and cauliflower.

    Science.gov (United States)

    Kocourek, František; Stará, Jitka; Holý, Kamil; Horská, Tereza; Kocourek, Vladimír; Kováčová, Jana; Kohoutková, Jana; Suchanová, Marie; Hajšlová, Jana

    2017-06-01

    Pesticide residues from the time of application until harvest were analysed for 20, 17 and 18 active insecticidal and fungicidal substances in Chinese cabbage, head cabbage and cauliflower, respectively. In total, 40 mathematical models of residue degradation were developed using a first-order kinetic equation, and from these models it was possible to forecast the action pre-harvest interval for a given action threshold for low-residue production in Brassica vegetables as a percentage of the maximum residue level. Additionally, it was possible to establish an action pre-harvest interval based on an action threshold of 0.01 mg kg ‒1 for the production of Brassica vegetables for baby food. Among the evaluated commodities, the speed of residue degradation was highest in head cabbage, medium in Chinese cabbage and lowest in cauliflower. The half-lives of pesticide in various vegetables were also determined: they ranged from 1.55 to 5.25 days in Chinese cabbage, from 0.47 to 6.54 days in head cabbage and from 1.88 to 7.22 days in cauliflower.

  2. 77 FR 24671 - Compliance Guide for Residue Prevention and Agency Testing Policy for Residues

    Science.gov (United States)

    2012-04-25

    ... Hazard Analysis and Critical Control Points (HACCP) inspection system, another important component of the NRP is to provide verification of residue control in HACCP systems. As part of the HACCP regulation... guide, and FSIS finds violative residues, the establishment's HACCP system may be inadequate under 9 CFR...

  3. 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

  4. 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.

  5. Residual flow patterns and morphological changes along a macro- and meso-tidal coastline

    Science.gov (United States)

    Leonardi, Nicoletta; Plater, Andrew James

    2017-11-01

    The hydrodynamic and residual transport patterns arising from oscillating tidal motion have important consequences for the transport of sediments, and for the evolution of the shoreline, especially under macro- and meso-tidal conditions. For many locations there are significant uncertainties about residual currents and sediment transport characteristics, and their possible influence on the morphological evolution of the coastline and on the character of the bed. Herein we use the coastline of SE England as a test case to investigate possible changes in residual currents, and residual transport patterns from neap to spring tide, the reciprocal interaction between residuals and the character of the bed, and the morphological evolution of the coastline at a century timescale. We found that in the long term the morphology of the system evolves toward a dynamic equilibrium configuration characterized by smaller, and spatially constant residual transport patterns. While the spatial distribution of residual currents maintains a similar trend during both neap and spring tide, during spring tide and for large areas residual currents switch between northerly and southerly directions, and their magnitude is doubled. Residual eddies develop in regions characterized by the presence of sand bars due to the interaction of the tide with the varying topography. Residual transport patterns are also computed for various sediment fractions, and based on the hydrodynamics and sediment availability at the bottom. We found that the distribution of sediments on the bed is significantly correlated with the intensity of residuals. Finally, the majority of long-term morphological changes tend to develop or augment sand banks features, with an increase in elevation and steepening of the bank contours.

  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

    OpenAIRE

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

    2015-01-01

    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 gra...

  7. Alternatives to crop residues for soil amendment

    OpenAIRE

    Powell, J.M.; Unger, P.W.

    1997-01-01

    Metadata only record In semiarid agroecosystems, crop residues can provide important benefits of soil and water conservation, nutrient cycling, and improved subsequent crop yields. However, there are frequently multiple competing uses for residues, including animal forage, fuel, and construction material. This chapter discusses the various uses of crop residues and examines alternative soil amendments when crop residues cannot be left on the soil.

  8. 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

    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......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......, 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...

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

    International Nuclear Information System (INIS)

    Donaldson, Stephanie B.; Bonington, Suzanne C.; Kershaw, Lucy E.; Cowan, Richard; Lyons, Jeanette; Elliott, Tony; Carrington, Bernadette M.

    2013-01-01

    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 2 -weighted MRI scans. Data were analysed semi-quantitatively and with a two-compartment exchange model to obtain parameters including relative signal intensity (rSI 80s ) and plasma perfusion (F 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 80s and F p were significantly higher in areas of residual tumour than Tr-Eff (rSI 80s = 2.9 vs 1.7, p < 0.001; F 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 80s ), 60% and 86% (F 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

  10. 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.

  11. Dynamic Biological Functioning Important for Simulating and Stabilizing Ocean Biogeochemistry

    Science.gov (United States)

    Buchanan, P. J.; Matear, R. J.; Chase, Z.; Phipps, S. J.; Bindoff, N. L.

    2018-04-01

    The biogeochemistry of the ocean exerts a strong influence on the climate by modulating atmospheric greenhouse gases. In turn, ocean biogeochemistry depends on numerous physical and biological processes that change over space and time. Accurately simulating these processes is fundamental for accurately simulating the ocean's role within the climate. However, our simulation of these processes is often simplistic, despite a growing understanding of underlying biological dynamics. Here we explore how new parameterizations of biological processes affect simulated biogeochemical properties in a global ocean model. We combine 6 different physical realizations with 6 different biogeochemical parameterizations (36 unique ocean states). The biogeochemical parameterizations, all previously published, aim to more accurately represent the response of ocean biology to changing physical conditions. We make three major findings. First, oxygen, carbon, alkalinity, and phosphate fields are more sensitive to changes in the ocean's physical state. Only nitrate is more sensitive to changes in biological processes, and we suggest that assessment protocols for ocean biogeochemical models formally include the marine nitrogen cycle to assess their performance. Second, we show that dynamic variations in the production, remineralization, and stoichiometry of organic matter in response to changing environmental conditions benefit the simulation of ocean biogeochemistry. Third, dynamic biological functioning reduces the sensitivity of biogeochemical properties to physical change. Carbon and nitrogen inventories were 50% and 20% less sensitive to physical changes, respectively, in simulations that incorporated dynamic biological functioning. These results highlight the importance of a dynamic biology for ocean properties and climate.

  12. Contribution of the residue at position 4 within classical nuclear localization signals to modulating interaction with importins and nuclear targeting.

    Science.gov (United States)

    Smith, Kate M; Di Antonio, Veronica; Bellucci, Luca; Thomas, David R; Caporuscio, Fabiana; Ciccarese, Francesco; Ghassabian, Hanieh; Wagstaff, Kylie M; Forwood, Jade K; Jans, David A; Palù, Giorgio; Alvisi, Gualtiero

    2018-08-01

    Nuclear import involves the recognition by importin (IMP) superfamily members of nuclear localization signals (NLSs) within protein cargoes destined for the nucleus, the best understood being recognition of classical NLSs (cNLSs) by the IMPα/β1 heterodimer. Although the cNLS consensus [K-(K/R)-X-(K/R) for positions P2-P5] is generally accepted, recent studies indicated that the contribution made by different residues at the P4 position can vary. Here, we apply a combination of microscopy, molecular dynamics, crystallography, in vitro binding, and bioinformatics approaches to show that the nature of residues at P4 indeed modulates cNLS function in the context of a prototypical Simian Virus 40 large tumor antigen-derived cNLS (KKRK, P2-5). Indeed, all hydrophobic substitutions in place of R impaired binding to IMPα and nuclear targeting, with the largest effect exerted by a G residue at P4. Substitution of R with neutral hydrophobic residues caused the loss of electrostatic and van der Waals interactions between the P4 residue side chains and IMPα. Detailed bioinformatics analysis confirmed the importance of the P4 residue for cNLS function across the human proteome, with specific residues such as G being associated with low activity. Furthermore, we validate our findings for two additional cNLSs from human cytomegalovirus (HCMV) DNA polymerase catalytic subunit UL54 and processivity factor UL44, where a G residue at P4 results in a 2-3-fold decrease in NLS activity. Our results thus showed that the P4 residue makes a hitherto poorly appreciated contribution to nuclear import efficiency, which is essential to determining the precise nuclear levels of cargoes. Copyright © 2018 Elsevier B.V. All rights reserved.

  13. 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.

  14. Computation of point reactor dynamics equations with thermal feedback via weighted residue method

    International Nuclear Information System (INIS)

    Suo Changan; Liu Xiaoming

    1986-01-01

    Point reactor dynamics equations with six groups of delayed neutrons have been computed via weighted-residual method in which the delta function was taken as a weighting function, and the parabolic with or without exponential factor as a trial function respectively for an insertion of large or smaller reactivity. The reactivity inserted into core can be varied with time, including insertion in forms of step function, polynomials up to second power and sine function. A thermal feedback of single flow channel model was added in. The thermal equations concerned were treated by use of a backward difference technique. A WRK code has been worked out, including implementation of an automatic selection of time span based on an input of error requirement and of an automatic change between computation with large reactivity and that with smaller one. On the condition of power varied slowly and without feedback, the results are not sensitive to the selection of values of time span. At last, the comparison of relevant results has shown that the agreement is quite well

  15. On the fractional systems fault detection: a comparison between fractional and rational residual sensitivity

    International Nuclear Information System (INIS)

    Aoun, M.; Aribi, A.; Najar, S.; Abdelkrim, M.N.

    2011-01-01

    This paper shows the interest of extending the dynamic parity space fault detection method for fractional systems. Accordingly, a comparison between fractional and rational residual generators using the later method is presented. An analysis of fractional and rational residuals sensitivity shows the merits of the fractional residual generators. A numerical example illustrating the advantage of using fractional residual generators for fractional systems diagnosis is given.

  16. Microbial association with the dynamics of particulate organic carbon in response to the amendment of elevated CO2-derived wheat residue into a Mollisol.

    Science.gov (United States)

    Wang, Yanhong; Yu, Zhenhua; Li, Yansheng; Wang, Guanghua; Liu, Junjie; Liu, Judong; Liu, Xiaobing; Jin, Jian

    2017-12-31

    As the chemical quality of crop residue is likely to be affected by elevated CO 2 (eCO 2 ), residue amendments may influence soil organic carbon (SOC) sequestration. However, in Mollisols, the dynamics of the SOC fractions in response to amendment with wheat residue produced under eCO 2 and the corresponding microbial community composition remain unknown. Such investigation is essential to residue management, which affects the soil quality and productivity of future farming systems. To narrow this knowledge gap, 13 C-labeled shoot and root residue derived from ambient CO 2 (aCO 2 ) or eCO 2 were amended into Mollisols and incubated for 200days. The soil was sampled during the incubation period to determine the residue-C retained in the three SOC fractions, i.e., coarse intra-aggregate particulate organic C (coarse iPOC), fine iPOC and mineral-associated organic C (MOC). The soil bacterial community was assessed using a MiSeq sequencing instrument. The results showed that the increase in SOC concentrations attributable to the application of the wheat residue primarily occurred in the coarse iPOC fraction. Compared with the aCO 2 -derived shoot residue, the amendment of eCO 2 -derived shoot residue resulted in greater SOC concentrations, whereas no significant differences (P>0.05) were observed between the aCO 2 - and eCO 2 -derived roots. Principal coordinates analysis (PCoA) showed that the residue amendment significantly (P≤0.05) altered the bacterial community composition compared with the non-residue amendment. Additionally, the bacterial community in the aCO 2 -derived shoot treatment differed from those in the other residue treatments until day 200 of the incubation period. The eCO 2 -derived shoot treatment significantly increased (P≤0.05) the relative abundances of the genera Acidobacteriaceae_(Subgroup_1)_uncultured, Bryobacter, Candidatus_Solibacter, Gemmatimonas and Nitrosomonadaceae_uncultured, whereas the opposite trend was observed in Nonomuraea

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

    OpenAIRE

    Kaminski, Lina; Eichler, Jerry

    2010-01-01

    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...

  18. Tyrosine residues modification studied by MALDI-TOF mass spectrometry

    International Nuclear Information System (INIS)

    Santrucek, Jiri; Strohalm, Martin; Kadlcik, Vojtech; Hynek, Radovan; Kodicek, Milan

    2004-01-01

    Amino acid residue-specific reactivity in proteins is of great current interest in structural biology as it provides information about solvent accessibility and reactivity of the residue and, consequently, about protein structure and possible interactions. In the work presented tyrosine residues of three model proteins with known spatial structure are modified with two tyrosine-specific reagents: tetranitromethane and iodine. Modified proteins were specifically digested by proteases and the mass of resulting peptide fragments was determined using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. Our results show that there are only small differences in the extent of tyrosine residues modification by tetranitromethane and iodine. However, data dealing with accessibility of reactive residues obtained by chemical modifications are not completely identical with those obtained by nuclear magnetic resonance and X-ray crystallography. These interesting discrepancies can be caused by local molecular dynamics and/or by specific chemical structure of the residues surrounding

  19. Handling of Solid Residues

    International Nuclear Information System (INIS)

    Medina Bermudez, Clara Ines

    1999-01-01

    The topic of solid residues is specifically of great interest and concern for the authorities, institutions and community that identify in them a true threat against the human health and the atmosphere in the related with the aesthetic deterioration of the urban centers and of the natural landscape; in the proliferation of vectorial transmitters of illnesses and the effect on the biodiversity. Inside the wide spectrum of topics that they keep relationship with the environmental protection, the inadequate handling of solid residues and residues dangerous squatter an important line in the definition of political and practical environmentally sustainable. The industrial development and the population's growth have originated a continuous increase in the production of solid residues; of equal it forms, their composition day after day is more heterogeneous. The base for the good handling includes the appropriate intervention of the different stages of an integral administration of residues, which include the separation in the source, the gathering, the handling, the use, treatment, final disposition and the institutional organization of the administration. The topic of the dangerous residues generates more expectation. These residues understand from those of pathogen type that are generated in the establishments of health that of hospital attention, until those of combustible, inflammable type, explosive, radio-active, volatile, corrosive, reagent or toxic, associated to numerous industrial processes, common in our countries in development

  20. Fission fragment distributions within dynamical approach

    Energy Technology Data Exchange (ETDEWEB)

    Mazurek, K. [Institute of Nuclear, Physics Polish Academy of Sciences, Krakow (Poland); Nadtochy, P.N. [Omsk State Technical University, Omsk (Russian Federation); Ryabov, E.G.; Adeev, G.D. [Omsk State University, Physics Department, Omsk (Russian Federation)

    2017-04-15

    The review covers recent developments and achievements in the dynamical description of fission process at high excitation energy. It is shown that the dynamical approach based on multidimensional Langevin equations combined with the statistical description of nuclear decay by particles evaporation is capable of fairly well describing the formation of fission fragment mass-energy, charge, and angular distributions of fission fragments in coincidence with the pre- and post-scission particle emission. The final yields of fission and evaporation residues channels products could be obtained. The detailed description of fission dynamics allows studying different stages of fission process, indicating the most important ingredients governing fission process and studying in detail such fundamental nuclear properties as nuclear viscosity and fission timescale. The tasks and perspectives of multidimensional dynamical approach are also discussed. (orig.)

  1. 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.

  2. Dissipation and residues of emamectin benzoate in cabbage.

    Science.gov (United States)

    Liu, Shuaigang; Zhang, Fengzu; Wang, Lei; Pan, Canping

    2012-09-01

    Emamectin benzoate residue dynamics and final residues in supervised field trials at GAP conditions were studied. An HPLC-MS analytical method for the determination of emamectin benzoate in cabbage and soil was developed. The recoveries of emamectin benzoate on cabbage and soil were observed from 71% to 102% at fortification levels of 0.01, 0.1 and 1.0 mg/kg. The reported limit of quantification (LOQ) was found to be 0.01 mg/kg. The dissipation experiments showed the half-lives (T(1/2)) of emamectin benzoate was around 1 days. At pre-harvest intervals (PHI) of 7 and 12 days, emamectin benzoate residue was observed to be below the LOQ.

  3. Combining protein sequence, structure, and dynamics: A novel approach for functional evolution analysis of PAS domain superfamily.

    Science.gov (United States)

    Dong, Zheng; Zhou, Hongyu; Tao, Peng

    2018-02-01

    PAS domains are widespread in archaea, bacteria, and eukaryota, and play important roles in various functions. In this study, we aim to explore functional evolutionary relationship among proteins in the PAS domain superfamily in view of the sequence-structure-dynamics-function relationship. We collected protein sequences and crystal structure data from RCSB Protein Data Bank of the PAS domain superfamily belonging to three biological functions (nucleotide binding, photoreceptor activity, and transferase activity). Protein sequences were aligned and then used to select sequence-conserved residues and build phylogenetic tree. Three-dimensional structure alignment was also applied to obtain structure-conserved residues. The protein dynamics were analyzed using elastic network model (ENM) and validated by molecular dynamics (MD) simulation. The result showed that the proteins with same function could be grouped by sequence similarity, and proteins in different functional groups displayed statistically significant difference in their vibrational patterns. Interestingly, in all three functional groups, conserved amino acid residues identified by sequence and structure conservation analysis generally have a lower fluctuation than other residues. In addition, the fluctuation of conserved residues in each biological function group was strongly correlated with the corresponding biological function. This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics. This is a new attempt to delineate functional evolution of proteins using the integrated information of sequence, structure, and dynamics. © 2017 The Protein Society.

  4. 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

    2017-08-01

    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

  5. 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.

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

    International Nuclear Information System (INIS)

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

    2009-01-01

    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.

  7. Entropy Transfer between Residue Pairs and Allostery in Proteins: Quantifying Allosteric Communication in Ubiquitin.

    Directory of Open Access Journals (Sweden)

    Aysima Hacisuleyman

    2017-01-01

    Full Text Available It has recently been proposed by Gunasakaran et al. that allostery may be an intrinsic property of all proteins. Here, we develop a computational method that can determine and quantify allosteric activity in any given protein. Based on Schreiber's transfer entropy formulation, our approach leads to an information transfer landscape for the protein that shows the presence of entropy sinks and sources and explains how pairs of residues communicate with each other using entropy transfer. The model can identify the residues that drive the fluctuations of others. We apply the model to Ubiquitin, whose allosteric activity has not been emphasized until recently, and show that there are indeed systematic pathways of entropy and information transfer between residues that correlate well with the activities of the protein. We use 600 nanosecond molecular dynamics trajectories for Ubiquitin and its complex with human polymerase iota and evaluate entropy transfer between all pairs of residues of Ubiquitin and quantify the binding susceptibility changes upon complex formation. We explain the complex formation propensities of Ubiquitin in terms of entropy transfer. Important residues taking part in allosteric communication in Ubiquitin predicted by our approach are in agreement with results of NMR relaxation dispersion experiments. Finally, we show that time delayed correlation of fluctuations of two interacting residues possesses an intrinsic causality that tells which residue controls the interaction and which one is controlled. Our work shows that time delayed correlations, entropy transfer and causality are the required new concepts for explaining allosteric communication in proteins.

  8. Entropy Transfer between Residue Pairs and Allostery in Proteins: Quantifying Allosteric Communication in Ubiquitin.

    Science.gov (United States)

    Hacisuleyman, Aysima; Erman, Burak

    2017-01-01

    It has recently been proposed by Gunasakaran et al. that allostery may be an intrinsic property of all proteins. Here, we develop a computational method that can determine and quantify allosteric activity in any given protein. Based on Schreiber's transfer entropy formulation, our approach leads to an information transfer landscape for the protein that shows the presence of entropy sinks and sources and explains how pairs of residues communicate with each other using entropy transfer. The model can identify the residues that drive the fluctuations of others. We apply the model to Ubiquitin, whose allosteric activity has not been emphasized until recently, and show that there are indeed systematic pathways of entropy and information transfer between residues that correlate well with the activities of the protein. We use 600 nanosecond molecular dynamics trajectories for Ubiquitin and its complex with human polymerase iota and evaluate entropy transfer between all pairs of residues of Ubiquitin and quantify the binding susceptibility changes upon complex formation. We explain the complex formation propensities of Ubiquitin in terms of entropy transfer. Important residues taking part in allosteric communication in Ubiquitin predicted by our approach are in agreement with results of NMR relaxation dispersion experiments. Finally, we show that time delayed correlation of fluctuations of two interacting residues possesses an intrinsic causality that tells which residue controls the interaction and which one is controlled. Our work shows that time delayed correlations, entropy transfer and causality are the required new concepts for explaining allosteric communication in proteins.

  9. Residual nilpotence and residual solubility of groups

    International Nuclear Information System (INIS)

    Mikhailov, R V

    2005-01-01

    The properties of the residual nilpotence and the residual solubility of groups are studied. The main objects under investigation are the class of residually nilpotent groups such that each central extension of these groups is also residually nilpotent and the class of residually soluble groups such that each Abelian extension of these groups is residually soluble. Various examples of groups not belonging to these classes are constructed by homological methods and methods of the theory of modules over group rings. Several applications of the theory under consideration are presented and problems concerning the residual nilpotence of one-relator groups are considered.

  10. Earthworms and Plant Residues Modify Nematodes in Tropical Cropping Soils (Madagascar): A Mesocosm Experiment

    International Nuclear Information System (INIS)

    Villenave, C.; Kichenin, E.; Djigal, D.; Blanchart, E.; Rabary, B.; Djigal, D.

    2010-01-01

    Free-living nematodes present several characteristics that have led to their use as bio indicators 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.

  11. 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.

  12. Residual stress concerns in containment analysis

    International Nuclear Information System (INIS)

    Costantini, F.; Kulak, R. F.; Pfeiffer, P. A.

    1997-01-01

    The manufacturing of steel containment vessels starts with the forming of flat plates into curved plates. A steel containment structure is made by welding individual plates together to form the sections that make up the complex shaped vessels. The metal forming and welding process leaves residual stresses in the vessel walls. Generally, the effect of metal forming residual stresses can be reduced or virtually eliminated by thermally stress relieving the vesseL In large containment vessels this may not be practical and thus the residual stresses due to manufacturing may become important. The residual stresses could possibly tiect the response of the vessel to internal pressurization. When the level of residual stresses is significant it will affect the vessel's response, for instance the yielding pressure and possibly the failure pressure. The paper will address the effect of metal forming residual stresses on the response of a generic pressure vessel to internal pressurization. A scoping analysis investigated the effect of residual forming stresses on the response of an internally pressurized vessel. A simple model was developed to gain understanding of the mechanics of the problem. Residual stresses due to the welding process were not considered in this investigation

  13. 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

  14. Liquid chromatography-electrospray ionization tandem mass spectrometry and dynamic multiple reaction monitoring method for determining multiple pesticide residues in tomato.

    Science.gov (United States)

    Andrade, G C R M; Monteiro, S H; Francisco, J G; Figueiredo, L A; Botelho, R G; Tornisielo, V L

    2015-05-15

    A quick and sensitive liquid chromatography-electrospray ionization tandem mass spectrometry method, using dynamic multiple reaction monitoring and a 1.8-μm particle size analytical column, was developed to determine 57 pesticides in tomato in a 13-min run. QuEChERS (quick, easy, cheap, effective, rugged, and safe) method for samples preparations and validations was carried out in compliance with EU SANCO guidelines. The method was applied to 58 tomato samples. More than 84% of the compounds investigated showed limits of detection equal to or lower than 5 mg kg(-1). A mild (50%) matrix effect was observed for 72%, 25%, and 3% of the pesticides studied, respectively. Eighty-one percent of the pesticides showed recoveries ranging between 70% and 120%. Twelve pesticides were detected in 35 samples, all below the maximum residue levels permitted in the Brazilian legislation; 15 samples exceeded the maximum residue levels established by the EU legislation for methamidophos; and 10 exceeded limits for acephate and four for bromuconazole. Copyright © 2014 Elsevier Ltd. All rights reserved.

  15. Evaporation channel as a tool to study fission dynamics

    Science.gov (United States)

    Di Nitto, A.; Vardaci, E.; La Rana, G.; Nadtochy, P. N.; Prete, G.

    2018-03-01

    The dynamics of the fission process is expected to affect the evaporation residue cross section because of the fission hindrance due to the nuclear viscosity. Systems of intermediate fissility constitute a suitable environment for testing such hypothesis since they are characterized by evaporation residue cross sections comparable or larger than the fission ones. Observables related to emitted charged particles, due to their relatively high emission probability, can be used to put stringent constraints on models describing the excited nucleus decay and to recognize the effects of fission dynamics. In this work model simulations are compared with the experimental data collected via the 32S +100 Mo reaction at Elab = 200 MeV. Consequently we pointed out, exploring an extended set of evaporation channel observables, the limits of the statistical model and the large improvement obtained with a dynamical model. Moreover we stress the importance of using an apparatus covering a large fraction of 4π to extract observables. Finally, we discuss the opportunity to measure more sensitive observables by a new detection device in operation at LNL.

  16. 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.

  17. Prediction of residual stress distributions due to surface machining and welding and crack growth simulation under residual stress distribution

    International Nuclear Information System (INIS)

    Ihara, Ryohei; Katsuyama, JInya; Onizawa, Kunio; Hashimoto, Tadafumi; Mikami, Yoshiki; Mochizuki, Masahito

    2011-01-01

    Research highlights: → Residual stress distributions due to welding and machining are evaluated by XRD and FEM. → Residual stress due to machining shows higher tensile stress than welding near the surface. → Crack growth analysis is performed using calculated residual stress. → Crack growth result is affected machining rather than welding. → Machining is an important factor for crack growth. - Abstract: In nuclear power plants, stress corrosion cracking (SCC) has been observed near the weld zone of the core shroud and primary loop recirculation (PLR) pipes made of low-carbon austenitic stainless steel Type 316L. The joining process of pipes usually includes surface machining and welding. Both processes induce residual stresses, and residual stresses are thus important factors in the occurrence and propagation of SCC. In this study, the finite element method (FEM) was used to estimate residual stress distributions generated by butt welding and surface machining. The thermoelastic-plastic analysis was performed for the welding simulation, and the thermo-mechanical coupled analysis based on the Johnson-Cook material model was performed for the surface machining simulation. In addition, a crack growth analysis based on the stress intensity factor (SIF) calculation was performed using the calculated residual stress distributions that are generated by welding and surface machining. The surface machining analysis showed that tensile residual stress due to surface machining only exists approximately 0.2 mm from the machined surface, and the surface residual stress increases with cutting speed. The crack growth analysis showed that the crack depth is affected by both surface machining and welding, and the crack length is more affected by surface machining than by welding.

  18. Extracting protein dynamics information from overlapped NMR signals using relaxation dispersion difference NMR spectroscopy.

    Science.gov (United States)

    Konuma, Tsuyoshi; Harada, Erisa; Sugase, Kenji

    2015-12-01

    Protein dynamics plays important roles in many biological events, such as ligand binding and enzyme reactions. NMR is mostly used for investigating such protein dynamics in a site-specific manner. Recently, NMR has been actively applied to large proteins and intrinsically disordered proteins, which are attractive research targets. However, signal overlap, which is often observed for such proteins, hampers accurate analysis of NMR data. In this study, we have developed a new methodology called relaxation dispersion difference that can extract conformational exchange parameters from overlapped NMR signals measured using relaxation dispersion spectroscopy. In relaxation dispersion measurements, the signal intensities of fluctuating residues vary according to the Carr-Purcell-Meiboon-Gill pulsing interval, whereas those of non-fluctuating residues are constant. Therefore, subtraction of each relaxation dispersion spectrum from that with the highest signal intensities, measured at the shortest pulsing interval, leaves only the signals of the fluctuating residues. This is the principle of the relaxation dispersion difference method. This new method enabled us to extract exchange parameters from overlapped signals of heme oxygenase-1, which is a relatively large protein. The results indicate that the structural flexibility of a kink in the heme-binding site is important for efficient heme binding. Relaxation dispersion difference requires neither selectively labeled samples nor modification of pulse programs; thus it will have wide applications in protein dynamics analysis.

  19. Extracting protein dynamics information from overlapped NMR signals using relaxation dispersion difference NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Konuma, Tsuyoshi [Icahn School of Medicine at Mount Sinai, Department of Structural and Chemical Biology (United States); Harada, Erisa [Suntory Foundation for Life Sciences, Bioorganic Research Institute (Japan); Sugase, Kenji, E-mail: sugase@sunbor.or.jp, E-mail: sugase@moleng.kyoto-u.ac.jp [Kyoto University, Department of Molecular Engineering, Graduate School of Engineering (Japan)

    2015-12-15

    Protein dynamics plays important roles in many biological events, such as ligand binding and enzyme reactions. NMR is mostly used for investigating such protein dynamics in a site-specific manner. Recently, NMR has been actively applied to large proteins and intrinsically disordered proteins, which are attractive research targets. However, signal overlap, which is often observed for such proteins, hampers accurate analysis of NMR data. In this study, we have developed a new methodology called relaxation dispersion difference that can extract conformational exchange parameters from overlapped NMR signals measured using relaxation dispersion spectroscopy. In relaxation dispersion measurements, the signal intensities of fluctuating residues vary according to the Carr-Purcell-Meiboon-Gill pulsing interval, whereas those of non-fluctuating residues are constant. Therefore, subtraction of each relaxation dispersion spectrum from that with the highest signal intensities, measured at the shortest pulsing interval, leaves only the signals of the fluctuating residues. This is the principle of the relaxation dispersion difference method. This new method enabled us to extract exchange parameters from overlapped signals of heme oxygenase-1, which is a relatively large protein. The results indicate that the structural flexibility of a kink in the heme-binding site is important for efficient heme binding. Relaxation dispersion difference requires neither selectively labeled samples nor modification of pulse programs; thus it will have wide applications in protein dynamics analysis.

  20. Management of NORM Residues

    International Nuclear Information System (INIS)

    2013-06-01

    The IAEA attaches great importance to the dissemination of information that can assist Member States in the development, implementation, maintenance and continuous improvement of systems, programmes and activities that support the nuclear fuel cycle and nuclear applications, and that address the legacy of past practices and accidents. However, radioactive residues are found not only in nuclear fuel cycle activities, but also in a range of other industrial activities, including: - Mining and milling of metalliferous and non-metallic ores; - Production of non-nuclear fuels, including coal, oil and gas; - Extraction and purification of water (e.g. in the generation of geothermal energy, as drinking and industrial process water; in paper and pulp manufacturing processes); - Production of industrial minerals, including phosphate, clay and building materials; - Use of radionuclides, such as thorium, for properties other than their radioactivity. Naturally occurring radioactive material (NORM) may lead to exposures at some stage of these processes and in the use or reuse of products, residues or wastes. Several IAEA publications address NORM issues with a special focus on some of the more relevant industrial operations. This publication attempts to provide guidance on managing residues arising from different NORM type industries, and on pertinent residue management strategies and technologies, to help Member States gain perspectives on the management of NORM residues

  1. 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.

  2. Important to investigate the dynamics of the stigma process.

    Science.gov (United States)

    Angermeyer, Matthias

    2004-01-01

    Studies have shown that the stigma of the most common mental disorder, namely depression, expose people with these disorders to a substantial amount of stigmatization in the workplace. Apart from the descriptive assessment of the magnitude of stigma, it is also important to investigate the dynamics of the stigma process. Agreeing with Dr. Stuart, three approaches to research on stigma and the workplace are proposed. The first is the dimension of social stigma, i.e., knowledge, attitudes and practices of employers. The second is the perspectives of the patients, i.e., self- stigmatization. The third is legal and policy frameworks, i.e., structural discrimination.

  3. Computational Prediction of Hot Spot Residues

    Science.gov (United States)

    Morrow, John Kenneth; Zhang, Shuxing

    2013-01-01

    Most biological processes involve multiple proteins interacting with each other. It has been recently discovered that certain residues in these protein-protein interactions, which are called hot spots, contribute more significantly to binding affinity than others. Hot spot residues have unique and diverse energetic properties that make them challenging yet important targets in the modulation of protein-protein complexes. Design of therapeutic agents that interact with hot spot residues has proven to be a valid methodology in disrupting unwanted protein-protein interactions. Using biological methods to determine which residues are hot spots can be costly and time consuming. Recent advances in computational approaches to predict hot spots have incorporated a myriad of features, and have shown increasing predictive successes. Here we review the state of knowledge around protein-protein interactions, hot spots, and give an overview of multiple in silico prediction techniques of hot spot residues. PMID:22316154

  4. Problems with Excessive Residual Lower Leg Length in Pediatric Amputees

    Science.gov (United States)

    Osebold, William R; Lester, Edward L; Christenson, Donald M

    2001-01-01

    We studied six pediatric amputees with long below-knee residual limbs, in order to delineate their functional and prosthetic situations, specifically in relation to problems with fitting for dynamic-response prosthetic feet. Three patients had congenital pseudoarthrosis of the tibia secondary to neurofibromatosis, one had fibular hemimelia, one had a traumatic amputation, and one had amputation secondary to burns. Five patients had Syme's amputations, one had a Boyd amputation. Ages at amputation ranged from nine months to five years (average age 3 years 1 month). After amputation, the long residual below-knee limbs allowed fitting with only the lowest-profile prostheses, such as deflection plates. In three patients, the femoral dome to tibial plafond length was greater on the amputated side than on the normal side. To allow room for more dynamic-response (and larger) foot prostheses, two patients have undergone proximal and distal tibial-fibular epiphyseodeses (one at age 5 years 10 months, the other at 3 years 7 months) and one had a proximal tibial-fibular epiphyseodesis at age 7 years 10 months. (All three patients are still skeletally immature.) The families of two other patients are considering epiphyseodeses, and one patient is not a candidate (skeletally mature). Scanogram data indicate that at skeletal maturity the epiphyseodesed patients will have adequate length distal to their residual limbs to fit larger and more dynamic-response prosthetic feet. PMID:11813953

  5. 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.

  6. Importance of the content and localization of tyrosine residues for thyroxine formation within the N-terminal part of human thyroglobulin

    NARCIS (Netherlands)

    den Hartog, M. T.; Sijmons, C. C.; Bakker, O.; Ris-Stalpers, C.; de Vijlder, J. J.

    1995-01-01

    Thyroxine (T4) is formed by coupling of iodinated tyrosine residues within thyroglobulin (TG). In mature TG, some iodinated tyrosine residues are involved preferentially in T4 formation. In order to investigate the specific role of various tyrosine residues in T4 formation, N-terminal TG fragments

  7. Hydrogen bond strengths in phosphorylated and sulfated amino acid residues.

    Directory of Open Access Journals (Sweden)

    Chaya Rapp

    Full Text Available Post-translational modification by the addition of an oxoanion functional group, usually a phosphate group and less commonly a sulfate group, leads to diverse structural and functional consequences in protein systems. Building upon previous studies of the phosphoserine residue (pSer, we address the distinct nature of hydrogen bonding interactions in phosphotyrosine (pTyr and sulfotyrosine (sTyr residues. We derive partial charges for these modified residues and then study them in the context of molecular dynamics simulation of model tripeptides and sulfated protein complexes, potentials of mean force for interacting residue pairs, and a survey of the interactions of modified residues among experimental protein structures. Overall, our findings show that for pTyr, bidentate interactions with Arg are particularly dominant, as has been previously demonstrated for pSer. sTyr interactions with Arg are significantly weaker, even as compared to the same interactions made by the Glu residue. Our work sheds light on the distinct nature of these modified tyrosine residues, and provides a physical-chemical foundation for future studies with the goal of understanding their roles in systems of biological interest.

  8. 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.

  9. The importance of correct specification of tribological parameters in dynamical systems modelling

    Science.gov (United States)

    Alaci, S.; Ciornei, F. C.; Romanu, I. C.; Ciornei, M. C.

    2018-01-01

    When modelling the behaviour of dynamical systems, the friction phenomenon cannot be neglected. Dry and fluid friction may occur, but dry friction has more severe effects upon the behaviour of the systems, based on the fact that the introduced discontinuities are more important. In the modelling of dynamical systems, dry friction is the main cause of occurrence of the bifurcation phenomenon. These aspects become more complex if, in the case of dry friction, static and dynamic frictions are put forward. The behaviour of a simple dynamical system is studied, consisting in a prismatic body linked to the ground by a spring, placed on a conveyor belt. The theoretical model is described by a nonlinear differential equation which after numerical integration leads to the conclusion that the steady motion of the prism is an un-damped oscillatory motion. The system was qualitatively modelled using specialised software for dynamical analysis. It was impractical to obtain a steady uniform translational motion of a rigid, therefore the conveyor belt was replaced by a metallic disc in uniform rotation motion. The attempts to compare the CAD model to the theoretical model were unsuccessful because the efforts of selecting the tribological parameters directed to the conclusion that the motion of the prism is a damped oscillation. To decide which of the methods depicts reality, a test-rig was assembled and it indicated a sustained oscillation. The conclusion is that the model employed by the dynamical analysis software cannot describe the actual model and a more complex model is required in the description of the friction phenomenon.

  10. 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. Copyright © 2014 Elsevier Ltd. All rights reserved.

  11. Residues from waste incineration. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Astrup, T.; Juul Pedersen, A.; Hyks, J.; Frandsen, F.J.

    2009-08-15

    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)

  12. Fluorescence imaging to quantify crop residue cover

    Science.gov (United States)

    Daughtry, C. S. T.; Mcmurtrey, J. E., III; Chappelle, E. W.

    1994-01-01

    Crop residues, the portion of the crop left in the field after harvest, can be an important management factor in controlling soil erosion. Methods to quantify residue cover are needed that are rapid, accurate, and objective. Scenes with known amounts of crop residue were illuminated with long wave ultraviolet (UV) radiation and fluorescence images were recorded with an intensified video camera fitted with a 453 to 488 nm band pass filter. A light colored soil and a dark colored soil were used as background for the weathered soybean stems. Residue cover was determined by counting the proportion of the pixels in the image with fluorescence values greater than a threshold. Soil pixels had the lowest gray levels in the images. The values of the soybean residue pixels spanned nearly the full range of the 8-bit video data. Classification accuracies typically were within 3(absolute units) of measured cover values. Video imaging can provide an intuitive understanding of the fraction of the soil covered by residue.

  13. Impact of Corn Residue Removal on Crop and Soil Productivity

    Science.gov (United States)

    Johnson, J. M.; Wilhelm, W. W.; Hatfield, J. L.; Voorhees, W. B.; Linden, D.

    2003-12-01

    Over-reliance on imported fuels, increasing atmospheric levels of greenhouses and sustaining food production for a growing population are three of the most important problems facing society in the mid-term. The US Department of Energy and private enterprise are developing technology necessary to use high cellulose feedstock, such as crop residues, for ethanol production. Based on production levels, corn (Zea mays L.) residue has potential as a biofuel feedstock. Crop residues are a renewable and domestic fuel source, which can reduce the rate of fossil fuel use (both imported and domestic) and provide an additional farm commodity. Crop residues protect the soil from wind and water erosion, provide inputs to form soil organic matter (a critical component determining soil quality) and play a role in nutrient cycling. Crop residues impact radiation balance and energy fluxes and reduce evaporation. Therefore, the benefits of using crop residues as fuel, which removes crop residues from the field, must be balanced against negative environmental impacts (e.g. soil erosion), maintaining soil organic matter levels, and preserving or enhancing productivity. All ramifications of new management practices and crop uses must be explored and evaluated fully before an industry is established. There are limited numbers of long-term studies with soil and crop responses to residue removal that range from negative to negligible. The range of crop and soil responses to crop residue removal was attributed to interactions with climate, management and soil type. Within limits, corn residue can be harvested for ethanol production to provide a renewable, domestic source of energy feedstock that reduces greenhouse gases. Removal rates must vary based on regional yield, climatic conditions and cultural practices. Agronomists are challenged to develop a protocol (tool) for recommending maximum permissible removal rates that ensure sustained soil productivity.

  14. Intercepts and residues of Regge poles in a stochastic-field multiparticle theory

    International Nuclear Information System (INIS)

    Arnold, R.C.

    1976-01-01

    A dynamical theory of multiparticle amplitudes, based on a functional integral representation embodying collective long-range correlations, is applied to the calculation of Regge intercepts and residues. Poles arising in conventional multiperipheral models will characteristically be modified in three ways: promotion, renormalization, and a proliferation of dynamical secondary trajectories, reminiscent of dual models

  15. 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.

  16. CONTRIBUTIONS OF INTRACELLULAR IONS TO Kv CHANNEL VOLTAGE SENSOR DYNAMICS.

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    Samuel eGoodchild

    2012-06-01

    Full Text Available Voltage sensing domains of Kv channels control ionic conductance through coupling of the movement of charged residues in the S4 segment to conformational changes at the cytoplasmic region of the pore domain, that allow K+ ions to flow. Conformational transitions within the voltage sensing domain caused by changes in the applied voltage across the membrane field are coupled to the conducting pore region and the gating of ionic conductance. However, several other factors not directly linked to the voltage dependent movement of charged residues within the voltage sensor impact the dynamics of the voltage sensor, such as inactivation, ionic conductance, intracellular ion identity and block of the channel by intracellular ligands. The effect of intracellular ions on voltage sensor dynamics is of importance in the interpretation of gating current measurements and the physiology of pore/voltage sensor coupling. There is a significant amount of variability in the reported kinetics of voltage sensor deactivation kinetics of Kv channels attributed to different mechanisms such as open state stabilization, immobilization and relaxation processes of the voltage sensor. Here we separate these factors and focus on the causal role that intracellular ions can play in allosterically modulating the dynamics of Kv voltage sensor deactivation kinetics. These considerations are of critical importance in understanding the molecular determinants of the complete channel gating cycle from activation to deactivation.

  17. Computational study of the activity, dynamics, energetics and conformations of insulin analogues using molecular dynamics simulations: Application to hyperinsulinemia and the critical residue B26

    Directory of Open Access Journals (Sweden)

    Anastasios Papaioannou

    2017-09-01

    Full Text Available Due to the increasing prevalence of diabetes, finding therapeutic analogues for insulin has become an urgent issue. While many experimental studies have been performed towards this end, they have limited scope to examine all aspects of the effect of a mutation. Computational studies can help to overcome these limitations, however, relatively few studies that focus on insulin analogues have been performed to date. Here, we present a comprehensive computational study of insulin analogues—three mutant insulins that have been identified with hyperinsulinemia and three mutations on the critical B26 residue that exhibit similar binding affinity to the insulin receptor—using molecular dynamics simulations with the aim of predicting how mutations of insulin affect its activity, dynamics, energetics and conformations. The time evolution of the conformers is studied in long simulations. The probability density function and potential of mean force calculations are performed on each insulin analogue to unravel the effect of mutations on the dynamics and energetics of insulin activation. Our conformational study can decrypt the key features and molecular mechanisms that are responsible for an enhanced or reduced activity of an insulin analogue. We find two key results: 1 hyperinsulinemia may be due to the drastically reduced activity (and binding affinity of the mutant insulins. 2 Y26BS and Y26BE are promising therapeutic candidates for insulin as they are more active than WT-insulin. The analysis in this work can be readily applied to any set of mutations on insulin to guide development of more effective therapeutic analogues.

  18. Five important advances in hematopathology.

    Science.gov (United States)

    Shi, Min; Xiao, Ruobing; Woda, Bruce A; Yu, Hongbo

    2014-03-01

    Hematopathology is a dynamic field that has always been on the frontier of clinical research within the scope of pathology. Several recent developments in hematopathology will likely affect its practice clinically. To review 5 important recent advances in hematopathology: (1) detection and prognostic implication of MYC in diffuse large B-cell lymphomas, (2) determining origin and prognosis through immunoglobulin gene usage in mature B-cell neoplasms, (3)detecting minimal residual disease in multiple myeloma, (4) using genome-wide analysis in myelodysplastic syndromes, and (5) employing whole-genome sequencing in acute myeloid leukemias. Literature review and the authors' experiences in an academic center. These advances will bring hematopathology into a new molecular era and help us to better understand the molecular, pathologic mechanisms of lymphomas, leukemias, myelomas, and myelodysplastic syndromes. They will help us to identify diagnostic and prognostic markers and eventually provide new therapeutic targets and treatments for these diseases.

  19. Quantification of Drive-Response Relationships Between Residues During Protein Folding.

    Science.gov (United States)

    Qi, Yifei; Im, Wonpil

    2013-08-13

    Mutual correlation and cooperativity are commonly used to describe residue-residue interactions in protein folding/function. However, these metrics do not provide any information on the causality relationships between residues. Such drive-response relationships are poorly studied in protein folding/function and difficult to measure experimentally due to technical limitations. In this study, using the information theory transfer entropy (TE) that provides a direct measurement of causality between two times series, we have quantified the drive-response relationships between residues in the folding/unfolding processes of four small proteins generated by molecular dynamics simulations. Instead of using a time-averaged single TE value, the time-dependent TE is measured with the Q-scores based on residue-residue contacts and with the statistical significance analysis along the folding/unfolding processes. The TE analysis is able to identify the driving and responding residues that are different from the highly correlated residues revealed by the mutual information analysis. In general, the driving residues have more regular secondary structures, are more buried, and show greater effects on the protein stability as well as folding and unfolding rates. In addition, the dominant driving and responding residues from the TE analysis on the whole trajectory agree with those on a single folding event, demonstrating that the drive-response relationships are preserved in the non-equilibrium process. Our study provides detailed insights into the protein folding process and has potential applications in protein engineering and interpretation of time-dependent residue-based experimental observables for protein function.

  20. Importance of vegetation dynamics for future terrestrial carbon cycling

    International Nuclear Information System (INIS)

    Ahlström, Anders; Smith, Benjamin; Xia, Jianyang; Luo, Yiqi; Arneth, Almut

    2015-01-01

    Terrestrial ecosystems currently sequester about one third of anthropogenic CO 2 emissions each year, an important ecosystem service that dampens climate change. The future fate of this net uptake of CO 2 by land based ecosystems is highly uncertain. Most ecosystem models used to predict the future terrestrial carbon cycle share a common architecture, whereby carbon that enters the system as net primary production (NPP) is distributed to plant compartments, transferred to litter and soil through vegetation turnover and then re-emitted to the atmosphere in conjunction with soil decomposition. However, while all models represent the processes of NPP and soil decomposition, they vary greatly in their representations of vegetation turnover and the associated processes governing mortality, disturbance and biome shifts. Here we used a detailed second generation dynamic global vegetation model with advanced representation of vegetation growth and mortality, and the associated turnover. We apply an emulator that describes the carbon flows and pools exactly as in simulations with the full model. The emulator simulates ecosystem dynamics in response to 13 different climate or Earth system model simulations from the Coupled Model Intercomparison Project Phase 5 ensemble under RCP8.5 radiative forcing. By exchanging carbon cycle processes between these 13 simulations we quantified the relative roles of three main driving processes of the carbon cycle; (I) NPP, (II) vegetation dynamics and turnover and (III) soil decomposition, in terms of their contribution to future carbon (C) uptake uncertainties among the ensemble of climate change scenarios. We found that NPP, vegetation turnover (including structural shifts, wild fires and mortality) and soil decomposition rates explained 49%, 17% and 33%, respectively, of uncertainties in modelled global C-uptake. Uncertainty due to vegetation turnover was further partitioned into stand-clearing disturbances (16%), wild fires (0%), stand

  1. Evidence of a double-lid movement in Pseudomonas aeruginosa lipase: insights from molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Subbulakshmi Latha Cherukuvada

    2005-08-01

    Full Text Available Pseudomonas aeruginosa lipase is a 29-kDa protein that, following the determination of its crystal structure, was postulated to have a lid that stretched between residues 125 and 148. In this paper, using molecular dynamics simulations, we propose that there exists, in addition to the above-mentioned lid, a novel second lid in this lipase. We further show that the second lid, covering residues 210-222, acts as a triggering lid for the movement of the first. We also investigate the role of hydrophobicity in the movement of the lids and show that two residues, Phe214 and Ala217, play important roles in lid movement. To our knowledge, this is the first time that a double-lid movement of the type described in our manuscript has been presented to the scientific community. This work also elucidates the interplay of hydrophobic interactions in the dynamics, and hence the function, of an enzyme.

  2. CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area.

    Directory of Open Access Journals (Sweden)

    Genki Terashi

    Full Text Available Proteins are flexible, and this flexibility has an essential functional role. Flexibility can be observed in loop regions, rearrangements between secondary structure elements, and conformational changes between entire domains. However, most protein structure alignment methods treat protein structures as rigid bodies. Thus, these methods fail to identify the equivalences of residue pairs in regions with flexibility. In this study, we considered that the evolutionary relationship between proteins corresponds directly to the residue-residue physical contacts rather than the three-dimensional (3D coordinates of proteins. Thus, we developed a new protein structure alignment method, contact area-based alignment (CAB-align, which uses the residue-residue contact area to identify regions of similarity. The main purpose of CAB-align is to identify homologous relationships at the residue level between related protein structures. The CAB-align procedure comprises two main steps: First, a rigid-body alignment method based on local and global 3D structure superposition is employed to generate a sufficient number of initial alignments. Then, iterative dynamic programming is executed to find the optimal alignment. We evaluated the performance and advantages of CAB-align based on four main points: (1 agreement with the gold standard alignment, (2 alignment quality based on an evolutionary relationship without 3D coordinate superposition, (3 consistency of the multiple alignments, and (4 classification agreement with the gold standard classification. Comparisons of CAB-align with other state-of-the-art protein structure alignment methods (TM-align, FATCAT, and DaliLite using our benchmark dataset showed that CAB-align performed robustly in obtaining high-quality alignments and generating consistent multiple alignments with high coverage and accuracy rates, and it performed extremely well when discriminating between homologous and nonhomologous pairs of proteins

  3. CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area.

    Science.gov (United States)

    Terashi, Genki; Takeda-Shitaka, Mayuko

    2015-01-01

    Proteins are flexible, and this flexibility has an essential functional role. Flexibility can be observed in loop regions, rearrangements between secondary structure elements, and conformational changes between entire domains. However, most protein structure alignment methods treat protein structures as rigid bodies. Thus, these methods fail to identify the equivalences of residue pairs in regions with flexibility. In this study, we considered that the evolutionary relationship between proteins corresponds directly to the residue-residue physical contacts rather than the three-dimensional (3D) coordinates of proteins. Thus, we developed a new protein structure alignment method, contact area-based alignment (CAB-align), which uses the residue-residue contact area to identify regions of similarity. The main purpose of CAB-align is to identify homologous relationships at the residue level between related protein structures. The CAB-align procedure comprises two main steps: First, a rigid-body alignment method based on local and global 3D structure superposition is employed to generate a sufficient number of initial alignments. Then, iterative dynamic programming is executed to find the optimal alignment. We evaluated the performance and advantages of CAB-align based on four main points: (1) agreement with the gold standard alignment, (2) alignment quality based on an evolutionary relationship without 3D coordinate superposition, (3) consistency of the multiple alignments, and (4) classification agreement with the gold standard classification. Comparisons of CAB-align with other state-of-the-art protein structure alignment methods (TM-align, FATCAT, and DaliLite) using our benchmark dataset showed that CAB-align performed robustly in obtaining high-quality alignments and generating consistent multiple alignments with high coverage and accuracy rates, and it performed extremely well when discriminating between homologous and nonhomologous pairs of proteins in both

  4. Variation in one residue associated with the metal ion-dependent adhesion site regulates αIIbβ3 integrin ligand binding affinity.

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    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.

  5. 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

  6. Research Progress on Pesticide Residue Analysis Techniques in Agro-products

    Directory of Open Access Journals (Sweden)

    HE Ze-ying

    2016-07-01

    Full Text Available There are constant occurrences of acute pesticide poisoning among consumers and pesticide residue violations in agro-products import/export trading. Pesticide residue analysis is the important way to protect the food safety and the interest of import/export enterprises. There has been a rapid development in pesticide residue analysis techniques in recent years. In this review, the research progress in the past five years were discussed in the respects of samples preparation and instrument determination. The application, modification and development of the QuEChERS method in samples preparation and the application of tandem mass spectrometry and high resolution mass spectrometry were reviewed. And the implications for the future of the field were discussed.

  7. Computational prediction of protein hot spot residues.

    Science.gov (United States)

    Morrow, John Kenneth; Zhang, Shuxing

    2012-01-01

    Most biological processes involve multiple proteins interacting with each other. It has been recently discovered that certain residues in these protein-protein interactions, which are called hot spots, contribute more significantly to binding affinity than others. Hot spot residues have unique and diverse energetic properties that make them challenging yet important targets in the modulation of protein-protein complexes. Design of therapeutic agents that interact with hot spot residues has proven to be a valid methodology in disrupting unwanted protein-protein interactions. Using biological methods to determine which residues are hot spots can be costly and time consuming. Recent advances in computational approaches to predict hot spots have incorporated a myriad of features, and have shown increasing predictive successes. Here we review the state of knowledge around protein-protein interactions, hot spots, and give an overview of multiple in silico prediction techniques of hot spot residues.

  8. Removal of heavy metals from aqueous solution by Carrot residues

    International Nuclear Information System (INIS)

    Eslamzadeh, T.; Nasernejad, B.; Bonakdar Pour, B.; Zamani, A.; Esmaail-Beygi, M.

    2004-01-01

    The removal of Copper(II), Zinc(II), and Chromium (III) from wastewater by carrot residues was investigated to evaluate cation exchange capacity. The effects of solution P H and co-ions were studied in batch experiments. Adsorption equilibria were initially rapidly established, and then decreased markedly after 10 min. Column experiments were carried out in a glass column filled with carrot residues to evaluate the metal removal capacity. The influences of the feed concentration and feed rate were also studied in order to compare the dynamic capacity for metal binding in different feed concentrations

  9. Bovine pancreatic polypeptide (bPP) undergoes significant changes in conformation and dynamics upon binding to DPC micelles.

    Science.gov (United States)

    Lerch, Mirjam; Gafner, Verena; Bader, Reto; Christen, Barbara; Folkers, Gerd; Zerbe, Oliver

    2002-10-04

    The pancreatic polypeptide (PP), a 36-residue, C-terminally amidated polypeptide hormone is a member of the neuropeptide Y (NPY) family. Here, we have studied the structure and dynamics of bovine pancreatic polypeptide (bPP) when bound to DPC-micelles as a membrane-mimicking model as well as the dynamics of bPP in solution. The comparison of structure and dynamics of bPP in both states reveals remarkable differences. The overall correlation time of 5.08ns derived from the 15N relaxation data proves unambiguously that bPP in solution exists as a dimer. Therein, intermolecular as well as intramolecular hydrophobic interactions from residues of both the amphiphilic helix and of the back-folded N terminus contribute to the stability of the PP fold. The overall rigidity is well-reflected in positive values for the heteronuclear NOE for residues 4-34. The membrane-bound species displays a partitioning into a more flexible N-terminal region and a well-defined alpha-helical region comprising residues 17-31. The average RMSD value for residues 17-31 is 0.22(+/-0.09)A. The flexibility of the N terminus is compatible with negative values of the heteronuclear NOE observed for the N-terminal residues 4-12 and low values of the generalized order parameter S(2). The membrane-peptide interface was investigated by micelle-integrating spin-labels and H,2H exchange measurements. It is formed by those residues which make contacts between the C-terminal alpha-helix and the polyproline helix. In contrast to pNPY, also residues from the N terminus display spatial proximity to the membrane interface. Furthermore, the orientation of the C terminus, that presumably contains residues involved in receptor binding, is different in the two environments. We speculate that this pre-positioning of residues could be an important requirement for receptor activation. Moreover, we doubt that the PP fold is of functional relevance for binding at the Y(4) receptor.

  10. 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.

  11. Comparing Residue Clusters from Thermophilic and Mesophilic Enzymes Reveals Adaptive Mechanisms.

    Science.gov (United States)

    Sammond, Deanne W; Kastelowitz, Noah; Himmel, Michael E; Yin, Hang; Crowley, Michael F; Bomble, Yannick J

    2016-01-01

    Understanding how proteins adapt to function at high temperatures is important for deciphering the energetics that dictate protein stability and folding. While multiple principles important for thermostability have been identified, we lack a unified understanding of how internal protein structural and chemical environment determine qualitative or quantitative impact of evolutionary mutations. In this work we compare equivalent clusters of spatially neighboring residues between paired thermophilic and mesophilic homologues to evaluate adaptations under the selective pressure of high temperature. We find the residue clusters in thermophilic enzymes generally display improved atomic packing compared to mesophilic enzymes, in agreement with previous research. Unlike residue clusters from mesophilic enzymes, however, thermophilic residue clusters do not have significant cavities. In addition, anchor residues found in many clusters are highly conserved with respect to atomic packing between both thermophilic and mesophilic enzymes. Thus the improvements in atomic packing observed in thermophilic homologues are not derived from these anchor residues but from neighboring positions, which may serve to expand optimized protein core regions.

  12. Unveiling the Mechanism of Arginine Transport through AdiC with Molecular Dynamics Simulations: The Guiding Role of Aromatic Residues.

    Directory of Open Access Journals (Sweden)

    Eva-Maria Krammer

    Full Text Available Commensal and pathogenic enteric bacteria have developed several systems to adapt to proton leakage into the cytoplasm resulting from extreme acidic conditions. One such system involves arginine uptake followed by export of the decarboxylated product agmatine, carried out by the arginine/agmatine antiporter (AdiC, which thus works as a virtual proton pump. Here, using classical and targeted molecular dynamics, we investigated at the atomic level the mechanism of arginine transport through AdiC of E. coli. Overall, our MD simulation data clearly demonstrate that global rearrangements of several transmembrane segments are necessary but not sufficient for achieving transitions between structural states along the arginine translocation pathway. In particular, local structural changes, namely rotameric conversions of two aromatic residues, are needed to regulate access to both the outward- and inward-facing states. Our simulations have also enabled identification of a few residues, overwhelmingly aromatic, which are essential to guiding arginine in the course of its translocation. Most of them belong to gating elements whose coordinated motions contribute to the alternating access mechanism. Their conservation in all known E. coli acid resistance antiporters suggests that the transport mechanisms of these systems share common features. Last but not least, knowledge of the functional properties of AdiC can advance our understanding of the members of the amino acid-carbocation-polyamine superfamily, notably in eukaryotic cells.

  13. Crop residue decomposition in Minnesota biochar-amended plots

    Science.gov (United States)

    Weyers, S. L.; Spokas, K. A.

    2014-06-01

    Impacts of biochar application at laboratory scales are routinely studied, but impacts of biochar application on decomposition of crop residues at field scales have not been widely addressed. The priming or hindrance of crop residue decomposition could have a cascading impact on soil processes, particularly those influencing nutrient availability. Our objectives were to evaluate biochar effects on field decomposition of crop residue, using plots that were amended with biochars made from different plant-based feedstocks and pyrolysis platforms in the fall of 2008. Litterbags containing wheat straw material were buried in July of 2011 below the soil surface in a continuous-corn cropped field in plots that had received one of seven different biochar amendments or a uncharred wood-pellet amendment 2.5 yr prior to start of this study. Litterbags were collected over the course of 14 weeks. Microbial biomass was assessed in treatment plots the previous fall. Though first-order decomposition rate constants were positively correlated to microbial biomass, neither parameter was statistically affected by biochar or wood-pellet treatments. The findings indicated only a residual of potentially positive and negative initial impacts of biochars on residue decomposition, which fit in line with established feedstock and pyrolysis influences. Overall, these findings indicate that no significant alteration in the microbial dynamics of the soil decomposer communities occurred as a consequence of the application of plant-based biochars evaluated here.

  14. On the Structural Context and Identification of Enzyme Catalytic Residues

    Directory of Open Access Journals (Sweden)

    Yu-Tung Chien

    2013-01-01

    Full Text Available Enzymes play important roles in most of the biological processes. Although only a small fraction of residues are directly involved in catalytic reactions, these catalytic residues are the most crucial parts in enzymes. The study of the fundamental and unique features of catalytic residues benefits the understanding of enzyme functions and catalytic mechanisms. In this work, we analyze the structural context of catalytic residues based on theoretical and experimental structure flexibility. The results show that catalytic residues have distinct structural features and context. Their neighboring residues, whether sequence or structure neighbors within specific range, are usually structurally more rigid than those of noncatalytic residues. The structural context feature is combined with support vector machine to identify catalytic residues from enzyme structure. The prediction results are better or comparable to those of recent structure-based prediction methods.

  15. Intermolecular dynamics studied by paramagnetic tagging

    Energy Technology Data Exchange (ETDEWEB)

    Xu Xingfu; Keizers, Peter H. J. [Leiden University, Institute of Chemistry (Netherlands); Reinle, Wolfgang; Hannemann, Frank; Bernhardt, Rita [Universitaet des Saarlandes, Naturwissenschaftlich-Technische Fakultaet III, Institut fuer Biochemie (Germany); Ubbink, Marcellus [Leiden University, Institute of Chemistry (Netherlands)], E-mail: m.ubbink@chem.leidenuniv.nl

    2009-04-15

    Yeast cytochrome c and bovine adrenodoxin form a dynamic electron transfer complex, which is a pure encounter complex. It is demonstrated that the dynamic nature of the interaction can readily be probed by using a rigid lanthanide tag attached to cytochrome c. The tag, Caged Lanthanide NMR Probe 5, induces pseudocontact shifts and residual dipolar couplings and does not perturb the binding interface. Due to the dynamics in the complex, residual dipolar couplings in adrenodoxin are very small. Simulation shows that cytochrome c needs to sample a large part of the surface of adrenodoxin to explain the small degree of alignment observed for adrenodoxin. The applied method provides a simple and straightforward way to observe dynamics in protein complexes or domain-domain mobility without the need for external alignment media.

  16. Intermolecular dynamics studied by paramagnetic tagging

    International Nuclear Information System (INIS)

    Xu Xingfu; Keizers, Peter H. J.; Reinle, Wolfgang; Hannemann, Frank; Bernhardt, Rita; Ubbink, Marcellus

    2009-01-01

    Yeast cytochrome c and bovine adrenodoxin form a dynamic electron transfer complex, which is a pure encounter complex. It is demonstrated that the dynamic nature of the interaction can readily be probed by using a rigid lanthanide tag attached to cytochrome c. The tag, Caged Lanthanide NMR Probe 5, induces pseudocontact shifts and residual dipolar couplings and does not perturb the binding interface. Due to the dynamics in the complex, residual dipolar couplings in adrenodoxin are very small. Simulation shows that cytochrome c needs to sample a large part of the surface of adrenodoxin to explain the small degree of alignment observed for adrenodoxin. The applied method provides a simple and straightforward way to observe dynamics in protein complexes or domain-domain mobility without the need for external alignment media

  17. Residual Stress Analysis of Aircraft Part using Neutron Beam

    Energy Technology Data Exchange (ETDEWEB)

    Shin, Eun Joo; Seong, Baek Seok; Sim, Cheul Muu [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2012-05-15

    A precise measurement of the residual stress magnitude and distribution is an important factor to evaluate the lifetime or safety of the materials, because the residual stress affects the material properties, such as the strength, fatigue, etc. In the case of a fighter jet, the lifetime and safety of the parts of the landing gear are more important than that of a passenger airplane because of its frequent take offs and landings. In particular in the case of training a fighter jet, a precise evaluation of life time for the parts of the landing gear is strongly required for economic reason. In this study, the residual stress of a part of the landing gear of the training fighter jet which is used to fix the landing gear to the aircraft body was investigated. The part was used for 2000 hours of flight, which corresponds to 10 years. During this period, the fighter jet normally takes off and lands more than 2000 times. These frequent take off and landing can generate residual stress and cause a crack in the part. By measuring the neutron diffraction peaks, we evaluated the residual stress of the landing gear part

  18. Residual stresses analysis of friction stir welding using one-way FSI simulation

    International Nuclear Information System (INIS)

    Kang, Sung Wook; Jang, Beom Seon; Song, Ha Cheol

    2015-01-01

    When certain mechanisms, such as plastic deformations and temperature gradients, occur and are released in a structure, stresses remain because of the shape of the structure and external constraints. These stresses are referred to as residual stresses. The base material locally expands during heating in the welding process. When the welding is completed and cooled to room temperature, the residual stresses are left at nearly the yield strength level. In the case of friction stir welding, the maximum temperature is 80% to 90% of the melting point of the materials. Thus, the residual stresses in the welding process are smaller than those in other fusion welding processes; these stresses have not been considered previously. However, friction stir welding residual stresses are sometimes measured at approximately 70% or above. These residual stresses significantly affect fatigue behavior and lifetime. The present study investigates the residual stress distributions in various welding conditions and shapes of friction stir welding. In addition, the asymmetric feature is considered in temperature and residual stress distribution. Heat transfer analysis is conducted using the commercial computational fluid dynamics program Fluent, and results are used in the finite element structural analysis with the ANSYS Multiphysics software. The calculated residual stresses are compared with experimental values using the X-ray diffraction method.

  19. [The importance of C-terminal aspartic acid residue (D141) to the antirestriction activity of the ArdB (R64) protein].

    Science.gov (United States)

    Kudryavtseva, A A; Osetrova, M S; Livinyuk, V Ya; Manukhov, I V; Zavilgelsky, G B

    2017-01-01

    Antirestriction proteins of the ArdB/KlcA family are specific inhibitors of restriction (endonuclease) activity of type-I restriction/modification enzymes. The effect of conserved amino acid residues on the antirestriction activity of the ArdB protein encoded by the transmissible R64 (IncI1) plasmid has been investigated. An analysis of the amino acid sequences of ArdB homologues demonstrated the presence of four groups of conserved residues ((1) R16, E32, and W51; (2) Y46 and G48; (3) S81, D83 and E132, and (4) N77, L(I)140, and D141) on the surface of the protein globule. Amino acid residues of the fourth group showed a unique localization pattern with the terminal residue protruding beyond the globule surface. The replacement of two conserved amino acids (D141 and N77) located in the close vicinity of each other on the globule surface showed that the C-terminal D141 is essential for the antirestriction activity of ArdB. The deletion of this residue, as well as replacement by a hydrophobic threonine residue (D141T), completely abolished the antirestriction activity of ArdB. The synonymous replacement of D141 by a glutamic acid residue (D141E) caused an approximately 30-fold decrease of the antirestriction activity of ArdB, and the point mutation N77A caused an approximately 20-fold decrease in activity. The residues D141 and N77 located on the surface of the protein globule are presumably essential for the formation of a contact between ArdB and a currently unknown factor that modulates the activity of type-I restriction/modification enzymes.

  20. Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings.

    Science.gov (United States)

    Al-Hashimi, Hashim M; Gosser, Yuying; Gorin, Andrey; Hu, Weidong; Majumdar, Ananya; Patel, Dinshaw J

    2002-01-11

    Ground-state dynamics in RNA is a critical precursor for structural adaptation observed ubiquitously in protein-RNA recognition. A tertiary conformational analysis of the stem-loop structural element in the transactivation response element (TAR) from human immunodeficiency virus type 1 (HIV-I) RNA is presented using recently introduced NMR methods that rely on the measurement of residual dipolar couplings (RDC) in partially oriented systems. Order matrix analysis of RDC data provides evidence for inter-helical motions that are of amplitude 46(+/-4) degrees, of random directional character, and that are executed about an average conformation with an inter-helical angle between 44 degrees and 54 degrees. The generated ensemble of TAR conformations have different organizations of functional groups responsible for interaction with the trans-activator protein Tat, including conformations similar to the previously characterized bound-state conformation. These results demonstrate the utility of RDC-NMR for simultaneously characterizing RNA tertiary dynamics and average conformation, and indicate an avenue for TAR complex formation involving tertiary structure capture. Copyright 2001 Academic Press.

  1. Structural dynamics and quantum mechanical aspects of shikonin derivatives as CREBBP bromodomain inhibitors.

    Science.gov (United States)

    Mitra, Sarmistha; Dash, Raju

    2018-05-04

    The Proteins involved in the chemical modification of lysine residues in histone, is currently being excessively focused as the therapeutic target for the treatment of cell related diseases like cancer. Among these proteins, the epigenetic reader, CREB-binding protein (CREBBP) bromodomain is one of the most prominent targets for effective anticancer drug design, which is responsible for the reorganization of acetylated histone lysine residues. Therefore, this study employed an integrative approach of structure based drug design, in combination with Molecular Dynamics (MD) and QM/MM study to identify as well as to describe the binding mechanism of two shikonin derivatives, acetylshikonin and propionylshikonin as inhibitors of CREBBP bromodomain. Here induced fit docking strategy was employed to explore the important intrinsic interactions of ligands with CREBBP bromodomain, consistently molecular dynamics simulation with two different methods and binding energy calculations by MM-GBSA and MM-PBSA were adopted to determine the stability of intermolecular interactions between protein and ligands. The results showed that both these derivatives made direct contacts with the important conserved residues of the active site, where propionylshikonin demonstrated stronger binding and stability than acetylshikonin, according to molecular dynamics simulation and binding free energy calculations. Further, QM/MM energy calculation was employed to study the chemical reactivity of the propionylshikonin and also to describe the mechanism of non bonded interactions between the propionylshikonin and CREBBP bromodomain. Though this study demands in vitro and in vivo experiments to evaluate the efficiency of the compound, these insights would assist to design more potent CREBBP bromodomain inhibitor, guiding the site of modification of propionylshikonin moiety for designing selective inhibitors. Copyright © 2018 Elsevier Inc. All rights reserved.

  2. Residual stresses

    International Nuclear Information System (INIS)

    Sahotra, I.M.

    2006-01-01

    The principal effect of unloading a material strained into the plastic range is to create a permanent set (plastic deformation), which if restricted somehow, gives rise to a system of self-balancing within the same member or reaction balanced by other members of the structure., known as residual stresses. These stresses stay there as locked-in stresses, in the body or a part of it in the absence of any external loading. Residual stresses are induced during hot-rolling and welding differential cooling, cold-forming and extruding: cold straightening and spot heating, fabrication and forced fitting of components constraining the structure to a particular geometry. The areas which cool more quickly develop residual compressive stresses, while the slower cooling areas develop residual tensile stresses, and a self-balancing or reaction balanced system of residual stresses is formed. The phenomenon of residual stresses is the most challenging in its application in surface modification techniques determining endurance mechanism against fracture and fatigue failures. This paper discusses the mechanism of residual stresses, that how the residual stresses are fanned and what their behavior is under the action of external forces. Such as in the case of a circular bar under limit torque, rectangular beam under limt moment, reclaiming of shafts welds and peening etc. (author)

  3. Comparing Residue Clusters from Thermophilic and Mesophilic Enzymes Reveals Adaptive Mechanisms.

    Directory of Open Access Journals (Sweden)

    Deanne W Sammond

    Full Text Available Understanding how proteins adapt to function at high temperatures is important for deciphering the energetics that dictate protein stability and folding. While multiple principles important for thermostability have been identified, we lack a unified understanding of how internal protein structural and chemical environment determine qualitative or quantitative impact of evolutionary mutations. In this work we compare equivalent clusters of spatially neighboring residues between paired thermophilic and mesophilic homologues to evaluate adaptations under the selective pressure of high temperature. We find the residue clusters in thermophilic enzymes generally display improved atomic packing compared to mesophilic enzymes, in agreement with previous research. Unlike residue clusters from mesophilic enzymes, however, thermophilic residue clusters do not have significant cavities. In addition, anchor residues found in many clusters are highly conserved with respect to atomic packing between both thermophilic and mesophilic enzymes. Thus the improvements in atomic packing observed in thermophilic homologues are not derived from these anchor residues but from neighboring positions, which may serve to expand optimized protein core regions.

  4. Obtention of ceramic pigments with residue from electroplating

    International Nuclear Information System (INIS)

    Boss, A.; Kniess, C.T.; Aguiar, B.M. de; Prates, P.B.; Milanez, K.

    2011-01-01

    The incorporation of industrial residues in industrial processes opens up new business opportunities and reduces the volume of extraction of raw materials, preserving natural resources, which are limited. An important residue is the mud from galvanic industry, consisting of alkali and transition metals. According to NBR 10004/2004, this residue can be classified as Class I (hazardous), depending on the concentration of metals present in the mud. This paper proposes a method for reusing the residue from electroplating in ceramic pigments. The characterization of residual plating was obtained by chemical analysis, mineralogical analysis and pH measurements. The electroplating waste was incorporated in different percentages on a standard pigment formula of industrial ceramic, consisting mainly of Zn, Fe and Cr. The obtained pigments were applied in ceramic glazes to colorimetric and visual analysis, which showed good results with the addition of up to 15% of industrial waste. (author)

  5. Local dynamics of proteins and DNA evaluated from crystallographic B factors

    International Nuclear Information System (INIS)

    Schneider, Bohdan; Gelly, Jean-Christophe; Brevern, Alexandre G. de; Černý, Jiří

    2014-01-01

    Distributions of scaled B factors from 704 protein–DNA complexes reflect primarily the neighbourhood of amino-acid and nucleotide residues: their flexibility grows from the protein core to protein–protein and protein–DNA interfaces, to solvent-exposed residues. Some of the findings clearly observed at higher resolution structures can no longer be observed for structures at low resolution indicating problems in refinement protocols. The dynamics of protein and nucleic acid structures is as important as their average static picture. The local molecular dynamics concealed in diffraction images is expressed as so-called B factors. To find out how the crystal-derived B factors represent the dynamic behaviour of atoms and residues of proteins and DNA in their complexes, the distributions of scaled B factors from a carefully curated data set of over 700 protein–DNA crystal structures were analyzed [Schneider et al. (2014 ▶), Nucleic Acids Res.42, 3381–3394]. Amino acids and nucleotides were categorized based on their molecular neighbourhood as solvent-accessible, solvent-inaccessible (i.e. forming the protein core) or lying at protein–protein or protein–DNA interfaces; the backbone and side-chain atoms were analyzed separately. The B factors of two types of crystal-ordered water molecules were also analyzed. The analysis confirmed several expected features of protein and DNA dynamics, but also revealed surprising facts. Solvent-accessible amino acids have B factors that are larger than those of residues at the biomolecular interfaces, and core-forming amino acids are the most restricted in their movement. A unique feature of the latter group is that their side-chain and backbone atoms are restricted in their movement to the same extent; in all other amino-acid groups the side chains are more floppy than the backbone. The low values of the B factors of water molecules bridging proteins with DNA and the very large fluctuations of DNA phosphates are

  6. Local dynamics of proteins and DNA evaluated from crystallographic B factors

    Energy Technology Data Exchange (ETDEWEB)

    Schneider, Bohdan, E-mail: bohdan.schneider@gmail.com [Institute of Biotechnology AS CR, Videnska 1083, 142 20 Prague (Czech Republic); Gelly, Jean-Christophe; Brevern, Alexandre G. de [INSERM, U1134, DSIMB, 75739 Paris (France); Université Paris Diderot, Sorbonne Paris Cité, UMR-S 1134, 75739 Paris (France); Institut National de la Transfusion Sanguine (INTS), 75739 Paris (France); Laboratoire d’Excellence GR-Ex, 75739 Paris (France); Černý, Jiří [Institute of Biotechnology AS CR, Videnska 1083, 142 20 Prague (Czech Republic)

    2014-09-01

    Distributions of scaled B factors from 704 protein–DNA complexes reflect primarily the neighbourhood of amino-acid and nucleotide residues: their flexibility grows from the protein core to protein–protein and protein–DNA interfaces, to solvent-exposed residues. Some of the findings clearly observed at higher resolution structures can no longer be observed for structures at low resolution indicating problems in refinement protocols. The dynamics of protein and nucleic acid structures is as important as their average static picture. The local molecular dynamics concealed in diffraction images is expressed as so-called B factors. To find out how the crystal-derived B factors represent the dynamic behaviour of atoms and residues of proteins and DNA in their complexes, the distributions of scaled B factors from a carefully curated data set of over 700 protein–DNA crystal structures were analyzed [Schneider et al. (2014 ▶), Nucleic Acids Res.42, 3381–3394]. Amino acids and nucleotides were categorized based on their molecular neighbourhood as solvent-accessible, solvent-inaccessible (i.e. forming the protein core) or lying at protein–protein or protein–DNA interfaces; the backbone and side-chain atoms were analyzed separately. The B factors of two types of crystal-ordered water molecules were also analyzed. The analysis confirmed several expected features of protein and DNA dynamics, but also revealed surprising facts. Solvent-accessible amino acids have B factors that are larger than those of residues at the biomolecular interfaces, and core-forming amino acids are the most restricted in their movement. A unique feature of the latter group is that their side-chain and backbone atoms are restricted in their movement to the same extent; in all other amino-acid groups the side chains are more floppy than the backbone. The low values of the B factors of water molecules bridging proteins with DNA and the very large fluctuations of DNA phosphates are

  7. 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

  8. An estimation of cogeneration potential by using refinery residuals in Mexico

    International Nuclear Information System (INIS)

    Marin-Sanchez, J.E.; Rodriguez-Toral, M.A.

    2007-01-01

    Electric power generation in Mexico is mainly based on fossil fuels, specifically heavy fuel oil, although the use of natural gas combined cycles (NGCC) is becoming increasingly important. This is the main destination that has promoted growing imports of natural gas, currently accounting for about 20% of the total national annual consumption. Available crude oil is becoming heavier; thus refineries should be able to process it, and to handle greater quantities of refinery residuals. If all refinery residuals are used in cogeneration plants serving petroleum refineries, the high heat/power ratio of refinery needs, leads to the availability of appreciable quantities of electricity that can be exported to the public utility. Thus, in a global perspective, Mexican imports of natural gas may be reduced by cogeneration using refinery residuals. This is not the authors' idea; in fact, PEMEX, the national oil company, has been entitled by the Mexican congress to sell its power leftovers to The Federal Electricity Commission (CFE) in order to use cogeneration in the way described for the years to come. A systematic way of determining the cogeneration potential by using refinery residuals from Mexican refineries is presented here, taking into account residual quantities and composition, from a national perspective, considering expected scenarios for Maya crude content going to local refineries in the years to come. Among different available technologies for cogeneration using refinery residuals, it is believed that the integrated gasification combined cycle (IGCC) would be the best option. Thus, considering IGCC plants supplying heat and power to refineries where it is projected to have refinery residuals for cogeneration, the expected electric power that can be sent to the public utility is quantified, along with the natural gas imports mitigation that may be attained. This in turn would contribute to a necessary fuel diversification policy balancing energy, economy and

  9. 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...... 302 of ATP8A2 with alanine (N302A), tyrosine (N302Y) and serine (N302S). Furthermore, a triple mutant of ATP8A2 (Q95GQ96AN302S) was studied to reveal any cooperativity between the two gates, as observed in yeast [1]. The affinities of the mutants for phosphatidylserine and phosphatidylethanolamine...

  10. The formation of fire residues associated with hunter-gatherers in humid tropical environments: A geo-ethnoarchaeological perspective

    Science.gov (United States)

    Friesem, David E.; Lavi, Noa; Madella, Marco; Boaretto, Elisabetta; Ajithparsad, P.; French, Charles

    2017-09-01

    Tropical forests have been an important human habitat and played a significant role in early human dispersal and evolution. Likewise, the use of fire, besides being one of the exceptional characteristics of humans, serves as a marker for human evolution. While the use of fire by prehistoric hunter-gatherers is relatively well documented in arid and temperate environments, the archaeological evidence in humid tropical environment is to date very limited. We first review the archaeological evidence for hunter-gatherer use of fire in humid tropical environments and suggest that better understanding of formation processes is required. We present a geo-ethnoarchaeological study from South India, involving ethnography, excavations and laboratory-based analyses in order to build a new framework to study fire residues in humid tropical forests associated with hunter-gatherer's use of fire. Ethnographic observations point to a dynamic and ephemeral use of hearths. Hearths location were dictated by the social and ever-changing social dynamics of the site. The hearths deposited small amount of residues which were later swept on a daily basis, re-depositing ash and charcoal in waste areas and leaving only a microscopic signal in the original location. Particular acidic conditions and intensive biological activity within tropical sediments result in the complete dissolution of ash and bones while favouring the preservation of charcoal and phytoliths. Consequently, the identification of fire residues in humid tropical forests and the reconstruction of the human use of fire must involve multi-proxy microscopic analysis to detect its micro-signatures.

  11. Residual generation with unknown input observer for linear systems in the presence of unmatched uncertainties

    International Nuclear Information System (INIS)

    Bagherpour, Esmaeel A.; HairiTazdi, Mohammad Reza; Mahjoob, Mohammad

    2014-01-01

    In this paper, we deal with residual vector generation for fault detection problems in linear systems via unknown input observer (UIO) when the so-called observer matching condition is not satisfied. Based on the relative degree between unknown input and output, a vector of the auxiliary output is introduced so that the observer matching condition is satisfied with respect to the vector. Auxiliary outputs are related to the derivatives of measured signals. However, differentiation leads to excessive amplification of measurement noise. A dynamically equivalent configuration of linear systems is developed using successive integrations to avoid differentiation. As such, auxiliary outputs are constructed without differentiation. Then, the equivalent dynamic system and its corresponding auxiliary outputs are used to generate the residual vector via an exponentially converging UIO. Fault detection in the generated residual vector is also investigated. Finally, the effectiveness of the proposed method is shown via numerical simulation.

  12. Management of municipal solid waste incineration residues

    International Nuclear Information System (INIS)

    Sabbas, T.; Polettini, A.; Pomi, R.; Astrup, T.; Hjelmar, O.; Mostbauer, P.; Cappai, G.; Magel, G.; Salhofer, S.; Speiser, C.; Heuss-Assbichler, S.; Klein, R.; Lechner, P.

    2003-01-01

    The management of residues from thermal waste treatment is an integral part of waste management systems. The primary goal of managing incineration residues is to prevent any impact on our health or environment caused by unacceptable particulate, gaseous and/or solute emissions. This paper provides insight into the most important measures for putting this requirement into practice. It also offers an overview of the factors and processes affecting these mitigating measures as well as the short- and long-term behavior of residues from thermal waste treatment under different scenarios. General conditions affecting the emission rate of salts and metals are shown as well as factors relevant to mitigating measures or sources of gaseous emissions

  13. Annotating Protein Functional Residues by Coupling High-Throughput Fitness Profile and Homologous-Structure Analysis

    Directory of Open Access Journals (Sweden)

    Yushen Du

    2016-11-01

    Full Text Available Identification and annotation of functional residues are fundamental questions in protein sequence analysis. Sequence and structure conservation provides valuable information to tackle these questions. It is, however, limited by the incomplete sampling of sequence space in natural evolution. Moreover, proteins often have multiple functions, with overlapping sequences that present challenges to accurate annotation of the exact functions of individual residues by conservation-based methods. Using the influenza A virus PB1 protein as an example, we developed a method to systematically identify and annotate functional residues. We used saturation mutagenesis and high-throughput sequencing to measure the replication capacity of single nucleotide mutations across the entire PB1 protein. After predicting protein stability upon mutations, we identified functional PB1 residues that are essential for viral replication. To further annotate the functional residues important to the canonical or noncanonical functions of viral RNA-dependent RNA polymerase (vRdRp, we performed a homologous-structure analysis with 16 different vRdRp structures. We achieved high sensitivity in annotating the known canonical polymerase functional residues. Moreover, we identified a cluster of noncanonical functional residues located in the loop region of the PB1 β-ribbon. We further demonstrated that these residues were important for PB1 protein nuclear import through the interaction with Ran-binding protein 5. In summary, we developed a systematic and sensitive method to identify and annotate functional residues that are not restrained by sequence conservation. Importantly, this method is generally applicable to other proteins about which homologous-structure information is available.

  14. Residual stress measurement method in MEMS microbeams using frequency shift data

    International Nuclear Information System (INIS)

    Somà, Aurelio; Ballestra, Alberto

    2009-01-01

    The dynamical behaviour of a set of gold microbeams affected by residual stress has been studied. Experimental frequency shift curves were obtained by increasing the dc voltage applied to the specimens. Comparison with different analytical and numerical models has been carried out in order to identify both analytical and finite element models in the presence of residual stress. Residual strain and stress, due to the fabrication process, have been widely reported in the literature in both out-of-plane microcantilevers and clamped–clamped microbeams by using mainly the value of pull-in voltage and static deflection data. In the case of a microcantilever, an accurate modelling includes the effect of the initial curvature due to microfabrication. In double-clamped microbeams, a pre-load applied by tensile stress is considered. A good correspondence is pointed out between measurements and numerical models so that the residual stress effect can be evaluated for different geometrical configurations

  15. Utility residual fuel oil market conditions: An update

    International Nuclear Information System (INIS)

    Mueller, H.A. Jr.

    1992-01-01

    Planning for residual fuel oil usage and management remains an important part of the generation fuel planning and management function for many utilities. EPRI's Utility Planning Methods Center has maintained its analytical overview of the fuel oil markets as part of its overall fuel planning and management research program. This overview provides an update of recent fuel oil market directions. Several key events of the past year have had important implications for residual fuel oil markets. The key events have been the changes brought about by the Persian Gulf War and its aftermath, as well as continuing environmental policy developments. The Persian Gulf conflict has created renewed interest in reducing fuel oil use by utilities as part of an overall reduction in oil imports. The policy analysis performed to date has generally failed to properly evaluate utility industry capability. The Persian Gulf conflict has also resulted in an important change in the structure of international oil markets. The result of this policy-based change is likely to be a shift in oil pricing strategy. Finally, continued change in environmental requirements is continuing to shift utility residual oil requirements, but is also changing the nature of the US resid market itself

  16. Measurement of residual stresses using fracture mechanics weight functions

    International Nuclear Information System (INIS)

    Fan, Y.

    2000-01-01

    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

  17. Measurement of residual stresses using fracture mechanics weight functions

    International Nuclear Information System (INIS)

    Fan, Y.

    2001-01-01

    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)

  18. A SUMOylation Motif in Aurora-A: Implications for Spindle Dynamics and Oncogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Pérez de Castro, Ignacio; Aguirre-Portolés, Cristina [Molecular Oncology Programme, Cell Division and Cancer Group, Centro Nacional de Investigaciones Oncológicas, Madrid (Spain); Martin, Benedicte [CNRS-UMR 6061, Institut de Génétique et Développement de Rennes, IFR 140 GFAS, Faculté de Médecine, Université Rennes 1, Rennes (France); Fernández-Miranda, Gonzalo [Molecular Oncology Programme, Cell Division and Cancer Group, Centro Nacional de Investigaciones Oncológicas, Madrid (Spain); Klotzbucher, Andrea; Kubbutat, Michael H. G. [ProQinase GmBH, Freiburg (Germany); Megías, Diego [Confocal Microscopy Core Unit, Centro Nacional de Investigaciones Oncológicas, Madrid (Spain); Arlot-Bonnemains, Yannick [CNRS-UMR 6061, Institut de Génétique et Développement de Rennes, IFR 140 GFAS, Faculté de Médecine, Université Rennes 1, Rennes (France); Malumbres, Marcos, E-mail: mmm@cnio.es, E-mail: iperez@cnio.es [Molecular Oncology Programme, Cell Division and Cancer Group, Centro Nacional de Investigaciones Oncológicas, Madrid (Spain)

    2011-12-14

    Aurora-A is a serine/threonine kinase that plays critical roles in centrosome maturation, spindle dynamics, and chromosome orientation and it is frequently over-expressed in human cancers. In this work, we show that Aurora-A interacts with the SUMO-conjugating enzyme UBC9 and co-localizes with SUMO1 in mitotic cells. Aurora-A can be SUMOylated in vitro and in vivo. Mutation of the highly conserved SUMOylation residue lysine 249 significantly disrupts Aurora-A SUMOylation and mitotic defects characterized by defective and multipolar spindles ensue. The Aurora-A{sup K249R} mutant has normal kinase activity but displays altered dynamics at the mitotic spindle. In addition, ectopic expression of the Aurora-A{sup K249R} mutant results in a significant increase in susceptibility to malignant transformation induced by the Ras oncogene. These data suggest that modification by SUMO residues may control Aurora-A function at the spindle and that deficiency of SUMOylation of this kinase may have important implications for tumor development.

  19. Statistical Measures to Quantify Similarity between Molecular Dynamics Simulation Trajectories

    Directory of Open Access Journals (Sweden)

    Jenny Farmer

    2017-11-01

    Full Text Available Molecular dynamics simulation is commonly employed to explore protein dynamics. Despite the disparate timescales between functional mechanisms and molecular dynamics (MD trajectories, functional differences are often inferred from differences in conformational ensembles between two proteins in structure-function studies that investigate the effect of mutations. A common measure to quantify differences in dynamics is the root mean square fluctuation (RMSF about the average position of residues defined by C α -atoms. Using six MD trajectories describing three native/mutant pairs of beta-lactamase, we make comparisons with additional measures that include Jensen-Shannon, modifications of Kullback-Leibler divergence, and local p-values from 1-sample Kolmogorov-Smirnov tests. These additional measures require knowing a probability density function, which we estimate by using a nonparametric maximum entropy method that quantifies rare events well. The same measures are applied to distance fluctuations between C α -atom pairs. Results from several implementations for quantitative comparison of a pair of MD trajectories are made based on fluctuations for on-residue and residue-residue local dynamics. We conclude that there is almost always a statistically significant difference between pairs of 100 ns all-atom simulations on moderate-sized proteins as evident from extraordinarily low p-values.

  20. Nitrous oxide emission from soils amended with crop residues

    NARCIS (Netherlands)

    Velthof, G.L.; Kuikman, P.J.; Oenema, O.

    2002-01-01

    Crop residues incorporated in soil are a potentially important source of nitrous oxide (N2O), though poorly quantified. Here, we report on the N2O emission from 10 crop residues added to a sandy and a clay soil, both with and without additional nitrate (NO3-). In the sandy soil, total nitrous oxide

  1. Vision for utilization of livestock residue as bioenergy resource in Japan

    International Nuclear Information System (INIS)

    Fujino, Junichi; Morita, Akihiro; Matsuoka, Yasunari; Sawayama, Shigeki

    2005-01-01

    Utilization of livestock residue is important not only for energy recovery and material recycling but also for preventing environmental pollution. This paper focuses on the following options from the viewpoint of the Law on Promoting Proper Management and Use of Livestock Excreta and the Kyoto protocol: energy use from livestock residue, reductions in CO 2 emissions resulting from substitution of fossil fuels, and reduction of other greenhouse gas emissions through appropriate treatment of livestock residue. Bioenergy potential of livestock residue in Japan was estimated to be 167 PJ in the year 2000. This is equivalent to about 0.7% of total primary energy supply. Biogas production with methane fermentation and burning poultry residue at power plants can produce 4.1 TWh of electricity and 46 PJ of heat. The amount of CO 2 substitution for fossil fuels is 6.9 Mt-CO 2 . This corresponds to about 0.6% of total CO 2 emissions in 1990. This also has an additional effect of reducing other greenhouse gas (CH 4 and N 2 O) emissions from conventional treatment of livestock residue. Development of biogas plants, promotion of biogas utilization, and effective use of fertilizer components extracted from livestock residue are expected to gain importance in the future

  2. Use of ultrasound in petroleum residue upgradation

    Energy Technology Data Exchange (ETDEWEB)

    Sawarkar, A.N.; Pandit, A.B.; Samant, S.D.; Joshi, J.B. [Mumbai Univ., Mumbai (India). Inst. of Chemical Technology

    2009-06-15

    The importance of bottom-of-the barrel upgrading has increased in the current petroleum refining scenario because of the progressively heavier nature of crude oil. Heavy residues contain large concentrations of metals such as vanadium and nickel which foul catalysts and reduce the potential effect of residue fluidized catalytic cracking. This study showed that the cavitational energy induced by ultrasound be be successfully used to upgrade hydrocarbon mixtures. Conventional processes for the upgrading of residual feedstocks, such as thermal cracking and catalytic cracking, were carried out in the temperature range of 400-520 degrees C. Experiments were performed on 2 vacuum residues, Arabian mix vacuum residue (AMVR) and Bombay high vacuum residue (BHVR) and 1 Haldia asphalt (HA). These were subjected to acoustic cavitation for different reaction times from 15 to 120 minutes at ambient temperature and pressure. Two acoustic cavitation devices were compared, namely the ultrasonic bath and ultrasonic horn. In particular, this study compared the ability of these 2 devices to upgrade the petroleum residues to lighter, more value-added products. Different surfactants were used to examine the effect of ultrasound on upgrading the residue when emulsified in water. In order to better understand the reaction mechanism, a kinetic model was developed based on the constituents of the residue. The ultrasonic horn was found to be more effective in bringing about the upgrading than ultrasonic bath. The study also showed that the acoustic cavitation of the aqueous emulsified hydrocarbon mixture could reduce the asphaltenes content to a greater extent than the acoustic cavitation of non-emulsified hydrocarbon mixture. 20 refs., 11 tabs., 17 figs.

  3. 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.

  4. The importance of monitoring minimal residual disease in childhood acute lymphoblastic leukemia

    International Nuclear Information System (INIS)

    Kolenova, A.; Subova, Z.; Cizmar, A.; Sejnova, D.; Kaiserova, E.; Hikkel, I.; Hikkelova, M.; Bubanska, E.; Oravkinova, I.

    2012-01-01

    Since the strong correlation between minimal residual disease (MRD) levels and risk of relapse in childhood acute lymphoblastic leukemia, monitoring of MRD provides unique information regarding treatment response. Because the significance of MRD monitoring has been strongly supported by several studies and because it has been implemented in the latest protocols, there has been a significant effort to develop MRD monitoring in the Slovak Republic. Between 1. 10. 2006 and 31. 12. 2009, 50 children with ALL who were treated at three Slovak centers were included in the RQ PCR MRD pilot project. Based on MRD stratification, we identified 26 patients who were stratified into the HRG (high risk group) 3 patients (11,5 %), IRG (intermediate risk group), 14 p. 54 % and SRG (standard risk group), 9 p. (34,5 %). (author)

  5. Structural and molecular dynamics studies of a C1-oxidizing lytic polysaccharide monooxygenase from Heterobasidion irregulare reveal amino acids important for substrate recognition

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Bing [Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala Sweden; Kognole, Abhishek A. [Department of Chemical and Materials Engineering, University of Kentucky, Lexington KY USA; Wu, Miao [Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala Sweden; Westereng, Bjørge [Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, Ås Norway; Crowley, Michael F. [Biosciences Center, National Renewable Energy Laboratory, Golden CO USA; Kim, Seonah [Biosciences Center, National Renewable Energy Laboratory, Golden CO USA; Dimarogona, Maria [Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala Sweden; Department of Chemical Engineering, University of Patras, Greece; Payne, Christina M. [Department of Chemical and Materials Engineering, University of Kentucky, Lexington KY USA; Directorate of Engineering, Division of Chemical, Bioengineering, Environmental, and Transport Systems, National Science Foundation, Alexandria VA USA; Sandgren, Mats [Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala Sweden

    2018-04-24

    Lytic polysaccharide monooxygenases (LPMOs) are a group of recently discovered enzymes that play important roles in the decomposition of recalcitrant polysaccharides. Here, we report the biochemical, structural, and computational characterization of an LPMO from the white-rot fungus Heterobasidion irregulare (HiLPMO9B). This enzyme oxidizes cellulose at the C1 carbon of glycosidic linkages. The crystal structure of HiLPMO9B was determined at 2.1 A resolution using X-ray crystallography. Unlike the majority of the currently available C1-specific LPMO structures, the HiLPMO9B structure contains an extended L2 loop, connecting ..beta..-strands ..beta..2 and ..beta..3 of the ..beta..-sandwich structure. Molecular dynamics (MD) simulations suggest roles for both aromatic and acidic residues in the substrate binding of HiLPMO9B, with the main contribution from the residues located on the extended region of the L2 loop (Tyr20) and the LC loop (Asp205, Tyr207, and Glu210). Asp205 and Glu210 were found to be involved in the hydrogen bonding with the hydroxyl group of the C6 carbon of glucose moieties directly or via a water molecule. Two different binding orientations were observed over the course of the MD simulations. In each orientation, the active-site copper of this LPMO preferentially skewed toward the pyranose C1 of the glycosidic linkage over the targeted glycosidic bond. This study provides additional insight into cellulose binding by C1-specific LPMOs, giving a molecular-level picture of active site substrate interactions.

  6. Stabilization and plant uptake of N from 15N-labelled pea residue 16.5 years after incorporation in soil

    DEFF Research Database (Denmark)

    Laberge, G.; Ambus, P.; Hauggaard-Nielsen, H.

    2006-01-01

    The decline of N from N-15-labelled mature pea residues was followed in unplanted soil over 16.5 yr. Eight years after residue incorporation, 24% of the residue N-15 input was still present in the soil and, after 16.5 yr, 16% of the residue N-15 input remained. A double exponential model......-amended soils were obtaining 1.7% of their N from residue N. This is, to our knowledge, the longest study on decay of N in soils from N-15-labelled crop residues. The current study thus provides a unique data set for our empirical understanding of N-dynamics in agricultural systems, which is a prerequisite...

  7. 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)

  8. Dynamics of Lithospheric Extension and Residual Topography in Southern Tibet

    Science.gov (United States)

    Chen, B.; Shahnas, M. H.; Pysklywec, R.; Sengul Uluocak, E.

    2017-12-01

    Although the north-south (N-S) convergence between India and Eurasia is ongoing, a number of north-south trending rifts (e.g., Tangra Yum Co Rift, Yadong-Gulu Rift and Cona Rift) and normal faulting are observed at the surface of southern Tibet, suggesting an east-west (E-W) extension tectonic regime. The earthquake focal mechanisms also show that deformation of southern Tibet is dominated by E-W extension across these N-S trending rifts. Because the structure of the lithosphere and underlying mantle is poorly understood, the origin of the east-west extension of southern Tibet is still under debate. Gravitational collapse, oblique convergence, and mantle upwelling are among possible responsible mechanisms. We employ a 3D-spherical control volume model of the present-day mantle flow to understand the relationship between topographic features (e.g., rifts and the west-east extension), intermediate-depth earthquakes, and tectonic stresses induced by mantle flow beneath the region. The thermal structure of the mantle and crust is obtained from P and S-wave seismic inversions and heat flow data. Power-law creep with viscous-plastic rheology, describing the behavior of the lithosphere and mantle material is employed. We determine the models which can best reconcile the observed features of southern Tibet including surface heat flow, residual topography with uplift and subsidence, reported GPS rates of the vertical movements, and the earthquake events. The 3D geodynamic modeling of the contemporary mantle flow-lithospheric response quantifies the relative importance of the various proposed mechanism responsible for the E-W extension and deep earthquakes in southern Tibet. The results also have further implications for the magmatic activities and crustal rheology of the region.

  9. The Effect of Drying-Wetting Cycle’s Repetition to the Characteristic of Natural and Stabilization Residual Soils Jawa Timur - Indonesia

    Science.gov (United States)

    Muntaha, M.

    2017-11-01

    Indonesia, which located in tropical region, continuously undergoes wetting and drying cycles due to the changeable seasons. An important role in activating the clay minerals on tropical residual soils is the main factor that affects the static and dynamic properties, such as: volume change, soil suction and dynamic modulus. The purpose of this paper is to evaluate the effect of drying-wetting cycles repetition on volume change, soil suction and mechanical characteristics of natural and stabilization of residual soils from Jawa Timur - Indonesia. The natural undisturbed and stabilized residual soil sample was naturally and gradually dried up with air to 25%, 50%, 75%, and 100 % of the initial water content. The wetting processes were carried out with the gradual increment water content of 25 %(wsat - wi), 50 %(wsat - wi), 75 %(wsat - wi), up to 100 %(wsat - wi). The Direct Shear test is used to measure the mechanic properties, and Whatman filter paper No. 42 is used to measure the soil suction. The drying-wetting processes were carried out for 1, 2, 4, and 6 cycles. The laboratory test results showed that, the void ratio decreased, the unit weight, cohesion and the internal friction angle were increasing due to stabilization. Drying-wetting cycle repetition reduces void ratio, negative pore-water pressure, cohesion and internal friction angle of natural and stabilized soils. Briefly, the decreased of mechanical soil properties was proven from the physical properties change observation.

  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

    2017-06-01

    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. Residual and Past Entropy for Concomitants of Ordered Random Variables of Morgenstern Family

    Directory of Open Access Journals (Sweden)

    M. M. Mohie EL-Din

    2015-01-01

    Full Text Available For a system, which is observed at time t, the residual and past entropies measure the uncertainty about the remaining and the past life of the distribution, respectively. In this paper, we have presented the residual and past entropy of Morgenstern family based on the concomitants of the different types of generalized order statistics (gos and give the linear transformation of such model. Characterization results for these dynamic entropies for concomitants of ordered random variables have been considered.

  12. Pesticide residues in food of plant origin from Southeast Asia – A Nordic project

    DEFF Research Database (Denmark)

    Skretteberg, L. G.; Lyrån, B.; Holen, B.

    2015-01-01

    Fruits and vegetables from Souteast Asia were analysed for the presence of pesticide residues. A total of 721 samples of 63 different commodities were collected in 2011. The products were imported to Denmark, Finland, Norway and Sweden from ten countries; about 80% were imported from Thailand....... The reason for the increased control for certain food products from Southeast Asia was that the official control had revealed many products with too high levels of pesticide residues. In 60% of the samples we did not find any residues, while 28% had residues below or at the MRLs. Results above the MRLs were...

  13. Proteins with Novel Structure, Function and Dynamics

    Science.gov (United States)

    Pohorille, Andrew

    2014-01-01

    Recently, a small enzyme that ligates two RNA fragments with the rate of 10(exp 6) above background was evolved in vitro (Seelig and Szostak, Nature 448:828-831, 2007). This enzyme does not resemble any contemporary protein (Chao et al., Nature Chem. Biol. 9:81-83, 2013). It consists of a dynamic, catalytic loop, a small, rigid core containing two zinc ions coordinated by neighboring amino acids, and two highly flexible tails that might be unimportant for protein function. In contrast to other proteins, this enzyme does not contain ordered secondary structure elements, such as alpha-helix or beta-sheet. The loop is kept together by just two interactions of a charged residue and a histidine with a zinc ion, which they coordinate on the opposite side of the loop. Such structure appears to be very fragile. Surprisingly, computer simulations indicate otherwise. As the coordinating, charged residue is mutated to alanine, another, nearby charged residue takes its place, thus keeping the structure nearly intact. If this residue is also substituted by alanine a salt bridge involving two other, charged residues on the opposite sides of the loop keeps the loop in place. These adjustments are facilitated by high flexibility of the protein. Computational predictions have been confirmed experimentally, as both mutants retain full activity and overall structure. These results challenge our notions about what is required for protein activity and about the relationship between protein dynamics, stability and robustness. We hypothesize that small, highly dynamic proteins could be both active and fault tolerant in ways that many other proteins are not, i.e. they can adjust to retain their structure and activity even if subjected to mutations in structurally critical regions. This opens the doors for designing proteins with novel functions, structures and dynamics that have not been yet considered.

  14. Importance of interactions between food quality, quantity, and gut transit time on consumer feeding, growth, and trophic dynamics.

    Science.gov (United States)

    Mitra, Aditee; Flynn, Kevin J

    2007-05-01

    Ingestion kinetics of animals are controlled by both external food availability and feedback from the quantity of material already within the gut. The latter varies with gut transit time (GTT) and digestion of the food. Ingestion, assimilation efficiency, and thus, growth dynamics are not related in a simple fashion. For the first time, the important linkage between these processes and GTT is demonstrated; this is achieved using a biomass-based, mechanistic multinutrient model fitted to experimental data for zooplankton growth dynamics when presented with food items of varying quality (stoichiometric composition) or quantity. The results show that trophic transfer dynamics will vary greatly between the extremes of feeding on low-quantity/high-quality versus high-quantity/low-quality food; these conditions are likely to occur in nature. Descriptions of consumer behavior that assume a constant relationship between the kinetics of grazing and growth irrespective of food quality and/or quantity, with little or no recognition of the combined importance of these factors on consumer behavior, may seriously misrepresent consumer activity in dynamic situations.

  15. A study of the influence of charged residues on β-hairpin formation by nuclear magnetic resonance and molecular dynamics.

    Science.gov (United States)

    Makowska, Joanna; Zmudzińska, Wioletta; Uber, Dorota; Chmurzyński, Lech

    2014-12-01

    Chain reversals are often nucleation sites in protein folding. The β-hairpins of FBP28 WW domain and IgG are stable and have been proved to initiate the folding and are, therefore, suitable for studying the influence of charged residues on β-hairpin conformation. In this paper, we carried out NMR examination of the conformations in solution of two fragments from the FPB28 protein (PDB code: 1E0L) (N-terminal part) namely KTADGKT-NH2 (1E0L 12-18, D7) and YKTADGKTY-NH2 (1E0L 11-19, D9), one from the B3 domain of the protein G (PDB code: 1IGD), namely DDATKT-NH2 (1IGD 51-56) (Dag1), and three variants of Dag1 peptide: DVATKT-NH2 (Dag2), OVATKT-NH2 (Dag3) and KVATKT-NH2 (Dag4), respectively, in which the original charged residue were replaced with non-polar residues or modified charged residues. It was found that both the D7 and D9 peptides form a large fraction bent conformations. However, no hydrophobic contacts between the terminal Tyr residues of D9 occur, which suggests that the presence of a pair of like-charged residues stabilizes chain reversal. Conversely, only the Dag1 and Dag2 peptides exhibit some chain reversal; replacing the second aspartic-acid residue with a valine and the first one with a basic residue results in a nearly extended conformation. These results suggest that basic residues farther away in sequence can result in stabilization of chain reversal owing to screening of the non-polar core. Conversely, smaller distance in sequence prohibits this screening, while the presence oppositely-charged residues can stabilize a turn because of salt-bridge formation.

  16. Probing the dynamic interface between trimethylamine dehydrogenase (TMADH) and electron transferring flavoprotein (ETF) in the TMADH-2ETF complex: role of the Arg-alpha237 (ETF) and Tyr-442 (TMADH) residue pair.

    Science.gov (United States)

    Burgess, Selena G; Messiha, Hanan Latif; Katona, Gergely; Rigby, Stephen E J; Leys, David; Scrutton, Nigel S

    2008-05-06

    We have used multiple solution state techniques and crystallographic analysis to investigate the importance of a putative transient interaction formed between Arg-alpha237 in electron transferring flavoprotein (ETF) and Tyr-442 in trimethylamine dehydrogenase (TMADH) in complex assembly, electron transfer, and structural imprinting of ETF by TMADH. We have isolated four mutant forms of ETF altered in the identity of the residue at position 237 (alphaR237A, alphaR237K, alphaR237C, and alphaR237E) and with each form studied electron transfer from TMADH to ETF, investigated the reduction potentials of the bound ETF cofactor, and analyzed complex formation. We show that mutation of Arg-alpha237 substantially destabilizes the semiquinone couple of the bound FAD and impedes electron transfer from TMADH to ETF. Crystallographic structures of the mutant ETF proteins indicate that mutation does not perturb the overall structure of ETF, but leads to disruption of an electrostatic network at an ETF domain boundary that likely affects the dynamic properties of ETF in the crystal and in solution. We show that Arg-alpha237 is required for TMADH to structurally imprint the as-purified semiquinone form of wild-type ETF and that the ability of TMADH to facilitate this structural reorganization is lost following (i) redox cycling of ETF, or simple conversion to the oxidized form, and (ii) mutagenesis of Arg-alpha237. We discuss this result in light of recent apparent conflict in the literature relating to the structural imprinting of wild-type ETF. Our studies support a mechanism of electron transfer by conformational sampling as advanced from our previous analysis of the crystal structure of the TMADH-2ETF complex [Leys, D. , Basran, J. , Sutcliffe, M. J., and Scrutton, N. S. (2003) Nature Struct. Biol. 10, 219-225] and point to a key role for the Tyr-442 (TMADH) and Arg-alpha237 (ETF) residue pair in transiently stabilizing productive electron transfer configurations. Our work

  17. Identification of Key Residues for Enzymatic Carboxylate Reduction

    Directory of Open Access Journals (Sweden)

    Holly Stolterfoht

    2018-02-01

    Full Text Available Carboxylate reductases (CARs, E.C. 1.2.1.30 generate aldehydes from their corresponding carboxylic acid with high selectivity. Little is known about the structure of CARs and their catalytically important amino acid residues. The identification of key residues for carboxylate reduction provides a starting point to gain deeper understanding of enzymatic carboxylate reduction. A multiple sequence alignment of CARs with confirmed activity recently identified in our lab and from the literature revealed a fingerprint of conserved amino acids. We studied the function of conserved residues by multiple sequence alignments and mutational replacements of these residues. In this study, single-site alanine variants of Neurospora crassa CAR were investigated to determine the contribution of conserved residues to the function, expressability or stability of the enzyme. The effect of amino acid replacements was investigated by analyzing enzymatic activity of the variants in vivo and in vitro. Supported by molecular modeling, we interpreted that five of these residues are essential for catalytic activity, or substrate and co-substrate binding. We identified amino acid residues having significant impact on CAR activity. Replacement of His 237, Glu 433, Ser 595, Tyr 844, and Lys 848 by Ala abolish CAR activity, indicating their key role in acid reduction. These results may assist in the functional annotation of CAR coding genes in genomic databases. While some other conserved residues decreased activity or had no significant impact, four residues increased the specific activity of NcCAR variants when replaced by alanine. Finally, we showed that NcCAR wild-type and mutants efficiently reduce aliphatic acids.

  18. Residual Resistance Data from Cavity Production Projects at Jefferson Lab

    International Nuclear Information System (INIS)

    Ciovati, Gianluigi; Geng, Rongli; Mammosser, John; Saunders, Jeffrey

    2010-01-01

    A fundamental limitation towards achieving high quality factors in superconducting radio-frequency cavities is the so-called residual resistance. Understanding and controlling the residual resistance has important implications towards improving the efficiency and reduce the operating cost of continuous wave superconducting linear accelerators. In this contribution we will report on the residual resistance values obtained from measurements of the quality factor of a large set of cavities, with resonant frequency between 805 MHz and 1.5 GHz, all of them processed and tested at Jefferson Lab. Surface treatments included both buffered chemical polishing and electropolishing. The results indicate an approximate value of the residual resistance of about 7-10 n Omega.

  19. Structural and dynamical insights into the membrane-bound α-synuclein.

    Directory of Open Access Journals (Sweden)

    Neha Jain

    Full Text Available Membrane-induced disorder-to-helix transition of α-synuclein, a presynaptic protein, has been implicated in a number of important neuronal functions as well as in the etiology of Parkinson's disease. In order to obtain structural insights of membrane-bound α-synuclein at the residue-specific resolution, we took advantage of the fact that the protein is devoid of tryptophan and incorporated single tryptophan at various residue positions along the sequence. These tryptophans were used as site-specific markers to characterize the structural and dynamical aspects of α-synuclein on the negatively charged small unilamellar lipid vesicles. An array of site-specific fluorescence readouts, such as the spectral-shift, quenching efficiency and anisotropy, allowed us to discern various features of the conformational rearrangements occurring at different locations of α-synuclein on the lipid membrane. In order to define the spatial localization of various regions of the protein near the membrane surface, we utilized a unique and sensitive indicator, namely, red-edge excitation shift (REES, which originates when a fluorophore is located in a highly ordered micro-environment. The extent of REES observed at different residue positions allowed us to directly identify the residues that are localized at the membrane-water interface comprising a thin (∼ 15 Å layer of motionally restrained water molecules and enabled us to construct a dynamic hydration map of the protein. The combination of site-specific fluorescence readouts allowed us to unravel the intriguing molecular details of α-synuclein on the lipid membrane in a direct model-free fashion. Additionally, the combination of methodologies described here are capable of distinguishing subtle but important structural alterations of α-synuclein bound to different negatively charged lipids with varied head-group chemistry. We believe that the structural modulations of α-synuclein on the membrane could

  20. Backbone dynamics of the human CC-chemokine eotaxin

    Energy Technology Data Exchange (ETDEWEB)

    Ye Jiqing; Mayer, Kristen L.; Stone, Martin J. [Indiana University, Department of Chemistry (United States)

    1999-10-15

    Eotaxin is a CC chemokine with potent chemoattractant activity towards eosinophils. {sup 15}N NMR relaxation data have been used to characterize the backbone dynamics of recombinant human eotaxin. {sup 15}N longitudinal (R{sub 1}) and transverse (R{sub 2}) auto relaxation rates, heteronuclear {sup 1}H-{sup 15}N steady-state NOEs, and transverse cross-relaxation rates ({eta}{sub xy}) were obtained at 30 deg. C for all resolved backbone secondary amide groups using {sup 1} H-detected two-dimensional NMR experiments. Ratios of transverse auto and cross relaxation rates were used to identify NH groups influenced by slow conformational rearrangement. Relaxation data were fit to the extended model free dynamics formalism, yielding parameters describing axially symmetric molecular rotational diffusion and the internal dynamics of each NH group. The molecular rotational correlation time ({tau}{sub m}) is 5.09{+-}0.02 ns, indicating that eotaxin exists predominantly as a monomer under the conditions of the NMR study. The ratio of diffusion rates about unique and perpendicular axes (D{sub parallel}/D{sub perpendicular}) is 0.81{+-}0.02. Residues with large amplitudes of subnanosecond motion are clustered in the N-terminal region (residues 1-19), the C-terminus (residues 68-73) and the loop connecting the first two {beta}-strands (residues 30-37). N-terminal flexibility appears to be conserved throughout the chemokine family and may have implications for the mechanism of chemokine receptor activation. Residues exhibiting significant dynamics on the microsecond-millisecond time scale are located close to the two conserved disulfide bonds, suggesting that these motions may be coupled to disulfide bond isomerization.

  1. Dynamic response of high speed centrifuge for reprocessing plant

    International Nuclear Information System (INIS)

    Rajput, Gaurav; Satish Kumar, V.; Selvaraj, T.; Ananda Rao, S.M.; Ravisankar, A.

    2012-01-01

    The standard for balancing the rotating bowl describes only the details about the selection of balance quality grade and the permissible residual unbalance for different operating speeds. This paper presents the effects of unbalance on the rotating bowl of high speed centrifuge used in reprocessing of spent nuclear fuel. In this study, the residual unbalance is evaluated for different recommended balancing grades in accordance with the ISO 1940. This unbalance mass generates dynamic force which acts on the rotor. The dynamic response of the rotor like displacements and stresses under this dynamic force are studied by numerical simulation. Finally, the effect of residual unbalance on the rotating bowl performance for different balancing grades is discussed. The experimental measurements are also carried out for the case of G 1.0 grade balanced rotating bowl to validate the resonance frequency as well as vibration amplitudes. (author)

  2. Structure-based network analysis of activation mechanisms in the ErbB family of receptor tyrosine kinases: the regulatory spine residues are global mediators of structural stability and allosteric interactions.

    Directory of Open Access Journals (Sweden)

    Kevin A James

    Full Text Available The ErbB protein tyrosine kinases are among the most important cell signaling families and mutation-induced modulation of their activity is associated with diverse functions in biological networks and human disease. We have combined molecular dynamics simulations of the ErbB kinases with the protein structure network modeling to characterize the reorganization of the residue interaction networks during conformational equilibrium changes in the normal and oncogenic forms. Structural stability and network analyses have identified local communities integrated around high centrality sites that correspond to the regulatory spine residues. This analysis has provided a quantitative insight to the mechanism of mutation-induced "superacceptor" activity in oncogenic EGFR dimers. We have found that kinase activation may be determined by allosteric interactions between modules of structurally stable residues that synchronize the dynamics in the nucleotide binding site and the αC-helix with the collective motions of the integrating αF-helix and the substrate binding site. The results of this study have pointed to a central role of the conserved His-Arg-Asp (HRD motif in the catalytic loop and the Asp-Phe-Gly (DFG motif as key mediators of structural stability and allosteric communications in the ErbB kinases. We have determined that residues that are indispensable for kinase regulation and catalysis often corresponded to the high centrality nodes within the protein structure network and could be distinguished by their unique network signatures. The optimal communication pathways are also controlled by these nodes and may ensure efficient allosteric signaling in the functional kinase state. Structure-based network analysis has quantified subtle effects of ATP binding on conformational dynamics and stability of the EGFR structures. Consistent with the NMR studies, we have found that nucleotide-induced modulation of the residue interaction networks is not

  3. Lysine as helix C-capping residue in a synthetic peptide.

    Science.gov (United States)

    Esposito, G; Dhanapal, B; Dumy, P; Varma, V; Mutter, M; Bodenhausen, G

    1997-01-01

    The structure of the synthetic peptide CH3CO(Leu-Ser-Leu-Leu-Leu-Ser-Leu)3Lys-NH2 in trifluoroethanol/water 60/40 (volume ratio) was characterized by two-dimensional nmr spectroscopy. The peptide, closely related to the amphiphilic helix models designed by W. F. De-Grado and co-workers to mimic protein ion channels [(1988) Science, Vol. 240, p. 1177-1181], folds into a regular helix spanning residues 1-20. Evidence for a helix C-terminal capping conformation, involving the terminal lysine residue, was observed from Overhauser effects and checked for consistency by restrained molecular dynamics simulations. The side-chain amino group of Lys22 forms a hydrogen bond with the carbonyl of Leu18, and the distorted helical geometry of the terminal dipeptide allows the inclusion of a water bridge between the backbone NH of the Lys22 residue and the carbonyls of Leu19 and Ser20.

  4. Topography of the Betics: crustal thickening, dynamic topography and relief inheritance

    Science.gov (United States)

    Janowski, Marianne; Loget, Nicolas; Bellahsen, Nicolas; Husson, Laurent; Le Pourhiet, Laetitia; Meyer, Bertrand

    2017-04-01

    The main mechanism that explains high orogenic topographies is the isostatic adjustment due to crustal thickening. However in the Betic Cordillera (South Spain), the present-day elevation and crustal thickness are not correlated. That is at odds with the general premise of isostasy and requires reappraising the question of the driving mechanisms leading to the current topography. The Betics are located at the western edge of the alpine Mediterranean belt. Its Cenozoic orogenic building was disrupted by a major crustal thinning event induced by a slab rollback in the internal zones (Alboran domain) during Neogene. Topography was largely levelled and flooded by the sea during Neogene extension, and then has been folded since the Late Tortonian inversion. The present-day topography shows flat summits still preserved from fluvial regression in the internal zones (central and eastern Betics). These low-relief surfaces may be inherited from the Neogene planation toward sea-level as rocks cooling histories inferred from low-temperature thermochronology seem to point it out. Post-Tortonian shortening estimated thanks to a crustal-scale N-S cross-section in the eastern Betics (at the Sierra Nevada longitude) does not exceed few kilometers which is much lower than the shortening required by isostatic equilibrium, and is thus insufficient to explain the post-Tortonian topography building. We tested the hypothesis that mantle dynamics could in fact be an important mechanism that explains the topography of the Betics. We first computed the residual topography (i.e. the non-isostatic component of the elevation) using the most recent published Moho mapping of the area. In the western Betics, our results show important negative residual topography (down to -3 km) possibly associated with the west-Alboran slab suction. In the eastern Betics however, positive residual topography is important (up to +3 km) and can be explained by the dynamic mantle support of the topography, possibly

  5. Combining specificity determining and conserved residues improves functional site prediction

    Directory of Open Access Journals (Sweden)

    Gelfand Mikhail S

    2009-06-01

    Full Text Available Abstract Background Predicting the location of functionally important sites from protein sequence and/or structure is a long-standing problem in computational biology. Most current approaches make use of sequence conservation, assuming that amino acid residues conserved within a protein family are most likely to be functionally important. Most often these approaches do not consider many residues that act to define specific sub-functions within a family, or they make no distinction between residues important for function and those more relevant for maintaining structure (e.g. in the hydrophobic core. Many protein families bind and/or act on a variety of ligands, meaning that conserved residues often only bind a common ligand sub-structure or perform general catalytic activities. Results Here we present a novel method for functional site prediction based on identification of conserved positions, as well as those responsible for determining ligand specificity. We define Specificity-Determining Positions (SDPs, as those occupied by conserved residues within sub-groups of proteins in a family having a common specificity, but differ between groups, and are thus likely to account for specific recognition events. We benchmark the approach on enzyme families of known 3D structure with bound substrates, and find that in nearly all families residues predicted by SDPsite are in contact with the bound substrate, and that the addition of SDPs significantly improves functional site prediction accuracy. We apply SDPsite to various families of proteins containing known three-dimensional structures, but lacking clear functional annotations, and discusse several illustrative examples. Conclusion The results suggest a better means to predict functional details for the thousands of protein structures determined prior to a clear understanding of molecular function.

  6. Prediction of Active Site and Distal Residues in E. coli DNA Polymerase III alpha Polymerase Activity.

    Science.gov (United States)

    Parasuram, Ramya; Coulther, Timothy A; Hollander, Judith M; Keston-Smith, Elise; Ondrechen, Mary Jo; Beuning, Penny J

    2018-02-20

    The process of DNA replication is carried out with high efficiency and accuracy by DNA polymerases. The replicative polymerase in E. coli is DNA Pol III, which is a complex of 10 different subunits that coordinates simultaneous replication on the leading and lagging strands. The 1160-residue Pol III alpha subunit is responsible for the polymerase activity and copies DNA accurately, making one error per 10 5 nucleotide incorporations. The goal of this research is to determine the residues that contribute to the activity of the polymerase subunit. Homology modeling and the computational methods of THEMATICS and POOL were used to predict functionally important amino acid residues through their computed chemical properties. Site-directed mutagenesis and biochemical assays were used to validate these predictions. Primer extension, steady-state single-nucleotide incorporation kinetics, and thermal denaturation assays were performed to understand the contribution of these residues to the function of the polymerase. This work shows that the top 15 residues predicted by POOL, a set that includes the three previously known catalytic aspartate residues, seven remote residues, plus five previously unexplored first-layer residues, are important for function. Six previously unidentified residues, R362, D405, K553, Y686, E688, and H760, are each essential to Pol III activity; three additional residues, Y340, R390, and K758, play important roles in activity.

  7. Long-term impact of reduced tillage and residue management on soil carbon stabilization: Implications for conservation agriculture on contrasting soil

    NARCIS (Netherlands)

    Chivenge, P.P.; Murwira, H.K.; Giller, K.E.; Mapfumo, P.; Six, J.

    2007-01-01

    Residue retention and reduced tillage are both conservation agricultural management options that may enhance soil organic carbon (SOC) stabilization in tropical soils. Therefore, we evaluated the effects of long-term tillage and residue management on SOC dynamics in a Chromic Luvisol (red clay soil)

  8. 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.

  9. Residual stress characterization of welds using x-ray diffraction techniques

    International Nuclear Information System (INIS)

    Pineault, J.A.; Brauss, M.E.

    1996-01-01

    Neglect of residual stresses created during processes lead to stress corrosion cracking, distortion, fatigue cracking, premature failures in components, and instances of over design. Automated residual stress mapping and truly portable equipment have now made the characterization of residual stresses using x-ray diffraction (XRI) practical. The nondestructive nature of the x-ray diffraction technique has made the tile residual stress characterization of welds a useful tool for process optimization and failure analysis, particularly since components can be measured before and after welding and post welding processes. This paper illustrates the importance of residual stress characterization in welds and presents examples where x-ray diffraction techniques were applied in the characterization of various kinds of welds. arc welds, TIG welds, resistance welds, laser welds and electron beam welds. Numerous techniques are available to help manage potentially harmfull residual stresses created during the welding process thus, the effects of a few example post weld processes such as grinding, heat treating and shot peening are also addressed

  10. Neutron diffraction measurement of residual stress in NPP construction materials

    International Nuclear Information System (INIS)

    Hinca, R.; Bokuchava, G.

    2000-01-01

    The aim of the investigation is to study the level of residual stresses induced by the surfacing in the weld deposit zone and in the base metal, where considerable thermal gradients are present. Surfacing high-nickel filler on an austenitic base metal is one of techniques in repair of primary collector the primary circuit of nuclear power plant type VVER. The repair technology was developed at Welding Research Institute Bratislava. Measurements of residual stresses in the weld overlay and the base metal are necessary for approving the mechanical analysis and verifying of residual stresses determination on welded material by numerical weld g computer simulation. Investigations of residual stresses are important for developing optimal welding techniques. (authors)

  11. Antimicrobial residues and resistance against critically important antimicrobials in non-typhoidal Salmonella from meat sold at wet markets and supermarkets in Vietnam.

    Science.gov (United States)

    Nhung, Nguyen Thi; Van, Nguyen Thi Bich; Cuong, Nguyen Van; Duong, Truong Thi Quy; Nhat, Tran Thi; Hang, Tran Thi Thu; Nhi, Nguyen Thi Hong; Kiet, Bach Tuan; Hien, Vo Be; Ngoc, Pham Thi; Campbell, James; Thwaites, Guy; Carrique-Mas, Juan

    2018-02-02

    Excessive antimicrobial usage and deficiencies in hygiene in meat production systems may result in undesirable human health hazards, such as the presence of antimicrobial drug residues and non-typhoidal Salmonella (NTS), including antimicrobial resistant (AMR) NTS. Recently, Vietnam has witnessed the emergence of integrated intensive animal production systems, coexisting with more traditional, locally-sourced wet markets. To date no systematic studies have been carried out to compare health hazards in beef, pork and chicken in different production systems. We aimed to: (1) estimate the prevalence of antimicrobial residues in beef, pork and chicken meat; (2) investigate the prevalence and levels of NTS contamination; and (3) investigate serovar distribution and AMR against critically important antimicrobials by animal species and type of retail (wet market vs. supermarket) in Vietnam. Fresh pork, beef and chicken meat samples (N=357) sourced from wet markets and supermarkets in Ho Chi Minh City (HCMC), Hanoi and Dong Thap were screened for antimicrobial residues by PremiTest, and were further investigated by Charm II. Samples from HCMC (N=113) were cultured using ISO 6579:2002/Amd 1:2007. NTS bacteria were quantified using a minimum probable number (MPN) technique. NTS isolates were assigned to serovar by Multilocus Sequence Typing (MLST), and were investigated for their phenotypic susceptibility against 32 antimicrobials. A total of 26 (7.3%) samples tested positive by PremiTest (9.5% beef, 4.1% pork and 8.4% chicken meat). Sulfonamides, tetracyclines and macrolides were detected by Charm in 3.1%, 2.8% and 2.0% samples, respectively. Overall, meat samples from wet markets had a higher prevalence of residues than those from supermarkets (9.6% vs. 2.6%) (p=0.016). NTS were isolated from 68.4% samples from HCMC. Chicken samples from wet markets had by far the highest NTS counts (median 3.2 logMPN/g). NTS isolates displayed high levels of resistance against quinolones

  12. Structural and dynamic properties of the C-terminal region of the Escherichia coli RNA chaperone Hfq: integrative experimental and computational studies.

    Science.gov (United States)

    Wen, Bin; Wang, Weiwei; Zhang, Jiahai; Gong, Qingguo; Shi, Yunyu; Wu, Jihui; Zhang, Zhiyong

    2017-08-09

    In Escherichia coli, hexameric Hfq is an important RNA chaperone that facilitates small RNA-mediated post-transcriptional regulation. The Hfq monomer consists of an evolutionarily conserved Sm domain (residues 1-65) and a flexible C-terminal region (residues 66-102). It has been recognized that the existence of the C-terminal region is important for the function of Hfq, but its detailed structural and dynamic properties remain elusive due to its disordered nature. In this work, using integrative experimental techniques, such as nuclear magnetic resonance spectroscopy and small-angle X-ray scattering, as well as multi-scale computational simulations, new insights into the structure and dynamics of the C-terminal region in the context of the Hfq hexamer are provided. Although the C-terminal region is intrinsically disordered, some residues (83-86) are motionally restricted. The hexameric core may affect the secondary structure propensity of the C-terminal region, due to transient interactions between them. The residues at the rim and the proximal side of the core have significantly more transient contacts with the C-terminal region than those residues at the distal side, which may facilitate the function of the C-terminal region in the release of double-stranded RNAs and the cycling of small non-coding RNAs. Structure ensembles constructed by fitting the experimental data also support that the C-terminal region prefers to locate at the proximal side. From multi-scale simulations, we propose that the C-terminal region may play a dual role of steric effect (especially at the proximal side) and recruitment (at the both sides) in the binding process of RNA substrates. Interestingly, we have found that these motionally restricted residues may serve as important binding sites for the incoming RNAs that is probably driven by favorable electrostatic interactions. These integrative studies may aid in our understanding of the functional role of the C-terminal region of Hfq.

  13. Three essays on price dynamics and causations among energy markets and macroeconomic information

    Science.gov (United States)

    Hong, Sung Wook

    This dissertation examines three important issues in energy markets: price dynamics, information flow, and structural change. We discuss each issue in detail, building empirical time series models, analyzing the results, and interpreting the findings. First, we examine the contemporaneous interdependencies and information flows among crude oil, natural gas, and electricity prices in the United States (US) through the multivariate generalized autoregressive conditional heteroscedasticity (MGARCH) model, Directed Acyclic Graph (DAG) for contemporaneous causal structures and Bernanke factorization for price dynamic processes. Test results show that the DAG from residuals of out-of-sample-forecast is consistent with the DAG from residuals of within-sample-fit. The result supports innovation accounting analysis based on DAGs using residuals of out-of-sample-forecast. Second, we look at the effects of the federal fund rate and/or WTI crude oil price shock on US macroeconomic and financial indicators by using a Factor Augmented Vector Autoregression (FAVAR) model and a graphical model without any deductive assumption. The results show that, in contemporaneous time, the federal fund rate shock is exogenous as the identifying assumption in the Vector Autoregression (VAR) framework of the monetary shock transmission mechanism, whereas the WTI crude oil price return is not exogenous. Third, we examine price dynamics and contemporaneous causality among the price returns of WTI crude oil, gasoline, corn, and the S&P 500. We look for structural break points and then build an econometric model to find the consistent sub-periods having stable parameters in a given VAR framework and to explain recent movements and interdependency among returns. We found strong evidence of two structural breaks and contemporaneous causal relationships among the residuals, but also significant differences between contemporaneous causal structures for each sub-period.

  14. Effects of single nucleotide polymorphisms on human N-acetyltransferase 2 structure and dynamics by molecular dynamics simulation.

    Directory of Open Access Journals (Sweden)

    M Rajasekaran

    Full Text Available BACKGROUND: Arylamine N-acetyltransferase 2 (NAT2 is an important catalytic enzyme that metabolizes the carcinogenic arylamines, hydrazine drugs and chemicals. This enzyme is highly polymorphic in different human populations. Several polymorphisms of NAT2, including the single amino acid substitutions R64Q, I114T, D122N, L137F, Q145P, R197Q, and G286E, are classified as slow acetylators, whereas the wild-type NAT2 is classified as a fast acetylator. The slow acetylators are often associated with drug toxicity and efficacy as well as cancer susceptibility. The biological functions of these 7 mutations have previously been characterized, but the structural basis behind the reduced catalytic activity and reduced protein level is not clear. METHODOLOGY/PRINCIPAL FINDINGS: We performed multiple molecular dynamics simulations of these mutants as well as NAT2 to investigate the structural and dynamical effects throughout the protein structure, specifically the catalytic triad, cofactor binding site, and the substrate binding pocket. None of these mutations induced unfolding; instead, their effects were confined to the inter-domain, domain 3 and 17-residue insert region, where the flexibility was significantly reduced relative to the wild-type. Structural effects of these mutations propagate through space and cause a change in catalytic triad conformation, cofactor binding site, substrate binding pocket size/shape and electrostatic potential. CONCLUSIONS/SIGNIFICANCE: Our results showed that the dynamical properties of all the mutant structures, especially in inter-domain, domain 3 and 17-residue insert region were affected in the same manner. Similarly, the electrostatic potential of all the mutants were altered and also the functionally important regions such as catalytic triad, cofactor binding site, and substrate binding pocket adopted different orientation and/or conformation relative to the wild-type that may affect the functions of the mutants

  15. Residual mass considerations in modal analysis of large dynamic structural systems

    International Nuclear Information System (INIS)

    Shulman, J.S.; Day, J.P.

    1991-01-01

    Industry guidelines have specified that the seismic evaluation of Moderate and High Hazard Department of Energy (DOE) facilities be accomplished by use of dynamic analysis. The recommended approach is elastic response spectrum dynamic analysis to evaluate the elastic system demand on facility components. The application of modal response spectrum analysis to the seismic evaluation of nuclear facility structures, systems and equipment involves approximations due to limitations on the number of modes typically addressed in the complete dynamic solution. A simplified approach for achieving improved rigor in accounting for responses of the higher frequency modes in a modal response spectrum analysis is demonstrated

  16. A Review on Recycling of Sunflower Residue for Sustaining Soil Health

    Directory of Open Access Journals (Sweden)

    Subhash Babu

    2014-01-01

    Full Text Available Modern agriculture is now at the crossroads ecologically, economically, technologically, and socially due to soil degradation. Critical analysis of available information shows that problems of degradation of soil health are caused due to imbalanced, inadequate and promacronutrient fertilizer use, inadequate use or no use of organic manures and crop residues, and less use of good quality biofertilizers. Although sizeable amount of crop residues and manure is produced in farms, it is becoming increasingly complex to recycle nutrients, even within agricultural systems. Therefore, there is a need to use all available sources of nutrients to maintain the productivity and fertility at a required level. Among the available organic sources of plant nutrients, crop residue is one of the most important sources for supplying nutrients to the crop and for improving soil health. Sunflower is a nontraditional oil seed crop produced in huge amount of crop residue. This much amount of crop residues is neither used as feed for livestock nor suitable for fuel due to low energy value per unit mass. However, its residue contains major plant nutrients in the range from 0.45 to 0.60% N, 0.15 to 0.22% P, and 1.80 to 1.94% K along with secondary and micronutrients, so recycling of its residue in the soil may be one of the best alternative practices for replenishing the depleted soil fertility and improving the physical, chemical, and biological properties of the soil in the present era of production. However, some researchers have reported allelopathic effects of sunflower residue on different crops. So, selection of suitable crops and management practices may play an important role to manage the sunflower residue at field level.

  17. Influences of conformations of peptides on stereoinversions and/or isomerizations of aspartic acid residues.

    Science.gov (United States)

    Oda, Akifumi; Nakayoshi, Tomoki; Fukuyoshi, Shuichi; Kurimoto, Eiji; Takahashi, Ohgi

    2018-07-01

    Recently, non-enzymatic stereoinversions of aspartic acid (Asp) residues in proteins and peptides have been reported. Here, we performed replica exchange molecular dynamics (REMD) simulations of model peptides (exon 6, 26A-1, and 26A-2) extracted from elastin to investigate their structural features, thereby revealing the factor that influences stereoinversions. For REMD trajectories, we calculated distances between carboxyl carbon in Asp and amide nitrogen in the (n + 1) residue (CN distances). Because bond formation between carbon and nitrogen is indispensable to the formation of a succinimide intermediate the distance between them seems to play an important role in stereoinversion. Moreover, we calculated polar surface areas (PSAs) for the trajectories, finding that CN distances and PSA were different for each peptide, with the longest CN distance and smallest PSA observed for exon 6 peptide, where stereoinversion of Asp is the slowest. Although the average CN distance was shorter for exon 26A-1 peptide than for exon 26A-2 peptide, the number of conformations with CN distances acids: biology in the mirror, edited by Dr. Loredano Pollegioni, Dr. Jean-Pierre Mothet and Dr. Molla Gianluca. Copyright © 2018 Elsevier B.V. All rights reserved.

  18. Environmental assessment of incinerator residue utilisation

    Energy Technology Data Exchange (ETDEWEB)

    Toller, Susanna

    2008-10-15

    In Sweden, utilisation of incinerator residues outside disposal areas is restricted by environmental concerns, as such residues commonly contain greater amounts of potentially toxic trace elements than the natural materials they replace. On the other hand, utilisation can also provide environmental benefits by decreasing the need for landfill and reducing raw material extraction. This thesis provides increased knowledge and proposes better approaches for environmental assessment of incinerator residue utilisation, particularly bottom ash from municipal solid waste incineration (MSWI). A life cycle assessment (LCA) based approach was outlined for environmental assessment of incinerator residue utilisation, in which leaching of trace elements as well as other emissions to air and water and the use of resources were regarded as constituting the potential environmental impact from the system studied. Case studies were performed for i) road construction with or without MSWI bottom ash, ii) three management scenarios for MSWI bottom ash and iii) three management scenarios for wood ash. Different types of potential environmental impact predominated in the activities of the system and the scenarios differed in use of resources and energy. Utilising MSWI bottom ash in road construction and recycling of wood ash on forest land saved more natural resources and energy than when these materials were managed according to the other scenarios investigated, including dumping in landfill. There is a potential for trace element leaching regardless of how the ash is managed. Trace element leaching, particularly of copper (Cu), was identified as being relatively important for environmental assessment of MSWI bottom ash utilisation. CuO is suggested as the most important type of Cu-containing mineral in weathered MSWI bottom ash, whereas in the leachate Cu is mainly present in complexes with dissolved organic matter (DOM). The hydrophilic components of the DOM were more important for Cu

  19. A survey of residual analysis and a new test of residual trend.

    Science.gov (United States)

    McDowell, J J; Calvin, Olivia L; Klapes, Bryan

    2016-05-01

    A survey of residual analysis in behavior-analytic research reveals that existing methods are problematic in one way or another. A new test for residual trends is proposed that avoids the problematic features of the existing methods. It entails fitting cubic polynomials to sets of residuals and comparing their effect sizes to those that would be expected if the sets of residuals were random. To this end, sampling distributions of effect sizes for fits of a cubic polynomial to random data were obtained by generating sets of random standardized residuals of various sizes, n. A cubic polynomial was then fitted to each set of residuals and its effect size was calculated. This yielded a sampling distribution of effect sizes for each n. To test for a residual trend in experimental data, the median effect size of cubic-polynomial fits to sets of experimental residuals can be compared to the median of the corresponding sampling distribution of effect sizes for random residuals using a sign test. An example from the literature, which entailed comparing mathematical and computational models of continuous choice, is used to illustrate the utility of the test. © 2016 Society for the Experimental Analysis of Behavior.

  20. 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.

  1. Potential ligand-binding residues in rat olfactory receptors identified by correlated mutation analysis

    Science.gov (United States)

    Singer, M. S.; Oliveira, L.; Vriend, G.; Shepherd, G. M.

    1995-01-01

    A family of G-protein-coupled receptors is believed to mediate the recognition of odor molecules. In order to identify potential ligand-binding residues, we have applied correlated mutation analysis to receptor sequences from the rat. This method identifies pairs of sequence positions where residues remain conserved or mutate in tandem, thereby suggesting structural or functional importance. The analysis supported molecular modeling studies in suggesting several residues in positions that were consistent with ligand-binding function. Two of these positions, dominated by histidine residues, may play important roles in ligand binding and could confer broad specificity to mammalian odor receptors. The presence of positive (overdominant) selection at some of the identified positions provides additional evidence for roles in ligand binding. Higher-order groups of correlated residues were also observed. Each group may interact with an individual ligand determinant, and combinations of these groups may provide a multi-dimensional mechanism for receptor diversity.

  2. Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism.

    Science.gov (United States)

    Goh, Garrett B; Hulbert, Benjamin S; Zhou, Huiqing; Brooks, Charles L

    2014-07-01

    pH is a ubiquitous regulator of biological activity, including protein-folding, protein-protein interactions, and enzymatic activity. Existing constant pH molecular dynamics (CPHMD) models that were developed to address questions related to the pH-dependent properties of proteins are largely based on implicit solvent models. However, implicit solvent models are known to underestimate the desolvation energy of buried charged residues, increasing the error associated with predictions that involve internal ionizable residue that are important in processes like hydrogen transport and electron transfer. Furthermore, discrete water and ions cannot be modeled in implicit solvent, which are important in systems like membrane proteins and ion channels. We report on an explicit solvent constant pH molecular dynamics framework based on multi-site λ-dynamics (CPHMD(MSλD)). In the CPHMD(MSλD) framework, we performed seamless alchemical transitions between protonation and tautomeric states using multi-site λ-dynamics, and designed novel biasing potentials to ensure that the physical end-states are predominantly sampled. We show that explicit solvent CPHMD(MSλD) simulations model realistic pH-dependent properties of proteins such as the Hen-Egg White Lysozyme (HEWL), binding domain of 2-oxoglutarate dehydrogenase (BBL) and N-terminal domain of ribosomal protein L9 (NTL9), and the pKa predictions are in excellent agreement with experimental values, with a RMSE ranging from 0.72 to 0.84 pKa units. With the recent development of the explicit solvent CPHMD(MSλD) framework for nucleic acids, accurate modeling of pH-dependent properties of both major class of biomolecules-proteins and nucleic acids is now possible. © 2013 Wiley Periodicals, Inc.

  3. Dynamic Nucleolar Targeting of Dengue Virus Polymerase NS5 in Response to Extracellular pH

    Science.gov (United States)

    Fraser, Johanna E.; Rawlinson, Stephen M.; Heaton, Steven M.

    2016-01-01

    ABSTRACT The nucleolar subcompartment of the nucleus is increasingly recognized as an important target of RNA viruses. Here we document for the first time the ability of dengue virus (DENV) polymerase, nonstructural protein 5 (NS5), to accumulate within the nucleolus of infected cells and to target green fluorescent protein (GFP) to the nucleolus of live transfected cells. Intriguingly, NS5 exchange between the nucleus and nucleolus is dynamically modulated by extracellular pH, responding rapidly and reversibly to pH change, in contrast to GFP alone or other nucleolar and non-nucleolar targeted protein controls. The minimal pH-sensitive nucleolar targeting region (pHNTR), sufficient to target GFP to the nucleolus in a pH-sensitive fashion, was mapped to NS5 residues 1 to 244, with mutation of key hydrophobic residues, Leu-165, Leu-167, and Val-168, abolishing pHNTR function in NS5-transfected cells, and severely attenuating DENV growth in infected cells. This is the first report of a viral protein whose nucleolar targeting ability is rapidly modulated by extracellular stimuli, suggesting that DENV has the ability to detect and respond dynamically to the extracellular environment. IMPORTANCE Infections by dengue virus (DENV) threaten 40% of the world's population yet there is no approved vaccine or antiviral therapeutic to treat infections. Understanding the molecular details that govern effective viral replication is key for the development of novel antiviral strategies. Here, we describe for the first time dynamic trafficking of DENV nonstructural protein 5 (NS5) to the subnuclear compartment, the nucleolus. We demonstrate that NS5's targeting to the nucleolus occurs in response to acidic pH, identify the key amino acid residues within NS5 that are responsible, and demonstrate that their mutation severely impairs production of infectious DENV. Overall, this study identifies a unique subcellular trafficking event and suggests that DENV is able to detect and respond

  4. Identification of key residues for pH dependent activation of violaxanthin de-epoxidase from Arabidopsis thaliana.

    Science.gov (United States)

    Fufezan, Christian; Simionato, Diana; Morosinotto, Tomas

    2012-01-01

    Plants are often exposed to saturating light conditions, which can lead to oxidative stress. The carotenoid zeaxanthin, synthesized from violaxanthin by Violaxanthin De-Epoxidase (VDE) plays a major role in the protection from excess illumination. VDE activation is triggered by a pH reduction in the thylakoids lumen occurring under saturating light. In this work the mechanism of the VDE activation was investigated on a molecular level using multi conformer continuum electrostatic calculations, site directed mutagenesis and molecular dynamics. The pK(a) values of residues of the inactive VDE were determined to identify target residues that could be implicated in the activation. Five such target residues were investigated closer by site directed mutagenesis, whereas variants in four residues (D98, D117, H168 and D206) caused a reduction in enzymatic activity indicating a role in the activation of VDE while D86 mutants did not show any alteration. The analysis of the VDE sequence showed that the four putative activation residues are all conserved in plants but not in diatoms, explaining why VDE in these algae is already activated at higher pH. Molecular dynamics showed that the VDE structure was coherent at pH 7 with a low amount of water penetrating the hydrophobic barrel. Simulations carried out with the candidate residues locked into their protonated state showed instead an increased amount of water penetrating the barrel and the rupture of the H121-Y214 hydrogen bond at the end of the barrel, which is essential for VDE activation. These results suggest that VDE activation relies on a robust and redundant network, in which the four residues identified in this study play a major role.

  5. Identification of key residues for pH dependent activation of violaxanthin de-epoxidase from Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Christian Fufezan

    Full Text Available Plants are often exposed to saturating light conditions, which can lead to oxidative stress. The carotenoid zeaxanthin, synthesized from violaxanthin by Violaxanthin De-Epoxidase (VDE plays a major role in the protection from excess illumination. VDE activation is triggered by a pH reduction in the thylakoids lumen occurring under saturating light. In this work the mechanism of the VDE activation was investigated on a molecular level using multi conformer continuum electrostatic calculations, site directed mutagenesis and molecular dynamics. The pK(a values of residues of the inactive VDE were determined to identify target residues that could be implicated in the activation. Five such target residues were investigated closer by site directed mutagenesis, whereas variants in four residues (D98, D117, H168 and D206 caused a reduction in enzymatic activity indicating a role in the activation of VDE while D86 mutants did not show any alteration. The analysis of the VDE sequence showed that the four putative activation residues are all conserved in plants but not in diatoms, explaining why VDE in these algae is already activated at higher pH. Molecular dynamics showed that the VDE structure was coherent at pH 7 with a low amount of water penetrating the hydrophobic barrel. Simulations carried out with the candidate residues locked into their protonated state showed instead an increased amount of water penetrating the barrel and the rupture of the H121-Y214 hydrogen bond at the end of the barrel, which is essential for VDE activation. These results suggest that VDE activation relies on a robust and redundant network, in which the four residues identified in this study play a major role.

  6. On machine surface to the unit event causing residual stress

    International Nuclear Information System (INIS)

    Arunachalama, R.M.; Mannanb, M.A.; Spowageca, A.

    2005-01-01

    Integrity and reduce overall costs. Within the framework of surface integrity investigations, special emphasis is given to the measurement of residual stresses because they contribute directly to premature failure of components. Since the highest residual stresses are to be found in surface layers, these deserve special attention when dealing with dynamically, heavily loaded machine parts such as gas turbine components used in aero engines. Of the many techniques available for the measurement of residual stresses, the most highly developed and widely used non-destructive method is based on X-ray diffraction (XRD). However, it is not possible to use this technique for inspection of all the components, since it is time consuming, complicated as well as expensive. In this paper, a method is being proposed that augments the XRD method but at the same time capable of inspecting all the components. A non-destructive, visual inspection technique has been developed that can correlate the characteristic features on the surface to the unit event causing the residual stress and the type of residual stress generated on the machined surface. Pictures of the machined surfaces have been taken using a digital video microscope at a magnification of 500 and the surface feature correlated to the unit event causing the residual stress. Sharp and well defined long grooves indicate that the plastic deformation is dominated by a mechanical unit event while appearance of streaks and small areas of smeared material indicate that the plastic deformation is dominated by a thermal unit event. These trends have been confirmed by measuring the residual stresses using XRD. The proposed technique is an attempt at establishing a simple methodology that would be useful to industries manufacturing aerospace and other components that require good surface integrity. (Author)

  7. 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...... testing and use in the field, consequences and recommendations are given. Failures, caused by harsh[1] customer environments, are not covered in this paper....

  8. Site-Mutation of Hydrophobic Core Residues Synchronically Poise Super Interleukin 2 for Signaling: Identifying Distant Structural Effects through Affordable Computations

    Directory of Open Access Journals (Sweden)

    Longcan Mei

    2018-03-01

    Full Text Available A superkine variant of interleukin-2 with six site mutations away from the binding interface developed from the yeast display technique has been previously characterized as undergoing a distal structure alteration which is responsible for its super-potency and provides an elegant case study with which to get insight about how to utilize allosteric effect to achieve desirable protein functions. By examining the dynamic network and the allosteric pathways related to those mutated residues using various computational approaches, we found that nanosecond time scale all-atom molecular dynamics simulations can identify the dynamic network as efficient as an ensemble algorithm. The differentiated pathways for the six core residues form a dynamic network that outlines the area of structure alteration. The results offer potentials of using affordable computing power to predict allosteric structure of mutants in knowledge-based mutagenesis.

  9. Is residual memory variance a valid method for quantifying cognitive reserve? A longitudinal application

    Science.gov (United States)

    Zahodne, Laura B.; Manly, Jennifer J.; Brickman, Adam M.; Narkhede, Atul; Griffith, Erica Y.; Guzman, Vanessa A.; Schupf, Nicole; Stern, Yaakov

    2016-01-01

    Cognitive reserve describes the mismatch between brain integrity and cognitive performance. Older adults with high cognitive reserve are more resilient to age-related brain pathology. Traditionally, cognitive reserve is indexed indirectly via static proxy variables (e.g., years of education). More recently, cross-sectional studies have suggested that reserve can be expressed as residual variance in episodic memory performance that remains after accounting for demographic factors and brain pathology (whole brain, hippocampal, and white matter hyperintensity volumes). The present study extends these methods to a longitudinal framework in a community-based cohort of 244 older adults who underwent two comprehensive neuropsychological and structural magnetic resonance imaging sessions over 4.6 years. On average, residual memory variance decreased over time, consistent with the idea that cognitive reserve is depleted over time. Individual differences in change in residual memory variance predicted incident dementia, independent of baseline residual memory variance. Multiple-group latent difference score models revealed tighter coupling between brain and language changes among individuals with decreasing residual memory variance. These results suggest that changes in residual memory variance may capture a dynamic aspect of cognitive reserve and could be a useful way to summarize individual cognitive responses to brain changes. Change in residual memory variance among initially non-demented older adults was a better predictor of incident dementia than residual memory variance measured at one time-point. PMID:26348002

  10. Diversity in crop residue management across an intensification gradient in southern Africa

    NARCIS (Netherlands)

    Rusinamhodzi, Leonard; Corbeels, Marc; Giller, Ken E.

    2016-01-01

    Crop residues are important for livestock feed and nutrient cycling among many other functions on smallholder farming systems of sub-Saharan Africa. The objective of this study was to assess differences in resource endowment, crop productivity and crop residue management in selected sites in

  11. New applications of partial residual methodology

    International Nuclear Information System (INIS)

    Uslu, V.R.

    1999-12-01

    The formulation of a problem of interest in the framework of a statistical analysis starts with collecting the data, choosing a model, making certain assumptions as described in the basic paradigm by Box (1980). This stage is is called model building. Then the estimation stage is in order by pretending as if the formulation of the problem was true to obtain estimates, to make tests and inferences. In the final stage, called diagnostic checking, checking of whether there are some disagreements between the data and the model fitted is done by using diagnostic measures and diagnostic plots. It is well known that statistical methods perform best under the condition that all assumptions related to the methods are satisfied. However it is true that having the ideal case in practice is very difficult. Diagnostics are therefore becoming important so are diagnostic plots because they provide a immediate assessment. Partial residual plots that are the main interest of the present study are playing the major role among the diagnostic plots in multiple regression analysis. In statistical literature it is admitted that partial residual plots are more useful than ordinary residual plots in detecting outliers, nonconstant variance, and especially discovering curvatures. In this study we consider the partial residual methodology in statistical methods rather than multiple regression. We have shown that for the same purpose as in the multiple regression the use of partial residual plots is possible particularly in autoregressive time series models, transfer function models, linear mixed models and ridge regression. (author)

  12. Some connections between importance sampling and enhanced sampling methods in molecular dynamics.

    Science.gov (United States)

    Lie, H C; Quer, J

    2017-11-21

    In molecular dynamics, enhanced sampling methods enable the collection of better statistics of rare events from a reference or target distribution. We show that a large class of these methods is based on the idea of importance sampling from mathematical statistics. We illustrate this connection by comparing the Hartmann-Schütte method for rare event simulation (J. Stat. Mech. Theor. Exp. 2012, P11004) and the Valsson-Parrinello method of variationally enhanced sampling [Phys. Rev. Lett. 113, 090601 (2014)]. We use this connection in order to discuss how recent results from the Monte Carlo methods literature can guide the development of enhanced sampling methods.

  13. Presence of pesticide residues on produce cultivated in Suriname.

    Science.gov (United States)

    Abdoel Wahid, F; Wickliffe, J; Wilson, M; Van Sauers, A; Bond, N; Hawkins, W; Mans, D; Lichtveld, M

    2017-06-01

    Agricultural pesticides are widely used in Suriname, an upper middle-income Caribbean country located in South America. Suriname imported 1.8 million kg of agricultural pesticides in 2015. So far, however, national monitoring of pesticides in crops is absent. Reports from the Netherlands on imported Surinamese produce from 2010 to 2015 consistently showed that samples exceeded plant-specific pesticide maximum residue limits (MRLs) of the European Union (EU). Consumption of produce containing unsafe levels of pesticide residues can cause neurological disorders, and particularly, pregnant women and children may be vulnerable. This pilot study assessed the presence of pesticide residues in commonly consumed produce items cultivated in Suriname. Thirty-two insecticides (organophosphates, organochlorines, carbamates, and pyrethroids) and 12 fungicides were evaluated for their levels in nine types of produce. Pesticide residue levels exceeding MRLs in this study regarded cypermethrin (0.32 μg/g) in tomatoes (USA MRL 0.20 μg/g), lambda-cyhalothrin (1.08 μg/g) in Chinese cabbage (USA MRL 0.40 μg/g), endosulfan (0.07 μg/g) in tannia (EU MRL 0.05 μg/g), and lindane (0.02 and 0.03 μg/g, respectively) in tannia (EU MRL 0.01 μg/g). While only a few pesticide residues were detected in this small pilot study, these residues included two widely banned pesticides (endosulfan and lindane). There is a need to address environmental policy gaps. A more comprehensive sampling and analysis of produce from Suriname is warranted to better understand the scope of the problem. Preliminary assessments, using intake rate, hazard quotient, and level of concern showed that it is unlikely that daily consumption of tannia leads to adverse health effects.

  14. Annotating Protein Functional Residues by Coupling High-Throughput Fitness Profile and Homologous-Structure Analysis.

    Science.gov (United States)

    Du, Yushen; Wu, Nicholas C; Jiang, Lin; Zhang, Tianhao; Gong, Danyang; Shu, Sara; Wu, Ting-Ting; Sun, Ren

    2016-11-01

    Identification and annotation of functional residues are fundamental questions in protein sequence analysis. Sequence and structure conservation provides valuable information to tackle these questions. It is, however, limited by the incomplete sampling of sequence space in natural evolution. Moreover, proteins often have multiple functions, with overlapping sequences that present challenges to accurate annotation of the exact functions of individual residues by conservation-based methods. Using the influenza A virus PB1 protein as an example, we developed a method to systematically identify and annotate functional residues. We used saturation mutagenesis and high-throughput sequencing to measure the replication capacity of single nucleotide mutations across the entire PB1 protein. After predicting protein stability upon mutations, we identified functional PB1 residues that are essential for viral replication. To further annotate the functional residues important to the canonical or noncanonical functions of viral RNA-dependent RNA polymerase (vRdRp), we performed a homologous-structure analysis with 16 different vRdRp structures. We achieved high sensitivity in annotating the known canonical polymerase functional residues. Moreover, we identified a cluster of noncanonical functional residues located in the loop region of the PB1 β-ribbon. We further demonstrated that these residues were important for PB1 protein nuclear import through the interaction with Ran-binding protein 5. In summary, we developed a systematic and sensitive method to identify and annotate functional residues that are not restrained by sequence conservation. Importantly, this method is generally applicable to other proteins about which homologous-structure information is available. To fully comprehend the diverse functions of a protein, it is essential to understand the functionality of individual residues. Current methods are highly dependent on evolutionary sequence conservation, which is

  15. Formulation of morning product using food residues

    Directory of Open Access Journals (Sweden)

    Maria do Rosário de Fátima Padilha

    2017-09-01

    Full Text Available In Brazil, there is resistance of the population to the use of stalks, leaves, peels and seeds of vegetables and fruits, leading to trash important parts of the food in good physiological conditions and with the presence of potential nutrients. In this research, a morning product was elaborated using green and dry coconut residue, jerimum and melon seed, crystallized sicilian lemon peel, cashew nut, common rapadura sweet and ginger. The bacteriological tests proved the hygienic-sanitary quality of the product, therefore suitable for consumption, that is, according to RDC 12/2001. It was also observed that the dehydration of all the residues reached the legal levels and accepted by ANVISA that limits in 25% the water content in the dehydrated foods. As for the centesimal composition, it was observed that the elaborated product with residues and other ingredients had a good content of macro nutrients. A use of the type of waste as a new food proposal constitutes an alternative to avoid and reduce: the serious environmental problem caused by the large residual volume generated, and the inadequate places in which they are stored or deposited, aggravating the scenario of food-borne pollutants.

  16. Measuring depth profiles of residual stress with Raman spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Enloe, W.S.; Sparks, R.G.; Paesler, M.A.

    1988-12-01

    Knowledge of the variation of residual stress is a very important factor in understanding the properties of machined surfaces. The nature of the residual stress can determine a part`s susceptibility to wear deformation, and cracking. Raman spectroscopy is known to be a very useful technique for measuring residual stress in many materials. These measurements are routinely made with a lateral resolution of 1{mu}m and an accuracy of 0.1 kbar. The variation of stress with depth; however, has not received much attention in the past. A novel technique has been developed that allows quantitative measurement of the variation of the residual stress with depth with an accuracy of 10nm in the z direction. Qualitative techniques for determining whether the stress is varying with depth are presented. It is also demonstrated that when the stress is changing over the volume sampled, errors can be introduced if the variation of the stress with depth is ignored. Computer aided data analysis is used to determine the depth dependence of the residual stress.

  17. Renewable energy potential from biomass residues in Egypt

    Energy Technology Data Exchange (ETDEWEB)

    Said, N.; Zamorano, M. [Civil Engineering Dept., Univ. of Granada, Campus de Fuentenueva, Granada (Spain); El-Shatoury, S.A. [Botany Dept., Faculty of Sciences, Suez Canal Univ., Ismailia (Egypt)

    2012-11-01

    Egypt has been one of the developing countries following successful programs for the development of renewable energy resources, with special emphasis on solar, wind and biomass. Utilization of biomass as a source of energy is important from energetic as well as environmental viewpoint. Furthermore, Egypt produces millions of biomass waste every year causing pollution and health problems. So, the incorporation of biomass with other renewable energy will increase the impact of solving energy and environmental problem. There is a good potential for the utilization of biomass energy resources in Egypt. Four main types of biomass energy sources are included in this study: agricultural residues, municipal solid wastes, animal wastes and sewage sludge. Analysis of the potential biomass resource quantity and its theoretical energy content has been computed according to literature review. The agriculture crop residue represents the main source of biomass waste with a high considerable amount of the theoretical potential energy in Egypt. Rice straw is considered one of the most important of such residue due to its high amount and its produced energy through different conversion techniques represent a suitable candidate for crop energy production in Egypt.

  18. Identification of mannose interacting residues using local composition.

    Directory of Open Access Journals (Sweden)

    Sandhya Agarwal

    Full Text Available BACKGROUND: Mannose binding proteins (MBPs play a vital role in several biological functions such as defense mechanisms. These proteins bind to mannose on the surface of a wide range of pathogens and help in eliminating these pathogens from our body. Thus, it is important to identify mannose interacting residues (MIRs in order to understand mechanism of recognition of pathogens by MBPs. RESULTS: This paper describes modules developed for predicting MIRs in a protein. Support vector machine (SVM based models have been developed on 120 mannose binding protein chains, where no two chains have more than 25% sequence similarity. SVM models were developed on two types of datasets: 1 main dataset consists of 1029 mannose interacting and 1029 non-interacting residues, 2 realistic dataset consists of 1029 mannose interacting and 10320 non-interacting residues. In this study, firstly, we developed standard modules using binary and PSSM profile of patterns and got maximum MCC around 0.32. Secondly, we developed SVM modules using composition profile of patterns and achieved maximum MCC around 0.74 with accuracy 86.64% on main dataset. Thirdly, we developed a model on a realistic dataset and achieved maximum MCC of 0.62 with accuracy 93.08%. Based on this study, a standalone program and web server have been developed for predicting mannose interacting residues in proteins (http://www.imtech.res.in/raghava/premier/. CONCLUSIONS: Compositional analysis of mannose interacting and non-interacting residues shows that certain types of residues are preferred in mannose interaction. It was also observed that residues around mannose interacting residues have a preference for certain types of residues. Composition of patterns/peptide/segment has been used for predicting MIRs and achieved reasonable high accuracy. It is possible that this novel strategy may be effective to predict other types of interacting residues. This study will be useful in annotating the function

  19. Nuclear magnetic resonance provides a quantitative description of protein conformational flexibility on physiologically important time scales.

    Science.gov (United States)

    Salmon, Loïc; Bouvignies, Guillaume; Markwick, Phineus; Blackledge, Martin

    2011-04-12

    A complete description of biomolecular activity requires an understanding of the nature and the role of protein conformational dynamics. In recent years, novel nuclear magnetic resonance-based techniques that provide hitherto inaccessible detail concerning biomolecular motions occurring on physiologically important time scales have emerged. Residual dipolar couplings (RDCs) provide precise information about time- and ensemble-averaged structural and dynamic processes with correlation times up to the millisecond and thereby encode key information for understanding biological activity. In this review, we present the application of two very different approaches to the quantitative description of protein motion using RDCs. The first is purely analytical, describing backbone dynamics in terms of diffusive motions of each peptide plane, using extensive statistical analysis to validate the proposed dynamic modes. The second is based on restraint-free accelerated molecular dynamics simulation, providing statistically sampled free energy-weighted ensembles that describe conformational fluctuations occurring on time scales from pico- to milliseconds, at atomic resolution. Remarkably, the results from these two approaches converge closely in terms of distribution and absolute amplitude of motions, suggesting that this kind of combination of analytical and numerical models is now capable of providing a unified description of protein conformational dynamics in solution.

  20. Evaluation of residue-residue contact predictions in CASP9

    KAUST Repository

    Monastyrskyy, Bohdan; Fidelis, Krzysztof; Tramontano, Anna; Kryshtafovych, Andriy

    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

  1. Endrin in birds: Lethal residues and secondary poisoning

    Science.gov (United States)

    Stickel, W.H.; Reichel, W.L.; Hughes, D.L.

    1979-01-01

    Endrin residues in brains that are diagnostic of death were determined for several species of birds. Residues of 0.8 ppm or more of endrin in brain meant death; 0.6 ppm or less meant survival; between was a zone of overlap. These criteria indicate that some wild birds of the U.S., particularly white pelicans in the Northwest and two bald eagles, have been killed by endrin. Signs of endrin poisoning in experimental birds are described. The important and highly toxic metabolite in rodents, 12-ketoendrin, was sought but not found.

  2. BROMOCEA Code: An Improved Grand Canonical Monte Carlo/Brownian Dynamics Algorithm Including Explicit Atoms.

    Science.gov (United States)

    Solano, Carlos J F; Pothula, Karunakar R; Prajapati, Jigneshkumar D; De Biase, Pablo M; Noskov, Sergei Yu; Kleinekathöfer, Ulrich

    2016-05-10

    All-atom molecular dynamics simulations have a long history of applications studying ion and substrate permeation across biological and artificial pores. While offering unprecedented insights into the underpinning transport processes, MD simulations are limited in time-scales and ability to simulate physiological membrane potentials or asymmetric salt solutions and require substantial computational power. While several approaches to circumvent all of these limitations were developed, Brownian dynamics simulations remain an attractive option to the field. The main limitation, however, is an apparent lack of protein flexibility important for the accurate description of permeation events. In the present contribution, we report an extension of the Brownian dynamics scheme which includes conformational dynamics. To achieve this goal, the dynamics of amino-acid residues was incorporated into the many-body potential of mean force and into the Langevin equations of motion. The developed software solution, called BROMOCEA, was applied to ion transport through OmpC as a test case. Compared to fully atomistic simulations, the results show a clear improvement in the ratio of permeating anions and cations. The present tests strongly indicate that pore flexibility can enhance permeation properties which will become even more important in future applications to substrate translocation.

  3. Measurement of residual stress in materials using neutrons. Proceedings of a technical meeting

    International Nuclear Information System (INIS)

    2005-06-01

    One of the objectives of the IAEA's project on effective utilization of research reactors is to promote the use of the existing research reactors based on their capabilities and is implemented through workshops and technical meetings. Measurement of residual stress is one of the techniques that find wide applications in materials development and testing. The Technical Meeting on Measurement of Residual Stress Using Neutrons was organized to meet this objective. This publication is the outcome of the deliberations during the meeting and the presentations by the participants and is addressed to the research reactor managers, users and designers of facilities for reactor utilization. It will especially benefit those seeking to develop new facilities or upgrade the existing ones to enhance the utilization of their research reactors. Experts with a long experience in developing and using neutron beam instruments in high flux and medium flux research reactors participated in this technical meeting. They presented the design, development and utilization of the facilities at their respective centres and reviewed the current status of the residual stress measurements using neutron beams from research reactors. The sessions included brainstorming on the methodology and data analysis, characterization and standardization of the equipment and identifying the scope for further development. This publication refers to the determination of residual and/or applied stresses in polycrystalline materials using neutron diffraction technique. Stress is developed during the synthesis and use of materials such as alloys and compounds. Measurement of residual stress is essential to improve the quality of synthesized materials and diagnosis of failure and/or reliability of fabricated components. Neutron scattering has played an important role in studying structure and dynamics of condensed matter. Neutron scattering is a non-destructive technique and is useful for testing large samples. The

  4. Dynamic MR imaging of pituitary adenoma

    International Nuclear Information System (INIS)

    Miki, Yukio; Nishizawa, Sadahiko; Kuroda, Yasumasa; Keyaki, Atsushi; Nabeshima, Sachio; Kawamura, Junichiro; Matsuo, Michimasa

    1990-01-01

    The authors performed serial dynamic MR imaging in patients with 10 normal pituitary and 21 pituitary adenoma utilizing spin-echo sequence with a very short repetition time (SE 100/15) every minute immediately after a bolus injection of Gd-DTPA. Usual T 1 -weighted images (SE 600/15) were also obtained before and after the dynamic study. Pituitary adenomas included 10 adenomas confirmed by surgery, 4 adenomas confirmed by biologic data, and 7 postoperative adenomas. Out of 10 patients who underwent surgery after dynamic MRI, 9 patients underwent postoperative dynamic MRI. In normal patients, the pituitary gland was markedly enhanced on the early-phase images of the dynamic study, followed by gradual decrease of intensity throughout the dynamic study. In cases of microadenomas, the contrast between the normal pituitary gland and adenoma is better than that on the usual T 1 -weighted images by marked enhancement of the normal pituitary gland. Dynamic images clearly showed the residual normal pituitary glands in all cases of macroadenoma larger than 15 mm in diameter, whereas usual contrast-enhanced images showed the normal pituitary gland only in one case. In all patients who underwent both preoperative and postoperative dynamic MRI, postoperative dynamic MRI showed the normal pituitary glands which are markedly enhanced on the early-phase images in the sites which correspond to the preoperative dynamic study. The normal residual anterior gland was also visualized in four out of 7 patients who received only postoperative dynamic MRI. Dynamic MRI is a strong diagnostic modality for visualizing microadenoma and for visualizing the normal pituitary gland in cases of preoperative and postoperative macroadenoma. (author)

  5. Residue-Specific Side-Chain Polymorphisms via Particle Belief Propagation.

    Science.gov (United States)

    Ghoraie, Laleh Soltan; Burkowski, Forbes; Li, Shuai Cheng; Zhu, Mu

    2014-01-01

    Protein side chains populate diverse conformational ensembles in crystals. Despite much evidence that there is widespread conformational polymorphism in protein side chains, most of the X-ray crystallography data are modeled by single conformations in the Protein Data Bank. The ability to extract or to predict these conformational polymorphisms is of crucial importance, as it facilitates deeper understanding of protein dynamics and functionality. In this paper, we describe a computational strategy capable of predicting side-chain polymorphisms. Our approach extends a particular class of algorithms for side-chain prediction by modeling the side-chain dihedral angles more appropriately as continuous rather than discrete variables. Employing a new inferential technique known as particle belief propagation, we predict residue-specific distributions that encode information about side-chain polymorphisms. Our predicted polymorphisms are in relatively close agreement with results from a state-of-the-art approach based on X-ray crystallography data, which characterizes the conformational polymorphisms of side chains using electron density information, and has successfully discovered previously unmodeled conformations.

  6. The Study of Residual Voltage of Induction Motor and the Influence of Various Parameters on the Residual Voltage

    Science.gov (United States)

    Zhang, Shuping; Zhao, Chen; Tan, Weipu

    2017-05-01

    The majority important load of industrial area is mainly composed of induction motor, it is more common that induction motor becomes sluggishness and even tripping due to the lose of power supply or other malfunction in the practical work. In this paper, space vector method is used to establish a reduced order model of induction motor, and then study the changes of motor electromagnetic after losing electricity. Based on motion equations of the rotor and magnetic flux conservation principle, it uses mathematical methods to deduce the expression of rotor current, rotor flux, the stator flux and the residual voltage of stator side. In addition, relying on thermal power plants, it uses the actual data of power plants, takes DIgsilent software to simulate the residual voltage of motor after losing electricity. analyses the influence on the residual voltage with the changes of the moment of inertia, load ratio, initial size of slip and the load characteristic of induction motor. By analysis of these, it has a more detailed understanding about the changes of residual voltage in practical application, in additional, it is more beneficial to put into standby power supply safely and effectively, moreover, reduce the influence of the input process to the whole system.

  7. Exploiting residual information in the parameter choice for discrete ill-posed problems

    DEFF Research Database (Denmark)

    Hansen, Per Christian; Kilmer, Misha E.; Kjeldsen, Rikke Høj

    2006-01-01

    Most algorithms for choosing the regularization parameter in a discrete ill-posed problem are based on the norm of the residual vector. In this work we propose a different approach, where we seek to use all the information available in the residual vector. We present important relations between...

  8. The Ising model for prediction of disordered residues from protein sequence alone

    International Nuclear Information System (INIS)

    Lobanov, Michail Yu; Galzitskaya, Oxana V

    2011-01-01

    Intrinsically disordered regions serve as molecular recognition elements, which play an important role in the control of many cellular processes and signaling pathways. It is useful to be able to predict positions of disordered residues and disordered regions in protein chains using protein sequence alone. A new method (IsUnstruct) based on the Ising model for prediction of disordered residues from protein sequence alone has been developed. According to this model, each residue can be in one of two states: ordered or disordered. The model is an approximation of the Ising model in which the interaction term between neighbors has been replaced by a penalty for changing between states (the energy of border). The IsUnstruct has been compared with other available methods and found to perform well. The method correctly finds 77% of disordered residues as well as 87% of ordered residues in the CASP8 database, and 72% of disordered residues as well as 85% of ordered residues in the DisProt database

  9. The evaluation of hierarchical structured superhydrophobic coatings for the alleviation of insect residue to aircraft laminar flow surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Kok, Mariana [Department of Mechanical, Aeronautical and Biomedical Engineering, University of Limerick, Limerick (Ireland); Materials and Surface Science Institute, University of Limerick, Limerick (Ireland); Young, Trevor M., E-mail: Trevor.Young@ul.ie [Department of Mechanical, Aeronautical and Biomedical Engineering, University of Limerick, Limerick (Ireland); Materials and Surface Science Institute, University of Limerick, Limerick (Ireland)

    2014-09-30

    Surface contamination caused by insects on laminar flow wing surfaces causes a disruption of the flow, resulting in an increase in drag and fuel consumption. Consequently, the use of superhydrophobic coatings to mitigate insect residue adhesion was investigated. A range of hierarchical superhydrophobic coatings with different surface chemistry and topography was examined. Candidate coatings were characterized in terms of their morphology and hydrophobic properties by scanning electron microscopy (SEM) and static and dynamic contact angle measurements, respectively. Arithmetic mean surface roughness (R{sub a}) values were measured using profilometry. Only superhydrophobic coatings with a specific topography showed complete mitigation against insect residue adhesion. A surface which exhibited a specific microstructure (R{sub a} = 5.26 μm) combined with a low sliding angle (SA = 7.6°) showed the best anti-contamination properties. The dynamics of an insect impact event and its influence on the wetting and adhesion mechanisms of insect residue to a surface were discussed.

  10. Effect of processing conditions on residual stress distributions by bead-on-plate welding after surface machining

    International Nuclear Information System (INIS)

    Ihara, Ryohei; Mochizuki, Masahito

    2014-01-01

    Residual stress is important factor for stress corrosion cracking (SCC) that has been observed near the welded zone in nuclear power plants. Especially, surface residual stress is significant for SCC initiation. In the joining processes of pipes, butt welding is conducted after surface machining. Residual stress is generated by both processes, and residual stress distribution due to surface machining is varied by the subsequent butt welding. In previous paper, authors reported that residual stress distribution generated by bead on plate welding after surface machining has a local maximum residual stress near the weld metal. The local maximum residual stress shows approximately 900 MPa that exceeds the stress threshold for SCC initiation. Therefore, for the safety improvement of nuclear power plants, a study on the local maximum residual stress is important. In this study, the effect of surface machining and welding conditions on residual stress distribution generated by welding after surface machining was investigated. Surface machining using lathe machine and bead on plate welding with tungsten inert gas (TIG) arc under various conditions were conducted for plate specimens made of SUS316L. Then, residual stress distributions were measured by X-ray diffraction method (XRD). As a result, residual stress distributions have the local maximum residual stress near the weld metal in all specimens. The values of the local maximum residual stresses are almost the same. The location of the local maximum residual stress is varied by welding condition. It could be consider that the local maximum residual stress is generated by same generation mechanism as welding residual stress in surface machined layer that has high yield stress. (author)

  11. Is residual memory variance a valid method for quantifying cognitive reserve? A longitudinal application.

    Science.gov (United States)

    Zahodne, Laura B; Manly, Jennifer J; Brickman, Adam M; Narkhede, Atul; Griffith, Erica Y; Guzman, Vanessa A; Schupf, Nicole; Stern, Yaakov

    2015-10-01

    Cognitive reserve describes the mismatch between brain integrity and cognitive performance. Older adults with high cognitive reserve are more resilient to age-related brain pathology. Traditionally, cognitive reserve is indexed indirectly via static proxy variables (e.g., years of education). More recently, cross-sectional studies have suggested that reserve can be expressed as residual variance in episodic memory performance that remains after accounting for demographic factors and brain pathology (whole brain, hippocampal, and white matter hyperintensity volumes). The present study extends these methods to a longitudinal framework in a community-based cohort of 244 older adults who underwent two comprehensive neuropsychological and structural magnetic resonance imaging sessions over 4.6 years. On average, residual memory variance decreased over time, consistent with the idea that cognitive reserve is depleted over time. Individual differences in change in residual memory variance predicted incident dementia, independent of baseline residual memory variance. Multiple-group latent difference score models revealed tighter coupling between brain and language changes among individuals with decreasing residual memory variance. These results suggest that changes in residual memory variance may capture a dynamic aspect of cognitive reserve and could be a useful way to summarize individual cognitive responses to brain changes. Change in residual memory variance among initially non-demented older adults was a better predictor of incident dementia than residual memory variance measured at one time-point. Copyright © 2015. Published by Elsevier Ltd.

  12. Production of ferrous sulfate from residue from the iron mining

    International Nuclear Information System (INIS)

    Cardoso, K.A; Riella, H.G.; Abreu, E.F.; Carvalho, E.F. Urano de; Durazzo, M.

    2012-01-01

    This paper was developed from a residue obtained by processing iron ore exploited by the mining company Samarco S/A. The residue was characterized and the analyses showed that it contains about 70% of the mineral hematite (Fe 2 O 3 ) and also that some economically important products could be produced. One is the ferrous sulfate that can be used in pharmaceuticals and also that can be used in the treatment of iron deficiency anemia. The iron, in addition to is importance for the industrial production of steel and parts in general, also has great biological importance in all living beings. In order to produce ferrous sulfate from the byproduct in question, it was developed a obtaining route using metallic iron as hematite reductor and sulfuric acid to form the salt. (author)

  13. Measurement of edge residual stresses in glass by the phase-shifting method

    Science.gov (United States)

    Ajovalasit, A.; Petrucci, G.; Scafidi, M.

    2011-05-01

    Control and measurement of residual stress in glass is of great importance in the industrial field. Since glass is a birefringent material, the residual stress analysis is based mainly on the photoelastic method. This paper considers two methods of automated analysis of membrane residual stress in glass sheets, based on the phase-shifting concept in monochromatic light. In particular these methods are the automated versions of goniometric compensation methods of Tardy and Sénarmont. The proposed methods can effectively replace manual methods of compensation (goniometric compensation of Tardy and Sénarmont, Babinet and Babinet-Soleil compensators) provided by current standards on the analysis of residual stresses in glasses.

  14. Dynamic effects of soil bulk density on denitrification and mineralisation by 15N labelled lettuce residue and paper wastes

    International Nuclear Information System (INIS)

    Hua Luo; Cheng Qing; Vinten, A.J.A.

    1997-10-01

    Two laboratory incubation experiments aimed to study the denitrification and mineralisation influenced by different additives ( 15 N labelled lettuce residue, paper wastes and mixture of both) and soil bulk densities were carried out by means of acetylene inhibition at the constant 15 degree C for 107 and 90 days, respectively. The results showed that the changes of N 2 O, CO 2 emission rates, inorganic nitrogen (NO 3 - and NH 4 + ), total N and 15 N abundance in the soils which were affected by adding lettuce residue, paper wastes and mixture of both were investigated. Soil denitrification rate increased after lettuce residue was added into soil for 8 days. The maximum rate of N 2 O emission was 15 times higher than that in soil without any additive. However, paper wastes did not increase N 2 O emission in the first 8 days compared with other treatments, mixed residue and paper wastes could promote soil microbial activity, but N 2 O emission was lower than that in the soil with lettuce residue added and higher than that with paper wastes, indicating that mixture of residue and paper wastes was benefit to soil nitrogen immobilisation. CO 2 emission in all the treatments were declined to the same level on the 107 th day. In the treatment added mixed residues and paper wastes, the released CO 2 quantities were higher than those in other treatments every day. Effect of different bulk density on N 2 O and CO 2 emission were response to the change of bulk density, it seems that N 2 O and CO 2 emission increased with bulk density. High bulk density could affect decomposition of paper wastes and NO 3 - , NH 4 + concentration. (30 ref., 10 tabs.)

  15. Application of backpropagation neural networks to evaluate residual properties of thermally damaged concrete

    International Nuclear Information System (INIS)

    Vasconcelos, W.L.; Shigaki, Y.; Tolentino, E.

    2009-01-01

    In this work it was analyzed the residual performance of Portland cement concretes, when cold after heat-treated up to 600 deg C. Granite-gneiss was used in the three concrete mix proportions as the coarse aggregate, and river sand with finesses modulus of 2.7 as the fine aggregate. Ultrasonic pulse tests were performed on all the specimens and ultrasonic dynamic modulus were obtained. An artificial neural network of the backpropagation type was trained to evaluate and apply models in predicting residual properties of Portland cement concretes. The input layer for both models consists of an external layer input vector of the temperature. The hidden layer has two processing units with hyperbolic tangent sigmoid transfer functions (tansig for short), and the output layer contains one processing unit that represents the network's output (ultrasonic pulse velocity or modulus of elasticity) for each input vector. The training phase of the network converged for reasonable results after 5.000 epochs approximately, resulting in mean squared errors less than 0.02 for the normalized data. The neural network developed for modeling residual properties of Portland cement concretes was shown to be efficient in both the training phase and the test. From the results reasonable predictions could be made for the ultrasonic pulse velocity or dynamic modulus of elasticity by using temperature. (author)

  16. Global Harmonization of Maximum Residue Limits for Pesticides.

    Science.gov (United States)

    Ambrus, Árpád; Yang, Yong Zhen

    2016-01-13

    International trade plays an important role in national economics. The Codex Alimentarius Commission develops harmonized international food standards, guidelines, and codes of practice to protect the health of consumers and to ensure fair practices in the food trade. The Codex maximum residue limits (MRLs) elaborated by the Codex Committee on Pesticide Residues are based on the recommendations of the FAO/WHO Joint Meeting on Pesticides (JMPR). The basic principles applied currently by the JMPR for the evaluation of experimental data and related information are described together with some of the areas in which further developments are needed.

  17. The prediction of the residual life of electromechanical equipment based on the artificial neural network

    Science.gov (United States)

    Zhukovskiy, Yu L.; Korolev, N. A.; Babanova, I. S.; Boikov, A. V.

    2017-10-01

    This article is devoted to the prediction of the residual life based on an estimate of the technical state of the induction motor. The proposed system allows to increase the accuracy and completeness of diagnostics by using an artificial neural network (ANN), and also identify and predict faulty states of an electrical equipment in dynamics. The results of the proposed system for estimation the technical condition are probability technical state diagrams and a quantitative evaluation of the residual life, taking into account electrical, vibrational, indirect parameters and detected defects. Based on the evaluation of the technical condition and the prediction of the residual life, a decision is made to change the control of the operating and maintenance modes of the electric motors.

  18. Catalytically important amino-acid residues of abalone alginate lyase HdAly assessed by site-directed mutagenesis

    OpenAIRE

    Yamamoto, Sayo; Sahara, Takehiko; Sato, Daisuke; Kawasaki, Kosei; Ohgiya, Satoru; Inoue, Akira; Ojima, Takao

    2008-01-01

    Alginate lyase is an enzyme that degrades alginate chains via β-elimination and has been used for the production of alginate oligosaccharides and protoplasts from brown algae. Previously, we deduced the amino-acid sequence of an abalone alginate lyase, HdAly, from its cDNA sequence and, through multiple amino-acid sequence alignment, found that several basic amino-acid residues were highly conserved among the polysaccharide-lyase family 14 (PL-14) enzymes including HdAly. In the present study...

  19. Residual stress analysis for engineering applications by means of neutron diffraction

    International Nuclear Information System (INIS)

    Gnaeupel-Herold, T.; Brand, P.C.; Prask, H.J.

    1999-01-01

    Residual stresses originate from spatial differences in plastic deformation, temperature, or phase distribution, introduced by manufacturing processes or during service. Engineering parts and materials experience mechanical, thermal, and chemical loads during their service, and most of these loads introduce stresses that are superimposed on the already existing residual stresses. Residual stresses can therefore limit or improve life and strength of engineering parts; knowledge and understanding of these stresses is therefore critical for optimizing strength and durability. The economic and scientific importance of neutron diffraction residual stress analysis has led to an increasing number of suitable instruments worldwide. All of the major sources due in the next several years will have instruments for the sole purpose of performing residual stress and texture measurements. Recently, a dedicated, state-of-the-art diffractometer has been installed at the National Institute of Standards and Technology reactor. It has been used for a variety of measurements on basic and engineering stress problems. Among the most prominent examples that have been investigated in collaboration with industrial and academic partners are residual stresses in rails, weldments, and plasma-sprayed coatings

  20. Residual gas analysis

    International Nuclear Information System (INIS)

    Berecz, I.

    1982-01-01

    Determination of the residual gas composition in vacuum systems by a special mass spectrometric method was presented. The quadrupole mass spectrometer (QMS) and its application in thin film technology was discussed. Results, partial pressure versus time curves as well as the line spectra of the residual gases in case of the vaporization of a Ti-Pd-Au alloy were demonstrated together with the possible construction schemes of QMS residual gas analysers. (Sz.J.)

  1. Assessing the Availability of Wood Residues and Residue Markets in Virginia

    OpenAIRE

    Alderman, Delton R. Jr.

    1998-01-01

    A statewide mail survey of primary and secondary wood product manufacturers was undertaken to quantify the production and consumption of wood residues in Virginia. Two hundred and sixty-six wood product manufacturers responded to the study and they provided information on the production, consumption, markets, income or disposal costs, and disposal methods of wood residues. Hardwood and pine sawmills produce approximately 66 percent of Virginia's wood residues. Virginia's wood product man...

  2. Biogas systems for sisal and other agro-industrial residues

    Energy Technology Data Exchange (ETDEWEB)

    Jungersen, G [Danish Technological Inst., Section for Biotechnology, Taastrup (Denmark)

    1998-12-31

    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)

  3. 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)

  4. The influence of alloy composition on residual stresses in heat treated aluminium alloys

    Energy Technology Data Exchange (ETDEWEB)

    Robinson, J.S., E-mail: jeremy.robinson@ul.ie [Department of Mechanical, Aeronautical and Biomedical Engineering, University of Limerick (Ireland); Redington, W. [Materials and Surface Science Institute, University of Limerick (Ireland)

    2015-07-15

    The as quenched properties of eight different heat treatable aluminium alloys are related to residual stress magnitudes with the objective being to establish if there is a relationship between the residual stress and the as quenched alloy hardness and strength. Near surface residual stresses were assessed with X-ray diffraction using both the established sin{sup 2}ψ method and the more recent cos α technique. Through thickness residual stresses were also characterised using neutron diffraction. The alloys were chosen to encompass a wide range of strengths. The low to medium strength alloys were 6060 and 6082, medium to high strength 2618A, 2014A, 7075, 7010 and two variants of 7449, while the very high strength alloy was the powder metallurgy alloy N707. To assess the as quenched strength, dynamic hardness and tensile properties were determined from samples tested immediately after quenching to minimise the influence of precipitation hardening by natural aging. In addition, hot hardness measurements were made in situ on samples cooled to simulate quench paths. Within the experimental constraints of the investigation, the distribution of residual stress through the thickness was found to follow the same pattern for all the alloys investigated, varying from tensile in the interior to surface compression. The influence of alloy strength was manifested as a change in the observed residual stress magnitudes, and surface residual stresses were found to vary linearly with as quenched hardness and strength. - Highlights: • As quenched aluminium alloys contain high magnitude residual stresses. • Surface is compressive balance by a tensile core. • As quenched surface residual stress is linear function of alloy strength. • In situ hot hardness demonstrates rapid change in intrinsic hardness during rapid cooling.

  5. Problems with Excessive Residual Lower Leg Length in Pediatric Amputees

    OpenAIRE

    Osebold, William R; Lester, Edward L; Christenson, Donald M

    2001-01-01

    We studied six pediatric amputees with long below-knee residual limbs, in order to delineate their functional and prosthetic situations, specifically in relation to problems with fitting for dynamic-response prosthetic feet. Three patients had congenital pseudoarthrosis of the tibia secondary to neurofibromatosis, one had fibular hemimelia, one had a traumatic amputation, and one had amputation secondary to burns. Five patients had Syme's amputations, one had a Boyd amputation. Ages at amputa...

  6. Partial alanine scan of mast cell degranulating peptide (MCD): importance of the histidine- and arginine residues.

    Science.gov (United States)

    Buku, Angeliki; Mendlowitz, Milton; Condie, Barry A; Price, Joseph A

    2004-06-01

    The influence of the two histidine and two arginine residues of mast cell degranulating peptide (MCD) in activity and binding was studied by replacing these amino acids in the MCD sequence with L-alanine. Their histamine releasing activity was determined on rat peritoneal mast cells. Their binding affinity to the FcepsilonRIalpha binding subunit of the human mast cell receptor protein, was carried out using fluorescence polarization. The histamine assay showed that replacement of His13 by Ala o ccurred without loss of activity compared with the activity of MCD. Alanine substitutions for Arg7 and His8 resulted in an approximately 40 fold increase, and for Arg16 in a 14-fold increase in histamine-releasing activity of MCD. The binding affinities of the analogs were tested by competitive displacement of bound fluorescent MCD peptide from the FcepsilonRIalpha binding protein of the mast cell receptor by the Ala analogs using fluorescence polarization. The analogs Ala8 (for His) and Ala16 (for Arg) showed the same binding affinities as MCD, whereas analog Ala7 (for Arg) and analog Ala13 (for His) showed slightly better binding affinity than the parent compound. This study showed that the introduction of alanine residues in these positions resulted in MCD agonists of diverse potency. These findings will be useful in further MCD structure-activity studies.

  7. Modeling Residual NAPL in Water-Wet Porous Media

    Directory of Open Access Journals (Sweden)

    R.J. Lenhard

    2002-06-01

    Full Text Available A model is outlined that predicts NAPL which is held in pore wedges and as films or lenses on solid and water surfaces and contributes negligibly to NAPL advection. This is conceptually referred to as residual NAPL. Since residual NAPL is immobile, it remains in the vadose zone after all free NAPL has drained. Residual NAPL is very important because it is a long-term source for groundwater contamination. Recent laboratory experiments have demonstrated that current models for predicting subsurface NAPL behavior are inadequate because they do not correctly predict residual NAPL. The main reason for the failure is a deficiency in the current constitutive theories for multiphase flow that are used in numerical simulators. Multiphase constitutive theory governs the relations among relative permeability, saturation, and pressure for fluid systems (i.e., air, NAPL, water. In this paper, we outline a model describing relations between fluid saturations and pressures that can be combined with existing multiphase constitutive theory to predict residual NAPL. We test the revised constitutive theory by applying it to a scenario involving NAPL imbibition and drainage, as well as water imbibition and drainage. The results suggest that the revised constitutive theory is able to predict the distribution of residual NAPL in the vadose zone as a function of saturation-path history. The revised model describing relations between fluid saturation and pressures will help toward developing or improving numerical multiphase flow simulators.

  8. Millisecond dynamics in glutaredoxin during catalytic turnover is dependent on substrate binding and absent in the resting states

    DEFF Research Database (Denmark)

    Jensen, Kristine Steen; Winther, Jakob R; Teilum, Kaare

    2011-01-01

    to the glutathione exchange rate was observed for 23 residues. Binding of reduced glutathione resulted in competitive inhibition of the reduced enzyme having kinetics similar to that of the reaction. This observation couples the motions observed during catalysis directly to substrate binding. Backbone motions......Conformational dynamics is important for enzyme function. Which motions of enzymes determine catalytic efficiency and whether the same motions are important for all enzymes, however, are not well understood. Here we address conformational dynamics in glutaredoxin during catalytic turnover...... with a combination of NMR magnetization transfer, R(2) relaxation dispersion, and ligand titration experiments. Glutaredoxins catalyze a glutathione exchange reaction, forming a stable glutathinoylated enzyme intermediate. The equilibrium between the reduced state and the glutathionylated state was biochemically...

  9. Low residual diet and hydration improving double contrast examination of the colon

    International Nuclear Information System (INIS)

    Virkki, R.; Maekelae, P.

    1983-01-01

    Light food diet and low residual diet with hydration, both combined with Proctosal and Bisacodyl cleansing, were compared in 268 patients in the preparation of the colon for double contrast examination. Low residual diet with hydration resulted in significantly less residual fecal material, no flocculation of the barium coating and significantly denser mucosal coating. The examination had to be repeated more often (8.6%) after light food diet than after low residual diet with hydration (1.7%), but there was no statistically significant difference in the diagnostic accuracy. The hydration is important in avoiding patient discomforts and flocculation of the barium coating. Despite the use of laxatives, a strict diet restriction is needed to obtain consistently clean colon. (orig.)

  10. Irradiation of residual muds and its use in the oat cultivation

    International Nuclear Information System (INIS)

    Moreno, A.J.; Colin, C.A.; Gomeztagle, M.M.; Frias, P.H.

    1997-01-01

    The irradiation of residual muds samples from a wastewater treatment plant at gamma radiation dose of 15 kGy removes from muds on average: fats and oils (33%), detergent (92%), phenols (50%) and over 99% of microorganisms of total account. The evaluation of irradiated residual mud and without irradiation as soil conditioner in oat growing (avena safira), was realized by triplicate, using different rates (80, 60, 40 and 20%) of frank sandy soil and irradiated and non-irradiated residual mud. The growing with rates 60/40 % of soil and irradiated mud respectively, resulted being more adequate as soil conditioner. It is important to clarify that for putting residual mud it is necessary that metals concentration not exceed the maximum permissible levels for the soil type and the corresponding growing. (Author)

  11. Measurement of the fluorescence of crop residues: A tool for controlling soil erosion

    Science.gov (United States)

    Daughtry, C. S. T.; Mcmurtrey, J. E., III; Chappelle, E. W.; Hunter, W. J.

    1994-01-01

    Management of crop residues, the portion of a crop left in the field after harvest, is an important conservation practice for minimizing soil erosion and for improving water quality. Quantification of crop residue cover is required to evaluate the effectiveness of conservation tillage practices. Methods are needed to quantify residue cover that are rapid, accurate, and objective. The fluorescence of crop residue was found to be a broadband phenomenon with emission maxima at 420 to 495 nm for excitations of 350 to 420 nm. Soils had low intensity broadband emissions over the 400 to 690 nm region for excitations of 300 to 600 nm. The range of relative fluorescence intensities for the crop residues was much greater than the fluorescence observed of the soils. As the crop residues decompose their blue fluorescence values approach the fluorescence of the soil. Fluorescence techniques are concluded to be less ambiguous and better suited for discriminating crop residues and soils than reflectance methods. If properly implemented, fluorescence techniques can be used to quantify, not only crop residue cover, but also photosynthetic efficiency in the field.

  12. 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.

  13. Stability of the anthocyanins extracted from residues of the wine industry

    Directory of Open Access Journals (Sweden)

    Edmar Clemente

    2011-09-01

    Full Text Available Anthocyanins are highly important due to their antioxidant capacity. They are the most important among the phenolic compounds and one of the main natural dyes used in the food industry. In this research, residue of processed grapes was used to investigate the presence of anthocyanins, the possibility of their extraction from the residue, and their stability. The extraction solution consisted of 70 mL of ethanol 70% and 30 mL of HCl 0.1% at pH 2.0. The results found for the processed grapes residue was 26.20 mg.100 g-1. In order to evaluate stability, caffeic acid was added at 0.5:1 w/v; 0.8:1 w/v; and 1:1 w/v concentrations. Anthocyanins extract reached the greatest stability at 0.5:1 w/v concentration, with 82.47% color retention and a half-life period of 15 days. Therefore, the use of this organic acid as a stabilizer for anthocyanins is feasible.

  14. Proceedings of the 7. biennial residue-to-revenue residual wood conference 2007

    International Nuclear Information System (INIS)

    Raulin, J.

    2007-01-01

    This conference provided information on the highest and best use of residual wood, which is quickly becoming a valuable commodity. Issues concerning forest residues, sawmill wastes, agricultural residues and urban organic materials were discussed along with trends in Canadian surplus mill waste production. The evolving nature and technologies of the biomass business were highlighted with particular focus on how to generate energy and save money through the use of residual wood. Residual wood energy projects and developments in Canada, North America and Europe were outlined along with biomass development in relation to forest fires and insect disturbances. Cogeneration technologies using wood wastes for thermal heat, steam and electricity were also presented, along with transportation fuel technologies for the production of ethanol. It was noted that with the rising cost of energy, the forest industry is seeking energy solutions based on the use of residual wood. The range of economically practical residual wood solutions continues to grow as energy prices increase. The conference was attended by more than 200 delegates from the forest industry, suppliers and government representatives, to discuss policies and procedures currently in place. Industry investment is being stimulated by the potential for biofuels and biochemicals, as well as the co-operation between the forest and energy sectors. The conference featured 23 presentations, of which 12 have been catalogued separately for inclusion in this database. refs., tabs., figs

  15. Prevalence of antimicrobial residues in eggs, tissue and feed samples in the State of Kuwait

    International Nuclear Information System (INIS)

    Alomirah, H.; Al-Mazeedi, H.; Al-Zenki, S.; Al-Faili, B.; Al-Foudary, M.; Abuzid, A.; Al-Sayed, I.; Sidhu, J.

    2007-01-01

    A total of 238 locally produced and imported eggs, tissue (meat, poultry and aquacultured fish) and feed and feedstuffs samples were collected at different seasonal periods from different farms and retail outlets in Kuwait and screened for presence of beta-lactams, tetracyclines, sulfonamides, streptomycin, macrolides and chloramphenicol (799 tests) using Charm II system. The results indicated that all of the 222 tests performed on table egg samples were negative for the analyzed antimicrobial residues indicating adherence to the guidelines for microbial use and withdrawal. Similarly, all of the 268 tests performed on tissue samples were negative for the analyzed antimicrobial residues except for chloramphenicol. These chloramphenicol positive samples, all of the 66 tests performed were negative for beta-lactams residues. Out of the 79 feed and feedstuff samples analyzed for teracyclines residues, broiler diet and concentrate samples (5%) were above the tetracyclines MRL (100 ppb.). On the other hands, results have revealed a widespread of sulfonamide residues and to a less extent chloramphenicol in tested feed and feedstuff samples. The Charm II system was reliable for rapid screening of antimicrobial residues. In general, results obtained in our study necessitate more effective and well planned national antimicrobial residues surveillance programs focusing particularly on samples imported from highly risk sources. (author)

  16. Bloqueio neuromuscular residual após o uso de rocurônio ou cisatracúrio Bloqueo neuromuscular residual después del uso de rocuronio o cisatracúrio Residual neuromuscular block after rocuronium or cisatracurium

    Directory of Open Access Journals (Sweden)

    Bruno Salomé de Morais

    2005-12-01

    (rocuronium. Residual neuromuscular block was unrelated to dose, age and use of antagonists, but was related to procedure length. In subgroup C, mean procedure length was 135 minutes for patients with neuromuscular block and 161 minutes for patients without (p < 0.029. In subgroup R, mean surgery length was 122 and 150 minutes, respectively (p < 0.039. CONCLUSIONS: Both groups had high incidence of residual neuromuscular block in the PACU. Residual postoperative curarization is still a problem even with new intermediary action neuromuscular blockers. It is highly important to objectively monitor all patients submitted to general anesthesia with neuromuscular blockers.

  17. Prediction of vitamin interacting residues in a vitamin binding protein using evolutionary information

    Directory of Open Access Journals (Sweden)

    Panwar Bharat

    2013-02-01

    Full Text Available Abstract Background The vitamins are important cofactors in various enzymatic-reactions. In past, many inhibitors have been designed against vitamin binding pockets in order to inhibit vitamin-protein interactions. Thus, it is important to identify vitamin interacting residues in a protein. It is possible to detect vitamin-binding pockets on a protein, if its tertiary structure is known. Unfortunately tertiary structures of limited proteins are available. Therefore, it is important to develop in-silico models for predicting vitamin interacting residues in protein from its primary structure. Results In this study, first we compared protein-interacting residues of vitamins with other ligands using Two Sample Logo (TSL. It was observed that ATP, GTP, NAD, FAD and mannose preferred {G,R,K,S,H}, {G,K,T,S,D,N}, {T,G,Y}, {G,Y,W} and {Y,D,W,N,E} residues respectively, whereas vitamins preferred {Y,F,S,W,T,G,H} residues for the interaction with proteins. Furthermore, compositional information of preferred and non-preferred residues along with patterns-specificity was also observed within different vitamin-classes. Vitamins A, B and B6 preferred {F,I,W,Y,L,V}, {S,Y,G,T,H,W,N,E} and {S,T,G,H,Y,N} interacting residues respectively. It suggested that protein-binding patterns of vitamins are different from other ligands, and motivated us to develop separate predictor for vitamins and their sub-classes. The four different prediction modules, (i vitamin interacting residues (VIRs, (ii vitamin-A interacting residues (VAIRs, (iii vitamin-B interacting residues (VBIRs and (iv pyridoxal-5-phosphate (vitamin B6 interacting residues (PLPIRs have been developed. We applied various classifiers of SVM, BayesNet, NaiveBayes, ComplementNaiveBayes, NaiveBayesMultinomial, RandomForest and IBk etc., as machine learning techniques, using binary and Position-Specific Scoring Matrix (PSSM features of protein sequences. Finally, we selected best performing SVM modules and

  18. Prediction of vitamin interacting residues in a vitamin binding protein using evolutionary information.

    Science.gov (United States)

    Panwar, Bharat; Gupta, Sudheer; Raghava, Gajendra P S

    2013-02-07

    The vitamins are important cofactors in various enzymatic-reactions. In past, many inhibitors have been designed against vitamin binding pockets in order to inhibit vitamin-protein interactions. Thus, it is important to identify vitamin interacting residues in a protein. It is possible to detect vitamin-binding pockets on a protein, if its tertiary structure is known. Unfortunately tertiary structures of limited proteins are available. Therefore, it is important to develop in-silico models for predicting vitamin interacting residues in protein from its primary structure. In this study, first we compared protein-interacting residues of vitamins with other ligands using Two Sample Logo (TSL). It was observed that ATP, GTP, NAD, FAD and mannose preferred {G,R,K,S,H}, {G,K,T,S,D,N}, {T,G,Y}, {G,Y,W} and {Y,D,W,N,E} residues respectively, whereas vitamins preferred {Y,F,S,W,T,G,H} residues for the interaction with proteins. Furthermore, compositional information of preferred and non-preferred residues along with patterns-specificity was also observed within different vitamin-classes. Vitamins A, B and B6 preferred {F,I,W,Y,L,V}, {S,Y,G,T,H,W,N,E} and {S,T,G,H,Y,N} interacting residues respectively. It suggested that protein-binding patterns of vitamins are different from other ligands, and motivated us to develop separate predictor for vitamins and their sub-classes. The four different prediction modules, (i) vitamin interacting residues (VIRs), (ii) vitamin-A interacting residues (VAIRs), (iii) vitamin-B interacting residues (VBIRs) and (iv) pyridoxal-5-phosphate (vitamin B6) interacting residues (PLPIRs) have been developed. We applied various classifiers of SVM, BayesNet, NaiveBayes, ComplementNaiveBayes, NaiveBayesMultinomial, RandomForest and IBk etc., as machine learning techniques, using binary and Position-Specific Scoring Matrix (PSSM) features of protein sequences. Finally, we selected best performing SVM modules and obtained highest MCC of 0.53, 0.48, 0.61, 0

  19. Highly Conserved Arg Residue of ERFNIN Motif of Pro-Domain is Important for pH-Induced Zymogen Activation Process in Cysteine Cathepsins K and L.

    Science.gov (United States)

    Aich, Pulakesh; Biswas, Sampa

    2018-06-01

    Pro-domain of a cysteine cathepsin contains a highly conserved Ex 2 Rx 2 Fx 2 Nx 3 Ix 3 N (ERFNIN) motif. The zymogen structure of cathepsins revealed that the Arg(R) residue of the motif is a central residue of a salt-bridge/H-bond network, stabilizing the scaffold of the pro-domain. Importance of the arginine is also demonstrated in studies where a single mutation (Arg → Trp) in human lysosomal cathepsin K (hCTSK) is linked to a bone-related genetic disorder "Pycnodysostosis". In the present study, we have characterized in vitro Arg → Trp mutant of hCTSK and the same mutant of hCTSL. The R → W mutant of hCTSK revealed that this mutation leads to an unstable zymogen that is spontaneously activated and auto-proteolytically degraded rapidly. In contrast, the same mutant of hCTSL is sufficiently stable and has proteolytic activity almost like its wild-type counterpart; however it shows an altered zymogen activation condition in terms of pH, temperature and time. Far and near UV circular dichroism and intrinsic tryptophan fluorescence experiments have revealed that the mutation has minimal effect on structure of the protease hCTSL. Molecular modeling studies shows that the mutated Trp31 in hCTSL forms an aromatic cluster with Tyr23 and Trp30 leading to a local stabilization of pro-domain and supplements the loss of salt-bridge interaction mediated by Arg31 in wild-type. In hCTSK-R31W mutant, due to presence of a non-aromatic Ser30 residue such interaction is not possible and may be responsible for local instability. These differences may cause detrimental effects of R31W mutation on the regulation of hCTSK auto-activation process compared to altered activation process in hCTSL.

  20. Solid residues

    International Nuclear Information System (INIS)

    Mulder, E.; Duin, P.J. van; Grootenboer, G.J.

    1995-01-01

    A summary is presented of the many investigations that have been done on solid residues of atmospheric fluid bed combustion (AFBC). These residues are bed ash, cyclone ash and bag filter ash. Physical and chemical properties are discussed and then the various uses of residues (in fillers, bricks, gravel, and for recovery of aluminium) are summarised. Toxicological properties of fly ash and stack ash are discussed as are risks of pneumoconiosis for workers handling fly ash, and contamination of water by ashes. On the basis of present information it is concluded that risks to public health from exposure to emissions of coal fly ash from AFBC appear small or negligible as are health risk to workers in the coal fly ash processing industry. 35 refs., 5 figs., 12 tabs

  1. Optimal temperature profiles for minimum residual stress in the cure process of polymer composites

    CSIR Research Space (South Africa)

    Gopal, AK

    2000-01-01

    Full Text Available include the minimum residual stresses, minimum cure cycle lime and full degree of cure. The development of residual stresses during the cure cycle is one of the most important problems as they affect the strength and the mechanical properties of the final...

  2. Chirality in the absence of rigid stereogenic elements: steric and electronic effects on the configurational stability of C3 symmetric residual tris-aryl phosphanes.

    Science.gov (United States)

    Rizzo, Simona; Cirilli, Roberto; Pierini, Marco

    2014-10-01

    Residual stereoisomers result whenever closed subsets of appropriately substituted interconverting isomers (the residual stereoisomers) are generated from a full set of stereoisomers under the operation of a favored stereomerization mechanism. In the case of the three-bladed propellers, differentiation of the edges of the blades and strict correlation in the motion of the rings are the prerequisites for the existence of residual stereoisomers. In these systems, the two-ring flip mechanism is the lowest energy process. It does not interconvert all possible conformational stereoisomers generated by helicity and the three-blade-hub rotors. In the case of C3 symmetric systems, two noninterconverting subgroups (the residual stereoisomers) are generated, each one constituted of quickly interconverting diastereoisomers. A series of tris-aryl phosphanes, structurally designed for existing as residual enantiomers or diastereoisomers, bearing substituents differing in size and electronic properties on the aryl rings, were synthesized and characterized. The configurational stability of residual phosphanes, evaluated by dynamic (1) H- and (31) P-NMR analysis and by dynamic enantioselective high-performance liquid chromatography (HPLC), was found 10 kcal mol(-1) lower than that shown by the corresponding phosphane-oxides. In accordance with the calculations, an unexpectedly low barrier for phosphorus pyramidal inversion was invoked as responsible for the scarce configurational stability of the residual tris-arylphosphanes. © 2014 Wiley Periodicals, Inc.

  3. Dynamic changes in the secondary structure of ECE-1 and XCE account for their different substrate specificities

    Directory of Open Access Journals (Sweden)

    Ul-Haq Zaheer

    2012-11-01

    Full Text Available Abstract Background X-converting enzyme (XCE involved in nervous control of respiration, is a member of the M13 family of zinc peptidases, for which no natural substrate has been identified yet. In contrast, it’s well characterized homologue endothelin-converting enzyme-1 (ECE-1 showed broad substrate specificity and acts as endopeptidase as well as dipeptidase. To explore the structural differences between XCE and ECE-1, homology model of XCE was built using the complex structure of ECE-1 with phosphoramidon (pdb-id: 3DWB as template. Phosphoramidon was docked into the binding site of XCE whereas phosphate oxygen of the inhibitor was used as water molecule to design the apo forms of both enzymes. Molecular dynamics simulation of both enzymes was performed to analyze the dynamic nature of their active site residues in the absence and presence of the inhibitor. Results Homology model of XCE explained the role of non-conserved residues of its S2’ subsite. Molecular dynamics (MD simulations identified the flexible transitions of F149/I150, N566/N571, W714/W719, and R145/R723 residues of ECE-1/XCE for the strong binding of the inhibitor. Secondary structure calculations using DSSP method reveals the folding of R145/R723 residue of ECE-1/XCE into β-sheet structure while unfolding of the S2’ subsite residues in aECE-1 and sustained compact folding of that of aXCE. The results evaluated are in good agreement with available experimental data, thus providing detailed molecular models which can explain the structural and specificities differences between both zinc peptidases. Conclusions Secondary structure changes of both enzymes during the simulation time revealed the importance of β-sheet structure of R145/R723 for its binding with the terminal carboxylate group of the inhibitor. Unfolding of the α-helix comprising the S2’ subsite residues in aECE-1 correlate well with its endopeptidase activity while their compact folding in aXCE may

  4. Application of Stable Isotope in Detection of Veterinary Drug Residues

    International Nuclear Information System (INIS)

    Wang Wei; Liu Zhanfeng; Du Xiaoning

    2010-01-01

    In recent years, there has happened a series of significant food safety events worldwide, which lower down consumers' confidence in food safety, and they are taking increasing care about the sources of their foods. The safety problem of animal-origin foods has become a global topic for discussion. Therefore, it is a pressing task to establish a precise, sensitive and reliable method for analyzing veterinary drug residue. An introduction of the present status regarding veterinary drug residue analysis was made in the paper, and it briefly summarized the limit of detection (LOD) and quantification (LOQ) which could be reached in veterinary drug residue analysis by isotopic internal standard method domestically and abroad. The paper also made a review of the progress in applied research of stable isotope labeled compound in veterinary drug residue analysis of, such as, antibiotic medicines, furans and sulfonamides. The paper elucidated the great importance of the application of stable isotopes in the sane development of China's food safety system. (authors)

  5. Gas-Phase Hydrogen-Deuterium Exchange Labeling of Select Peptide Ion Conformer Types: a Per-Residue Kinetics Analysis.

    Science.gov (United States)

    Khakinejad, Mahdiar; Kondalaji, Samaneh Ghassabi; Tafreshian, Amirmahdi; Valentine, Stephen J

    2015-07-01

    The per-residue, gas-phase hydrogen deuterium exchange (HDX) kinetics for individual amino acid residues on selected ion conformer types of the model peptide KKDDDDDIIKIIK have been examined using ion mobility spectrometry (IMS) and HDX-tandem mass spectrometry (MS/MS) techniques. The [M + 4H](4+) ions exhibit two major conformer types with collision cross sections of 418 Å(2) and 446 Å(2); the [M + 3H](3+) ions also yield two different conformer types having collision cross sections of 340 Å(2) and 367 Å(2). Kinetics plots of HDX for individual amino acid residues reveal fast- and slow-exchanging hydrogens. The contributions of each amino acid residue to the overall conformer type rate constant have been estimated. For this peptide, N- and C-terminal K residues exhibit the greatest contributions for all ion conformer types. Interior D and I residues show decreased contributions. Several charge state trends are observed. On average, the D residues of the [M + 3H](3+) ions show faster HDX rate contributions compared with [M + 4H](4+) ions. In contrast the interior I8 and I9 residues show increased accessibility to exchange for the more elongated [M + 4H](4+) ion conformer type. The contribution of each residue to the overall uptake rate showed a good correlation with a residue hydrogen accessibility score model calculated using a distance from charge site and initial incorporation site for nominal structures obtained from molecular dynamic simulations (MDS).

  6. Availability and conversion to energy potentials of wood-based industry residues in Cameroon

    International Nuclear Information System (INIS)

    Simo, A.; Siyam Siew, S.

    2000-01-01

    The importance of biomass as the most accessible primary energy source in Cameroon is presented. The valorization of wood wastes and residues is seen as a way of implementing the sustainable use of biomass resources. A recent survey of wood-based industries in Cameroon reveals that large volumes of industrial wood residues are generated in the rain forest areas and are inefficiently used. Important quantities are lost in the form of burning in the four main forestry provinces, while other parts of the country suffer from fuelwood shortage. With the exception of the plywood factories, the wood industry is essentially dependent on commercial energy. An analysis made to show the economic and environmental benefits of converting wood residues to energy for industrial and domestic use is presented. (author)

  7. Chemical modelling of pore water composition from PFBC residues

    International Nuclear Information System (INIS)

    Karlsson, L.G.

    1991-01-01

    The concentration of trace elements varies depending on the source of the coal and also due to the combustion process used. Mercury is one important element among the trace elements in the coal residues, generally recognised as potentially harmful to the biological system. To predict the pore water concentrations of mercury and other important constituents leached from coal combustion residues disposal sites, mechanistic data on chemical reactions are required. The present study is an application of a basially thermodynamical approach using the geochemical code EQ3NR. The presence of discrete solid phases that control the aqueous concentrations of major elements such as aluminium, calcium and silicon are identified. Solid phases are modelled in equilibrium with a hypothetical pore water at a pH range of 7-11. In this study the thermodynamic database of EQ3NR has been complemented with data for cadmium, mercury and lead taken from the OECD/NEA Thermodynamic Database and from a compilation made by Lindsay. Possible solubility limiting phases for the important trace elements arsenic, cadmium, chromium, copper, mercury, nickel and lead have been identified. Concentrations of these trace elements as a function of pH in the hypothetical pore water were calculated using mechanistic thermodynamial data. The thermodynamical approach in this study seems justified because most solid residues that are either present or expected to form during weathering have relatively fast precipitation/dissolution kinetics. (21 refs., 18 figs., 5 tabs.)

  8. Diffraction measurements of residual stress in titanium matrix composites

    International Nuclear Information System (INIS)

    James, M.R.; Bourke, M.A.; Goldstone, J.A.; Lawson, A.C.

    1993-01-01

    Metal matrix composites develop residual strains after consolidation due to the thermal expansion mismatch between the reinforcement fiber and the matrix. X-ray and neutron diffraction measured values for the longitudinal residual stress in the matrix of four titanium MMCs are reported. For thick composites (> 6 plies) the surface stress measured by x-ray diffraction matches that determined by neutron diffraction and therefore represents the stress in the bulk region consisting of the fibers and matrix. For thin sheet composites, the surface values are lower than in the interior and increase as the outer rows of fibers are approached. While a rationale for the behavior in the thin sheet has yet to be developed, accounting for composite thickness is important when using x-ray measured values to validate analytic and finite element calculations of the residual stress state

  9. Sampling and sample processing in pesticide residue analysis.

    Science.gov (United States)

    Lehotay, Steven J; Cook, Jo Marie

    2015-05-13

    Proper sampling and sample processing in pesticide residue analysis of food and soil have always been essential to obtain accurate results, but the subject is becoming a greater concern as approximately 100 mg test portions are being analyzed with automated high-throughput analytical methods by agrochemical industry and contract laboratories. As global food trade and the importance of monitoring increase, the food industry and regulatory laboratories are also considering miniaturized high-throughput methods. In conjunction with a summary of the symposium "Residues in Food and Feed - Going from Macro to Micro: The Future of Sample Processing in Residue Analytical Methods" held at the 13th IUPAC International Congress of Pesticide Chemistry, this is an opportune time to review sampling theory and sample processing for pesticide residue analysis. If collected samples and test portions do not adequately represent the actual lot from which they came and provide meaningful results, then all costs, time, and efforts involved in implementing programs using sophisticated analytical instruments and techniques are wasted and can actually yield misleading results. This paper is designed to briefly review the often-neglected but crucial topic of sample collection and processing and put the issue into perspective for the future of pesticide residue analysis. It also emphasizes that analysts should demonstrate the validity of their sample processing approaches for the analytes/matrices of interest and encourages further studies on sampling and sample mass reduction to produce a test portion.

  10. Combined Role of Two Tryptophane Residues of α-Factor Pheromone

    Energy Technology Data Exchange (ETDEWEB)

    Hong, Eun Young [Yeungnam Univ., Gyungsan (Korea, Republic of); Hong, Nam Joo [Seoul National Univ., Seoul (Korea, Republic of)

    2013-02-15

    Amide analogs of tridecapeptide α-factor (WHWLQLKPGQPMYCONH{sub 2}) of Saccharomyces cerevisiae, in which Trp at position 1 and 3 were replaced with other residues, were synthesized to ascertain whether cooperative interactions between two Trp residues occurred upon binding with its receptor. Analogs containing Ala or Aib at position 3 of the peptide [Ala{sup 3}]α-factor amide (2) and [Aib{sup 3}]α-factor amide (5) exhibited greater decreases in bioactivity than analogs with same residue at position one [Ala{sup 1}]α-factor amide (1) and [Aib{sup 1}]α-factor amide (4), reflecting that Trp{sup 3} may plays more important role than Trp{sup 1} for agonist activity. Analogs containing Ala or Aib in both position one and three 3, 6 exhibited complete loss of bioactivity, emphasizing both the essential role and the combined role of two indole rings for triggering cell signaling. In contrast, double substituted analog with D-Trp in both positions 9 exhibited greater activity than single substituted analog with D-Trp 8 or deleted analog 7, reflecting the combined contribution of two tryptophane residues of α-factor ligand to activation of Ste2p through interaction with residue Tyr{sup 266} and importance of the proper parallel orientation of two indole rings for efficient triggering of signal G protein coupled activation. Among ten amide analogs, [Ala{sup 1,3}]α-factor amide (3), [Aib{sup 1,3}]α-factor amide (6), [D-Trp{sup 3}]α-factor amide (8) and [des-Trp{sup 1},Phe{sup 3}]α-factor amide (10) were found to have antagonistic activity. Analogs 3 and 6 showed greater antagonistic activity than analogs 8 and 10.

  11. Combined Role of Two Tryptophane Residues of α-Factor Pheromone

    International Nuclear Information System (INIS)

    Hong, Eun Young; Hong, Nam Joo

    2013-01-01

    Amide analogs of tridecapeptide α-factor (WHWLQLKPGQPMYCONH 2 ) of Saccharomyces cerevisiae, in which Trp at position 1 and 3 were replaced with other residues, were synthesized to ascertain whether cooperative interactions between two Trp residues occurred upon binding with its receptor. Analogs containing Ala or Aib at position 3 of the peptide [Ala 3 ]α-factor amide (2) and [Aib 3 ]α-factor amide (5) exhibited greater decreases in bioactivity than analogs with same residue at position one [Ala 1 ]α-factor amide (1) and [Aib 1 ]α-factor amide (4), reflecting that Trp 3 may plays more important role than Trp 1 for agonist activity. Analogs containing Ala or Aib in both position one and three 3, 6 exhibited complete loss of bioactivity, emphasizing both the essential role and the combined role of two indole rings for triggering cell signaling. In contrast, double substituted analog with D-Trp in both positions 9 exhibited greater activity than single substituted analog with D-Trp 8 or deleted analog 7, reflecting the combined contribution of two tryptophane residues of α-factor ligand to activation of Ste2p through interaction with residue Tyr 266 and importance of the proper parallel orientation of two indole rings for efficient triggering of signal G protein coupled activation. Among ten amide analogs, [Ala 1,3 ]α-factor amide (3), [Aib 1,3 ]α-factor amide (6), [D-Trp 3 ]α-factor amide (8) and [des-Trp 1 ,Phe 3 ]α-factor amide (10) were found to have antagonistic activity. Analogs 3 and 6 showed greater antagonistic activity than analogs 8 and 10

  12. Computation of a Reference Model for Robust Fault Detection and Isolation Residual Generation

    Directory of Open Access Journals (Sweden)

    Emmanuel Mazars

    2008-01-01

    Full Text Available This paper considers matrix inequality procedures to address the robust fault detection and isolation (FDI problem for linear time-invariant systems subject to disturbances, faults, and polytopic or norm-bounded uncertainties. We propose a design procedure for an FDI filter that aims to minimize a weighted combination of the sensitivity of the residual signal to disturbances and modeling errors, and the deviation of the faults to residual dynamics from a fault to residual reference model, using the ℋ∞-norm as a measure. A key step in our procedure is the design of an optimal fault reference model. We show that the optimal design requires the solution of a quadratic matrix inequality (QMI optimization problem. Since the solution of the optimal problem is intractable, we propose a linearization technique to derive a numerically tractable suboptimal design procedure that requires the solution of a linear matrix inequality (LMI optimization. A jet engine example is employed to demonstrate the effectiveness of the proposed approach.

  13. Characteristics of purple nonsulfur bacteria grown under Stevia residue extractions.

    Science.gov (United States)

    Xu, J; Feng, Y; Wang, Y; Lin, X

    2013-11-01

    As a consequence of the large-scale cultivation of Stevia plants, releases of plant residues, the byproduct after sweetener extraction, to the environment are inevitable. Stevia residue and its effluent after batching up contain large amounts of organic matters with small molecular weight, which therefore are a potential pollution source. Meanwhile, they are favourite substrates for micro-organism growths. This investigation was aimed to utilize the simulated effluent of Stevia residue to enrich the representative purple nonsulfur bacterium (PNSB), Rhodopseudomonas palustris (Rps. palustris), which has important economic values. The growth profile and quality of Rps. palustris were characterized by spectrophotometry, compared to those grown in common PNSB mineral synthetic medium. Our results revealed that the simulated effluent of Stevia residue not only stimulated Rps. palustris growth to a greater extent, but also increased its physiologically active cytochrome concentrations and excreted indole-3-acetic acid (IAA) content. This variation in phenotype of Rps. palustris could result from the shift in its genotype, further revealed by the repetitive sequence-based PCR (rep-PCR) fingerprinting analysis. Our results showed that the effluent of Stevia residue was a promising substrate for microbial growth. © 2013 The Society for Applied Microbiology.

  14. Residual Stress Analysis for Engineering Applications by Means of Neutron Diffraction

    International Nuclear Information System (INIS)

    Gndupel-Herold, Thomas; Brand, Paul C.; Prask, Henry J.

    1999-01-01

    The economic and scientific importance of neutron diffraction residual stress analysis has led to an increasing number of suitable instruments worldwide. Recently, a dedicated state-of-the-art diffractometer has been installed at the National Institute of Standards and Technology reactor. It has been used for a variety of measurements on basic and engineering stress problems. Among the most prominent examples that have been investigated are residual stresses in rails, weldments, and plasma-sprayed coatings

  15. Modeling seasonal redox dynamics and the corresponding fate of the pharmaceutical residue phenazone during artificial recharge of groundwater.

    Science.gov (United States)

    Greskowiak, Janek; Prommer, Henning; Massmann, Gudrun; Nützmann, Gunnar

    2006-11-01

    Reactive multicomponent transport modeling was used to investigate and quantify the factors that affect redox zonation and the fate of the pharmaceutical residue phenazone during artificial recharge of groundwater at an infiltration site in Berlin, Germany. The calibrated model and the corresponding sensitivity analysis demonstrated thattemporal and spatial redox zonation at the study site was driven by seasonally changing, temperature-dependent organic matter degradation rates. Breakthrough of phenazone at monitoring wells occurred primarily during the warmer summer months, when anaerobic conditions developed. Assuming a redox-sensitive phenazone degradation behavior the model results provided an excellent agreement between simulated and measured phenazone concentrations. Therefore, the fate of phenazone was shown to be indirectly controlled by the infiltration water temperature through its effect on the aquifer's redox conditions. Other factors such as variable residence times appeared to be of less importance.

  16. CHARACTERIZING RESIDUE TRANSFER EFFICIENCIES USING A FLUORESCENT IMAGING TECHNIQUE

    Science.gov (United States)

    To reduce the uncertainty associated with current estimates of children's exposure to pesticides by dermal contact and indirect ingestion, residue transfer data are required. Prior to conducting exhaustive studies, a screening study to identify the important parameters for chara...

  17. Modeling of residual stress state in turning of 304L

    International Nuclear Information System (INIS)

    Valiorgue, F.; Rech, J.; Bergheau, J.M.

    2010-01-01

    Research presented in this paper aims to link machining parameters to residual stress state and helps understanding mechanisms responsible of machined surface properties modifications. The first presented works are based on an experimental campaign. They reproduce the finishing turning operation of 304L and allow observing the residual stress state evolution at the work piece surface and for an affected depth of 0.2 mm for such processes. Then, the finishing turning operation is simulated numerically in order to realize the same sensitivity study to cutting parameters. This simulation is based on an hybrid approach mixing experimental data and numerical simulation. This method allows getting round the classical difficulties of turning simulation by applying equivalent thermo mechanical loadings onto the work piece surface without modeling the material separation phenomena. Moreover the numerical model uses an hardening law taking into account dynamic recrystallization phenomena. (authors)

  18. Visualization of residual organic liquid trapped in aquifers

    International Nuclear Information System (INIS)

    Conrad, S.H.; Wilson, J.L.; Mason, W.R.; Peplinski, W.J.

    1992-01-01

    Organic liquids that are essentially immiscible with water migrate through the subsurface under the influence of capillary, viscous, and buoyancy forces. These liquids originate from the improper disposal of hazardous wastes, and the spills and leaks of petroleum hydrocarbons and solvents. The flow visualization experiments described in this study examined the migration of organic liquids through the saturated zone of aquifers, with a primary focus on the behavior of the residual organic liquid saturation, referring to that portion of the organic liquid that is trapped by capillary forces. Etched glass micromodels were used to visually observe dynamic multiphase displacement processes in pore networks. The resulting fluid distributions were photographed. Pore and blob casts were produced by a technique in which an organic liquid was solidified in place within a sand column at the conclusion of a displacement. The columns were sectioned and examined under optical and scanning electron microscopes. Photomicrographs of these sections show the morphology of the organic phase and its location within the sand matrix. The photographs from both experimental techniques reveal that in the saturated zone large amounts of residual organic liquid are trapped as isolated blobs of microscopic size. The size, shape, and spatial distribution of these blobs of residual organic liquid affect the dissolution of organic liquid into the water phase and the biotransformation of organic components. These processes are of concern for the prediction of pollution migration and the design of aquifer remediation schemes

  19. Dynamics of a Highly Flexible Protein

    DEFF Research Database (Denmark)

    Andersen, Lisbeth

    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...

  20. The effect of glycosylation on the transferrin structure: A molecular dynamic simulation analysis.

    Science.gov (United States)

    Ghanbari, Z; Housaindokht, M R; Bozorgmehr, M R; Izadyar, M

    2016-09-07

    Transferrins have been defined by the highly cooperative binding of iron and a carbonate anion to form a Fe-CO3-Tf ternary complex. As such, the layout of the binding site residues affects transferrin function significantly; In contrast to N-lobe, C-lobe binding site of the transferrin structure has been less characterized and little research which surveyed the interaction of carbonate with transferrin in the C-lobe binding site has been found. In the present work, molecular dynamic simulation was employed to gain access into the molecular level understanding of carbonate binding site and their interactions in each lobe. Residues responsible for carbonate binding of transferrin structure were pointed out. In addition, native human transferrin is a glycoprotein that two N-linked complex glycan chains located in the C-lobe. Usually, in the molecular dynamic simulation for simplifying, glycan is removed from the protein structure. Here, we explore the effect of glycosylation on the transferrin structure. Glycosylation appears to have an effect on the layout of the binding site residue and transferrin structure. On the other hand, sometimes the entire transferrin formed by separated lobes that it allows the results to be interpreted in a straightforward manner rather than more parameters required for full length protein. But, it should be noted that there are differences between the separated lobe and full length transferrin, hence, a comparative analysis by the molecular dynamic simulation was performed to investigate such structural variations. Results revealed that separation in C-lobe caused a significant structural variation in comparison to N-lobe. Consequently, the separated lobes and the full length one are different, showing the importance of the interlobe communication and the impact of the lobes on each other in the transferrin structure. Copyright © 2016 Elsevier Ltd. All rights reserved.

  1. 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.

  2. Importance of ecotone type to landscape dynamics at biome transition zones

    Science.gov (United States)

    Landscapes in biome transition zones consist of a mosaic of patches dominated or codominated by species from adjacent biomes. Shifts in the vegetation composition and dynamics of a biome transition zone depend upon the underlying patch dynamics of the ecotones between these dominant species. Landsc...

  3. Tillering dynamics in pastures of guinea grass subjected to grazing severities under intermittent stocking

    Directory of Open Access Journals (Sweden)

    Denise Baptaglin Montagner

    2012-03-01

    Full Text Available This experiment was carried out to analyze the tillering dynamics of the species Panicum maximum cv. Mombaca subjected to three post-grazing heights: residue of 30 cm (30; residue of 50 cm (50; and residue of 50 cm during spring and summer, lowered to 40 cm in the first fall season grazing and to 30 cm in the following grazing cycle, resuming to 50 cm after the first grazing of the following spring season (50-30. Grazings were initiated whenever the swards intercepted 95% of the incident light. The post-grazing heights were allocated in the experimental units in a completely randomized block design with three replications. The density of basal tillers did not vary between the residual heights evaluated. Swards managed with variable residual height (50-30 presented higher rates of appearance and mortality of basal tillers during the summer of 2007, indicating high tiller renovation. Regardless of the post-grazing height evaluated, lower rates of appearance of basal tillers were found in the spring of 2006. The stability index of guinea grass cv. Mombaca was close to 1.0 throughout the experimental period. Swards managed with variable post-grazing present structural changes able to improve the regrowth vigor, which may be important to maximize the use of the forage species in the production system.

  4. 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.

  5. Optimizing Biomass Feedstock Logistics for Forest Residue Processing and Transportation on a Tree-Shaped Road Network

    Directory of Open Access Journals (Sweden)

    Hee Han

    2018-03-01

    Full Text Available An important task in forest residue recovery operations is to select the most cost-efficient feedstock logistics system for a given distribution of residue piles, road access, and available machinery. Notable considerations include inaccessibility of treatment units to large chip vans and frequent, long-distance mobilization of forestry equipment required to process dispersed residues. In this study, we present optimized biomass feedstock logistics on a tree-shaped road network that take into account the following options: (1 grinding residues at the site of treatment and forwarding ground residues either directly to bioenergy facility or to a concentration yard where they are transshipped to large chip vans, (2 forwarding residues to a concentration yard where they are stored and ground directly into chip vans, and (3 forwarding residues to a nearby grinder location and forwarding the ground materials. A mixed-integer programming model coupled with a network algorithm was developed to solve the problem. The model was applied to recovery operations on a study site in Colorado, USA, and the optimal solution reduced the cost of logistics up to 11% compared to the conventional system. This is an important result because this cost reduction propagates downstream through the biomass supply chain, reducing production costs for bioenergy and bioproducts.

  6. Dynamic Modelling Reveals 'Hotspots' on the Pathway to Enzyme-Substrate Complex Formation.

    Directory of Open Access Journals (Sweden)

    Shane E Gordon

    2016-03-01

    Full Text Available Dihydrodipicolinate synthase (DHDPS catalyzes the first committed step in the diaminopimelate pathway of bacteria, yielding amino acids required for cell wall and protein biosyntheses. The essentiality of the enzyme to bacteria, coupled with its absence in humans, validates DHDPS as an antibacterial drug target. Conventional drug design efforts have thus far been unsuccessful in identifying potent DHDPS inhibitors. Here, we make use of contemporary molecular dynamics simulation and Markov state models to explore the interactions between DHDPS from the human pathogen Staphylococcus aureus and its cognate substrate, pyruvate. Our simulations recover the crystallographic DHDPS-pyruvate complex without a priori knowledge of the final bound structure. The highly conserved residue Arg140 was found to have a pivotal role in coordinating the entry of pyruvate into the active site from bulk solvent, consistent with previous kinetic reports, indicating an indirect role for the residue in DHDPS catalysis. A metastable binding intermediate characterized by multiple points of intermolecular interaction between pyruvate and key DHDPS residue Arg140 was found to be a highly conserved feature of the binding trajectory when comparing alternative binding pathways. By means of umbrella sampling we show that these binding intermediates are thermodynamically metastable, consistent with both the available experimental data and the substrate binding model presented in this study. Our results provide insight into an important enzyme-substrate interaction in atomistic detail that offers the potential to be exploited for the discovery of more effective DHDPS inhibitors and, in a broader sense, dynamic protein-drug interactions.

  7. A primary simulation for residual stress neutron diffractometer

    International Nuclear Information System (INIS)

    Wang Shuying; Liu Lijuan; Sun Liangwei

    2012-01-01

    At present, neutron diffraction method is the unique and nondestructive method that can directly measure the residual stress distribution in deep materials and engineering components. It has an important application in engineering. A simulation of the flux at the position of the sample table was reported, and the resolution of the residual stress instrument was computed at the same time. The effect of the parameters of the second collimator on the flux at the sample position and the resolution of the instrument have been analyzed. The result indicated that the second collimator empress much on the neutron flux and the instrument resolution is well when the sample's diffraction angle is less than 120°. (authors)

  8. Tidal residual current and its role in the mean flow on the Changjiang Bank

    Science.gov (United States)

    Xuan, Jiliang; Yang, Zhaoqing; Huang, Daji; Wang, Taiping; Zhou, Feng

    2016-02-01

    The 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 on 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%.

  9. 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%.

  10. Prediction of the residual strength of clay using functional networks

    Directory of Open Access Journals (Sweden)

    S.Z. Khan

    2016-01-01

    Full Text Available Landslides are common natural hazards occurring in most parts of the world and have considerable adverse economic effects. Residual shear strength of clay is one of the most important factors in the determination of stability of slopes or landslides. This effect is more pronounced in sensitive clays which show large changes in shear strength from peak to residual states. This study analyses the prediction of the residual strength of clay based on a new prediction model, functional networks (FN using data available in the literature. The performance of FN was compared with support vector machine (SVM and artificial neural network (ANN based on statistical parameters like correlation coefficient (R, Nash--Sutcliff coefficient of efficiency (E, absolute average error (AAE, maximum average error (MAE and root mean square error (RMSE. Based on R and E parameters, FN is found to be a better prediction tool than ANN for the given data. However, the R and E values for FN are less than SVM. A prediction equation is presented that can be used by practicing geotechnical engineers. A sensitivity analysis is carried out to ascertain the importance of various inputs in the prediction of the output.

  11. Conserved residues of the human mitochondrial holocytochrome c synthase mediate interactions with heme.

    Science.gov (United States)

    Babbitt, Shalon E; San Francisco, Brian; Bretsnyder, Eric C; Kranz, Robert G

    2014-08-19

    C-type cytochromes are distinguished by the covalent attachment of a heme cofactor, a modification that is typically required for its subsequent folding, stability, and function. Heme attachment takes place in the mitochondrial intermembrane space and, in most eukaryotes, is mediated by holocytochrome c synthase (HCCS). HCCS is the primary component of the eukaryotic cytochrome c biogenesis pathway, known as System III. The catalytic function of HCCS depends on its ability to coordinate interactions between its substrates: heme and cytochrome c. Recent advancements in the recombinant expression and purification of HCCS have facilitated comprehensive analyses of the roles of conserved residues in HCCS, as demonstrated in this study. Previously, we proposed a four-step model describing HCCS-mediated cytochrome c assembly, identifying a conserved histidine residue (His154) as an axial ligand to the heme iron. In this study, we performed a systematic mutational analysis of 17 conserved residues in HCCS, and we provide evidence that the enzyme contains two heme-binding domains. Our data indicate that heme contacts mediated by residues within these domains modulate the dynamics of heme binding and contribute to the stability of the HCCS-heme-cytochrome c steady state ternary complex. While some residues are essential for initial heme binding (step 1), others impact the subsequent release of the holocytochrome c product (step 4). Certain HCCS mutants that were defective in heme binding were corrected for function by exogenous aminolevulinic acid (ALA, the precursor to heme). This chemical "correction" supports the proposed role of heme binding for the corresponding residues.

  12. a System Dynamics Model to Study the Importance of Infrastructure Facilities on Quality of Primary Education System in Developing Countries

    Science.gov (United States)

    Pedamallu, Chandra Sekhar; Ozdamar, Linet; Weber, Gerhard-Wilhelm; Kropat, Erik

    2010-06-01

    The system dynamics approach is a holistic way of solving problems in real-time scenarios. This is a powerful methodology and computer simulation modeling technique for framing, analyzing, and discussing complex issues and problems. System dynamics modeling and simulation is often the background of a systemic thinking approach and has become a management and organizational development paradigm. This paper proposes a system dynamics approach for study the importance of infrastructure facilities on quality of primary education system in developing nations. The model is proposed to be built using the Cross Impact Analysis (CIA) method of relating entities and attributes relevant to the primary education system in any given community. We offer a survey to build the cross-impact correlation matrix and, hence, to better understand the primary education system and importance of infrastructural facilities on quality of primary education. The resulting model enables us to predict the effects of infrastructural facilities on the access of primary education by the community. This may support policy makers to take more effective actions in campaigns.

  13. Expression and mutagenesis of the sea anemone toxin Av2 reveals key amino acid residues important for activity on voltage-gated sodium channels.

    Science.gov (United States)

    Moran, Yehu; Cohen, Lior; Kahn, Roy; Karbat, Izhar; Gordon, Dalia; Gurevitz, Michael

    2006-07-25

    Type I sea anemone toxins are highly potent modulators of voltage-gated Na-channels (Na(v)s) and compete with the structurally dissimilar scorpion alpha-toxins on binding to receptor site-3. Although these features provide two structurally different probes for studying receptor site-3 and channel fast inactivation, the bioactive surface of sea anemone toxins has not been fully resolved. We established an efficient expression system for Av2 (known as ATX II), a highly insecticidal sea anemone toxin from Anemonia viridis (previously named A. sulcata), and mutagenized it throughout. Each toxin mutant was analyzed in toxicity and binding assays as well as by circular dichroism spectroscopy to discern the effects derived from structural perturbation from those related to bioactivity. Six residues were found to constitute the anti-insect bioactive surface of Av2 (Val-2, Leu-5, Asn-16, Leu-18, and Ile-41). Further analysis of nine Av2 mutants on the human heart channel Na(v)1.5 expressed in Xenopus oocytes indicated that the bioactive surfaces toward insects and mammals practically coincide but differ from the bioactive surface of a structurally similar sea anemone toxin, Anthopleurin B, from Anthopleura xanthogrammica. Hence, our results not only demonstrate clear differences in the bioactive surfaces of Av2 and scorpion alpha-toxins but also indicate that despite the general conservation in structure and importance of the Arg-14 loop and its flanking residues Gly-10 and Gly-20 for function, the surface of interaction between different sea anemone toxins and Na(v)s varies.

  14. Construction of second order accurate monotone and stable residual distribution schemes for unsteady flow problems

    International Nuclear Information System (INIS)

    Abgrall, Remi; Mezine, Mohamed

    2003-01-01

    The aim of this paper is to construct upwind residual distribution schemes for the time accurate solution of hyperbolic conservation laws. To do so, we evaluate a space-time fluctuation based on a space-time approximation of the solution and develop new residual distribution schemes which are extensions of classical steady upwind residual distribution schemes. This method has been applied to the solution of scalar advection equation and to the solution of the compressible Euler equations both in two space dimensions. The first version of the scheme is shown to be, at least in its first order version, unconditionally energy stable and possibly conditionally monotonicity preserving. Using an idea of Csik et al. [Space-time residual distribution schemes for hyperbolic conservation laws, 15th AIAA Computational Fluid Dynamics Conference, Anahein, CA, USA, AIAA 2001-2617, June 2001], we modify the formulation to end up with a scheme that is unconditionally energy stable and unconditionally monotonicity preserving. Several numerical examples are shown to demonstrate the stability and accuracy of the method

  15. Effect of preemptive weld overlay on residual stress of repaired weldment in surge nozzle

    Energy Technology Data Exchange (ETDEWEB)

    Oh, Chang Young; Song, Tae Kwang; Bae, Hong Yeol; Chun, Yun Bae; Kim, Yun Jae [Korea Univ., Seoul (Korea, Republic of); Lee, Kyoung Soo; Park, Chi Yong [Korea Electric Power Research Institute, Daejeon (Korea, Republic of)

    2008-07-01

    In the welding process, weldments usually include repair weld during the manufacturing process. Repair welds is supposed to cause strong tensile residual stress. Moreover weldments, usually made by Alloy 82/182, is susceptible to PWSCC. Therefore, mitigation of welding residual stress in weldments is important for reliable operating. PWOL is one of the methods for mitigation and verified for over twenty years. In this paper, residual stress distribution of repaired weldments and the effect of PWOL on mitigation is examined for surge nozzle.

  16. Reverse Conservation Analysis Reveals the Specificity Determining Residues of Cytochrome P450 Family 2 (CYP 2

    Directory of Open Access Journals (Sweden)

    Tai-Sung Lee

    2008-01-01

    Full Text Available The concept of conservation of amino acids is widely used to identify important alignment positions of orthologs. The assumption is that important amino acid residues will be conserved in the protein family during the evolutionary process. For paralog alignment, on the other hand, the opposite concept can be used to identify residues that are responsible for specificity. Assuming that the function-specific or ligand-specific residue positions will have higher diversity since they are under evolutionary pressure to fit the target specificity, these function-specific or ligand-specific residues positions will have a lower degree of conservation than other positions in a highly conserved paralog alignment. This study assessed the ability of reverse conservation analysis to identify function-specific and ligand-specific residue positions in closely related paralog. Reverse conservation analysis of paralog alignments successfully identified all six previously reported substrate recognition sites (SRSs in cytochrome P450 family 2 (CYP 2. Further analysis of each subfamily identified the specificity-determining residues (SDRs that have been experimentally found. New potential SDRs were also predicted and await confirmation by further experiments or modeling calculations. This concept may be also applied to identify SDRs in other protein families.

  17. Persistence of DDT and parathion residues on a plant surface as influenced by weather factors

    NARCIS (Netherlands)

    Fahmy, H.S.M.

    1961-01-01

    The decay of DDT and parathion deposits under the influence of temperature, rain and ultraviolet radiation was described. Temperature and solar radiation were the main factors limiting the residual effect. High mean temperatures were more important than high maxima.

    DDT residues were more

  18. PENETAPAN RESIDU DAN PERKIRAAN PENETAPAN BATAS MAKSIMUM RESIDU (BMR ORGANOKLORIN PADA SIMPLISIA

    Directory of Open Access Journals (Sweden)

    Ani Isnawati

    2012-10-01

    Full Text Available Penggunaaan bahan obat tradisional (simplisia untuk skala industri dan peningkatan produksi tanaman obat dalam skala besar menjadi tidak ekonomis tanpa pestisida. Disatu sisi penggunaan pestisida dapat menguntungkan yaitu menyebabkan toksis pada hama namun disisi lain toksisitas dapat terjadi juga pada manusia, sehingga residu pestisida dalam tanaman obat yang dikonsumsi dalam jangka panjang akan merugikan kesehatan. Batas maksimum Residu (BMR pestisida dalam simplisia baik di Indonesia maupun di negara lain belum ditetapkan. Sehingga untuk itu untuk mengetahui adanya residu pestisida jenis organoklorin yang telah dilarang penggunaannya melalui Permentan No.434.1/kpts/TP.270/7/2001 dan untuk mengetahui batas keamanannya, maka perlu dilakukan penetapan residu organoklorin dalam simplisia dan menetapkan batas keamanan berdasarkan perhitungan secara teoritis. Pengujian residu dilakukan terhadap golongan pestisida organoklorin pada 4 jenis simplisia (daun wungu (Graptophyllum pictum (L Grifl, daun sambiloto Andrographis paniculata Ness, herba pegagan (Centella  asiatica (L Urban, daun tempuyung (Sonchus arvensis (L yang berasal dari 3 lokasi penanaman, yaitu : perkebunan Tanaman Obat Manako (Jawa Barat, Balai Penelitian Tanaman Obat Tawangmangu (BPTO di Jawa Tengah dan Perkebunan Tanaman Obat Purwodadi (Jawa Timur. Pemeriksaan residu pestisida organoklorin menggunakan kromatografi gas dan perhitungan batas keamanan dihitung dengan adanya nilai ADI (Acceptable daily intake yang telah ditetapkan bersama antara JAO dan WHO serta perkiraan banyaknya konsumsi simplisia. Hasil Pengujian residu pestisida organoklorin diperoleh bahwa simplisia daun Wungu (Tawangmangu mengandung residu lindan dengan kadar 0,24 mg/kg, pegagan (Purwodadi, mengandung lindan 0,36 mg/kg dan aldrin 0,31 mg/kg serta pegagan (Manako mengandung heptaklor 0,15 mg/kg dan op-DDE 0,11 mg/kg. Adapun penghitungan BMR heptaklor dan lindan secara teoritis dengan asumsi rata

  19. Dynamics of fragment capture for cluster structures of weakly bound 7Li

    Directory of Open Access Journals (Sweden)

    Shrivastava A.

    2013-12-01

    Full Text Available Role of cluster structures of 7Li on reaction dynamics have been studied by performing exclusive measurements of prompt-γ rays from residues with scattered particles at energy, E/Vb = 1.6, with 198Pt target. Yields of the residues resulting after capture of t and 4,5,6He, corresponding to different excitation energies of the composite system were estimated. The results were compared with three body classical-dynamical model for breakup fusion, constrained by the measured fusion, α and t capture cross-sections. The cross-section of residues from capture of α and t agreed well with the prediction of the model showing dominance of the two step process - breakup fusion, while those from tightly bound 6He showed massive transfer to be the dominant mechanism.

  20. Residual magnetic field in rotary machines; Campo magnetico residual en maquinas rotatorias

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez V, Esteban A; Apanco R, Marcelino [Instituto de Investigaciones Electricas, Cuernavaca, Morelos (Mexico)

    2007-07-01

    The residual magnetism is a phenomenon in which the magnetic dipoles of a substance are oriented in a certain degree. On the other hand, when internal forces exist capable of aligning elementary magnetic dipoles of a material, a permanent magnet is obtained. Just as in a conductor or in a material, in the elements of a rotary electrical machine magnetic fields can be induced that produce a residual magnetism or magnetization. In the rotary electrical machines, the magnetization phenomenon causes serious problems, such as the generation of induced currents that propitiate the mechanical wear in bearings, collars, trunnions and inclusive in the shaft, by effects known as pitting, frosting and spark tracks, as well as erroneous readings in vibration and temperature sensors, that in some cases can cause the shut down of the machine. In this article are presented the general concepts on the residual magnetism in rotary electrical machines, the causes that originate it and the problems that arises, as well as the demagnetization of the components that have residual magnetic field. The results obtained by the area of Electrical Equipment of the Instituto de Investigaciones Electricas are revised, during the execution of activities related to the measurement and elimination of the residual magnetic field in rotary electrical machines. [Spanish] El magnetismo residual es un fenomeno en el que los dipolos magneticos de una sustancia se encuentran orientados en un grado determinado. Por otro lado, cuando existen fuerzas internas capaces de alinear los dipolos magneticos elementales de un material, se tiene un iman permanente. Al igual que en un conductor o un material, en los elementos de una maquina electrica rotatoria se pueden inducir campos magneticos que producen un magnetismo residual o magnetizacion. En las maquinas electricas rotatorias, el fenomeno de magnetizacion causa graves problemas, como la generacion de corrientes inducidas que propician el desgaste mecanico

  1. 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...... pronounces. For this the well accepted NREL 5MW reference turbine simulated with FAST is used. The main result is a reduction in tower fatigue load at 22% while power error, rotor speed error, generator torque and pitch rate is improved from 2 to 33%....

  2. Development of Radiometric and Allied Analytical Methods and Strategies to Strengthen National Residue Control Programmes for Antibiotic and Anthelmintic Veterinary Drug Residues. Final Report of a Coordinated Research Project

    International Nuclear Information System (INIS)

    2016-08-01

    Awareness of food safety is rising among consumers, and many importing countries implement food control regulations to guarantee the quality and safety of imported foods for their consumers. Many developing countries have also taken steps to put in place control systems that encourage responsible use of veterinary medicines to combat possible drug resistance, control drug residues and ensure compliance with international and national standards. However, these countries still require the necessary know-how and skills to protect local consumers and to access international markets. One significant constraint is the capacity of laboratory services to generate surveillance data using reliable and cost effective analytical methods validated to national and international standards. The IAEA coordinated research project (CRP) on the Development of Radiometric and Allied Analytical Methods to Strengthen National Residue Control Programmes for Antibiotic and Anthelmintic Veterinary Drug Residues was initiated in 2009 to conduct work on robust nuclear and related technologies suitable for the screening and confirmatory analysis of residues of veterinary medicines, including antimicrobials and anthelmintics commonly used in animal production, with public health and trade significance. The CRP also explored mechanisms to enhance networking among research institutions involved in research on pharmacologically active veterinary drug residues in food (primarily) and environmental samples. The project was implemented by the Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture between 2009 and 2014 and involved eleven research contracts and one technical contract, five research agreements and one institution. The CRP was a continuation of the CRP on the Development of Strategies for the Effective Monitoring of Veterinary Drug Residues in Livestock and Livestock Products in Developing Countries and the key findings are also summarized in this publication.

  3. Coastal tomographic mapping of nonlinear tidal currents and residual currents

    Science.gov (United States)

    Zhu, Ze-Nan; Zhu, Xiao-Hua; Guo, Xinyu

    2017-07-01

    Depth-averaged current data, which were obtained by coastal acoustic tomography (CAT) July 12-13, 2009 in Zhitouyang Bay on the western side of the East China Sea, are used to estimate the semidiurnal tidal current (M2) as well as its first two overtide currents (M4 and M6). Spatial mean amplitude ratios M2:M4:M6 in the bay are 1.00:0.15:0.11. The shallow-water equations are used to analyze the generation mechanisms of M4 and M6. In the deep area, where water depths are larger than 60 m, M4 velocity amplitudes measured by CAT agree well with those predicted by the advection terms in the shallow water equations, indicating that M4 in the deep area is predominantly generated by the advection terms. M6 measured by CAT and M6 predicted by the nonlinear quadratic bottom friction terms agree well in the area where water depths are less than 20 m, indicating that friction mechanisms are predominant for generating M6 in the shallow area. In addition, dynamic analysis of the residual currents using the tidally averaged momentum equation shows that spatial mean values of the horizontal pressure gradient due to residual sea level and of the advection of residual currents together contribute about 75% of the spatial mean values of the advection by the tidal currents, indicating that residual currents in this bay are induced mainly by the nonlinear effects of tidal currents. This is the first ever nonlinear tidal current study by CAT.

  4. Interfacial Tryptophan Residues: A Role for the Cation-{pi} Effect?

    DEFF Research Database (Denmark)

    Petersen, Frederic Nicolas Rønne; Jensen, Morten Ø.; Helix Nielsen, Claus

    2005-01-01

    Integral membrane proteins are characterized by having a preference for aromatic residues, e.g., tryptophan (W), at the interface between the lipid bilayer core and the aqueous phase. The reason for this is not clear, but it seems that the preference is related to a complex interplay between steric...... between the nitrogen moiety of lipid molecule headgroups and the pi-electron distribution of gramicidin (gA) tryptophan residues (W(9), W(11), W(13), and W(15)) using molecular dynamics (MD) simulations of gA embedded in two hydrated lipid bilayers composed of 1-palmitoyl-2-oleoylphosphatidylethanolamine....... Our criteria for cation-pi interactions are based on distance and angular requirements, and the results from our model suggest that cation-pi interactions are relevant for W(PE)(11), W(PE)(13), W(PE)(15), and, to some extent, W(PC)(11) and W(PC)(13). In our model, W(9)does not seem to engage in cation...

  5. Single particle dynamics in circular accelerators

    International Nuclear Information System (INIS)

    Ruth, R.D.

    1986-10-01

    The purpose of this paper is to introduce the reader to the theory associated with the transverse dynamics of single particle, in circular accelerators. The discussion begins with a review of Hamiltonian dynamics and canonical transformations. The case of a single particle in a circular accelerator is considered with a discussion of non-linear terms and chromaticity. The canonical perturbation theory is presented and nonlinear resonances are considered. Finally, the concept of renormalization and residue criterion are examined. (FI)

  6. 76 FR 23914 - National Organic Program; Periodic Residue Testing

    Science.gov (United States)

    2011-04-29

    ... NOP. Residue testing plays an important role in organic certification by providing a means for... OFPA (7 U.S.C. 6503 through 6507) from creating certification programs to certify organic farms or... State organic certification program may contain additional requirements for the production and handling...

  7. Three-dimensional dynamic magnetic resonance angiography for the evaluation of radiosurgically treated cerebral arteriovenous malformations

    International Nuclear Information System (INIS)

    Gauvrit, Jean-Yves; Oppenheim, Catherine; Naggara, Olivier; Trystram, Denis; Fredy, Daniel; Meder, Jean-Francois; Nataf, Francois; Roux, Francois-Xavier; Munier, Thierry; Pruvo, Jean-Pierre; Leclerc, Xavier

    2006-01-01

    We assessed the value of three-dimensional (3D) dynamic magnetic resonance angiography (MRA) for the follow-up of patients with radiosurgically treated cerebral arteriovenous malformations (AVMs). Fifty-four patients with cerebral AVMs treated by radiosurgery (RS) were monitored using conventional catheter angiography (CCA) and 3D dynamic MRA with sensitivity encoding based on the parallel imaging. Cerebral AVM was qualitatively classified by two radiologists into one of five categories in terms of residual nidus size and persistence of early draining vein (I, >6 cm; II, 3-6 cm; III, <3 cm; IV, isolated early draining vein; V, complete obliteration). 3D MRA findings showed a good agreement with CCA in 40 cases (κ=0.62). Of 23 nidus detected on CCA, 3D dynamic MRA showed 14 residual nidus. Of 28 occluded nidus on 3D dynamic MRA, 22 nidus were occluded on CCA. The sensitivity and specificity of 3D dynamic MRA for the detection of residual AVM were 81% and 100%. 3D dynamic MRA after RS may therefore be useful in association with MRI and can be repeated as long as opacification of the nidus or early venous drainage persists, one CCA remaining indispensable to affirm the complete occlusion at the end of follow-up. (orig.)

  8. Calcium silicates synthesised from industrial residues with the ability for CO2 sequestration.

    Science.gov (United States)

    Morales-Flórez, Victor; Santos, Alberto; López, Antonio; Moriña, Isabel; Esquivias, Luis

    2014-12-01

    This work explored several synthesis routes to obtain calcium silicates from different calcium-rich and silica-rich industrial residues. Larnite, wollastonite and calcium silicate chloride were successfully synthesised with moderate heat treatments below standard temperatures. These procedures help to not only conserve natural resources, but also to reduce the energy requirements and CO2 emissions. In addition, these silicates have been successfully tested as carbon dioxide sequesters, to enhance the viability of CO2 mineral sequestration technologies using calcium-rich industrial by-products as sequestration agents. Two different carbon sequestration experiments were performed under ambient conditions. Static experiments revealed carbonation efficiencies close to 100% and real-time resolved experiments characterised the dynamic behaviour and ability of these samples to reduce the CO2 concentration within a mixture of gases. The CO2 concentration was reduced up to 70%, with a carbon fixation dynamic ratio of 3.2 mg CO2 per g of sequestration agent and minute. Our results confirm the suitability of the proposed synthesis routes to synthesise different calcium silicates recycling industrial residues, being therefore energetically more efficient and environmentally friendly procedures for the cement industry. © The Author(s) 2014.

  9. Dermal insecticide residues from birds inhabiting an orchard

    Science.gov (United States)

    Vyas, N.B.; Spann, J.W.; Hulse, C.S.; Gentry, S.; Borges, S.L.

    2007-01-01

    The US Environmental Protection Agency conducts risk assessments of insecticide applications to wild birds using a model that is limited to the dietary route of exposure. However, free-flying birds are also exposed to insecticides via the inhalation and dermal routes. We measured azinphos-methyl residues on the skin plus feathers and the feet of brown-headed cowbirds (Molothrus ater) in order to quantify dermal exposure to songbirds that entered and inhabited an apple (Malus x domestica) orchard following an insecticide application. Exposure to azinphos-methyl was measured by sampling birds from an aviary that was built around an apple tree. Birds sampled at 36 h and 7-day post-application were placed in the aviary within 1 h after the application whereas birds exposed for 3 days were released into the aviary 4-day post-application. Residues on vegetation and soil were also measured. Azinphos-methyl residues were detected from the skin plus feathers and the feet from all exposure periods. Our results underscore the importance of incorporating dermal exposure into avian pesticide risk assessments.

  10. Effect of washing on pesticide residues in olives.

    Science.gov (United States)

    Guardia-Rubio, M; Ayora-Cañada, M J; Ruiz-Medina, A

    2007-03-01

    The present work aims at contributing to the knowledge of the fate of 5 pesticides in olives in order to evaluate how washing may affect the presence of these residues in this fruit (and consequently in olive oil). For this purpose, olives were sprayed with commercial formulations containing the active ingredients and a series of analyses were performed for 64 d by using gas chromatography with mass spectrometric detection. Selected pesticides, ranked by their importance, were diuron, terbuthylazine, simazine, alpha-endosulfan, and beta-endosulfan. The pesticide fraction, which was not removable from olives by washing, increased with time after treatment until their degradation started at week 6. Washing performed 1 d after treatment was the most effective in reducing residues, especially for simazine. Consequently, the washing step performed in olive mills could be effective in removing those herbicide residues present in olives as a consequence of contact with contaminated soil for a short time. This happens when olives are dropped and harvested off the ground by means of brushes or suction equipment.

  11. Dynamic features of apo and bound HIV-Nef protein reveal the anti-HIV dimerization inhibition mechanism.

    Science.gov (United States)

    Moonsamy, Suri; Bhakat, Soumendranath; Soliman, Mahmoud E S

    2015-01-01

    The first account on the dynamic features of Nef or negative factor, a small myristoylated protein located in the cytoplasm believes to increase HIV-1 viral titer level, is reported herein. Due to its major role in HIV-1 pathogenicity, Nef protein is considered an emerging target in anti-HIV drug design and discovery process. In this study, comparative long-range all-atom molecular dynamics simulations were employed for apo and bound protein to unveil molecular mechanism of HIV-Nef dimerization and inhibition. Results clearly revealed that B9, a newly discovered Nef inhibitor, binds at the dimeric interface of Nef protein and caused significant separation between orthogonally opposed residues, namely Asp108, Leu112 and Gln104. Large differences in magnitudes were observed in the radius of gyration (∼1.5 Å), per-residue fluctuation (∼2 Å), C-alpha deviations (∼2 Å) which confirm a comparatively more flexible nature of apo conformation due to rapid dimeric association. Compared to the bound conformer, a more globally correlated motion in case of apo structure of HIV-Nef confirms the process of dimeric association. This clearly highlights the process of inhibition as a result of ligand binding. The difference in principal component analysis (PCA) scatter plot and per-residue mobility plot across first two normal modes further justifies the same findings. The in-depth dynamic analyses of Nef protein presented in this report would serve crucial in understanding its function and inhibition mechanisms. Information on inhibitor binding mode would also assist in designing of potential inhibitors against this important HIV target.

  12. Characterization Report on Sand, Slag, and Crucible Residues and on Fluoride Residues

    International Nuclear Information System (INIS)

    Murray, A.M.

    1999-01-01

    This paper reports on the chemical characterization of the sand, slag, and crucible (SS and C) residues and the fluoride residues that may be shipped from the Rocky Flats Environmental Technology Site (RFETS) to Savannah River Site (SRS)

  13. Investigation of the Residual Stress State in an Epoxy Based Specimen

    DEFF Research Database (Denmark)

    Baran, Ismet; Jakobsen, Johnny; Andreasen, Jens Henrik

    2015-01-01

    Abstract. Process induced residual stresses may play an important role under service loading conditions for fiber reinforced composite. They may initiate premature cracks and alter the internal stress level. Therefore, the developed numerical models have to be validated with the experimental...... observations. In the present work, the formation of the residual stresses/strains are captured from experimental measurements and numerical models. An epoxy/steel based sample configuration is considered which creates an in-plane biaxial stress state during curing of the resin. A hole drilling process...... material models, i.e. cure kinetics, elastic modulus, CTE, chemical shrinkage, etc. together with the drilling process using the finite element method. The measured and predicted in-plane residual strain states are compared for the epoxy/metal biaxial stress specimen....

  14. Studies of the magnitude and nature of pesticide residues in stored products, using radiotracer techniques

    International Nuclear Information System (INIS)

    1990-01-01

    Growing world population and food demand have dictated the introduction of intensive agricultural practices, including the use of an increasing range of agrochemicals. The utilization of these chemicals has a positive and often dramatic impact on agricultural production, but every effort has to be made to ensure safety in use. This is a dynamic challenge for many countries and necessitates the implementation of adequate monitoring programmes. Even when pesticide use conforms to currently adopted standards of good management practice, undesirable side effects may occur and could, at times, endanger public health. Nuclear techniques provide a valuable tool for studying pesticide residues in stored food commodities. Radioisotopes can be used to determine total quantities of residue present, the nature of the residue (i.e. both undecomposed parent material and reaction products), rates of breakdown and loss and distribution in the food material. All of this information is essential for health and regulatory authorities to establish and maintain comprehensive tolerance standards that will protect the health of the consumer. The use of 14 C labelled compounds constitutes a superior and unrivalled tool, in particular for the detection and quantification of grain bound residues. All pesticide residues remaining on or in food materials are of potential concern to human health. Surface residues that remain on commodities such as grain may present an occupational risk to workers exposed to dust emanating from the commodity; residues that remain in food may be a hazard to the consumer. The nature of the residue, the quantity present and its toxicological significance should be known so that tolerance levels can be established and complied with. Refs, figs and tabs

  15. A residue-specific shift in stability and amyloidogenicity of antibody variable domains.

    Science.gov (United States)

    Nokwe, Cardine N; Zacharias, Martin; Yagi, Hisashi; Hora, Manuel; Reif, Bernd; Goto, Yuji; Buchner, Johannes

    2014-09-26

    Variable (V) domains of antibodies are essential for antigen recognition by our adaptive immune system. However, some variants of the light chain V domains (VL) form pathogenic amyloid fibrils in patients. It is so far unclear which residues play a key role in governing these processes. Here, we show that the conserved residue 2 of VL domains is crucial for controlling its thermodynamic stability and fibril formation. Hydrophobic side chains at position 2 stabilize the domain, whereas charged residues destabilize and lead to amyloid fibril formation. NMR experiments identified several segments within the core of the VL domain to be affected by changes in residue 2. Furthermore, molecular dynamic simulations showed that hydrophobic side chains at position 2 remain buried in a hydrophobic pocket, and charged side chains show a high flexibility. This results in a predicted difference in the dissociation free energy of ∼10 kJ mol(-1), which is in excellent agreement with our experimental values. Interestingly, this switch point is found only in VL domains of the κ family and not in VLλ or in VH domains, despite a highly similar domain architecture. Our results reveal novel insight into the architecture of variable domains and the prerequisites for formation of amyloid fibrils. This might also contribute to the rational design of stable variable antibody domains. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  16. Recovery of biogas as a source of renewable energy from ice-cream production residues and wastewater.

    Science.gov (United States)

    Demirel, Burak; Orok, Murat; Hot, Elif; Erkişi, Selin; Albükrek, Metin; Onay, Turgut T

    2013-01-01

    Proper management of waste streams and residues from agro-industry is very important to prevent environmental pollution. In particular, the anaerobic co-digestion process can be used as an important tool for safe disposal and energy recovery from agro-industry waste streams and residues. The primary objective of this laboratory-scale study was to determine whether it was possible to recover energy (biogas) from ice-cream production residues and wastewater, through a mesophilic anaerobic co-digestion process. A high methane yield of 0.338 L CH4/gCOD(removed) could be achieved from anaerobic digestion of ice-cream wastewater alone, with almost 70% of methane in biogas, while anaerobic digestion of ice-cream production residue alone did not seem feasible. When wastewater and ice-cream production residue were anaerobically co-digested at a ratio of 9:1 by weight, the highest methane yield of 0.131 L CH4/gCOD(removed) was observed. Buffering capacity seemed to be imperative in energy recovery from these substrates in the anaerobic digestion process.

  17. Verification and Validation of Residual Stresses in Bi-Material Composite Rings

    Energy Technology Data Exchange (ETDEWEB)

    Nelson, Stacy Michelle [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Hanson, Alexander Anthony [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Briggs, Timothy [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Werner, Brian T. [Sandia National Lab. (SNL-CA), Livermore, CA (United States)

    2017-07-01

    Process-induced residual stresses commonly occur in composite structures composed of dissimilar materials. These residual stresses form due to differences in the composite materials’ coefficients of thermal expansion and the shrinkage upon cure exhibited by polymer matrix materials. Depending upon the specific geometric details of the composite structure and the materials’ curing parameters, it is possible that these residual stresses could result in interlaminar delamination or fracture within the composite. Therefore, the consideration of potential residual stresses is important when designing composite parts and their manufacturing processes. However, the experimental determination of residual stresses in prototype parts can be time and cost prohibitive. As an alternative to physical measurement, it is possible for computational tools to be used to quantify potential residual stresses in composite prototype parts. Therefore, the objectives of the presented work are to demonstrate a simplistic method for simulating residual stresses in composite parts, as well as the potential value of sensitivity and uncertainty quantification techniques during analyses for which material property parameters are unknown. Specifically, a simplified residual stress modeling approach, which accounts for coefficient of thermal expansion mismatch and polymer shrinkage, is implemented within the Sandia National Laboratories’ developed SIERRA/SolidMechanics code. Concurrent with the model development, two simple, bi-material structures composed of a carbon fiber/epoxy composite and aluminum, a flat plate and a cylinder, are fabricated and the residual stresses are quantified through the measurement of deformation. Then, in the process of validating the developed modeling approach with the experimental residual stress data, manufacturing process simulations of the two simple structures are developed and undergo a formal verification and validation process, including a mesh

  18. Radiotracer studies of fungicide residues in food plants

    International Nuclear Information System (INIS)

    1990-04-01

    Agricultural fungicides are chemicals used on seeds, crops and in soils throughout the growing season. Fungicide treatments may lead to various levels of chemical residues in food commodities. Primary emphasis has been placed on ethylenebisdithiocarbamates (EBDCs), an important group of agrofungicides used in preparations for spraying or dusting major crops such as apples, pears, broccoli, cabbages, egg plants, cauliflower, grapes, lettuce, peppers, celery, cucumbers and tomatoes. Treatments with EBDCs result in terminal residues containing ethylenthiourea (ETU). This is a toxicologically significant decomposition product which has attracted considerable attention in recent years due to indications of its potential goitrogenic and carcinogenic properties. In recognition of the need for a coordinated examination of ETU levels in food, particularly under tropical conditions, the program of radiotracer techniques as a tool for studying fungicide residue problems on food was initiated in 1984. In current studies, three EBDCs, maneb, zineb and mancozeb from different manufacturers in different countries were analysed. This report describes the model protocols (Annexes I, II and III) as they were set up for determination of residues in commodities and soil, using radiotracer and conventional chromatographic techniques . In the 16 papers presented in this report C 14 -labelled EBDCs are determined in plants, vegetables, and soils, before and after cooking, as a function of time and of other agricultural parameters. Refs, figs and tabs

  19. Development of residual stress analysis procedure for fitness-for-service assessment of welded structure

    International Nuclear Information System (INIS)

    Kim, Jong Sung; Jin, Tae Eun; Dong, P.; Prager, M.

    2003-01-01

    In this study, a state of art review of existing residual stress analysis techniques and representative solutions is presented in order to develop the residual stress analysis procedure for Fitness-For-Service(FFS) assessment of welded structure. Critical issues associated with existing residual stress solutions and their treatments in performing FFS are discussed. It should be recognized that detailed residual stress evolution is an extremely complicated phenomenon that typically involves material-specific thermomechanical/metallurgical response, welding process physics, and structural interactions within a component being welded. As a result, computational procedures can vary significantly from highly complicated numerical techniques intended only to elucidate a small part of the process physics to cost-effective procedures that are deemed adequate for capturing some of the important features in a final residual stress distribution. Residual stress analysis procedure for FFS purposes belongs to the latter category. With this in mind, both residual stress analysis techniques and their adequacy for FFS are assessed based on both literature data and analyses performed in this investigation

  20. Release of bound residues of atrazine from soils through autoclaving and gamma radiation sterilization

    International Nuclear Information System (INIS)

    Nakagawa, L.E.; Andréa, M.M.

    1997-01-01

    The sterilization methods are particularly important to study the influence of microorganisms on the pesticide dissipation in soils. This study, conducted in the laboratories of the Instituto Biológico of São Paulo in august 1996, tested the influence of two methods of soil sterilization - moist heat (autoclaving) and γ radiation - on the release of nonextractable or bound residues. It was studied, as example, bound residues of the herbicide atrazine in two types of soil (gley humic and dark red latosol). In the soil samples submitted to the moist heat sterilization, the recovery of the previously bound residues as reextractable residues was 5.6 and 5.9 times higher than in the control soils, not submitted to any sterilization process. Therefore, the method itself released the residues, indicating that the autoclaving is not the most appropriate method for studies on the influence of microorganisms on the release of bound residues. Otherwise, the γ radiation did not modify the residues recovery when compared to the controls. (author) [pt

  1. Application of preservatives for residual fuels

    International Nuclear Information System (INIS)

    Gorozpe y Munoz, Tomas

    2000-01-01

    Due to the high costs of the combust oils (fuel oil 6) used in generators of vapor and in other treatments, makes important consider the use of preservatives that improve the operation of the units from the operative point of view and of environmental control. The author enumerates several of the problems of corrosion, of efficiency in the combustion and of thermal efficiency; in a same way it enumerates several useful preservatives, to be used in residual fuel

  2. Residual symptoms and specific functional impairments in euthymic patients with bipolar disorder.

    Science.gov (United States)

    Samalin, Ludovic; de Chazeron, Ingrid; Vieta, Eduard; Bellivier, Frank; Llorca, Pierre-Michel

    2016-03-01

    The aims of the present study were to confirm the impact of residual symptoms on overall functioning in a large sample of euthymic patients with bipolar disorder in real-life conditions and to explore the relationship between residual symptoms and specific areas of functional impairment. This was a multicenter, cross-sectional, non-interventional study of euthymic outpatients with bipolar disorder. The Functioning Assessment Short Test was used to assess overall and specific domains of functioning (autonomy, occupational functioning, cognitive functioning, financial issues, interpersonal relationships, and leisure time). Various residual symptoms were assessed (residual mood symptoms, emotional dysregulation, sleep and sexual disorders, stigma, and perceived cognitive impairment). Logistic regression was used to determine the best model of association between functional domains and residual symptoms. Almost half of the 468 patients included (42%) had poor overall functioning. Residual depressive symptoms appeared to have an impact on overall functioning and in nearly all areas of functioning. In addition, specific residual symptoms had significantly more negative effects on some domains of functioning in euthymic patients with bipolar disorder (residual manic symptoms and occupational stigma on autonomy, emotional inhibition on occupational functioning, residual manic symptoms on financial issues, family stigma on interpersonal relationships, and sexual function and occupational stigma on leisure time). Our findings highlight the importance of evaluating overall functioning in clinical practice as well as functional domains. They also indicate that some residuals symptoms in patients with bipolar disorder should be targeted in personalized treatment plans, in order to improve functioning in the domains in which the patient is most impaired. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  3. Prosthetics socket that incorporates an air splint system focusing on dynamic interface pressure.

    Science.gov (United States)

    Razak, Nasrul Anuar Abd; Osman, Noor Azuan Abu; Gholizadeh, Hossein; Ali, Sadeeq

    2014-08-01

    The interface pressure between the residual limb and prosthetic socket has a significant effect on an amputee's satisfaction and comfort. This paper presents the design and performance of a new prosthetic socket that uses an air splint system. The air splint prosthetic socket system was implemented by combining the air splint with a pressure sensor that the transhumeral user controls through the use of a microcontroller. The modular construction of the system developed allows the FSR pressure sensors that are placed inside the air splint socket to determine the required size and fitting for the socket used. Fifteen transhumeral amputees participated in the study. The subject's dynamic pressure on the socket that's applied while wearing the air splint systems was recorded using F-socket transducers and microcontroller analysis. The values collected by the F-socket sensor for the air splint prosthetic socket system were determined accordingly by comparing the dynamic pressure applied using statically socket. The pressure volume of the air splint fluctuated and was recorded at an average of 38 kPa (2.5) to 41 kPa (1.3) over three hours. The air splint socket might reduce the pressure within the interface of residual limb. This is particularly important during the daily life activities and may reduce the pain and discomfort at the residual limb in comparison to the static socket. The potential development of an auto-adjusted socket that uses an air splint system as the prosthetic socket will be of interest to researchers involved in rehabilitation engineering, prosthetics and orthotics.

  4. Residual stress by repair welds

    International Nuclear Information System (INIS)

    Mochizuki, Masahito; Toyoda, Masao

    2003-01-01

    Residual stress by repair welds is computed using the thermal elastic-plastic analysis with phase-transformation effect. Coupling phenomena of temperature, microstructure, and stress-strain fields are simulated in the finite-element analysis. Weld bond of a plate butt-welded joint is gouged and then deposited by weld metal in repair process. Heat source is synchronously moved with the deposition of the finite-element as the weld deposition. Microstructure is considered by using CCT diagram and the transformation behavior in the repair weld is also simulated. The effects of initial stress, heat input, and weld length on residual stress distribution are studied from the organic results of numerical analysis. Initial residual stress before repair weld has no influence on the residual stress after repair treatment near weld metal, because the initial stress near weld metal releases due to high temperature of repair weld and then stress by repair weld regenerates. Heat input has an effect for residual stress distribution, for not its magnitude but distribution zone. Weld length should be considered reducing the magnitude of residual stress in the edge of weld bead; short bead induces high tensile residual stress. (author)

  5. Infra-red finiteness in quantum electro-dynamics

    International Nuclear Information System (INIS)

    Kawai, Takahiro

    1984-01-01

    The authors report some mathematical aspects of a recent solution of the infra-red catastrophe in quantum electro-dynamics. A principal result is that the coordinate space Feynman function can be separated into two factors the first of which is a unitary operator in photon space representing the classical electro-magnetic contribution to the amplitude, and the second of which is a residual factor representing the quantum fluctuation about the classical contribution. The main objectives were to verify: (i) the residual factor is free of infra-red divergences, and (ii) the dominant part of the singularity of the residual factor on the positive-α Landau surface has the same analytic form as it would have if the photons were massive. (Auth.)

  6. Computational and Experimental Investigations of the Molecular Scale Structure and Dynamics of Gologically Important Fluids and Mineral-Fluid Interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Bowers, Geoffrey [Alfred Univ., NY (United States)

    2017-04-05

    United States Department of Energy grant DE-FG02-10ER16128, “Computational and Spectroscopic Investigations of the Molecular Scale Structure and Dynamics of Geologically Important Fluids and Mineral-Fluid Interfaces” (Geoffrey M. Bowers, P.I.) focused on developing a molecular-scale understanding of processes that occur in fluids and at solid-fluid interfaces using the combination of spectroscopic, microscopic, and diffraction studies with molecular dynamics computer modeling. The work is intimately tied to the twin proposal at Michigan State University (DOE DE-FG02-08ER15929; same title: R. James Kirkpatrick, P.I. and A. Ozgur Yazaydin, co-P.I.).

  7. Zaccai neutron resilience and site-specific hydration dynamics in a globular protein

    Energy Technology Data Exchange (ETDEWEB)

    Miao, Yinglong [Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Hong, Liang [Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Yi, Zheng [Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Smith, Jeremy C. [Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2013-07-16

    A discussion is presented of contributions of the Zaccai group to the understanding of flexibility in biological macromolecules using dynamic neutron scattering. The concept of resilience as introduced by Zaccai is discussed and investigated using molecular dynamics simulation on camphor-bound cytochrome P450. The resilience of hydrophilic residues is found to be more strongly affected by hydration than that of hydrophobic counterparts. The hydration-induced softening of protein propagates from the surface into the dry core. Furthermore, buried hydrophilic residues behave more like those exposed on the protein surface, and are different from their hydrophobic counterparts.

  8. Characterizing the Dynamics of α-Synuclein Oligomers Using Hydrogen/Deuterium Exchange Monitored by Mass Spectrometry

    DEFF Research Database (Denmark)

    Mysling, Simon; Betzer, Cristine; Jensen, Poul Henning

    2013-01-01

    Soluble oligomers formed by α-synuclein (αSN) are suspected to play a central role in neuronal cell death during Parkinson's disease. While studies have probed the surface structure of these oligomers, little is known about the backbone dynamics of αSN when they form soluble oligomers. Using...... analyses performed on αSN fibrils and indicated a possible zipperlike maturation mechanism for αSN aggregates. We find the protected N-terminus (residues 4-17) to be of particular interest, as this region has previously been observed to be highly dynamic for both monomeric and fibrillar αSN. This region...... has mainly been described in relation to membrane binding of αSN, and structuring may be important in relation to disease....

  9. Three-residue turns in alpha/beta-peptides and their application in the design of tertiary structures.

    Science.gov (United States)

    Sharma, Gangavaram V M; Nagendar, Pendem; Ramakrishna, Kallaganti V S; Chandramouli, Nagula; Choudhary, Madavi; Kunwar, Ajit C

    2008-06-02

    A new three-residue turn was serendipitously discovered in alpha/beta hybrid peptides derived from alternating C-linked carbo-beta-amino acids (beta-Caa) and L-Ala residues. The three-residue beta-alpha-beta turn at the C termini, nucleated by a helix at the N termini, resulted in helix-turn (HT) supersecondary structures in these peptides. The turn in the HT motif is stabilized by two H bonds-CO(i-2)-NH(i), with a seven-membered pseudoring (gamma turn) in the backward direction, and NH(i-2)-CO(i), with a 13-membered pseudoring in the forward direction (i being the last residue)--at the C termini. The study was extended to generalize the new three-residue turn (beta-alpha-beta) by using different alpha- and beta-amino acids. Furthermore, the HT motifs were efficiently converted, by an extension with helical oligomers at the C termini, into peptides with novel helix-turn-helix (HTH) tertiary structures. However, this resulted in the destabilization of the beta-alpha-beta turn with the concomitant nucleation of another three-residue turn, alpha-beta-beta, which is stabilized by 11- and 15-membered bifurcated H bonds. Extensive NMR spectroscopic studies were carried out to delineate the secondary and tertiary structures in these peptides, which are further supported by molecular dynamics (MD) investigations.

  10. Properties of Direct Coal Liquefaction Residue Modified Asphalt Mixture

    Directory of Open Access Journals (Sweden)

    Jie Ji

    2017-01-01

    Full Text Available The objectives of this paper are to use Direct Coal Liquefaction Residue (DLCR to modify the asphalt binders and mixtures and to evaluate the performance of modified asphalt mixtures. The dynamic modulus and phase angle of DCLR and DCLR-composite modified asphalt mixture were analyzed, and the viscoelastic properties of these modified asphalt mixtures were compared to the base asphalt binder SK-90 and Styrene-Butadiene-Styrene (SBS modified asphalt mixtures. The master curves of the asphalt mixtures were shown, and dynamic and viscoelastic behaviors of asphalt mixtures were described using the Christensen-Anderson-Marasteanu (CAM model. The test results show that the dynamic moduli of DCLR and DCLR-composite asphalt mixtures are higher than those of the SK-90 and SBS modified asphalt mixtures. Based on the viscoelastic parameters of CAM models of the asphalt mixtures, the high- and low-temperature performance of DLCR and DCLR-composite modified asphalt mixtures are obviously better than the SK-90 and SBS modified asphalt mixtures. In addition, the DCLR and DCLR-composite modified asphalt mixtures are more insensitive to the frequency compared to SK-90 and SBS modified asphalt mixtures.

  11. Calculation method for residual stress analysis of filament-wound spherical pressure vessels

    International Nuclear Information System (INIS)

    Knight, C.E. Jr.

    1976-01-01

    Filament wound spherical pressure vessels may be produced with very high performance factors. These performance factors are a calculation of contained pressure times enclosed volume divided by structure weight. A number of parameters are important in determining the level of performance achieved. One of these is the residual stress state in the fabricated unit. A significant level of an unfavorable residual stress state could seriously impair the performance of the vessel. Residual stresses are of more concern for vessels with relatively thick walls and/or vessels constructed with the highly anisotropic graphite or aramid fibers. A method is established for measuring these stresses. A theoretical model of the composite structure is required. Data collection procedures and techniques are developed. The data are reduced by means of the model and result in the residual stress analysis. The analysis method can be used in process parameter studies to establish the best fabrication procedures

  12. The Motion Planning of Overhead Crane Based on Suppressing Payload Residual Swing

    Directory of Open Access Journals (Sweden)

    Liu Hua-sen

    2016-01-01

    Full Text Available Since the overhead crane system is subject to under actuation system due to that overhead crane and payload are connected by flexibility wire rope. The payload generates residual swing when the overhead crane is accelerating/ decelerating the motions. This may cause trouble for the payload precise positioning and motion planning. Hence, an optimization input shaping control method is presented to reduce the under actuated overhead crane’s payload swing caused via the inertia force. The dynamic model of the overhead crane is proposed according to the physics structure of the crane. The input shaper based on the motion planning of the crane is used as the feed forward input to suppress payload residual swing. Simulation and experiment results indicate that the ZV input shaper and ZVD input shaper can reduce the payload swing of the overhead crane.

  13. Crop residues as raw materials for biorefinery systems - A LCA case study

    International Nuclear Information System (INIS)

    Cherubini, Francesco; Ulgiati, Sergio

    2010-01-01

    Our strong dependence on fossil fuels results from the intensive use and consumption of petroleum derivatives which, combined with diminishing oil resources, causes environmental and political concerns. The utilization of agricultural residues as raw materials in a biorefinery is a promising alternative to fossil resources for production of energy carriers and chemicals, thus mitigating climate change and enhancing energy security. This paper focuses on a biorefinery concept which produces bioethanol, bioenergy and biochemicals from two types of agricultural residues, corn stover and wheat straw. These biorefinery systems are investigated using a Life Cycle Assessment (LCA) approach, which takes into account all the input and output flows occurring along the production chain. This approach can be applied to almost all the other patterns that convert lignocellulosic residues into bioenergy and biochemicals. The analysis elaborates on land use change aspects, i.e. the effects of crop residue removal (like decrease in grain yields, change in soil N 2 O emissions and decrease of soil organic carbon). The biorefinery systems are compared with the respective fossil reference systems producing the same amount of products/services from fossils instead of biomass. Since climate change mitigation and energy security are the two most important driving forces for biorefinery development, the assessment focuses on greenhouse gas (GHG) emissions and cumulative primary energy demand, but other environmental categories are evaluated as well. Results show that the use of crop residues in a biorefinery saves GHG emissions and reduces fossil energy demand. For instance, GHG emissions are reduced by about 50% and more than 80% of non-renewable energy is saved. Land use change effects have a strong influence in the final GHG balance (about 50%), and their uncertainty is discussed in a sensitivity analysis. Concerning the investigation of the other impact categories, biorefinery systems

  14. Fasting, but Not Aging, Dramatically Alters the Redox Status of Cysteine Residues on Proteins in Drosophila melanogaster

    Directory of Open Access Journals (Sweden)

    Katja E. Menger

    2015-06-01

    Full Text Available Altering the redox state of cysteine residues on protein surfaces is an important response to environmental challenges. Although aging and fasting alter many redox processes, the role of cysteine residues is uncertain. To address this, we used a redox proteomic technique, oxidative isotope-coded affinity tags (OxICAT, to assess cysteine-residue redox changes in Drosophila melanogaster during aging and fasting. This approach enabled us to simultaneously identify and quantify the redox state of several hundred cysteine residues in vivo. Cysteine residues within young flies had a bimodal distribution with peaks at ∼10% and ∼85% reversibly oxidized. Surprisingly, these cysteine residues did not become more oxidized with age. In contrast, 24 hr of fasting dramatically oxidized cysteine residues that were reduced under fed conditions while also reducing cysteine residues that were initially oxidized. We conclude that fasting, but not aging, dramatically alters cysteine-residue redox status in D. melanogaster.

  15. MODEL FOR THE CORRECTION OF THE SPECIFIC GRAVITY OF BIODIESEL FROM RESIDUAL OIL

    Directory of Open Access Journals (Sweden)

    Tatiana Aparecida Rosa da Silva

    2013-06-01

    Full Text Available Biodiesel is a important fuel with economic benefits, social and environmental. The production cost of the biodiesel can be significantly lowered if the raw material is replaced by a alternative material as residual oil. In this study, the variation of specific gravity with temperature increase for diesel and biodiesel from residual oil obtained by homogeneous basic catalysis. All properties analyzed for biodiesel are within specification Brazil. The determination of the correction algorithm for the specific gravity function of temperature is also presented, and the slope of the line to diesel fuel, methylic biodiesel (BMR and ethylic biodiesel (BER from residual oil were respectively the values -0.7089, -0.7290 and -0.7277. This demonstrates the existence of difference of the model when compared chemically different fuels, like diesel and biodiesel from different sources, indicating the importance of determining the specific algorithm for the operations of conversion of volume to the reference temperature.

  16. Variation behavior of residual stress distribution by manufacturing processes in welded pipes of austenitic stainless steel

    International Nuclear Information System (INIS)

    Ihara, Ryohei; Hashimoto, Tadafumi; Mochizuki, Masahito

    2012-01-01

    Stress corrosion cracking (SCC) has been observed near heat affected zone (HAZ) of primary loop recirculation pipes made of low-carbon austenitic stainless steel type 316L in the nuclear power plants. For the non-sensitization material, residual stress is the important factor of SCC, and it is generated by machining and welding. In the actual plants, welding is conducted after machining as manufacturing processes of welded pipes. It could be considered that residual stress generated by machining is varied by welding as a posterior process. This paper presents residual stress variation due to manufacturing processes of pipes using X-ray diffraction method. Residual stress distribution due to welding after machining had a local maximum stress in HAZ. Moreover, this value was higher than residual stress generated by welding or machining. Vickers hardness also had a local maximum hardness in HAZ. In order to clarify hardness variation, crystal orientation analysis with EBSD method was performed. Recovery and recrystallization were occurred by welding heat near the weld metal. These lead hardness decrease. The local maximum region showed no microstructure evolution. In this region, machined layer was remained. Therefore, the local maximum hardness was generated at machined layer. The local maximum stress was caused by the superposition effect of residual stress distributions due to machining and welding. Moreover, these local maximum residual stress and hardness are exceeded critical value of SCC initiation. In order to clarify the effect of residual stress on SCC initiation, evaluation including manufacturing processes is important. (author)

  17. Spin distribution of evaporation residues formed in complete and incomplete fusion in 16O+154Sm system

    Science.gov (United States)

    Singh, D.; Linda, Sneha B.; Giri, Pankaj K.; Mahato, Amritraj; Tripathi, R.; Kumar, Harish; Afzal Ansari, M.; Sathik, N. P. M.; Ali, Rahbar; Kumar, Rakesh; Muralithar, S.; Singh, R. P.

    2017-11-01

    Spin distributions for several evaporation residues populated in the 16O+154Sm system have been measured at projectile energy ≈ 6.2 MeV/A by using the charged particle-γ-coincidence technique. The measured spin distributions of the evaporation residues populated through incomplete fusion associated with 'fast' α and 2α-emission channels are found to be entirely different from fusion-evaporation channels. It is observed that the mean input angular momentum for the evaporation residues formed in incomplete fusion channel is relatively higher than that observed for evaporation residues in complete fusion channels. The feeding intensity profile of evaporation residues populated through complete fusion and incomplete fusion have also been studied. The incomplete fusion channels are found to have narrow range feeding only for high spin states, while complete fusion channels are strongly fed over a broad spin range and widely populated. Comparison of present results with earlier data suggests that the mean input angular momentum values are relatively smaller for spherical target than that of deformed target using the same projectile and incident energy highlighting the role of target deformation in incomplete fusion dynamics.

  18. Spin distribution of evaporation residues formed in complete and incomplete fusion in 16O+154Sm system

    Directory of Open Access Journals (Sweden)

    D. Singh

    2017-11-01

    Full Text Available Spin distributions for several evaporation residues populated in the 16O+154Sm system have been measured at projectile energy ≈ 6.2 MeV/A by using the charged particle–γ-coincidence technique. The measured spin distributions of the evaporation residues populated through incomplete fusion associated with ‘fast’ α and 2α-emission channels are found to be entirely different from fusion–evaporation channels. It is observed that the mean input angular momentum for the evaporation residues formed in incomplete fusion channel is relatively higher than that observed for evaporation residues in complete fusion channels. The feeding intensity profile of evaporation residues populated through complete fusion and incomplete fusion have also been studied. The incomplete fusion channels are found to have narrow range feeding only for high spin states, while complete fusion channels are strongly fed over a broad spin range and widely populated. Comparison of present results with earlier data suggests that the mean input angular momentum values are relatively smaller for spherical target than that of deformed target using the same projectile and incident energy highlighting the role of target deformation in incomplete fusion dynamics.

  19. Securing a bioenergy future without imports

    International Nuclear Information System (INIS)

    Welfle, Andrew; Gilbert, Paul; Thornley, Patricia

    2014-01-01

    The UK has legally binding renewable energy and greenhouse gas targets. Energy from biomass is anticipated to make major contributions to these. However there are concerns about the availability and sustainability of biomass for the bioenergy sector. A Biomass Resource Model has been developed that reflects the key biomass supply-chain dynamics and interactions determining resource availability, taking into account climate, food, land and other constraints. The model has been applied to the UK, developing four biomass resource scenarios to analyse resource availability and energy generation potential within different contexts. The model shows that indigenous biomass resources and energy crops could service up to 44% of UK energy demand by 2050 without impacting food systems. The scenarios show, residues from agriculture, forestry and industry provide the most robust resource, potentially providing up to 6.5% of primary energy demand by 2050. Waste resources are found to potentially provide up to 15.4% and specifically grown biomass and energy crops up to 22% of demand. The UK is therefore projected to have significant indigenous biomass resources to meet its targets. However the dominant biomass resource opportunities identified in the paper are not consistent with current UK bioenergy strategies, risking biomass deficit despite resource abundance. - Highlights: • Biomass Resource Model and Scenarios reflect biomass supply-chain dynamics to 2050. • High potential availability of biomass and energy crops without food systems impacts. • UK Indigenous biomass resource could service up to 44% of UK energy demand by 2050. • Robust residue resource from ongoing activities and large potential waste resource. • Indigenous resource abundance and the UK’s path towards increased resource deficit

  20. Identification of residue pairing in interacting β-strands from a predicted residue contact map.

    Science.gov (United States)

    Mao, Wenzhi; Wang, Tong; Zhang, Wenxuan; Gong, Haipeng

    2018-04-19

    Despite the rapid progress of protein residue contact prediction, predicted residue contact maps frequently contain many errors. However, information of residue pairing in β strands could be extracted from a noisy contact map, due to the presence of characteristic contact patterns in β-β interactions. This information may benefit the tertiary structure prediction of mainly β proteins. In this work, we propose a novel ridge-detection-based β-β contact predictor to identify residue pairing in β strands from any predicted residue contact map. Our algorithm RDb 2 C adopts ridge detection, a well-developed technique in computer image processing, to capture consecutive residue contacts, and then utilizes a novel multi-stage random forest framework to integrate the ridge information and additional features for prediction. Starting from the predicted contact map of CCMpred, RDb 2 C remarkably outperforms all state-of-the-art methods on two conventional test sets of β proteins (BetaSheet916 and BetaSheet1452), and achieves F1-scores of ~ 62% and ~ 76% at the residue level and strand level, respectively. Taking the prediction of the more advanced RaptorX-Contact as input, RDb 2 C achieves impressively higher performance, with F1-scores reaching ~ 76% and ~ 86% at the residue level and strand level, respectively. In a test of structural modeling using the top 1 L predicted contacts as constraints, for 61 mainly β proteins, the average TM-score achieves 0.442 when using the raw RaptorX-Contact prediction, but increases to 0.506 when using the improved prediction by RDb 2 C. Our method can significantly improve the prediction of β-β contacts from any predicted residue contact maps. Prediction results of our algorithm could be directly applied to effectively facilitate the practical structure prediction of mainly β proteins. All source data and codes are available at http://166.111.152.91/Downloads.html or the GitHub address of https://github.com/wzmao/RDb2C .

  1. 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

    2014-01-01

    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. PMID:24963997

  2. Mapping and quantification of organic agro-industrial residues in East Africa

    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 East-African agro-industries generate very large quantities of organic residues from production and processing of different crops. These residues form a major contribution to the pollution of air, soil and water ways, but, at the same time they constitute a large potential for production of bioenergy through anaerobic digestion as well as potential substrate for other biological fermentation processes. The utilization of these resources for production of valuable products would contribute significantly to: Improvement of the local energy supply, through production of bio-energy; Improvement of the economy of the East African agro-industry; Reduction of the environmental impact from the agro-industrial sector. Except for production of cane sugar, most agro-industrial residues are generated from cash crops, which are produced and processed in the developing countries and where the final products mainly are used for export. In the East-African Region the most important of these crops are: Sisal, coffee, Cashew nuts and Pineapple. In addition significant quantities of organic residues are generated from other food processing activities like breweries, consumption of bananas etc. The total potential methane production of the residues available for use in biomethanization systems in East Africa is 189.61 million m{sup 3} of methane per year. Converted to diesel oil equivalents and including the residues only feasible for combustion systems, the total bioenergy potential of agro-industrial residues in Eastern Africa is 279,176 TOE. If this potential was fully utilized for production of electricity, it would correspond to installed effects of 37,68 and 31 MW in Tanzania, Kenya and Uganda, respectively, equivalent to 10%, 11% and 18% of the currently installed effect is these countries. Residues from sisal and coffee processing constitute the main part of the bioenergy potential, on average approximately 75%, while the remaining 25% of the potential are formed by the

  3. Prokaryote community dynamics in anaerobic co-digestion of swine manure, rice straw and industrial clay residuals.

    Science.gov (United States)

    Jiménez, Janet; Theuerl, Susanne; Bergmann, Ingo; Klocke, Michael; Guerra, Gilda; Romero-Romero, Osvaldo

    The aim of this study was to analyze the effect of the addition of rice straw and clay residuals on the prokaryote methane-producing community structure in a semi-continuously stirred tank reactor fed with swine manure. Molecular techniques, including terminal restriction fragment length polymorphism and a comparative nucleotide sequence analyses of the prokaryotic 16S rRNA genes, were performed. The results showed a positive effect of clay addition on methane yield during the co-digestion of swine manure and rice straw. At the digestion of swine manure, the bacterial phylum Firmicutes and the archaeal family Methanosarcinaceae, particularly Methanosarcina species, were predominant. During the co-digestion of swine manure and rice straw the microbial community changed, and with the addition of clay residual, the phylum Bacteroidetes predominated. The new nutritional conditions resulted in a shift in the archaeal family Methanosarcinaceae community as acetoclastic Methanosaeta species became dominant.

  4. Residuals and the Residual-Based Statistic for Testing Goodness of Fit of Structural Equation Models

    Science.gov (United States)

    Foldnes, Njal; Foss, Tron; Olsson, Ulf Henning

    2012-01-01

    The residuals obtained from fitting a structural equation model are crucial ingredients in obtaining chi-square goodness-of-fit statistics for the model. The authors present a didactic discussion of the residuals, obtaining a geometrical interpretation by recognizing the residuals as the result of oblique projections. This sheds light on the…

  5. Energy Management Dynamic Control Topology In MANET

    Science.gov (United States)

    Madhusudan, G.; Kumar, TNR

    2017-08-01

    Topology management via per-node transmission power adjustment has been shown effective in extending network lifetime. The existing algorithms constructs static topologies which fail to take the residual energy of network nodes, and cannot balance energy consumption efficiently. To address this problem, a Light Weighted Distributed Topology Control algorithm EMDCT(Energy Management Dynamic Control Topology ) is proposed in this paper. Based on the link metric of the network, both the energy consumption rate level and residual energy levels at the two end nodes are considered. EMDCT generates a Dynamic Topology that changes with the variation of node energy without the aid of location information, each node determines its transmission power according to local network information, which reduces the overhead complexity of EMDCT greatly. The experiment results show that EMDCT preserves network connectivity and manitains minimum-cost property of the network also it can extend network lifetime more remarkably.

  6. Molecular Dynamics Simulations of Orai Reveal How the Third Transmembrane Segment Contributes to Hydration and Ca2+ Selectivity in Calcium Release-Activated Calcium Channels.

    Science.gov (United States)

    Alavizargar, Azadeh; Berti, Claudio; Ejtehadi, Mohammad Reza; Furini, Simone

    2018-04-26

    Calcium release-activated calcium (CRAC) channels open upon depletion of Ca 2+ from the endoplasmic reticulum, and when open, they are permeable to a selective flux of calcium ions. The atomic structure of Orai, the pore domain of CRAC channels, from Drosophila melanogaster has revealed many details about conduction and selectivity in this family of ion channels. However, it is still unclear how residues on the third transmembrane helix can affect the conduction properties of the channel. Here, molecular dynamics and Brownian dynamics simulations were employed to analyze how a conserved glutamate residue on the third transmembrane helix (E262) contributes to selectivity. The comparison between the wild-type and mutated channels revealed a severe impact of the mutation on the hydration pattern of the pore domain and on the dynamics of residues K270, and Brownian dynamics simulations proved that the altered configuration of residues K270 in the mutated channel impairs selectivity to Ca 2+ over Na + . The crevices of water molecules, revealed by molecular dynamics simulations, are perfectly located to contribute to the dynamics of the hydrophobic gate and the basic gate, suggesting a possible role in channel opening and in selectivity function.

  7. Identification of key residues for protein conformational transition using elastic network model.

    Science.gov (United States)

    Su, Ji Guo; Xu, Xian Jin; Li, Chun Hua; Chen, Wei Zu; Wang, Cun Xin

    2011-11-07

    Proteins usually undergo conformational transitions between structurally disparate states to fulfill their functions. The large-scale allosteric conformational transitions are believed to involve some key residues that mediate the conformational movements between different regions of the protein. In the present work, a thermodynamic method based on the elastic network model is proposed to predict the key residues involved in protein conformational transitions. In our method, the key functional sites are identified as the residues whose perturbations largely influence the free energy difference between the protein states before and after transition. Two proteins, nucleotide binding domain of the heat shock protein 70 and human/rat DNA polymerase β, are used as case studies to identify the critical residues responsible for their open-closed conformational transitions. The results show that the functionally important residues mainly locate at the following regions for these two proteins: (1) the bridging point at the interface between the subdomains that control the opening and closure of the binding cleft; (2) the hinge region between different subdomains, which mediates the cooperative motions between the corresponding subdomains; and (3) the substrate binding sites. The similarity in the positions of the key residues for these two proteins may indicate a common mechanism in their conformational transitions.

  8. Comparison of Dynamic Contrast-Enhanced MRI and PET/CT in the Evaluation of Laryngeal Cancer After Inadequate CT Results

    International Nuclear Information System (INIS)

    Citil, Serdal; Dogan, Serap; Atilgan, Hasan Ikbal; Menzilcioglu, Mehmet Sait; Sahin, Tuna; Abdulrezzak, Ummuhan; Duymus, Mahmut; Ozturk, Mustafa

    2015-01-01

    To investigate the diagnostic value of dynamic magnetic resonance imaging (MRI) and positron emission tomography/computed tomography (PET/CT) for laryngeal cancers after inadequate CT results. The study comprised 45 patients investigated for primary laryngeal cancer or recurrence-residue in which CT was considered inadequate. A mass was found in 20 patients. Dynamic MRI and PET/CT were compared for diagnosis of mass, lymph node involvement, recurrence and residue. The dynamic curves formed in dynamic MRI were investigated for diagnostic contributions. The sensitivity and specificity of the dynamic MRI, for supraglottic, glottic and subglottic location, was 100%, 80%, and 92%; 100%, 85%, and 100%, respectively. In PET/CT the sensitivity and specificity were 100% for all of those localizations. For lymph node involvement, the sensitivity of dynamic MRI and PET/CT was 100%, the specificity was 100% and 93%, respectively. For recurrence-residue, the sensitivity and specificity of dynamic MRI were 86% and 67%, respectively, with 100% sensitivity and specificity in PET/CT. The sensitivity of type A curve for detection of malignancy was 40%, and specificity was 100%. When type A and B curves were included, the sensitivity was 100%. For patients investigated for laryngeal cancer in which CT is considered inadequate, dynamic MRI or PET/CT is useful

  9. Comparison of Dynamic Contrast-Enhanced MRI and PET/CT in the Evaluation of Laryngeal Cancer After Inadequate CT Results.

    Science.gov (United States)

    Citil, Serdal; Dogan, Serap; Atilgan, Hasan Ikbal; Menzilcioglu, Mehmet Sait; Sahin, Tuna; Abdulrezzak, Ummuhan; Duymus, Mahmut; Ozturk, Mustafa

    2015-01-01

    To investigate the diagnostic value of dynamic magnetic resonance imaging (MRI) and positron emission tomography/computed tomography (PET/CT) for laryngeal cancers after inadequate CT results. The study comprised 45 patients investigated for primary laryngeal cancer or recurrence-residue in which CT was considered inadequate. A mass was found in 20 patients. Dynamic MRI and PET/CT were compared for diagnosis of mass, lymph node involvement, recurrence and residue. The dynamic curves formed in dynamic MRI were investigated for diagnostic contributions. The sensitivity and specificity of the dynamic MRI, for supraglottic, glottic and subglottic location, was 100%, 80%, and 92%; 100%, 85%, and 100%, respectively. In PET/CT the sensitivity and specificity were 100% for all of those localizations. For lymph node involvement, the sensitivity of dynamic MRI and PET/CT was 100%, the specificity was 100% and 93%, respectively. For recurrence-residue, the sensitivity and specificity of dynamic MRI were 86% and 67%, respectively, with 100% sensitivity and specificity in PET/CT. The sensitivity of type A curve for detection of malignancy was 40%, and specificity was 100%. When type A and B curves were included, the sensitivity was 100%. For patients investigated for laryngeal cancer in which CT is considered inadequate, dynamic MRI or PET/CT is useful.

  10. Computational design of a Diels-Alderase from a thermophilic esterase: the importance of dynamics

    Science.gov (United States)

    Linder, Mats; Johansson, Adam Johannes; Olsson, Tjelvar S. G.; Liebeschuetz, John; Brinck, Tore

    2012-09-01

    A novel computational Diels-Alderase design, based on a relatively rare form of carboxylesterase from Geobacillus stearothermophilus, is presented and theoretically evaluated. The structure was found by mining the PDB for a suitable oxyanion hole-containing structure, followed by a combinatorial approach to find suitable substrates and rational mutations. Four lead designs were selected and thoroughly modeled to obtain realistic estimates of substrate binding and prearrangement. Molecular dynamics simulations and DFT calculations were used to optimize and estimate binding affinity and activation energies. A large quantum chemical model was used to capture the salient interactions in the crucial transition state (TS). Our quantitative estimation of kinetic parameters was validated against four experimentally characterized Diels-Alderases with good results. The final designs in this work are predicted to have rate enhancements of ≈103-106 and high predicted proficiencies. This work emphasizes the importance of considering protein dynamics in the design approach, and provides a quantitative estimate of the how the TS stabilization observed in most de novo and redesigned enzymes is decreased compared to a minimal, `ideal' model. The presented design is highly interesting for further optimization and applications since it is based on a thermophilic enzyme ( T opt = 70 °C).

  11. Residual, restarting and Richardson iteration for the matrix exponential

    NARCIS (Netherlands)

    Bochev, Mikhail A.; Grimm, Volker; Hochbruck, Marlis

    2013-01-01

    A well-known problem in computing some matrix functions iteratively is the lack of a clear, commonly accepted residual notion. An important matrix function for which this is the case is the matrix exponential. Suppose the matrix exponential of a given matrix times a given vector has to be computed.

  12. Residual, restarting and Richardson iteration for the matrix exponential

    NARCIS (Netherlands)

    Bochev, Mikhail A.

    2010-01-01

    A well-known problem in computing some matrix functions iteratively is a lack of a clear, commonly accepted residual notion. An important matrix function for which this is the case is the matrix exponential. Assume, the matrix exponential of a given matrix times a given vector has to be computed. We

  13. The Effect of Creep on the Residual Stresses Generated During Silicon Sheet Growth

    Science.gov (United States)

    Hutchinson, J. W.; Lambropoulos, J. C.

    1984-01-01

    The modeling of stresses generated during the growth of thin silicon sheets at high speeds is an important part of the EFG technique since the experimental measurement of the stresses is difficult and prohibitive. The residual stresses which arise in such a growth process lead to serious problems which make thin Si ribbons unsuitable for fabrication. The constitutive behavior is unrealistic because at high temperature (close to the melting point) Si exhibits considerable creep which significantly relaxes the residual stresses. The effect of creep on the residual stresses generated during the growth of Si sheets at high speeds was addressed and the basic qualitative effect of creep are reported.

  14. Insight into interaction mechanism of the inhibitor pDI5W with MDM2 based on molecular dynamics

    International Nuclear Information System (INIS)

    Chen Jianzhong; Liang Zhiqiang; Wang Wei; Liu Jinqing; Zhang Qinggang; Liu Xiaoyang

    2012-01-01

    The p53-MDM2 interaction has been an important target of drug design curing cancers. In this work, molecular dynamics (MD) simulation coupled with molecular mechanics/Poisson Boltzmann surface area method (MM-PBSA) was performed to calculate the binding free energy of peptide inhibitor pDI6W to MDM2. The results show that van der Waals energy is the dominant factor of the pDI6W— MDM2 interaction. Cross-correlation matrix calculated suggests that the main motion of the residues in MMDM2 induced by the inhibitor binding is anti-correlation motion. The calculations of residue-residue interactions between pDI6W and MDM2 not only prove that five residues Phe19', Trp22', Trp23', Leu26' and Thr27' from pDI6W can produce strong interaction with MDM2, but also show that CH-π, CH-CH and π-π interactions drive the binding of pDI6W in the hydrophobic cleft of MDM2. This study can provide theoretical helps for anti-cancer drug designs. (authors)

  15. Machine for compacting solid residues

    International Nuclear Information System (INIS)

    Herzog, J.

    1981-11-01

    Machine for compacting solid residues, particularly bulky radioactive residues, constituted of a horizontally actuated punch and a fixed compression anvil, in which the residues are first compacted horizontally and then vertically. Its salient characteristic is that the punch and the compression anvil have embossments on the compression side and interpenetrating plates in the compression position [fr

  16. An approach to the estimation of the value of agricultural residues used as biofuels

    International Nuclear Information System (INIS)

    Kumar, A.; Purohit, P.; Rana, S.; Kandpal, T.C.

    2002-01-01

    A simple demand side approach for estimating the monetary value of agricultural residues used as biofuels is proposed. Some of the important issues involved in the use of biomass feedstocks in coal-fired boilers are briefly discussed along with their implications for the maximum acceptable price estimates for the agricultural residues. Results of some typical calculations are analysed along with the estimates obtained on the basis of a supply side approach (based on production cost) developed earlier. The prevailing market prices of some agricultural residues used as feedstocks for briquetting are also indicated. The results obtained can be used as preliminary indicators for identifying niche areas for immediate/short-term utilization of agriculture residues in boilers for process heating and power generation. (author)

  17. Computational design, construction, and characterization of a set of specificity determining residues in protein-protein interactions.

    Science.gov (United States)

    Nagao, Chioko; Izako, Nozomi; Soga, Shinji; Khan, Samia Haseeb; Kawabata, Shigeki; Shirai, Hiroki; Mizuguchi, Kenji

    2012-10-01

    Proteins interact with different partners to perform different functions and it is important to elucidate the determinants of partner specificity in protein complex formation. Although methods for detecting specificity determining positions have been developed previously, direct experimental evidence for these amino acid residues is scarce, and the lack of information has prevented further computational studies. In this article, we constructed a dataset that is likely to exhibit specificity in protein complex formation, based on available crystal structures and several intuitive ideas about interaction profiles and functional subclasses. We then defined a "structure-based specificity determining position (sbSDP)" as a set of equivalent residues in a protein family showing a large variation in their interaction energy with different partners. We investigated sequence and structural features of sbSDPs and demonstrated that their amino acid propensities significantly differed from those of other interacting residues and that the importance of many of these residues for determining specificity had been verified experimentally. Copyright © 2012 Wiley Periodicals, Inc.

  18. Modelling residual stresses in friction stir welding of Al alloys - a review of possibilities and future trends

    DEFF Research Database (Denmark)

    Hattel, Jesper Henri; Sonne, Mads Rostgaard; Tutum, Cem C.

    2015-01-01

    Residual stresses are very important in any joining process of materials since they act as pre-stresses in the loading situation of the joint, thereby affecting the final mechanical performance of the component. This is also the case for friction stir welding (FSW) which is a complex solid-state ......, numerical framework and application as well as putting them into proper context with respect to some of the new trends in the field, e.g. coupling with subsequent load analyses of the in-service situation or applying residual stress models of FSWin numerical optimization.......Residual stresses are very important in any joining process of materials since they act as pre-stresses in the loading situation of the joint, thereby affecting the final mechanical performance of the component. This is also the case for friction stir welding (FSW) which is a complex solid......-state joining process characterized by a pronounced multiphysical behaviour involving phenomena such as change of temperature, material flow, change of microstructures and formation of residual stresses. Thus, models of FSWare typically divided into thermal models, flow models, residual stress models...

  19. Economic factors influencing potential use of cellulosic crop residues for electricity generation

    International Nuclear Information System (INIS)

    Maung, Thein A.; McCarl, Bruce A.

    2013-01-01

    This study examines cellulosic crop residues for biopower production in the context of (greenhouse gas) GHG emission mitigation. We employ sector modeling to simulate future market potential for biopower production from crop residues. Our findings suggest that in order for crop residues to have any role in electricity generation either the carbon or (carbon dioxide) CO 2 equivalent GHG price must rise to about 15 dollars per ton or the price of coal has to increase to about 43 dollars per ton. We find that crop residues with higher heat content have greater opportunities in biopower production than the residues with lower heat content. In addition, our evidence shows that improvements in crop yields do not have much impact on biopower production. However, the energy recovery efficiency does have significant positive impact but only if the CO 2 equivalent price rises substantially. Moreover, our analysis indicates the desirability of cofiring biomass as opposed to 100% replacement because this reduces transportation cost and increases the efficiency of heat recovery. In terms of policy implications, imposing carbon emission pricing could be an important step in inducing electric power producers to include biomass feedstocks in their fuel-mix power generation portfolios and achieve GHG emission reductions. - Highlights: • Crop residues with higher heat content have greater market opportunities. • Improvement in crop and residue yields does not have much impact on biopower production. • Advancement in biopower production technology does not encourage more use of crop residues. • The main factor that induces biopower production is an increase in future carbon prices

  20. Degradation kinetics and safety evaluation of buprofezin residues in grape (Vitis vinifera L.) and three different soils of India.

    Science.gov (United States)

    Oulkar, Dasharath P; Banerjee, Kaushik; Patil, Sangram H; Upadhyay, Ajay K; Taware, Praveen B; Deshmukh, Madhukar B; Adsule, Pandurang G

    2009-02-01

    This work was undertaken to determine the preharvest interval (PHI) of buprofezin to minimize its residues in grapes and thereby ensure consumer safety and avoid possible non-compliance in terms of residue violations in export markets. Furthermore, the residue dynamics in three grapevine soils of India was explored to assess its environmental safety. Residues dissipated following non-linear two-compartment first + first-order kinetics. In grapes, the PHI was 31 days at both treatments (312.5 and 625 g a.i. ha(-1)), with the residues below the maximum permissible intake even 1 h after foliar spraying. Random sampling of 5 kg comprising small bunchlets (8-10 berries) collected from a 1 ha area gave satisfactory homogeneity and representation of the population. A survey on the samples harvested after the PHI from supervised vineyards that received treatment at the recommended dose showed residues below the maximum residue limit (MRL) of 0.02 mg kg(-1) applicable for the European Union. In soil, the degradation rate was fastest in clay soil, followed by sandy loam and silty clay, with a half-life within 16 days in all the soils. The recommendation of the PHI proved to be effective in minimizing buprofezin residues in grapes. Thus, this work is of high practical significance to the domestic and export grape industry of India to ensure safety compliance in respect of buprofezin residues, keeping in view the requirements of international trade.

  1. The influence of mean climate trends and climate variance on beaver survival and recruitment dynamics.

    Science.gov (United States)

    Campbell, Ruairidh D; Nouvellet, Pierre; Newman, Chris; Macdonald, David W; Rosell, Frank

    2012-09-01

    Ecologists are increasingly aware of the importance of environmental variability in natural systems. Climate change is affecting both the mean and the variability in weather and, in particular, the effect of changes in variability is poorly understood. Organisms are subject to selection imposed by both the mean and the range of environmental variation experienced by their ancestors. Changes in the variability in a critical environmental factor may therefore have consequences for vital rates and population dynamics. Here, we examine ≥90-year trends in different components of climate (precipitation mean and coefficient of variation (CV); temperature mean, seasonal amplitude and residual variance) and consider the effects of these components on survival and recruitment in a population of Eurasian beavers (n = 242) over 13 recent years. Within climatic data, no trends in precipitation were detected, but trends in all components of temperature were observed, with mean and residual variance increasing and seasonal amplitude decreasing over time. A higher survival rate was linked (in order of influence based on Akaike weights) to lower precipitation CV (kits, juveniles and dominant adults), lower residual variance of temperature (dominant adults) and lower mean precipitation (kits and juveniles). No significant effects were found on the survival of nondominant adults, although the sample size for this category was low. Greater recruitment was linked (in order of influence) to higher seasonal amplitude of temperature, lower mean precipitation, lower residual variance in temperature and higher precipitation CV. Both climate means and variance, thus proved significant to population dynamics; although, overall, components describing variance were more influential than those describing mean values. That environmental variation proves significant to a generalist, wide-ranging species, at the slow end of the slow-fast continuum of life histories, has broad implications for

  2. Effects of fretting fatigue on the residual stress of shot peened Ti-6Al-4V samples

    International Nuclear Information System (INIS)

    Martinez, S.A.; Sathish, S.; Blodgett, M.P.; Mall, S.; Namjoshi, S.

    2005-01-01

    X-ray diffraction residual stress measurement has been utilized as nondestructive tool for the characterization of fretting fatigue damage in shot peened samples of Ti-6Al-4V. Prior to fretting fatigue damage, compressive residual stresses were found to be uniform over the entire face of the sample and independent of the measurement direction. After fretting fatigue, inside and in the vicinity of the fretting damage zone large relaxation of compressive residual stress was observed. An anisotropic residual stress distribution has been observed in the fretting fatigue damaged region. Residual stress measurements in interrupted fretting fatigue experiments showed that the relaxation of residual stress increases as the number of fretting fatigue cycles increase. The results are discussed in the light of their importance in establishing X-ray diffraction residual stress measurement technique as a nondestructive tool to characterize fretting fatigue damage

  3. 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. Copyright © 2013 Elsevier GmbH. All rights reserved.

  4. Effect of subseabed salt domes on Tidal Residual currents in the Persian Gulf

    Science.gov (United States)

    Mashayekh Poul, Hossein; Backhaus, Jan; Dehghani, Ali; Huebner, Udo

    2016-05-01

    Geological studies in the Persian Gulf (PG) have revealed the existence of subseabed salt-domes. With suitable filtering of a high-resolution PG seabed topography, it is seen that the domes leave their signature in the seabed, i.e., numerous hills and valleys with amplitudes of several tens of meters and radii from a few up to tens of kilometers. It was suspected that the "shark skin" of the PG seabed may affect the tidal residual flow. The interaction of tidal dynamics and these obstacles was investigated in a nonlinear hydrodynamic numerical tidal model of the PG. The model was first used to characterize flow patterns of residual currents generated by a tidal wave passing over symmetric, elongated and tilted obstacles. Thereafter it was applied to the entire PG. The model was forced at its open boundary by the four dominant tidal constituents residing in the PG. Each tidal constituent was simulated separately. Results, i.e., tidal residual currents in the PG, as depicted by Lagrangian trajectories reveal a stationary flow that is very rich in eddies. Each eddy can be identified with a topographic obstacle. This confirms that the tidal residual flow field is strongly influenced by the nonlinear interaction of the tidal wave with the bottom relief which, in turn, is deformed by salt-domes beneath the seabed. Different areas of maximum residual current velocities are identified for major tidal constituents. The pattern of trajectories indicates the presence of two main cyclonic gyres and several adjacent gyres rotating in opposite directions and a strong coastal current in the northern PG.

  5. Residual stresses in a co-sintered SOC half-cell during post-sintering cooling

    DEFF Research Database (Denmark)

    Charlas, Benoit; Chatzichristodoulou, Christodoulos; Brodersen, Karen

    2014-01-01

    .e. the reference temperature (Tref) or the strain difference based on the curvature. This approximation gives good results for bilayers with a defined cooling temperature profile, where the curvature of the bilayer defines a unique balance between the two unknown residual stress states in the two layers......Due to the thermal expansion mismatch between the layers of a Solid Oxide Cell, residual stresses (thermal stresses) develop during the cooling after sintering. Residual stresses can induce cell curvature for asymmetric cells but more importantly they also result in more fragile cells. Depending...... on the loading conditions, the additional stress needed to break the cells can indeed be smaller due to the initial thermo-mechanical stress state. The residual stresses can for a bilayer cell be approximated by estimating the temperature at which elastic stresses start to build up during the cooling, i...

  6. Characterization and treatment of sisal fiber residues for cement-based composite application

    OpenAIRE

    Lima,Paulo R. L.; Santos,Rogério J.; Ferreira,Saulo R.; Toledo Filho,Romildo D.

    2014-01-01

    Sisal fiber is an important agricultural product used in the manufacture of ropes, rugs and also as a reinforcement of polymeric or cement-based composites. However, during the fiber production process a large amount of residues is generated which currently have a low potential for commercial use. The aim of this study is to characterize the agricultural residues by the production and improvement of sisal fiber, called field bush and refugo and verify the potentiality of their use in the rein...

  7. 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

    International Nuclear Information System (INIS)

    Demicheli, Romano; Ardoino, Ilaria; Boracchi, Patrizia; Coradini, Danila; Agresti, Roberto; Ferraris, Cristina; Gennaro, Massimiliano; Hrushesky, William JM; Biganzoli, Elia

    2010-01-01

    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. 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. 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. 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

  8. Dynamics differentiate between active and inactive inteins.

    Science.gov (United States)

    Cronin, Melissa; Coolbaugh, Michael J; Nellis, David; Zhu, Jianwei; Wood, David W; Nussinov, Ruth; Ma, Buyong

    2015-02-16

    The balance between stability and dynamics for active enzymes can be somewhat quantified by studies of intein splicing and cleaving reactions. Inteins catalyze the ligation of flanking host exteins while excising themselves. The potential for applications led to engineering of a mini-intein splicing domain, where the homing endonuclease domain of the Mycobacterium tuberculosis RecA (Mtu recA) intein was removed. The remaining domains were linked by several short peptides, but splicing activity in all was substantially lower than the full-length intein. Native splicing activity was restored in some cases by a V67L mutation. Using computations and experiments, we examine the impact of this mutation on the stability and conformational dynamics of the mini-intein splicing domain. Molecular dynamics simulations were used to delineate the factors that determine the active state, including the V67L mini-intein mutant, and peptide linker. We found that (1) the V67L mutation lowers the global fluctuations in all modeled mini-inteins, stabilizing the mini-intein constructs; (2) the connecting linker length affects intein dynamics; and (3) the flexibilities of the linker and intein core are higher in the active structure. We have observed that the interaction of the linker region and a turn region around residues 35-41 provides the pathway for the allostery interaction. Our experiments reveal that intein catalysis is characterized by non-linear Arrhenius plot, confirming the significant contribution of protein conformational dynamics to intein function. We conclude that while the V67L mutation stabilizes the global structure, cooperative dynamics of all intein regions appear more important for intein function than high stability. Our studies suggest that effectively quenching the conformational dynamics of an intein through engineered allosteric interactions could deactivate intein splicing or cleaving. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  9. Leaching Behavior of Circulating Fluidised Bed MSWI Air Pollution Control Residue in Washing Process

    Directory of Open Access Journals (Sweden)

    Zhiliang Chen

    2016-09-01

    Full Text Available In this study, air pollution control (APC residue is conducted with water washing process to reduce its chloride content. A novel electrical conductivily (EC measurement method is proposed to monitor the dynamic change of chloride concentrations in leachate as well as the chloride content of the residue. The method equally applies to various washing processes with different washing time, liquid/solid ratio and washing frequency. The results show that washing effectively extracts chloride salts from APC residues, including those from circulating fluidized bed (CFB municipal solid waste incineration (MSWI. The most appropriate liquid/solid ratio and washing time in the first washing are found to be around 4 L water per kg of APC residue and 30 min, respectively, and washing twice is required to obtain maximum dissolution. The pH value is the major controlling factor of the heavy metals speciation in leachate, while chloride concentration also affects the speciation of Cd. Water washing causes no perceptible transfer of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs from the APC residue to leachate. The chloride concentration is strongly related with electrical conductivity (EC, as well as with the concentrations of calcium, sodium and potassium of washing water. Their regression analyses specify that soluble chloride salts and EC could act as an indirect indicator to monitor the change of chloride concentration and remaining chloride content, thus, contributing to the selection of the optimal washing conditions.

  10. Analysis of residual stress relief mechanisms in post-weld heat treatment

    International Nuclear Information System (INIS)

    Dong, Pingsha; Song, Shaopin; Zhang, Jinmiao

    2014-01-01

    This paper presents a recent study on weld residual stress relief mechanisms associated with furnace-based uniform post-weld heat treatment (PWHT). Both finite element and analytical methods are used to quantitatively examine how plastic deformation and creep relaxation contribute to residual stress relief process at different stages of PWHT process. The key contribution of this work to an improved understanding of furnace based uniform PWHT can be summarized as follows: (1)Plastic deformation induced stress relief during PWHT can be analytically expressed by the change in material elastic deformation capacity (or elastic deformation limit) measured in terms of material yield strength to Young's modulus ratio, which has a rather limited role in overall residual stress relief during furnace based uniform PWHT. (2)The most dominant stress relief mechanism is creep strain induced stress relaxation, as expected. However, a rapid creep strain development accompanied by a rapid residual stress reduction during heating stage before reaching PWHT temperature is shown to contribute to most of the stress relief seen in overall PWHT process, suggesting PWHT hold time can be significantly reduced as far as residual stress relief is concerned. (3)A simple engineering scheme for estimating residual stress reduction is proposed based on this study by relating material type, PWHT temperature, and component wall thickness. - Highlights: • The paper clarified effects of plastic deformation and creep relaxation on weld residual stress relief during uniform PWHT. • Creep strain development is far more important than plastic strain, mostly completed even before hold time starts. • Plastic strain development is insignificant and be analytically described by a material elastic deformation capacity parameter. • An engineering estimation scheme is proposed for determining residual stress reduction resulted from furnace based PWHT

  11. Characterization of Hospital Residuals

    International Nuclear Information System (INIS)

    Blanco Meza, A.; Bonilla Jimenez, S.

    1997-01-01

    The main objective of this investigation is the characterization of the solid residuals. A description of the handling of the liquid and gassy waste generated in hospitals is also given, identifying the source where they originate. To achieve the proposed objective the work was divided in three stages: The first one was the planning and the coordination with each hospital center, in this way, to determine the schedule of gathering of the waste can be possible. In the second stage a fieldwork was made; it consisted in gathering the quantitative and qualitative information of the general state of the handling of residuals. In the third and last stage, the information previously obtained was organized to express the results as the production rate per day by bed, generation of solid residuals for sampled services, type of solid residuals and density of the same ones. With the obtained results, approaches are settled down to either determine design parameters for final disposition whether for incineration, trituration, sanitary filler or recycling of some materials, and storage politics of the solid residuals that allow to determine the gathering frequency. The study concludes that it is necessary to improve the conditions of the residuals handling in some aspects, to provide the cleaning personnel of the equipment for gathering disposition and of security, minimum to carry out this work efficiently, and to maintain a control of all the dangerous waste, like sharp or polluted materials. In this way, an appreciable reduction is guaranteed in the impact on the atmosphere. (Author) [es

  12. Mutation of charged residues to neutral ones accelerates urea denaturation of HP-35.

    Science.gov (United States)

    Wei, Haiyan; Yang, Lijiang; Gao, Yi Qin

    2010-09-16

    Following the studies of urea denaturation of β-hairpins using molecular dynamics, in this paper, molecular dynamics simulations of two peptides, a 35 residue three helix bundle villin headpiece protein HP-35 and its doubly norleucine-substituent mutant (Lys24Nle/Lys29Nle) HP-35 NleNle, were undertaken in urea solutions to understand the molecular mechanism of urea denaturation of α-helices. The mutant HP-35 NleNle was found to denature more easily than the wild type. During the expansion of the small hydrophobic core, water penetration occurs first, followed by that of urea molecules. It was also found that the initial hydration of the peptide backbone is achieved through water hydrogen bonding with the backbone CO groups during the denaturation of both polypeptides. The mutation of the two charged lysine residues to apolar norleucine enhances the accumulation of urea near the hydrophobic core and facilitates the denaturation process. Urea also interacts directly with the peptide backbone as well as side chains, thereby stabilizing nonnative conformations. The mechanism revealed here is consistent with the previous study on secondary structure of β-hairpin polypeptide, GB1, PEPTIDE 1, and TRPZIP4, suggesting that there is a general mechanism in the denaturation of protein backbone hydrogen bonds by urea.

  13. Applications of bauxite residue: A mini-review.

    Science.gov (United States)

    Verma, Ajay S; Suri, Narendra M; Kant, Suman

    2017-10-01

    Bauxite residue is the waste generated during alumina production by Bayer's process. The amount of bauxite residue (40-50 wt%) generated depends on the quality of bauxite ore used for the processing. High alkalinity and high caustic content in bauxite residue causes environmental risk for fertile soil and ground water contamination. The caustic (NaOH) content in bauxite residue leads to human health risks, like dermal problems and irritation to eyes. Moreover, disposal of bauxite residue requires a large area; such problems can only be minimised by utilising bauxite residue effectively. For two decades, bauxite residue has been used as a binder in cement industries and filler/reinforcement for composite materials in the automobile industry. Valuable metals and oxides, like alumina (Al 2 O 3 ), titanium oxide (TiO 2 ) and iron oxide Fe 2 O 3 , were extracted from bauxite residue to reduce waste. Bauxite residue was utilised in construction and structure industries to make geopolymers. It was also used in the making of glass-ceramics and a coating material. Recently bauxite residue has been utilised to extract rare earth elements like scandium (Sc), yttrium (Y), lanthanum (La), cerium (Ce), neodymium (Nd) and dysprosium (Dy). In this review article, the mineralogical characteristics of bauxite residue are summarised and current progresses on utilisation of bauxite residue in different fields of science and engineering are presented in detail.

  14. Willingness of nonindustrial private forest owners in Norway to supply logging residues for wood energy

    Science.gov (United States)

    Hanne K. Sjolie; Dennis Becker; Daniel Habesland; Birger Solberg; Berit Hauger Lindstad; Stephanie Snyder; Mike. Kilgore

    2016-01-01

    Norway has set ambitious targets for increasing bioenergy production. Forest residue extraction levels are currently very low, but residues have the potential to be an important component of the wood energy supply chain. A representative sample of Norwegian nonindustrial private forest owners having at least 8 ha (20 acres) of productive forest land was surveyed about...

  15. Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity

    Directory of Open Access Journals (Sweden)

    Lyngsø Rune

    2010-04-01

    Full Text Available Abstract Background The dynamic motions of many proteins are central to their function. It therefore follows that the dynamic requirements of a protein are evolutionary constrained. In order to assess and quantify this, one needs to compare the dynamic motions of different proteins. Comparing the dynamics of distinct proteins may also provide insight into how protein motions are modified by variations in sequence and, consequently, by structure. The optimal way of comparing complex molecular motions is, however, far from trivial. The majority of comparative molecular dynamics studies performed to date relied upon prior sequence or structural alignment to define which residues were equivalent in 3-dimensional space. Results Here we discuss an alternative methodology for comparative molecular dynamics that does not require any prior alignment information. We show it is possible to align proteins based solely on their dynamics and that we can use these dynamics-based alignments to quantify the dynamic similarity of proteins. Our method was tested on 10 representative members of the PDZ domain family. Conclusions As a result of creating pair-wise dynamics-based alignments of PDZ domains, we have found evolutionarily conserved patterns in their backbone dynamics. The dynamic similarity of PDZ domains is highly correlated with their structural similarity as calculated with Dali. However, significant differences in their dynamics can be detected indicating that sequence has a more refined role to play in protein dynamics than just dictating the overall fold. We suggest that the method should be generally applicable.

  16. 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.

  17. Confirmatory analysis of the AP1000 passive residual heat removal heat exchanger with 3-D computational fluid dynamic analysis

    International Nuclear Information System (INIS)

    Schwall, James R.; Karim, Naeem U.; Thakkar, Jivan G.; Taylor, Creed; Schulz, Terry; Wright, Richard F.

    2006-01-01

    The AP1000 is an 1100 MWe advanced nuclear power plant that uses passive safety features to enhance plant safety and to provide significant and measurable improvements in plant simplification, reliability, investment protection and plant costs. The AP1000 received final design approval from the US-NRC in 2004. The AP1000 design is based on the AP600 design that received final design approval in 1999. Wherever possible, the AP1000 plant configuration and layout was kept the same as AP600 to take advantage of the maturity of the design and to minimize new design efforts. As a result, the two-loop configuration was maintained for AP1000, and the containment vessel diameter was kept the same. It was determined that this significant power up-rate was well within the capability of the passive safety features, and that the safety margins for AP1000 were greater than those of operating PWRs. A key feature of the passive core cooling system is the passive residual heat removal heat exchanger (PRHR HX) that provides decay heat removal for postulated LOCA and non-LOCA events. The PRHR HX is a C-tube heat exchanger located in the in-containment refueling water storage tank (IRWST) above the core promoting natural circulation heat removal between the reactor cooling system and the tank. Component testing was performed for the AP600 PRHR HX to determine the heat transfer characteristics and to develop correlations to be used for the AP1000 safety analysis codes. The data from these tests were confirmed by subsequent integral tests at three separate facilities including the ROSA facility in Japan. Owing to the importance of this component, an independent analysis has been performed using the ATHOS-based computational fluid dynamics computer code PRHRCFD. Two separate models of the PRHR HX and IRWST have been developed representing the ROSA test geometry and the AP1000 plant geometry. Confirmation of the ROSA test results were used to validate PRHRCFD, and the AP1000 plant model

  18. Prediction of Weld Residual Stress of Narrow Gap Welds

    International Nuclear Information System (INIS)

    Yang, Jun Seog; Huh, Nam Su

    2010-01-01

    The conventional welding technique such as shield metal arc welding has been mostly applied to the piping system of the nuclear power plants. It is well known that this welding technique causes the overheating and welding defects due to the large groove angle of weld. On the other hand, the narrow gap welding(NGW) technique has many merits, for instance, the reduction of welding time, the shrinkage of weld and the small deformation of the weld due to the small groove angle and welding bead width comparing with the conventional welds. These characteristics of NGW affect the deformation behavior and the distribution of welding residual stress of NGW, thus it is believed that the residual stress results obtained from conventional welding procedure may not be applied to structural integrity evaluation of NGW. In this paper, the welding residual stress of NGW was predicted using the nonlinear finite element analysis to simulate the thermal and mechanical effects of the NGW. The present results can be used as the important information to perform the flaw evaluation and to improve the weld procedure of NGW

  19. Immobilization of acid digestion residue

    International Nuclear Information System (INIS)

    Greenhalgh, W.O.; Allen, C.R.

    1983-01-01

    Acid digestion treatment of nuclear waste is similar to incineration processes and results in the bulk of the waste being reduced in volume and weight to some residual solids termed residue. The residue is composed of various dispersible solid materials and typically contains the resultant radioactivity from the waste. This report describes the immobilization of the residue in portland cement, borosilicate glass, and some other waste forms. Diagrams showing the cement and glass virtification parameters are included in the report as well as process steps and candidate waste product forms. Cement immobilization is simplest and probably least expensive; glass vitrification exhibits the best overall volume reduction ratio

  20. The importance of residues 195-206 of human blood clotting factor VII in the interaction of factor VII with tissue factor

    International Nuclear Information System (INIS)

    Wildgoose, P.; Kisiel, W.; Kazim, A.L.

    1990-01-01

    Previous studies indicated that human and bovine factor VII exhibit 71% amino acid sequence identity. In the present study, competition binding experiments revealed that the interaction of human factor VII with cell-surface human tissue factor was not inhibited by 100-fold molar excess of bovine factor VII. This finding indicated that bovine and human factor VII are not structurally homologous in the region(s) where human factor VII interacts with human tissue factor. On this premise, the authors synthesized three peptides corresponding to regions of human factor VII that exhibited marked structural dissimilarity to bovine factor VII; these regions of dissimilarity included residues 195-206, 263-274, and 314-326. Peptide 195-206 inhibited the interaction of factor VII with cell-surface tissue factor and the activation of factor X by a complex of factor VIIa and tissue factor half-maximally at concentrations of 1-2 mM. A structurally rearranged form of peptide 195-206 containing an aspartimide residue inhibited these reactions half-maximally at concentrations of 250-300 μM. In contrast, neither peptide 263-274 nor peptide 314-326, at 2 mM concentration, significantly affected either factor VIIa interaction with tissue factor or factor VIIa-mediated activation of factor X. The data provide presumptive evidence that residues 195-206 of human factor VII are involved in the interaction of human factor VII with the extracellular domain of human tissue factor apoprotein

  1. Influence of ion irradiation on internal residual stress in DLC films

    Energy Technology Data Exchange (ETDEWEB)

    Karaseov, Platon A., E-mail: platon.karaseov@rphf.spbstu.r [St. Petersburg State Polytechnic University, Polytechnicheskaya St. 29, 195251 St. Petersburg (Russian Federation); Podsvirov, Oleg A.; Karabeshkin, Konstantin V. [St. Petersburg State Polytechnic University, Polytechnicheskaya St. 29, 195251 St. Petersburg (Russian Federation); Vinogradov, Andrei Ya. [Ioffe Physicotechnical Institute RAS, Polytechnicheskaya 26, 195252 St. Petersburg (Russian Federation); Azarov, Alexander Yu. [St. Petersburg State Polytechnic University, Polytechnicheskaya St. 29, 195251 St. Petersburg (Russian Federation); Karasev, Nikita N. [State University of Information Technologies, Mechanics and Optics, Sablinskaya Str. 14, 197101 St. Petersburg (Russian Federation); Titov, Andrei I.; Smirnov, Alexander S. [St. Petersburg State Polytechnic University, Polytechnicheskaya St. 29, 195251 St. Petersburg (Russian Federation)

    2010-10-01

    The dependence of internal residual stress in thin diamond-like carbon films grown on Si substrate by PECVD technique on most important growth parameters, namely RF-power, DC bias voltage and substrate temperature, is described. Results show that compressive stress reaches the highest value of 2.7 GPa at low RF-power and DC bias. Increase of substrate temperature from 250 to 350 {sup o}C leads to nonlinear increase of stress value. Inhomogeneity of residual stress along the film surface disappears when film is deposited at temperatures above 275 {sup o}C. Post-growth film irradiation by P{sup +} and In{sup +} ions cause decrease of compressive stress followed by its inversion to tensile. For all ion energy combinations used residual stress changes linearly with normalized fluence up to 0.2 DPA with slope (8.7 {+-} 1.3) GPa/DPA.

  2. Qualitative screening method for pesticide residues detection in fruits and vegetables

    Directory of Open Access Journals (Sweden)

    Iván Mauricio Huérfano Barco

    2018-01-01

    Full Text Available Because of the importance of developing methodologies that allow agricultural residues analysis, a rapid screening qualitative method for the determination of pesticides residues in fruits and vegetables was validated. The methodology was based on the European QuEChERS extraction method with an additional cleaning step by gel permeation chromatography (GPC, which helped to reduce the number of matrix components in the final extract. The analysis was carried out by gas chromatography coupled to mass spectrometry with a single quadrupole analyzer. The methodology was appropriate for the qualitative analysis of 31 pesticides at their respective maximum residue limits. Consistent results were obtained with respect to a quantitative routine methodology in the analysis of real samples, hence the methodology was proven to be a good alternative for the fast analysis of these contaminants in fruits and vegetables.

  3. Modeling of human operator dynamics in simple manual control utilizing time series analysis. [tracking (position)

    Science.gov (United States)

    Agarwal, G. C.; Osafo-Charles, F.; Oneill, W. D.; Gottlieb, G. L.

    1982-01-01

    Time series analysis is applied to model human operator dynamics in pursuit and compensatory tracking modes. The normalized residual criterion is used as a one-step analytical tool to encompass the processes of identification, estimation, and diagnostic checking. A parameter constraining technique is introduced to develop more reliable models of human operator dynamics. The human operator is adequately modeled by a second order dynamic system both in pursuit and compensatory tracking modes. In comparing the data sampling rates, 100 msec between samples is adequate and is shown to provide better results than 200 msec sampling. The residual power spectrum and eigenvalue analysis show that the human operator is not a generator of periodic characteristics.

  4. The effect of Residual Stress on the Stress Intensity Factor of Nuclear Material

    International Nuclear Information System (INIS)

    Song, Taek Ho

    2008-01-01

    As NPP (Nuclear Power Plant) gets aged, the importance of the pressure boundary integrity increases very much to those who are trying to operate their plant beyond its design life. Not long ago, Boric acid crystal was found at the RPV outlet nozzle of V.C. Summer plant during the visual examination in 2000. After this finding, non-destructive examination was taken to find out what's taken place. As a result of this examination, circumferential and axial cracks were found. With Metallurgical structure examination, it was shown that crack had been developed at the mid-point between Inco-alloy buttering and weld metal. It was turned out that high welding residual stress was the main cause of the cracking. Because of the through wall crack, nozzle and welding parts were replaced. Many other nuclear power plants experienced similar pressure boundary stress corrosion cracks (SCCs). KEPRI (Korea Electric Power Research Institute) has carried out research projects for managing and preventing these kinds of cracks in nuclear power plants (NPPs). The titles of these research projects are 'Development of Stress Corrosion Cracking Management Technology and Aging Monitor for NPP Main Components' and 'Development of Analysis Technology for Crack Management of Dissimilar Metal Weld'. Through these projects, residual stress measurement techniques have been exercised at various points in mock-up test specimens to simulate nuclear power plant dissimilar base metal and weldment residual stress. X-ray test and hole drilling method have been reviewed to measure residual stresses of the dissimilar metal welds. This paper shows some point of view in residual stress measurement. Fracture mechanics analysis has been performed to explain the importance of residual stress measurement in association with nuclear power plant safety

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

    Science.gov (United States)

    Skolnick, Jeffrey

    2016-09-01

    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.

  6. [Situation analysis and standard formulation of pesticide residues in traditional Chinese medicines].

    Science.gov (United States)

    Yang, Wan-Zhen; Kang, Chuan-Zhi; Ji, Rui-Feng; Zhou, L I; Wang, Sheng; Li, Zhen-Hao; Ma, Zhong-Hua; Guo, Lan-Ping

    2017-06-01

    Chinese Pharmacopoeia provides nine pesticide Maximum Residual Limits(MRLs) of traditional Chinese medicines(TCMs), The number of pesticides used in production are far more than those listed in pharmacopoeia. The lack of the standards make it's hard to reflect the real situation of pesticide residues in TCMs correctly. The paper is aimed to analyze the data of pesticide residues in TCMs from 7 089 items in 140 reports, and judging the exceedance rate of pesticides in TCMs using the MRLs of European pharmacopoeia,which is widely accepted in many countries. The results show that:①Pesticide residues in 18 kinds of TCMs are higher than MRLs,while in 137 kinds are below MRLs, such as Atractylodis Macrocephalae Rhizoma, Menthae Haplocalycis Herba and Fritillariae Thunbergii Bulbus. The average exceedance rate of all TCMs is 1.72%. The average exceedance rates of organochlorine, organophosphorus and pyrethroid are 2.26%, 1.51%, 0.37%,respectively. ②The average exceedance rate of pesticides is 2.00%, and the exceedance rate is more than 5%, accounting for 8.33%, the exceedance rate is between 1%-5%, accounting for 18.75%. the exceedance rate is between 0%-1%, accounting for 18.75%. The remaining 29 kinds of pesticides were not exceeded, accounting for 60.42%.Some reports like Greenpeace's organization exaggerated the pesticide residues in TCMs.But the pesticide residue question is still worthy of attention, so we proposed to amend the Chinese Pharmacopoeia pesticide residues standards, to increase the pesticide species of traditional Chinese medicine in production on the basis of retaining the existing types of pesticide residues, to strengthen the system research of pesticide residues in TCMs, providing a basis for making standard and promoting import and export trade in TCMs. Copyright© by the Chinese Pharmaceutical Association.

  7. Residual stress characterization of steel TIG welds by neutron diffraction and by residual magnetic stray field mappings

    Science.gov (United States)

    Stegemann, Robert; Cabeza, Sandra; Lyamkin, Viktor; Bruno, Giovanni; Pittner, Andreas; Wimpory, Robert; Boin, Mirko; Kreutzbruck, Marc

    2017-03-01

    The residual stress distribution of tungsten inert gas welded S235JRC+C plates was determined by means of neutron diffraction (ND). Large longitudinal residual stresses with maxima around 600 MPa were found. With these results as reference, the evaluation of residual stress with high spatial resolution GMR (giant magneto resistance) sensors was discussed. The experiments performed indicate a correlation between changes in residual stresses (ND) and the normal component of local residual magnetic stray fields (GMR). Spatial variations in the magnetic field strength perpendicular to the welds are in the order of the magnetic field of the earth.

  8. Sensitivity Analysis for Residual Stress on DVI (Direct Vessel Injection) Nozzle Welded Joint

    International Nuclear Information System (INIS)

    Noh, Byeong Wook; Chung, Sung Ho; Lee, Jung Hun; Kim, Oak Sug

    2008-01-01

    Generally, any welding process produces high compressive or tensile residual stresses in the heat affected zone depending on the method, shape and procedures of the weldment. In particular, the tensile residual stresses have a considerable effect on the material strength, fatigue strength and corrosion cracking. For this reason, it is important that some knowledge of the internal stress state be deduced either from measurements or from modeling predictions. In this study, the residual stresses after a multi-pass welding process for DVI nozzle welding joint were evaluated by a numerical simulation method. The welding joint considered three weld joint angles of 40 deg., 6 deg. and 2 deg. Computations were made using a 2-D finite element model based on the simulation of cooling from the heat treatment temperature to room temperature with two cooling conditions at the inside surface. In these results, it is shown that the residual stress increased at the inner surface, when water cooling was applied to the inner surface, and axial compressive residual stress increased at the inner surface when the joint angle was decreased. (authors)

  9. Sensitivity Analysis for Residual Stress on DVI (Direct Vessel Injection) Nozzle Welded Joint

    Energy Technology Data Exchange (ETDEWEB)

    Noh, Byeong Wook; Chung, Sung Ho; Lee, Jung Hun; Kim, Oak Sug [DOOSAN Heavy Industries and Construction Co. LTD, Reactor Design Team, 555 Guygok-dong Changwon (Korea, Republic of)

    2008-07-01

    Generally, any welding process produces high compressive or tensile residual stresses in the heat affected zone depending on the method, shape and procedures of the weldment. In particular, the tensile residual stresses have a considerable effect on the material strength, fatigue strength and corrosion cracking. For this reason, it is important that some knowledge of the internal stress state be deduced either from measurements or from modeling predictions. In this study, the residual stresses after a multi-pass welding process for DVI nozzle welding joint were evaluated by a numerical simulation method. The welding joint considered three weld joint angles of 40 deg., 6 deg. and 2 deg. Computations were made using a 2-D finite element model based on the simulation of cooling from the heat treatment temperature to room temperature with two cooling conditions at the inside surface. In these results, it is shown that the residual stress increased at the inner surface, when water cooling was applied to the inner surface, and axial compressive residual stress increased at the inner surface when the joint angle was decreased. (authors)

  10. Specific features of the determination of residual stresses in materials by diffraction techniques

    Science.gov (United States)

    Gorkunov, E. S.; Zadvorkin, S. M.; Goruleva, L. S.

    2017-12-01

    Residual stresses arising in separate machine parts and structural components during production and use to a large extent govern their lifetime. In this connection, the development and improvement of nondestructive methods for the determination of residual stresses is an important task for nondestructive testing. Standards regulate only the determination of macroscopic stresses, and in practice these stresses are most often determined with the application of the sin2ψ method. This paper, using quenched structural steels as an example, compares the results of residual stress determination by the sin2ψ method with those obtained by the method based on the analysis of the diffraction line profile as dependent on the value of the irradiated volume. It is demonstrated that, as the irradiated volume decreases, the value of residual stresses determined by the sin2ψ method may vary considerably, up to the change of the sign. For a more complete characteristic of residual stresses it is proposed to use, besides the determination of macrostresses by the shift of the diffraction lines, the value of microscopic stresses calculated from the line profile analysis.

  11. Nitrogen mineralization from selected 15N-labelled crop residues and humus as affected by inorganic nitrogen

    International Nuclear Information System (INIS)

    Santos, J.A.

    1987-01-01

    The use of cover crops or crop residues as a source of N to succeeding crops has become a matter of increasing importance for economic and environmental reason. Greenhouse and field studies were conducted to determine the N contribution of four 15 N labelled crop residues, rye (Secale cereale L.), wheat (Triticum aestivum L.), crimson clover (Trifolium encarnatum L.), and hairy vetch (Vicia sativa L.), to successive crops and to evaluate the effect of different organic (ON) and inorganic N (IN) combinations on mineralization of the above residues. Total 15 N recovery from the residues ranged from 51% to 85% and 4% to 74% for the greenhouse and field studies, respectively

  12. Radioactive material in residues of health services residues

    International Nuclear Information System (INIS)

    Costa R, A. Jr.; Recio, J.C.

    2006-01-01

    The work presents the operational actions developed by the one organ responsible regulator for the control of the material use radioactive in Brazil. Starting from the appearance of coming radioactive material of hospitals and clinical with services of nuclear medicine, material that that is picked up and transported in specific trucks for the gathering of residuals of hospital origin, and guided one it manufactures of treatment of residuals of services of health, where they suffer radiological monitoring before to guide them for final deposition in sanitary embankment, in the city of Sao Paulo, Brazil. The appearance of this radioactive material exposes a possible one violation of the norms that govern the procedures and practices in that sector in the country. (Author)

  13. Improved crop residue cover estimates by coupling spectral indices for residue and moisture

    Science.gov (United States)

    Remote sensing assessment of soil residue cover (fR) and tillage intensity will improve our predictions of the impact of agricultural practices and promote sustainable management. Spectral indices for estimating fR are sensitive to soil and residue water content, therefore, the uncertainty of estima...

  14. Greater utilization of wood residue fuels through improved financial planning

    International Nuclear Information System (INIS)

    Billings, C.D.; Ziemke, M.C.; Stanford, R.

    1991-01-01

    Recent events have focused attention on the promotion of greater utilization of biomass fuel. Considerations include the need to reduce increases in global warming and also to improve ground level air quality by limiting the use of fossil fuels. However, despite all these important environmentally related considerations, economics remains the most important factor in the decision process used to determine the feasibility of using available renewable fuels instead of more convenient fossil fuels. In many areas of the Southeast, this decision process involves choosing between wood residue fuels such as bark, sawdust and shavings and presently plentiful natural gas. The primary candidate users of wood residue fuels are industries that use large amounts of heat and electric power and are located near centers of activity in the forest products industry such as sawmills, veneer mills and furniture factories. Given that such facilities both produce wood residues and need large amounts of heat and electricity, it is understandable that these firms are often major users of wood-fired furnaces and boilers. The authors have observed that poor or incomplete financial planning by the subject firms is a major barrier to economic utilization of inexpensive and widely available renewable fuels. In this paper, the authors suggest that wider usage of improved financial planning could double the present modest annual incidence of new commercial wood-fueled installation

  15. Pesticides residue levels in selected fruits from some Ghanaian markets

    International Nuclear Information System (INIS)

    Bempah, K.C.

    2009-02-01

    The amount of some pesticide residues in fruits was monitored at five (5) Accra Metropolis markets. Locally produced fruits (pawpaw and tomato) and imported apples were purchased from two supermarkets and three urban markets in Accra metropolis and analyzed by gas chromatography equipped with electron capture detector for pesticide residues. A total of 220 samples of fruits were extracted and analyzed for pesticide residues, mainly organochlorines (γ-HCH, δ-HCH, aldrin, heptachlor, γ-chlordane, heptachlor epoxide, α-endosulfan, p,p'-DDE, endrin, β-endosulfan, o,p'-DDT, endrin aldehyde, p,p'- DDT, endrin ketone and methoxychlor). The data showed that most of the fruit samples analyzed contain residues of the monitored pesticides above the accepted maximum residue limit (MRL) as adopted by the FAO/WHO Codex Alimentarius Commission (CAC). The results obtained showed that 38.6 % fruit samples showed results above the MRL, 48.7 % were below the MRL and 12.7 % contained no detectable level of the monitored pesticides. Data analysis of health risk estimates indicated that, particularly γ-HCH, δ-HCH, o,p'-DDT, p,p'-DDE or p,p'-DDT do not pose a direct hazard to human health, although present in the three fruits (pawpaw, tomato and apple). However, heptachlor, heptachlor epoxide, endrin aldehyde, and endrin ketone levels exceeded the reference dose, indicating a great potential for systemic toxicity, especially in children who are considered to be the most vulnerable population subgroup. Lastly, the public is aware of pesticide residues in fruits and advocates for the curtailing of pesticide use on horticulture produce or strong educational programmes for farmers on control and safer use of pesticides. (au)

  16. A highly Conserved Aspartic Acid Residue of the Chitosanase from Bacillus Sp. TS Is Involved in the Substrate Binding.

    Science.gov (United States)

    Zhou, Zhanping; Zhao, Shuangzhi; Liu, Yang; Chang, Zhengying; Ma, Yanhe; Li, Jian; Song, Jiangning

    2016-11-01

    The chitosanase from Bacillus sp. TS (CsnTS) is an enzyme belonging to the glycoside hydrolase family 8. The sequence of CsnTS shares 98 % identity with the chitosanase from Bacillus sp. K17. Crystallography analysis and site-direct mutagenesis of the chitosanase from Bacillus sp. K17 identified the important residues involved in the catalytic interaction and substrate binding. However, despite progress in understanding the catalytic mechanism of the chitosanase from the family GH8, the functional roles of some residues that are highly conserved throughout this family have not been fully elucidated. This study focused on one of these residues, i.e., the aspartic acid residue at position 318. We found that apart from asparagine, mutation of Asp318 resulted in significant loss of enzyme activity. In-depth investigations showed that mutation of this residue not only impaired enzymatic activity but also affected substrate binding. Taken together, our results showed that Asp318 plays an important role in CsnTS activity.

  17. A sensitive fluorescent probe for the polar solvation dynamics at protein-surfactant interfaces.

    Science.gov (United States)

    Singh, Priya; Choudhury, Susobhan; Singha, Subhankar; Jun, Yongwoong; Chakraborty, Sandipan; Sengupta, Jhimli; Das, Ranjan; Ahn, Kyo-Han; Pal, Samir Kumar

    2017-05-17

    Relaxation dynamics at the surface of biologically important macromolecules is important taking into account their functionality in molecular recognition. Over the years it has been shown that the solvation dynamics of a fluorescent probe at biomolecular surfaces and interfaces account for the relaxation dynamics of polar residues and associated water molecules. However, the sensitivity of the dynamics depends largely on the localization and exposure of the probe. For noncovalent fluorescent probes, localization at the region of interest in addition to surface exposure is an added challenge compared to the covalently attached probes at the biological interfaces. Here we have used a synthesized donor-acceptor type dipolar fluorophore, 6-acetyl-(2-((4-hydroxycyclohexyl)(methyl)amino)naphthalene) (ACYMAN), for the investigation of the solvation dynamics of a model protein-surfactant interface. A significant structural rearrangement of a model histone protein (H1) upon interaction with anionic surfactant sodium dodecyl sulphate (SDS) as revealed from the circular dichroism (CD) studies is nicely corroborated in the solvation dynamics of the probe at the interface. The polarization gated fluorescence anisotropy of the probe compared to that at the SDS micellar surface clearly reveals the localization of the probe at the protein-surfactant interface. We have also compared the sensitivity of ACYMAN with other solvation probes including coumarin 500 (C500) and 4-(dicyanomethylene)-2-methyl-6-(p-dimethylamino-styryl)-4H-pyran (DCM). In comparison to ACYMAN, both C500 and DCM fail to probe the interfacial solvation dynamics of a model protein-surfactant interface. While C500 is found to be delocalized from the protein-surfactant interface, DCM becomes destabilized upon the formation of the interface (protein-surfactant complex). The timescales obtained from this novel probe have also been compared with other femtosecond resolved studies and molecular dynamics simulations.

  18. 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.

  19. Tyrosine Residues Regulate Multiple Nuclear Functions of P54nrb.

    Science.gov (United States)

    Lee, Ahn R; Hung, Wayne; Xie, Ning; Liu, Liangliang; He, Leye; Dong, Xuesen

    2017-04-01

    The non-POU-domain-containing octamer binding protein (NONO; also known as p54nrb) has various nuclear functions ranging from transcription, RNA splicing, DNA synthesis and repair. Although tyrosine phosphorylation has been proposed to account for the multi-functional properties of p54nrb, direct evidence on p54nrb as a phosphotyrosine protein remains unclear. To investigate the tyrosine phosphorylation status of p54nrb, we performed site-directed mutagenesis on the five tyrosine residues of p54nrb, replacing the tyrosine residues with phenylalanine or alanine, and immunoblotted for tyrosine phosphorylation. We then preceded with luciferase reporter assays, RNA splicing minigene assays, co-immunoprecipitation, and confocal microscopy to study the function of p54nrb tyrosine residues on transcription, RNA splicing, protein-protein interaction, and cellular localization. We found that p54nrb was not phosphorylated at tyrosine residues. Rather, it has non-specific binding affinity to anti-phosphotyrosine antibodies. However, replacement of tyrosine with phenylalanine altered p54nrb activities in transcription co-repression and RNA splicing in gene context-dependent fashions by means of differential regulation of p54nrb protein association with its interacting partners and co-regulators of transcription and splicing. These results demonstrate that tyrosine residues, regardless of phosphorylation status, are important for p54nrb function. J. Cell. Physiol. 232: 852-861, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  20. Optimizing biomass feedstock logistics for forest residue processing and transportation on a tree-shaped road network

    Science.gov (United States)

    Hee Han; Woodam Chung; Lucas Wells; Nathaniel Anderson

    2018-01-01

    An important task in forest residue recovery operations is to select the most cost-efficient feedstock logistics system for a given distribution of residue piles, road access, and available machinery. Notable considerations include inaccessibility of treatment units to large chip vans and frequent, long-distance mobilization of forestry equipment required to process...

  1. A mutational analysis and molecular dynamics simulation of quinolone resistance proteins QnrA1 and QnrC from Proteus mirabilis

    Directory of Open Access Journals (Sweden)

    Ye Xinyu

    2010-10-01

    Full Text Available Abstract Background The first report on the transferable, plasmid-mediated quinolone-resistance determinant qnrA1 was in 1998. Since then, qnr alleles have been discovered worldwide in clinical strains of Gram-negative bacilli. Qnr proteins confer quinolone resistance, and belong to the pentapeptide repeat protein (PRP family. Several PRP crystal structures have been solved, but little is known about the functional significance of their structural arrangement. Results We conducted random and site-directed mutagenesis on qnrA1 and on qnrC, a newly identified quinolone-resistance gene from Proteus mirabilis. Many of the Qnr mutants lost their quinolone resistance function. The highly conserved hydrophobic Leu or Phe residues at the center of the pentapeptide repeats are known as i sites, and loss-of-function mutations included replacement of the i site hydrophobic residues with charged residues, replacing the i-2 site, N-terminal to the i residues, with bulky side-chain residues, introducing Pro into the β-helix coil, deletion of the N- and C-termini, and excision of a central coil. Molecular dynamics simulations and homology modeling demonstrated that QnrC overall adopts a stable β-helix fold and shares more similarities with MfpA than with other PRP structures. Based on homology modeling and molecular dynamics simulation, the dysfunctional point mutations introduced structural deformations into the quadrilateral β-helix structure of PRPs. Of the pentapeptides of QnrC, two-thirds adopted a type II β-turn, while the rest adopted type IV turns. A gap exists between coil 2 and coil 3 in the QnrC model structure, introducing a structural flexibility that is similar to that seen in MfpA. Conclusion The hydrophobic core and the β-helix backbone conformation are important for maintaining the quinolone resistance property of Qnr proteins. QnrC may share structural similarity with MfpA.

  2. DnaK as Antibiotic Target: Hot Spot Residues Analysis for Differential Inhibition of the Bacterial Protein in Comparison with the Human HSP70.

    Directory of Open Access Journals (Sweden)

    Federica Chiappori

    Full Text Available DnaK, the bacterial homolog of human Hsp70, plays an important role in pathogens survival under stress conditions, like antibiotic therapies. This chaperone sequesters protein aggregates accumulated in bacteria during antibiotic treatment reducing the effect of the cure. Although different classes of DnaK inhibitors have been already designed, they present low specificity. DnaK is highly conserved in prokaryotes (identity 50-70%, which encourages the development of a unique inhibitor for many different bacterial strains. We used the DnaK of Acinetobacter baumannii as representative for our analysis, since it is one of the most important opportunistic human pathogens, exhibits a significant drug resistance and it has the ability to survive in hospital environments. The E.coli DnaK was also included in the analysis as reference structure due to its wide diffusion. Unfortunately, bacterial DnaK and human Hsp70 have an elevated sequence similarity. Therefore, we performed a differential analysis of DnaK and Hsp70 residues to identify hot spots in bacterial proteins that are not present in the human homolog, with the aim of characterizing the key pharmacological features necessary to design selective inhibitors for DnaK. Different conformations of DnaK and Hsp70 bound to known inhibitor-peptides for DnaK, and ineffective for Hsp70, have been analysed by molecular dynamics simulations to identify residues displaying stable and selective interactions with these peptides. Results achieved in this work show that there are some residues that can be used to build selective inhibitors for DnaK, which should be ineffective for the human Hsp70.

  3. Estimation of residual stress distribution for pressurizer nozzle of Kori nuclear power plant considering safe end

    Energy Technology Data Exchange (ETDEWEB)

    Song, Tae Kwang; Bae, Hong Yeol; Chun, Yun Bae; Oh, Chang Young; Kim, Yun Jae [Korea University, Seoul (Korea, Republic of); Lee, Kyoung Soo; Park, Chi Yong [Korea Electric Power Research Institute, Daejeon (Korea, Republic of)

    2008-08-15

    In nuclear power plants, ferritic low alloy steel nozzle was connected with austenitic stainless steel piping system through alloy 82/182 butt weld. Accurate estimation of residual stress for weldment is important in the sense that alloy 82/182 is susceptible to stress corrosion cracking. There are many results which predict residual stress distribution for alloy 82/182 weld between nozzle and pipe. However, nozzle and piping system usually connected through safe end which has short length. In this paper, residual stress distribution for pressurizer nozzle of Kori nuclear power plant was predicted using FE analysis, which considered safe end. As a result, existing residual stress profile was redistributed and residual stress of inner surface was decreased specially. It means that safe end should be considered to reduce conservatism when estimating the piping system.

  4. Joining of molybdenum disilicide to stainless steel using amorphous metal brazes - residual stress analysis

    Energy Technology Data Exchange (ETDEWEB)

    Vaidya, R.U.; Gallegos, D.E.; Kautz, D.D. [Los Alamos National Lab. (United States)

    2007-07-01

    Molybdenum disilicide (MoSi{sub 2})/stainless steel 316 L joints were produced by high temperature brazing using a cobalt-based metallic-glass (METGLAS trademark 2714A). Successful joining was completed in two different ways; either by feeding excess braze into the braze gap upon heating or by constraining the MoSi{sub 2}/stainless steel assembly with an alumina (Al{sub 2}O{sub 3}) fixture during the heating cycle. These steps were necessary to ensure the production of a high quality void free joint. Residual stress measurements were completed on these joints. Indentation results show higher tensile residual stresses in the stainless steel for the joint with the external constraint, in comparison to the unconstrained state. In contrast, the compressive residual stresses in the MoSi{sub 2} (as measured by X-ray diffraction) were lower in the constrained state relative to the unconstrained state. These results and a lack of residual stress balance indicate that the stress state in the braze is significantly different under the two joining conditions and the volume of the braze plays an important role in the development of the residual stresses. Push-out tests carried out on these joints gave higher joint strengths in the unconstrained as compared to the constrained condition. The results of this study have important implications on the selection of the appropriate joining process (use of constraint versus extra braze). (orig.)

  5. Effect of residual gas on structural, electrical and mechanical properties of niobium films deposited by magnetron sputtering deposition

    Science.gov (United States)

    Wang, Lanruo; Zhong, Yuan; Li, Jinjin; Cao, Wenhui; Zhong, Qing; Wang, Xueshen; Li, Xu

    2018-04-01

    Magnetron sputtering is an important method in the superconducting thin films deposition. The residual gas inside the vacuum chamber will directly affect the quality of the superconducting films. In this paper, niobium films are deposited by magnetron sputtering under different chamber residual gas conditions. The influence of baking and sputtering process on residual gas are studied as well. Surface morphology, electrical and mechanical properties of the films are analysed. The residual gas analysis result before the sputtering process could be regarded as a reference condition to achieve high quality superconducting thin films.

  6. Modelling of the long-term fate of pesticide residues in agricultural soils and their surface exchange with the atmosphere: Part II. Projected long-term fate of pesticide residues.

    Science.gov (United States)

    Scholtz, M T; Bidleman, T F

    2007-05-01

    In the first part of this paper, a simple coupled dynamic soil-atmosphere model for studying the gaseous exchange of pesticide soil residues with the atmosphere is described and evaluated by comparing model results with published measurements of pesticide concentrations in air and soil. In Part II, the model is used to study the concentration profiles of pesticide residues in both undisturbed and annually tilled agricultural soils. Future trends are estimated for the measured air and soil concentrations of lindane and six highly persistent pesticides (toxaphene, p,p'-DDE, dieldrin, cis- and trans-chlordane and trans-nonachlor) over a twenty-year period due to volatilization and leaching into the deeper soil. Wet deposition and particle associated pesticide deposition (that increase soil residue concentrations) and soil erosion, degradation in the soil (other than for lindane) and run-off in precipitation are not considered in this study. Estimates of the rain deposition fluxes are reported that show that, other than for lindane, net volatilization fluxes greatly exceed rain deposition fluxes. The model shows that the persistent pesticides studied are highly immobile in soil and that loss of these highly persistent residues from the soil is by volatilization rather than leaching into the deeper soil. The soil residue levels of these six pesticides are currently sources of net volatilization to the atmosphere and will remain so for many years. The maximum rate of volatilization from the soil was simulated by setting the atmospheric background concentration to zero; these simulations show that the rates of volatilization will not be significantly increased since soil resistance rather than the atmospheric concentration controls the volatilization rates. Annual tilling of the soils increases the volatilization loss to the atmosphere. Nonetheless, the model predicts that, if only air-soil exchange is considered, more than 76% of current persistent pesticide residues

  7. Distortion and residual stresses in structures reinforced with titanium straps for improved damage tolerance

    International Nuclear Information System (INIS)

    Liljedahl, C.D.M.; Fitzpatrick, M.E.; Edwards, L.

    2008-01-01

    Distortion and residual stresses induced during the manufacturing process of bonded crack retarders have been investigated. Titanium alloy straps were adhesively bonded to an aluminium alloy SENT specimen to promote fatigue crack growth retardation. The effect of three different strap dimensions was investigated. The spring-back of a component when released from the autoclave and the residual stresses are important factors to take into account when designing a selective reinforcement, as this may alter the local aerodynamic characteristics and reduce the crack bridging effect of the strap. The principal problem with residual stresses is that the tensile nature of the residual stresses in the primary aluminium structure has a negative impact on the crack initiation and crack propagation behaviour in the aluminium. The residual stresses were measured with neutron diffraction and the distortion of the specimens was measured with a contour measurement machine. The bonding process was simulated with a three-dimensional FE model. The residual stresses were found to be tensile close to the strap and slightly compressive on the un-bonded side. Both the distortion and the residual stresses increased with the thickness and the width of the strap. Very good agreement between the measured stresses and the measured distortion and the FE simulation was found

  8. An adjoint method of sensitivity analysis for residual vibrations of structures subject to impacts

    Science.gov (United States)

    Yan, Kun; Cheng, Gengdong

    2018-03-01

    For structures subject to impact loads, the residual vibration reduction is more and more important as the machines become faster and lighter. An efficient sensitivity analysis of residual vibration with respect to structural or operational parameters is indispensable for using a gradient based optimization algorithm, which reduces the residual vibration in either active or passive way. In this paper, an integrated quadratic performance index is used as the measure of the residual vibration, since it globally measures the residual vibration response and its calculation can be simplified greatly with Lyapunov equation. Several sensitivity analysis approaches for performance index were developed based on the assumption that the initial excitations of residual vibration were given and independent of structural design. Since the resulting excitations by the impact load often depend on structural design, this paper aims to propose a new efficient sensitivity analysis method for residual vibration of structures subject to impacts to consider the dependence. The new method is developed by combining two existing methods and using adjoint variable approach. Three numerical examples are carried out and demonstrate the accuracy of the proposed method. The numerical results show that the dependence of initial excitations on structural design variables may strongly affects the accuracy of sensitivities.

  9. Residual Structures in Latent Growth Curve Modeling

    Science.gov (United States)

    Grimm, Kevin J.; Widaman, Keith F.

    2010-01-01

    Several alternatives are available for specifying the residual structure in latent growth curve modeling. Two specifications involve uncorrelated residuals and represent the most commonly used residual structures. The first, building on repeated measures analysis of variance and common specifications in multilevel models, forces residual variances…

  10. A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein

    Directory of Open Access Journals (Sweden)

    Mingyuan Xu

    2018-05-01

    Full Text Available A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC method is proposed for ab initio molecular dynamic simulation of proteins. In this approach, the energy of the protein is computed by a linear combination of the QM energies of individual residues and molecular fragments that account for the two-body interaction of hydrogen bond between backbone peptides. The atomic forces on the caped H atoms were corrected to conserve the total force of the protein. Using this approach, ab initio molecular dynamic simulation of an Ace-(ALA9-NME linear peptide showed the conservation of the total energy of the system throughout the simulation. Further a more robust 110 ps ab initio molecular dynamic simulation was performed for a protein with 56 residues and 862 atoms in explicit water. Compared with the classical force field, the ab initio molecular dynamic simulations gave better description of the geometry of peptide bonds. Although further development is still needed, the current approach is highly efficient, trivially parallel, and can be applied to ab initio molecular dynamic simulation study of large proteins.

  11. 4D-PET reconstruction using a spline-residue model with spatial and temporal roughness penalties

    Science.gov (United States)

    Ralli, George P.; Chappell, Michael A.; McGowan, Daniel R.; Sharma, Ricky A.; Higgins, Geoff S.; Fenwick, John D.

    2018-05-01

    4D reconstruction of dynamic positron emission tomography (dPET) data can improve the signal-to-noise ratio in reconstructed image sequences by fitting smooth temporal functions to the voxel time-activity-curves (TACs) during the reconstruction, though the optimal choice of function remains an open question. We propose a spline-residue model, which describes TACs as weighted sums of convolutions of the arterial input function with cubic B-spline basis functions. Convolution with the input function constrains the spline-residue model at early time-points, potentially enhancing noise suppression in early time-frames, while still allowing a wide range of TAC descriptions over the entire imaged time-course, thus limiting bias. Spline-residue based 4D-reconstruction is compared to that of a conventional (non-4D) maximum a posteriori (MAP) algorithm, and to 4D-reconstructions based on adaptive-knot cubic B-splines, the spectral model and an irreversible two-tissue compartment (‘2C3K’) model. 4D reconstructions were carried out using a nested-MAP algorithm including spatial and temporal roughness penalties. The algorithms were tested using Monte-Carlo simulated scanner data, generated for a digital thoracic phantom with uptake kinetics based on a dynamic [18F]-Fluromisonidazole scan of a non-small cell lung cancer patient. For every algorithm, parametric maps were calculated by fitting each voxel TAC within a sub-region of the reconstructed images with the 2C3K model. Compared to conventional MAP reconstruction, spline-residue-based 4D reconstruction achieved  >50% improvements for five of the eight combinations of the four kinetics parameters for which parametric maps were created with the bias and noise measures used to analyse them, and produced better results for 5/8 combinations than any of the other reconstruction algorithms studied, while spectral model-based 4D reconstruction produced the best results for 2/8. 2C3K model-based 4D reconstruction generated

  12. Comparison of residual stress measurement in thin films using surface micromachining method

    International Nuclear Information System (INIS)

    He, Q.; Luo, Z.X.; Chen, X.Y.

    2008-01-01

    Conductive, dielectric, semiconducting, piezoelectric and ferroelectric thin films are extensively used for MEMS/NEMS applications. One of the important parameters of thin films is residual stress. The residual stress can seriously affect the properties, performance and long-term stability of the films. Excessive compressive or tensile stress results in buckling, cracking, splintering and sticking problems. Stress measurement techniques are therefore essential for both process development and process monitoring. Many suggestions for stress measurement in thin films have been made over the past several decades. This paper is concentrated on the in situ stress measurement using surface micromachining techniques to determine the residual stress. The authors review and compare several types of stress measurement methods including buckling technique, rotating technique, micro strain gauge and long-short beam strain sensor

  13. Residual stresses evaluation in a gas-pipeline crossing

    Energy Technology Data Exchange (ETDEWEB)

    Fonseca, Maria Cindra [Universidade Federal Fluminense (UFF), Niteroi, RJ (Brazil); Almeida, Manoel Messias [COMPAGAS, Curitiba, PR (Brazil); Rebello, Joao Marcos Alcoforado [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil); Souza Filho, Byron Goncalves de [PETROBRAS, Rio de Janeiro, RJ (Brazil)

    2009-07-01

    The X-rays diffraction technique is a well established and effectiveness method in the determination of the residual and applied stresses in fine grained crystalline materials. It allows to characterize and to quantify the magnitude and direction of the existing surface stresses in the studied point of the material. The objective of this work is the evaluation of the surface stresses in a 10 in diameter Natural Gas Distribution Pipeline manufactured from API 5 L Gr B steel of COMPAGAS company, in a crossing with a Natural Gas Transportation Pipeline, in Araucaria-PR. This kind of evaluation is important to establish weather you have to perform a repositioning of one of the pipeline or not. The measurements had been made in two transversal sections of the pipe, the one upstream (170 mm of the external wall of the pipeline) and another one downstream (840 mm of the external wall of the pipeline). Each transversal section measurements where carried out in 3 points: 9 hours, 12 hours and 3 hours. In each measured point of the pipe surface, the longitudinal and transversal stresses had been measured. The magnitude of the surface residual stresses in the pipe varied of +180 MPa at the -210 MPa. The residual stress state on the surface of the points 12 hours region is characterized by tensile stresses and by compressive stresses in the points of 3 and 9 hours region. The surface residual stresses in gas-pipeline have been measured using X-ray diffraction method, by double exposure technique, using a portable apparatus, with Cr-K-alpha radiation. (author)

  14. Residual stress and its effect on the mechanical properties of Y-doped Mg alloy fabricated via back-pressure assisted equal channel angular pressing (ECAP-BP)

    Energy Technology Data Exchange (ETDEWEB)

    Shen, Jianghua, E-mail: j_shen@live.cn [Department of Mechanical Engineering, University of North Carolina at Charlotte, Charlotte, NC 28223-0001 (United States); School of Aeronautics, Northwestern Polytechnical University, Xi’an 710072 (China); Gärtnerová, Viera [Laboratory of Nanostructures and Nanomaterials, Institute of Physics of the ASCR, Na Slovance 2, CZ – 182 21, Prague 8 (Czech Republic); Kecskes, Laszlo J. [US Army Research Laboratory, Aberdeen Proving Ground, MD 21005-5069 (United States); Kondoh, Katsuyoshi [Joining and Welding Research Institute, Osaka University, 11-1 Mihogaoka, Ibaragi, Osaka 567-0047 (Japan); Jäger, Aleš, E-mail: jager@fzu.cz [Laboratory of Nanostructures and Nanomaterials, Institute of Physics of the ASCR, Na Slovance 2, CZ – 182 21, Prague 8 (Czech Republic); Wei, Qiuming [Department of Mechanical Engineering, University of North Carolina at Charlotte, Charlotte, NC 28223-0001 (United States)

    2016-07-04

    In this study, pure magnesium (Mg) and Mg-0.6 wt% yttrium (Y) binary alloy were fabricated via casting followed by room temperature equal channel angular pressing (ECAP) using an applied back pressure (BP). Microstructural examination after ECAP-BP revealed a fine-grained Mg-Y alloy with a high residual stress level, whereas, the pure Mg exhibited a well-recrystallized microstructure with uniform and equiaxed grains, but retaining very little residual stress. The Y atoms were present in the Mg matrix as solid solutes and acted as dislocation and grain boundary blockers, thus suppressing dynamic recovery and/or recrystallization during the ECAP process. The Mg-Y alloy had an average grain size of ~400 nm, approximately one order smaller than that of pure Mg. The combination of high residual stress and ultrafine grains of the Mg-Y alloy gave rise to a significant difference in its mechanical behavior from that of the pure Mg, under both quasi-static and dynamic compressive loading.

  15. Residual stress analysis in linear friction welded in-service Inconel 718 superalloy via neutron diffraction and contour method approaches

    Energy Technology Data Exchange (ETDEWEB)

    Smith, M. [University of British Columbia – Okanagan, School of Engineering, 3333 University Way, Kelowna, Canada V1V 1V7 (Canada); Levesque, J.-B. [Institut de recherche d' Hydro-Québec (IREQ), 1800 Lionel-Boulet Blvd., Varennes, Canada J3X 1S1 (Canada); Bichler, L., E-mail: lukas.bichler@ubc.ca [University of British Columbia – Okanagan, School of Engineering, 3333 University Way, Kelowna, Canada V1V 1V7 (Canada); Sediako, D. [Canadian Nuclear Laboratories, Building 459, Station 18, Chalk River, Canada K0J 1J0 (Canada); Gholipour, J.; Wanjara, P. [National Research Council of Canada, Aerospace 5145 Decelles Ave., Montreal, Canada H3T 2B2 (Canada)

    2017-04-13

    In this study, an analysis of elastic residual stress in Inconel{sup ®} 718 (IN 718) linear friction welds (LFWs) was carried out. In particular, the suitability of LFW for manufacturing and repair of aero engine components was emulated by joining virgin and in-service (extracted from a turbine disk) materials. The evolution in the residual strains and stresses in the heat-affected zone (HAZ), thermomechanically affected zone (TMAZ) and dynamically recrystallized zone (DRX) of the weld was characterized using the neutron diffraction and contour methods. The results provided insight into diverse challenges in quantitative analysis of residual stresses in welded IN 718 using diffraction techniques. Specifically, judicious selection of the beam width, height and stress-free lattice spacing were seen to be crucial to minimize measurement error and increase accuracy. Further, the contour method – a destructive technique relying on capturing the stress relaxation after electrical discharge machining – was used to characterize the residual stress distribution on two-dimensional plane sections of the welds. Both techniques suggested an increasing magnitude of residual stress originating from the base metal that reached a peak at the weld interface. Both methods indicated that the peak magnitude of residual stresses were below the yield stress of IN 718.

  16. Natural radioactivity in petroleum residues

    International Nuclear Information System (INIS)

    Gazineu, M.H.P.; Gazineu, M.H.P.; Hazin, C.A.; Hazin, C.A.

    2006-01-01

    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 238 U and 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 226 Ra, 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 226 Ra, 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 226 Ra, 40.5 to 1,550.0 kBq/kg for 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)

  17. Computing Decoupled Residuals for Compact Disc Players

    DEFF Research Database (Denmark)

    Odgaard, Peter Fogh; Stoustrup, Jakob; Andersen, Palle

    2006-01-01

    a pair of residuals generated by Compact Disc Player. However, these residuals depend on the performance of position servos in the Compact Disc Player. In other publications of the same authors a pair of decoupled residuals is derived. However, the computation of these alternative residuals has been...

  18. Dynamic viscosity study of barley malt and chicory concentrates

    Directory of Open Access Journals (Sweden)

    G. O. Magomedov

    2016-01-01

    Full Text Available The purpose of research is to find optimal conditions for dispersing and subsequent dehydration of liquid food environments in the nozzle spray drying chamber through the study of dynamic changes in viscosity according to temperature, velocities gradients and dry residue content. The objects of study were roasted chicory and malt barley concentrates with dry residue content of 20, 40, 60 and 80%. Research of dynamic viscosity were carried out at the measuring complex based on the rotational viscometer Rheotest II, analog-to-digital converter, module Laurent and a personal computer with a unique software that allows to record in real time (not only on a tape recorder, but also in the form of graphic files the behavior of the viscosity characteristics of concentrates. Registration of changes of dynamic viscosity was carried out at a shear rate gradient from 1,0 с -1 to 27,0 с -1 and the products temperature thermostating : 35, 55, 75˚ C. The research results are presented in the form of graphic dependences of effective viscosity on shear rate and flow curves (dependencies of shear stresses on the velocity gradient, which defined flow regimes, the optimal modes of dispersion concentrates into spray dryer chambers in obtaining of powdered semi-finished products and instanting were found: dry residue content - 40 %, concentrate temperature - 75 ˚C, velocity gradient in the air channel of the nozzle at least 20 c-1

  19. Characterisation and management of concrete grinding residuals.

    Science.gov (United States)

    Kluge, Matt; Gupta, Nautasha; Watts, Ben; Chadik, Paul A; Ferraro, Christopher; Townsend, Timothy G

    2018-02-01

    Concrete grinding residue is the waste product resulting from the grinding, cutting, and resurfacing of concrete pavement. Potential beneficial applications for concrete grinding residue include use as a soil amendment and as a construction material, including as an additive to Portland cement concrete. Concrete grinding residue exhibits a high pH, and though not hazardous, it is sufficiently elevated that precautions need to be taken around aquatic ecosystems. Best management practices and state regulations focus on reducing the impact on such aquatic environment. Heavy metals are present in concrete grinding residue, but concentrations are of the same magnitude as typically recycled concrete residuals. The chemical composition of concrete grinding residue makes it a useful product for some soil amendment purposes at appropriate land application rates. The presence of unreacted concrete in concrete grinding residue was examined for potential use as partial replacement of cement in new concrete. Testing of Florida concrete grinding residue revealed no dramatic reactivity or improvement in mortar strength.

  20. Characterization of particulate residues from greenlandic mswi for use as secondary resources

    DEFF Research Database (Denmark)

    Kirkelund, Gunvor Marie; Dias-Ferreira, Célia; Jensen, Pernille Erland

    2016-01-01

    In Greenland, waste incineration is used in the larger towns to treat the municipal solid waste. The incineration reduces the amount of waste, but produces particulate incineration residues such as fly and bottom ash that are disposed of. Most construction materials are imported to Arctic areas...... as secondary material. The bottom ashes consisted of coarser particles and exhibited lower heavy metal leaching than the fly ash. All residue samples were different and evaluation of reuse should be made individually, however the fly ash shows potential as cement replacement and bottom ash as sand replacement...

  1. Structural and sequence features of two residue turns in beta-hairpins.

    Science.gov (United States)

    Madan, Bharat; Seo, Sung Yong; Lee, Sun-Gu

    2014-09-01

    Beta-turns in beta-hairpins have been implicated as important sites in protein folding. In particular, two residue β-turns, the most abundant connecting elements in beta-hairpins, have been a major target for engineering protein stability and folding. In this study, we attempted to investigate and update the structural and sequence properties of two residue turns in beta-hairpins with a large data set. For this, 3977 beta-turns were extracted from 2394 nonhomologous protein chains and analyzed. First, the distribution, dihedral angles and twists of two residue turn types were determined, and compared with previous data. The trend of turn type occurrence and most structural features of the turn types were similar to previous results, but for the first time Type II turns in beta-hairpins were identified. Second, sequence motifs for the turn types were devised based on amino acid positional potentials of two-residue turns, and their distributions were examined. From this study, we could identify code-like sequence motifs for the two residue beta-turn types. Finally, structural and sequence properties of beta-strands in the beta-hairpins were analyzed, which revealed that the beta-strands showed no specific sequence and structural patterns for turn types. The analytical results in this study are expected to be a reference in the engineering or design of beta-hairpin turn structures and sequences. © 2014 Wiley Periodicals, Inc.

  2. Antimicrobial residues in tissues and eggs of laying hens at Chittagong, Bangladesh

    Directory of Open Access Journals (Sweden)

    Ariful Islam

    2016-12-01

    Full Text Available Aim: Antimicrobial residue in animal food products is an important index of food safety. Antimicrobial residues could result from chemotherapeutic or chemoprophylactic use of drugs in food animals. This occurrence of residue in animal food products has received enormous worldwide attention from some local, international, and public health agencies. A crosssectional study was conducted from July to December 2009 to detect the antibiotic residues in tissues and eggs of laying hens at Chittagong of Bangladesh. Materials and Methods: Microbial inhibition test (MIT and thin layer chromatography (TLC methods were used to detect antibacterial residues in poultry tissues (liver, kidney, breast, and thigh muscles and eggs. The bacteria and pH of the MIT method were as follows: Bacillus subtilis on test agar medium with a pH of 7.2, Bacillus cereus with a pH of 6.0, and Escherichia coli at pH with an 8.0. Results: The overall prevalence of antibiotic residues detected by MIT was 64% in liver, 63% in kidney, 56% in breast muscle, 50% in thigh muscle, and 60% in eggs. There was significant variation in results between MIT and TLC (p<0.05. Tetracycline residues were found in 48% in liver, 24% in kidneys, 20% in thigh muscles, 26% in breast muscles, and 36% in eggs. Ciprofloxacin residues were found 46% in liver, 42% in kidneys, 34% in thigh muscles, 30% in breast muscles, and 30% in eggs. Enrofloxacin residues were found 40% in livers, 36% in kidneys, 24% in thigh muscles, 20% in breast muscles, and 26% in eggs. Amoxicillin residues were found 48% in livers, 30% in kidneys, 26% in thigh muscles, 22% in breast muscles, and 24% in eggs. The most frequently detected antibiotic residues by both MIT and TLC were found in liver tissue, tetracycline (48%, ciprofloxacin (46%, enrofloxacin (40%, and amoxicillin (42% were found in liver. Breast muscle tissue was least likely to contain antibiotic residues (24%. Tetracycline (p=0.01 and amoxicillin (p=0.03 residues had

  3. Residual symptoms and functioning in depression, does the type of residual symptom matter? A post-hoc analysis

    Directory of Open Access Journals (Sweden)

    Romera Irene

    2013-02-01

    Full Text Available Abstract Background The degrees to which residual symptoms in major depressive disorder (MDD adversely affect patient functioning is not known. This post-hoc analysis explored the association between different residual symptoms and patient functioning. Methods Patients with MDD who responded (≥50% on the 17-item Hamilton Rating Scale for Depression; HAMD-17 after 3 months of treatment (624/930 were included. Residual core mood-symptoms (HAMD-17 core symptom subscale ≥1, residual insomnia-symptoms (HAMD-17 sleep subscale ≥1, residual anxiety-symptoms (HAMD-17-anxiety subscale ≥1, residual somatic-symptoms (HAMD-17 Item 13 ≥1, pain (Visual Analogue Scale ≥30, and functioning were assessed after 3 months treatment. A stepwise logistic regression model with normal functioning (Social and Occupational Functioning Assessment Scale ≥80 as the dependent variable was used. Results After 3 months, 59.5% of patients (371/624 achieved normal functioning and 66.0% (412/624 were in remission. Residual symptom prevalence was: core mood symptoms 72%; insomnia 63%; anxiety 78%; and somatic symptoms 41%. Pain reported in 18%. Factors associated with normal functioning were absence of core mood symptoms (odds ratio [OR] 8.7; 95% confidence interval [CI], 4.6–16.7, absence of insomnia symptoms (OR 1.8; 95% CI, 1.2–2.7, episode length (4–24 weeks vs. ≥24 weeks [OR 2.0; 95% CI, 1.1–3.6] and better baseline functioning (OR 1.0; 95% CI, 1.0–1.1. A significant interaction between residual anxiety symptoms and pain was found (p = 0.0080. Conclusions Different residual symptoms are associated to different degrees with patient functioning. To achieve normal functioning, specific residual symptoms domains might be targeted for treatment.

  4. 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.

  5. Monitoring of Some Pesticides Residue in Consumed tea in Tehran Market

    Directory of Open Access Journals (Sweden)

    Maryam Amirahmadi

    2013-01-01

    Full Text Available Tea is an agricultural product of the leaves, leaf buds, and internodes of various cultivars and sub-varieties of the Camellia sinensis plant, processed and vulcanized using various methods. Tea is a main beverage in Iranian food basket so should be free from toxic elements such as pesticides residue. There is no data bank on the residue of pesticides in the consumed black tea in Iran. The present study is the first attempt for monitoring of 25 pesticide residues from different chemical groups in tea samples obtained from local markets in Tehran, I.R. Iran during the period 2011. A reliable and accurate method based on spiked calibration curve and QuEChERS sample preparation was developed for determination of pesticide residues in tea by gas chromatography--mass spectrometry (GC/MS. The using of spiked calibration standards for constructing the calibration curve substantially reduced adverse matrix-related effects and negative recovery affected by GCB on pesticides. The recovery of pesticides at 3 concentration levels (n = 3 was in range of 81.4 - 99.4%. The method was proved to be repeatable with RSDr lower than 20%. The limits of quantification for all pesticides were <=20 ng/g. 53 samples from 17 imported and manufactured brand were analyzed. Detectable pesticides residues were found in 28.3% (15 samples of the samples. All of the positive samples were contaminated with unregulated pesticides (Endosulfan Sulfate or Bifenthrin which are established by ISIRI. None of the samples had contamination higher than maximum residue limit set by EU and India.

  6. Monitoring of some pesticides residue in consumed tea in Tehran market

    Directory of Open Access Journals (Sweden)

    Hamedani Morteza Pirali

    2013-01-01

    Full Text Available Abstract Tea is an agricultural product of the leaves, leaf buds, and internodes of various cultivars and sub-varieties of the Camellia sinensis plant, processed and vulcanized using various methods. Tea is a main beverage in Iranian food basket so should be free from toxic elements such as pesticides residue. There is no data bank on the residue of pesticides in the consumed black tea in Iran. The present study is the first attempt for monitoring of 25 pesticide residues from different chemical groups in tea samples obtained from local markets in Tehran, I.R. Iran during the period 2011. A reliable and accurate method based on spiked calibration curve and QuEChERS sample preparation was developed for determination of pesticide residues in tea by gas chromatography–mass spectrometry (GC/MS. The using of spiked calibration standards for constructing the calibration curve substantially reduced adverse matrix-related effects and negative recovery affected by GCB on pesticides. The recovery of pesticides at 3 concentration levels (n = 3 was in range of 81.4 - 99.4%. The method was proved to be repeatable with RSDr lower than 20%. The limits of quantification for all pesticides were ≤20 ng/g. 53 samples from 17 imported and manufactured brand were analyzed. Detectable pesticides residues were found in 28.3% (15 samples of the samples. All of the positive samples were contaminated with unregulated pesticides (Endosulfan Sulfate or Bifenthrin which are established by ISIRI. None of the samples had contamination higher than maximum residue limit set by EU and India.

  7. Is increased residual shank length a competitive advantage for elite transtibial amputee long jumpers?

    Science.gov (United States)

    Nolan, Lee; Patritti, Benjamin L; Stana, Laura; Tweedy, Sean M

    2011-07-01

    The purpose of this study was to evaluate the extent to which residual shank length affects long jump performance of elite athletes with a unilateral transtibial amputation. Sixteen elite, male, long jumpers with a transtibial amputation were videoed while competing in major championships (World Championships 1998, 2002 and Paralympic Games, 2004). The approach, take-off, and landing of each athlete's best jump was digitized to determine residual and intact shank lengths, jump distance, and horizontal and vertical velocity of center of mass at touchdown. Residual shank length ranged from 15 cm to 38 cm. There were weak, nonsignificant relationships between residual shank length and (a) distance jumped (r = 0.30), (b) horizontal velocity (r = 0.31), and vertical velocity (r = 0.05). Based on these results, residual shank length is not an important determinant of long jump performance, and it is therefore appropriate that all long jumpers with transtibial amputation compete in the same class. The relationship between residual shank length and key performance variables was stronger among athletes that jumped off their prosthetic leg (N = 5), and although this result must be interpreted cautiously, it indicates the need for further research.

  8. Influence of ageing of residues on the availability of herbicides for leaching

    International Nuclear Information System (INIS)

    Walker, A.; Rodriguez-Cruz, M.S.; Mitchell, M.J.

    2005-01-01

    Losses by leaching of chlorotoluron, isoproturon and triasulfuron from small intact columns of a structured clay loam and an unstructured sandy loam soil were measured in five separate field experiments. In general, losses of all three herbicides were greater from the clay loam than from the sandy loam soil and the order between herbicides was always triasulfuron>>isoproturon>chlorotoluron. Differences between experiments were also consistent for every soil/herbicide combination. There was no relationship between total loss and either total rainfall or cumulative leachate volume. When weighting factors were applied to the rainfall data to make early rainfall more important than later rainfall, there were significant positive relationships between cumulative weighted rainfall and total losses. Also, there were significant negative correlations between total losses and the delay to accumulation of 25 mm rainfall (equivalent to one pore volume of available water) in the different experiments. In laboratory incubations, there was a more rapid decline in aqueous (0.01 M calcium chloride) extractable residues than in total solvent extractable residues indicating increasing sorption with residence time. However, the rate of change in water extractable residues could not completely explain the decrease in leachability with ageing of residues in the field. Short-term sorption studies with aggregates of the two soils indicated slower sorption by those of the clay loam than by those of the sandy loam suggesting that diffusion into and out of aggregates may affect availability for leaching in the more structured soil. Small scale leaching studies with aggregates of the soils also demonstrated reductions in availability for leaching as residence time in soil was increased, which could not be explained by degradation. These results therefore indicate that time-dependent sorption processes are important in controlling pesticide movement in soils, although the data do not give a

  9. Influence of ageing of residues on the availability of herbicides for leaching

    Energy Technology Data Exchange (ETDEWEB)

    Walker, A.; Rodriguez-Cruz, M.S.; Mitchell, M.J

    2005-01-01

    Losses by leaching of chlorotoluron, isoproturon and triasulfuron from small intact columns of a structured clay loam and an unstructured sandy loam soil were measured in five separate field experiments. In general, losses of all three herbicides were greater from the clay loam than from the sandy loam soil and the order between herbicides was always triasulfuron>>isoproturon>chlorotoluron. Differences between experiments were also consistent for every soil/herbicide combination. There was no relationship between total loss and either total rainfall or cumulative leachate volume. When weighting factors were applied to the rainfall data to make early rainfall more important than later rainfall, there were significant positive relationships between cumulative weighted rainfall and total losses. Also, there were significant negative correlations between total losses and the delay to accumulation of 25 mm rainfall (equivalent to one pore volume of available water) in the different experiments. In laboratory incubations, there was a more rapid decline in aqueous (0.01 M calcium chloride) extractable residues than in total solvent extractable residues indicating increasing sorption with residence time. However, the rate of change in water extractable residues could not completely explain the decrease in leachability with ageing of residues in the field. Short-term sorption studies with aggregates of the two soils indicated slower sorption by those of the clay loam than by those of the sandy loam suggesting that diffusion into and out of aggregates may affect availability for leaching in the more structured soil. Small scale leaching studies with aggregates of the soils also demonstrated reductions in availability for leaching as residence time in soil was increased, which could not be explained by degradation. These results therefore indicate that time-dependent sorption processes are important in controlling pesticide movement in soils, although the data do not give a

  10. SDI: Statistical dynamic interactions

    International Nuclear Information System (INIS)

    Blann, M.; Mustafa, M.G.; Peilert, G.; Stoecker, H.; Greiner, W.

    1991-01-01

    We focus on the combined statistical and dynamical aspects of heavy ion induced reactions. The overall picture is illustrated by considering the reaction 36 Ar + 238 U at a projectile energy of 35 MeV/nucleon. We illustrate the time dependent bound excitation energy due to the fusion/relaxation dynamics as calculated with the Boltzmann master equation. An estimate of the mass, charge and excitation of an equilibrated nucleus surviving the fast (dynamic) fusion-relaxation process is used as input into an evaporation calculation which includes 20 heavy fragment exit channels. The distribution of excitations between residue and clusters is explicitly calculated, as is the further deexcitation of clusters to bound nuclei. These results are compared with the exclusive cluster multiplicity measurements of Kim et al., and are found to give excellent agreement. We consider also an equilibrated residue system at 25% lower initial excitation, which gives an unsatisfactory exclusive multiplicity distribution. This illustrates that exclusive fragment multiplicity may provide a thermometer for system excitation. This analysis of data involves successive binary decay with no compressional effects nor phase transitions. Several examples of primary versus final (stable) cluster decay probabilities for an A = 100 nucleus at excitations of 100 to 800 MeV are presented. From these results a large change in multifragmentation patterns may be understood as a simple phase space consequence, invoking neither phase transitions, nor equation of state information. These results are used to illustrate physical quantities which are ambiguous to deduce from experimental fragment measurements. 14 refs., 4 figs

  11. Residual stresses around Vickers indents

    International Nuclear Information System (INIS)

    Pajares, A.; Guiberteau, F.; Steinbrech, R.W.

    1995-01-01

    The residual stresses generated by Vickers indentation in brittle materials and their changes due to annealing and surface removal were studied in 4 mol% yttria partially stabilized zirconia (4Y-PSZ). Three experimental methods to gain information about the residual stress field were applied: (i) crack profile measurements based on serial sectioning, (ii) controlled crack propagation in post indentation bending tests and (iii) double indentation tests with smaller secondary indents located around a larger primary impression. Three zones of different residual stress behavior are deduced from the experiments. Beneath the impression a crack free spherical zone of high hydrostatic stresses exists. This core zone is followed by a transition regime where indentation cracks develop but still experience hydrostatic stresses. Finally, in an outward third zone, the crack contour is entirely governed by the tensile residual stress intensity (elastically deformed region). Annealing and surface removal reduce this crack driving stress intensity. The specific changes of the residual stresses due to the post indentation treatments are described and discussed in detail for the three zones

  12. Minimization of zirconium chlorinator residues

    International Nuclear Information System (INIS)

    Green, G.K.; Harbuck, D.D.

    1995-01-01

    Zirconium chlorinator residues contain an array of rare earths, scandium, unreacted coke, and radioactive thorium and radium. Because of the radioactivity, the residues must be disposed in special waste containment facilities. As these sites become more congested, and with stricter environmental regulations, disposal of large volumes of wastes may become more difficult. To reduce the mass of disposed material, the US Bureau of Mines (USBM) developed technology to recover rare earths, thorium and radium, and unreacted coke from these residues. This technology employs an HCl leach to solubilize over 99% of the scandium and thorium, and over 90% of the rare earths. The leach liquor is processed through several solvent extraction stages to selectively recover scandium, thorium, and rare earths. The leach residue is further leached with an organic acid to solubilize radium, thus allowing unreacted coke to be recycled to the chlorinator. The thorium and radium waste products, which comprise only 2.1% of the original residue mass, can then be sent to the radioactive waste facility

  13. A review of experimental methods for determining residual creep life

    International Nuclear Information System (INIS)

    Bolton, C.J.

    1977-11-01

    Experimental methods available for determining how much creep life remains at a particular time in the high temperature service of a component are reviewed. After a brief consideration of the limitations of stress rupture extrapolation techniques, the application of post-exposure creep testing is considered. Ways of assessing the effect of microstructural degradation on residual life are then reviewed. It is pointed out that while this type of work will be useful for certain materials, there are other materials in which 'mechanical damage' such as cavitation will be more important. Cavitation measurement techniques are therefore reviewed. The report ends with a brief consideration of the use of crack growth measurements in assessing the residual life of cracked components. (author)

  14. 9 CFR 311.39 - Biological residues.

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 2 2010-01-01 2010-01-01 false Biological residues. 311.39 Section... Biological residues. Carcasses, organs, or other parts of carcasses of livestock shall be condemned if it is determined that they are adulterated because of the presence of any biological residues. ...

  15. Cover crops and crop residue management under no-till systems improve soils and environmental quality

    Science.gov (United States)

    Kumar, Sandeep; Wegner, Brianna; Vahyala, Ibrahim; Osborne, Shannon; Schumacher, Thomas; Lehman, Michael

    2015-04-01

    Crop residue harvest is a common practice in the Midwestern USA for the ethanol production. However, excessive removal of crop residues from the soil surface contributes to the degradation of important soil quality indicators such as soil organic carbon (SOC). Addition of a cover crop may help to mitigate these negative effects. The present study was set up to assess the impacts of corn (Zea mays L.) residue removal and cover crops on various soil quality indicators and surface greenhouse gas (GHG) fluxes. The study was being conducted on plots located at the North Central Agricultural Research Laboratory (NCARL) in Brookings, South Dakota, USA. Three plots of a corn and soybean (Glycine max (L.) Merr.) rotation under a no-till (NT) system are being monitored for soils and surface gas fluxes. Each plot has three residue removal (high residue removal, HRR; medium residue removal, MRR; and low residue removal, LRR) treatments and two cover crops (cover crops and no cover crops) treatments. Both corn and soybean are represented every year. Gas flux measurements were taken weekly using a closed static chamber method. Data show that residue removal significantly impacted soil quality indicators while more time was needed for an affect from cover crop treatments to be noticed. The LRR treatment resulted in higher SOC concentrations, increased aggregate stability, and increased microbial activity. The LRR treatment also increased soil organic matter (SOM) and particulate organic matter (POM) concentrations. Cover crops used in HRR (high corn residue removal) improved SOC (27 g kg-1) by 6% compared to that without cover crops (25.4 g kg-1). Cover crops significantly impacted POM concentration directly after the residue removal treatments were applied in 2012. CO2 fluxes were observed to increase as temperature increased, while N2O fluxes increased as soil moisture increased. CH4 fluxes were responsive to both increases in temperature and moisture. On average, soils under

  16. Residual stresses associated with the hydraulic expansion of steam generator tubing into tubesheets

    International Nuclear Information System (INIS)

    Middlebrooks, W.B.; Harrod, D.L.; Gold, R.E.

    1991-01-01

    Westinghouse has used three different processes for the full depth expansion of tubes into the tube sheets of recirculating nuclear steam generators: mechanical rolling, explosive expansion and hydraulic expansion. Each process aims at expanding tubes tightly to tube sheets, leaving the smallest possible secondary side crevice depth, and minimizing the residual stress in the expanded tubes, all for the purpose of mitigating the effect of corrosion phenomena. The hydraulic expansion process was qualified and has been implemented since 1978, and more than 1.1 million tube ends have been hydraulically expanded into production units. In this paper, the results of the recent analytical studies related to the residual stress in the expanded tubes are summarized. The method of hydraulic expansion is explained, and some important parameters are given. Finite element method, theoretical incremental analysis, tube sheet yielding and residual stress, contact pressure, sensitivity analysis and temperature effect in the central region of tube sheets, and the residual stress in the transition zone are described. (K.I.)

  17. 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).

  18. Current perspectives on the dynamics of antibiotic resistance in different reservoirs.

    Science.gov (United States)

    Caniça, Manuela; Manageiro, Vera; Jones-Dias, Daniela; Clemente, Lurdes; Gomes-Neves, Eduarda; Poeta, Patrícia; Dias, Elsa; Ferreira, Eugénia

    2015-09-01

    Antibiotic resistance consists of a dynamic web. In this review, we describe the path by which different antibiotic residues and antibiotic resistance genes disseminate among relevant reservoirs (human, animal, and environmental settings), evaluating how these events contribute to the current scenario of antibiotic resistance. The relationship between the spread of resistance and the contribution of different genetic elements and events is revisited, exploring examples of the processes by which successful mobile resistance genes spread across different niches. The importance of classic and next generation molecular approaches, as well as action plans and policies which might aid in the fight against antibiotic resistance, are also reviewed. Copyright © 2015 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  19. Polycrystalline models for the calculation of residual stresses in zirconium alloys tubes

    International Nuclear Information System (INIS)

    Signorelli, J.W.; Turner, P.A.; Lebensohn, R.A.; Pochettino, A.A.

    1995-01-01

    Tubes made of different Zirconium alloys are used in various types of reactors. The final texture of tubes as well as the distribution of residual stresses depend on the mechanical treatments done during their manufacturing process. The knowledge and prediction of both the final texture and the distribution of residual stresses in a tube for nuclear applications are of outstanding importance in relation with in-reactor performance of the tube, especially in what concerns to its irradiation creep and growth behaviour. The viscoplastic and the elastoplastic self consistent polycrystal models are used to investigate the influence of different mechanical treatments, performed during rolling processes on the final distribution of intergranular residual stresses of zirconium alloys tubes. The residual strains predictions with both formulations show a non linear dependence with the orientation, but they are qualitatively different. This discrepancy could be explain in terms of the relative plastic activity between the -type and -type deformation modes predicted with the viscoplastic and elastoplastic models. (author). 10 refs., 4 figs., 1 tab

  20. Importance of dynamic topography in Himalaya-Tibetan plateau region

    Science.gov (United States)

    Ghosh, A.; Singh, S.

    2017-12-01

    Himalaya-Tibetan plateau region has the highest topography in the world. Various studies have been done to understand the mechanisms responsible for sustaining this high topography. However, the existence of dynamic topography in this region is still uncertain, though there have been some studies exploring the role of channel flow in lower crust leading to some topography. We investigated the role of radial mantle flow in this region by studying the relationship between geoid and topography. High geoid-to-topography ratios (GTR) were observed along the Himalayas suggesting deeper compensation mechanisms. However, further north, the geoid and topography relationship became a lot more complex as high as well as low GTR values were observed. The high GTR regions also coincided with area of high filtered free air gravity anomalies, indicating dynamic support. We also looked at the spectral components of gravity, geoid and topography, and calculated response functions to distinguish between different compensation mechanisms. We estimated the average elastic thickness of the whole region to be around 40 km from coherence and admittance studies. The GTR and admittance-coherence studies suggest deeper mass anomalies playing a role in supporting the topography along Himalayas and the area between Altyn Tagh and Kunlun faults.

  1. Measurement of neutron importance by a dynamic method

    International Nuclear Information System (INIS)

    Dmitriev, V.M.; Matusevich, E.S.; Regushevskij, V.I.; Sazonov, S.P.; Usikov, D.A.

    1977-01-01

    A procedure is proposed for measuring neutron importance spatial distribution in a critical reactor by determining the parameters of its run-up with a constant neutron source. 252 Cf quasiisotropic point source was used. The measurements were performed at a critical assembly with a highly enriched uranium core and beryllium reflector. Importance distributions in critical and subsritical assemblies were compared for various degrees of subcriticality. Absolute normalization for the importance was obtained, and some new integral reactor characteristics were determined experimentally on its basis. An experimental data acquisition and processing system was developed on the basis of the ELECTRONIKA-100 computer. An algorithm was also developed for statistical treatment of the data. The importance distributions in critical and subcritical assemblies proved to coincide up to a rather deep subcriticality

  2. Driving Calmodulin Protein towards Conformational Shift by Changing Ionization States of Select Residues

    International Nuclear Information System (INIS)

    Negi, Sunita; Atilgan, Ali Rana; Atilgan, Canan

    2012-01-01

    Proteins are complex systems made up of many conformational sub-states which are mainly determined by the folded structure. External factors such as solvent type, temperature, pH and ionic strength play a very important role in the conformations sampled by proteins. Here we study the conformational multiplicity of calmodulin (CaM) which is a protein that plays an important role in calcium signaling pathways in the eukaryotic cells. CaM can bind to a variety of other proteins or small organic compounds, and mediates different physiological processes by activating various enzymes. Binding of calcium ions and proteins or small organic molecules to CaM induces large conformational changes that are distinct to each interacting partner. In particular, we discuss the effect of pH variation on the conformations of CaM. By using the pKa values of the charged residues as a basis to assign protonation states, the conformational changes induced in CaM by reducing the pH are studied by molecular dynamics simulations. Our current view suggests that at high pH, barrier crossing to the compact form is prevented by repulsive electrostatic interactions between the two lobes. At reduced pH, not only is barrier crossing facilitated by protonation of residues, but also conformations which are on average more compact are attained. The latter are in accordance with the fluorescence resonance energy transfer experiment results of other workers. The key events leading to the conformational change from the open to the compact conformation are (i) formation of a salt bridge between the N-lobe and the linker, stabilizing their relative motions, (ii) bending of the C-lobe towards the N-lobe, leading to a lowering of the interaction energy between the two-lobes, (iii) formation of a hydrophobic patch between the two lobes, further stabilizing the bent conformation by reducing the entropic cost of the compact form, (iv) sharing of a Ca +2 ion between the two lobes.

  3. Driving Calmodulin Protein towards Conformational Shift by Changing Ionization States of Select Residues

    Science.gov (United States)

    Negi, Sunita; Rana Atilgan, Ali; Atilgan, Canan

    2012-12-01

    Proteins are complex systems made up of many conformational sub-states which are mainly determined by the folded structure. External factors such as solvent type, temperature, pH and ionic strength play a very important role in the conformations sampled by proteins. Here we study the conformational multiplicity of calmodulin (CaM) which is a protein that plays an important role in calcium signaling pathways in the eukaryotic cells. CaM can bind to a variety of other proteins or small organic compounds, and mediates different physiological processes by activating various enzymes. Binding of calcium ions and proteins or small organic molecules to CaM induces large conformational changes that are distinct to each interacting partner. In particular, we discuss the effect of pH variation on the conformations of CaM. By using the pKa values of the charged residues as a basis to assign protonation states, the conformational changes induced in CaM by reducing the pH are studied by molecular dynamics simulations. Our current view suggests that at high pH, barrier crossing to the compact form is prevented by repulsive electrostatic interactions between the two lobes. At reduced pH, not only is barrier crossing facilitated by protonation of residues, but also conformations which are on average more compact are attained. The latter are in accordance with the fluorescence resonance energy transfer experiment results of other workers. The key events leading to the conformational change from the open to the compact conformation are (i) formation of a salt bridge between the N-lobe and the linker, stabilizing their relative motions, (ii) bending of the C-lobe towards the N-lobe, leading to a lowering of the interaction energy between the two-lobes, (iii) formation of a hydrophobic patch between the two lobes, further stabilizing the bent conformation by reducing the entropic cost of the compact form, (iv) sharing of a Ca+2 ion between the two lobes.

  4. Dynamics of many-body localization in the presence of particle loss

    Science.gov (United States)

    van Nieuwenburg, EPL; Yago Malo, J.; Daley, AJ; Fischer, MH

    2018-01-01

    At long times, residual couplings to the environment become relevant even in the most isolated experiments, a crucial difficulty for the study of fundamental aspects of many-body dynamics. A particular example is many-body localization in a cold-atom setting, where incoherent photon scattering introduces both dephasing and particle loss. Whereas dephasing has been studied in detail and is known to destroy localization already on the level of non-interacting particles, the effect of particle loss is less well understood. A difficulty arises due to the ‘non-local’ nature of the loss process, complicating standard numerical tools using matrix product decomposition. Utilizing symmetries of the Lindbladian dynamics, we investigate the particle loss on both the dynamics of observables, as well as the structure of the density matrix and the individual states. We find that particle loss in the presence of interactions leads to dissipation and a strong suppression of the (operator space) entanglement entropy. Our approach allows for the study of the interplay of dephasing and loss for pure and mixed initial states to long times, which is important for future experiments using controlled coupling of the environment.

  5. Dynamic Coupling and Allosteric Networks in the α Subunit of Heterotrimeric G Proteins.

    Science.gov (United States)

    Yao, Xin-Qiu; Malik, Rabia U; Griggs, Nicholas W; Skjærven, Lars; Traynor, John R; Sivaramakrishnan, Sivaraj; Grant, Barry J

    2016-02-26

    G protein α subunits cycle between active and inactive conformations to regulate a multitude of intracellular signaling cascades. Important structural transitions occurring during this cycle have been characterized from extensive crystallographic studies. However, the link between observed conformations and the allosteric regulation of binding events at distal sites critical for signaling through G proteins remain unclear. Here we describe molecular dynamics simulations, bioinformatics analysis, and experimental mutagenesis that identifies residues involved in mediating the allosteric coupling of receptor, nucleotide, and helical domain interfaces of Gαi. Most notably, we predict and characterize novel allosteric decoupling mutants, which display enhanced helical domain opening, increased rates of nucleotide exchange, and constitutive activity in the absence of receptor activation. Collectively, our results provide a framework for explaining how binding events and mutations can alter internal dynamic couplings critical for G protein function. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  6. On the relationship between residue structural environment and sequence conservation in proteins.

    Science.gov (United States)

    Liu, Jen-Wei; Lin, Jau-Ji; Cheng, Chih-Wen; Lin, Yu-Feng; Hwang, Jenn-Kang; Huang, Tsun-Tsao

    2017-09-01

    Residues that are crucial to protein function or structure are usually evolutionarily conserved. To identify the important residues in protein, sequence conservation is estimated, and current methods rely upon the unbiased collection of homologous sequences. Surprisingly, our previous studies have shown that the sequence conservation is closely correlated with the weighted contact number (WCN), a measure of packing density for residue's structural environment, calculated only based on the C α positions of a protein structure. Moreover, studies have shown that sequence conservation is correlated with environment-related structural properties calculated based on different protein substructures, such as a protein's all atoms, backbone atoms, side-chain atoms, or side-chain centroid. To know whether the C α atomic positions are adequate to show the relationship between residue environment and sequence conservation or not, here we compared C α atoms with other substructures in their contributions to the sequence conservation. Our results show that C α positions are substantially equivalent to the other substructures in calculations of various measures of residue environment. As a result, the overlapping contributions between C α atoms and the other substructures are high, yielding similar structure-conservation relationship. Take the WCN as an example, the average overlapping contribution to sequence conservation is 87% between C α and all-atom substructures. These results indicate that only C α atoms of a protein structure could reflect sequence conservation at the residue level. © 2017 Wiley Periodicals, Inc.

  7. Heating oil, distillates and residuals outlook

    International Nuclear Information System (INIS)

    Ervin, M.J.

    2004-01-01

    M.J. Ervin and Associates offers strategic planning support to the downstream petroleum industry in terms of price market monitoring, market analysis, media commentary and benchmarking of marketing operations. This presentation included graphs depicting supply and demand for heating oil distillates and residuals from the mid 1990s to 2004. It was noted that the long-term decline in residuals demand in the United States and Canada are due to environmental issues, the use of natural gas as an alternative, and the increasing complexity of refineries. Graphs depicting market impacts of refinery utilization and inventory trends showed that middle distillate production will increase at the expense of gasoline production. Middle distillates and gasoline markets will be more sensitive to supply disruptions, resulting in more frequent price spikes. Inventory trends indicate a greater reliance on product imports. The demand for heating fuel has stabilized due to the continued penetration of natural gas in eastern states and provinces. The demand for diesel fuel has growth 1.5 to 2 per cent while the demand for jet fuel has remained relatively flat and depends greatly on the growth of the gross national product (GNP). tabs., figs

  8. Determination of Pesticides Residues in Cucumbers Grown in Greenhouse and the Effect of Some Procedures on Their Residues.

    Science.gov (United States)

    Leili, Mostafa; Pirmoghani, Amin; Samadi, Mohammad Taghi; Shokoohi, Reza; Roshanaei, Ghodratollah; Poormohammadi, Ali

    2016-11-01

    The objective of this study was to determine the residual concentrations of ethion and imidacloprid in cucumbers grown in greenhouse. The effect of some simple processing procedures on both ethion and imidacloprid residues were also studied. Ten active greenhouses that produce cucumber were randomly selected. Ethion and imidacloprid as the most widely used pesticides were measured in cucumber samples of studied greenhouses. Moreover, the effect of storing, washing, and peeling as simple processing procedures on both ethion and imidacloprid residues were investigated. One hour after pesticide application; the maximum residue levels (MRLs) of ethion and imidacloprid were higher than that of Codex standard level. One day after pesticide application, the levels of pesticides were decreased about 35 a