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Sample records for residual interaction parameters

  1. Novel feature for catalytic protein residues reflecting interactions with other residues.

    Directory of Open Access Journals (Sweden)

    Yizhou Li

    Full Text Available Owing to their potential for systematic analysis, complex networks have been widely used in proteomics. Representing a protein structure as a topology network provides novel insight into understanding protein folding mechanisms, stability and function. Here, we develop a new feature to reveal correlations between residues using a protein structure network. In an original attempt to quantify the effects of several key residues on catalytic residues, a power function was used to model interactions between residues. The results indicate that focusing on a few residues is a feasible approach to identifying catalytic residues. The spatial environment surrounding a catalytic residue was analyzed in a layered manner. We present evidence that correlation between residues is related to their distance apart most environmental parameters of the outer layer make a smaller contribution to prediction and ii catalytic residues tend to be located near key positions in enzyme folds. Feature analysis revealed satisfactory performance for our features, which were combined with several conventional features in a prediction model for catalytic residues using a comprehensive data set from the Catalytic Site Atlas. Values of 88.6 for sensitivity and 88.4 for specificity were obtained by 10-fold cross-validation. These results suggest that these features reveal the mutual dependence of residues and are promising for further study of structure-function relationship.

  2. Bioinformatic prediction and in vivo validation of residue-residue interactions in human proteins

    Science.gov (United States)

    Jordan, Daniel; Davis, Erica; Katsanis, Nicholas; Sunyaev, Shamil

    2014-03-01

    Identifying residue-residue interactions in protein molecules is important for understanding both protein structure and function in the context of evolutionary dynamics and medical genetics. Such interactions can be difficult to predict using existing empirical or physical potentials, especially when residues are far from each other in sequence space. Using a multiple sequence alignment of 46 diverse vertebrate species we explore the space of allowed sequences for orthologous protein families. Amino acid changes that are known to damage protein function allow us to identify specific changes that are likely to have interacting partners. We fit the parameters of the continuous-time Markov process used in the alignment to conclude that these interactions are primarily pairwise, rather than higher order. Candidates for sites under pairwise epistasis are predicted, which can then be tested by experiment. We report the results of an initial round of in vivo experiments in a zebrafish model that verify the presence of multiple pairwise interactions predicted by our model. These experimentally validated interactions are novel, distant in sequence, and are not readily explained by known biochemical or biophysical features.

  3. Universal relationship connecting various two-body effective residual interactions

    International Nuclear Information System (INIS)

    Knuepfer, W.; Huber, M.G.

    1976-01-01

    Starting from a momentum space analysis of the two-body matrix elements, a relation has been established between the size of the model space actually used in a specific calculation and the relevant properties of the effective residual interaction. It turns out that the two-body transition density acts like a filter function on the Fourier transform of the force; it exhibits a distinct structure which clearly reflects the size and the detailed properties of the configuration space actually used. From an investigation of this filter function an equivalence criterion for different effective residual two-body interactions has been established both for closed and open shell nuclei. This result can be used to construct simple although realistic effective forces. As an example, a model for a separable residual interaction is proposed in which the corresponding parameters are being clearly related to the nuclear radius (i.e., the mass number), to the quantum numbers (i.e., the angular momentum) of the state under consideration and to the size of the configuration space used. For a number of examples this force has been applied successfully for the description of low energy properties of both closed and open shell nuclei

  4. Improved Interaction Potentials for Charged Residues in Proteins

    DEFF Research Database (Denmark)

    Kepp, Kasper Planeta

    2008-01-01

    -consistent, experimental set of hydration free energies for acetate (Asp), propionate (Glu), 4-methylimidazolium (Hip), n-butylammonium (Lys), and n-propylguanidinium (Arg), all resembling charged residue side chains, including -carbons. It is shown that OPLS-AA free energies depend critically on the type of water model......, TIP4P or TIP3P; i.e., each water model requires specific water-charged molecule interaction potentials. New models (models 1 and 3) are thus described for both water models. Uncertainties in relative free energies of charged residues are ~2 kcal/mol with the new parameters, due to variations in system...... setup (MAEs of ca. 1 kcal/mol) and noise from simulations (ca. 1 kcal/mol). The latter error of ~1 kcal/mol contrasts MAEs from standard OPLS-AA of up to 13 kcal/mol for the entire series of charged residues or up to 5 kcal/mol for the cationic series Lys, Arg, and Hip. The new parameters can be used...

  5. Optimization of machining and vibration parameters for residual stresses minimization in ultrasonic assisted turning of 4340 hardened steel.

    Science.gov (United States)

    Sharma, Varun; Pandey, Pulak M

    2016-08-01

    The residual stresses generated in the machined work piece have detrimental effect on fatigue life, corrosion resistance and tribological properties. However, the effect of cutting and vibration parameters on residual stresses in Ultrasonic Assisted Turning (UAT) has not been dealt with. The present paper highlights the effect of feed rate, depth of cut, cutting velocity and percentage intensity of ultrasonic power on residual stress generation. XRD analysis has been carried out to measure the residual stress while turning 4340 hardened steel using UAT. The experiments were performed based on response surface methodology to develop statistical model for residual stress. The outcome of ANOVA revealed that percentage intensity and feed rate significantly affect the residual stress generation. The significant interactions between process parameters have also been presented tin order to understand the thermo-mechanical mechanism responsible for residual stress generation. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. Hubble Parameter Corrected Interactions in Cosmology

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    J. Sadeghi

    2014-01-01

    character opening a room for different kinds of manipulations. In this paper we will consider a modification of an interaction Q, where we accept that interaction parameter b1 (order of unity in Q=3Hb1ρ is time dependent and presented as a linear function of Hubble parameter H of the form b0+btH, where b and b0 are constants. We consider two different models including modified Chaplygin gas and polytropic gas which have bulk viscosity. Then, we investigate problem numerically and analyze behavior of different cosmological parameters concerning fluids and behavior of the universe.

  7. Profile Monitors Based on Residual Gas Interaction

    CERN Document Server

    Forck, P; Giacomini, T; Peters, A

    2005-01-01

    The precise determination of transverse beam profiles at high current hadron accelerators has to be performed non-interceptingly. Two methods will be discussed based on the excitation of the residual gas molecules by the beam particles: Firstly, by beam induced fluorescence (BIF) light is emitted from the residual gas molecules and is observed with an image intensified CCD camera. At most laboratories N2 gas is inserted, which has a large cross section for emission in the blue wave length region. Secondly, a larger signal strength is achieved by detecting the ionization products in an Ionization Profile Monitor (IPM). By applying an electric field all ionization products are accelerated toward a spatial resolving Micro-Channel Plate. The signal read-out can either be performed by observing the light from a phosphor screen behind the MCP or electronically by a wire array. Methods to achieve a high spatial resolution and a fast turn-by-turn readout capability are discussed. Even though various approaches at dif...

  8. Identification of mannose interacting residues using local composition.

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    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

  9. Modeling and Parameter Optimization for Surface Roughness and Residual Stress in Dry Turning Process

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    M. H. El-Axir

    2017-10-01

    Full Text Available The influence of some turning variables and tool overhang on surface roughness parameters and residual stress induced due to machining 6061-T6 aluminum alloy is investigated in this paper. Four input parameters (cutting speed, feed rate, depth of cut and tool overhang are considered. Tests are carried out by precision turning operation on a lathe. Design of experiment techniques, i.e. response surface methodology (RSM and Taguchi's technique have been used to accomplish the objective of the experimental study. Surface roughness parameters are measured using a portable surface roughness device while residual stresses are measured employing deflection-etching technique using electrochemical analysis. The results obtained reveal that feed and rotational speed play significant role in determining the average surface roughness. Furthermore, the depth of cut and tool overhang are less significant parameters, whereas tool overhang interacts with feed rate. The best result of surface roughness was obtained using low or medium values of overhang with low speed and /or feed rate. Minimum maximum tensile residual stress can be obtained with a combination of tool overhang of 37 mm with very low depth of cut, low rotational speed and feed rate of 0.188 mm/rev.

  10. Immunological parameters and residual feed intake of Nellore heifers

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    Cleisy Ferreira Nascimento

    2012-12-01

    Full Text Available The residual feed intake (RFI is a parameter used in the identification of animals with respect to more efficient feed utilization. However, physiological basis are still unknown, however, the interrelationships between nutrition an immunity of the animal can contribute to the investigation of biological phenomena relevant to the RFI, since the defense system to oxidative effects caused by free radicals, is formed by acid polyunsaturated fatty acids, water soluble substances and enzymes, which derive mainly from the use of nutrients in the diet. The objective of this study was to evaluate the immunological parameters of Nellore heifers classified according to RFI. It were evaluated 176 heifers (born between 2008 and 2010, Traditional Nellore herd from Instituto de Zootecnia - Sertãozinho/SP, forming three groups of evaluation, submitted to test post weaning feed efficiency and classified into high (> mean + 0.5 SD, n= 55, medium (± 0.5 SD, n= 65 and low RFI (< mean – 0.5 SD, n= 56. The diet was formulated based on Brachiaria decumbens hay, corn, cottonseed meal and mineral mixture (45:55, forage: concentrate. The weight of the animals were performed in fasting blood samples collected by venipuncture vein, using tubes of 10 ml type vacuntainer with EDTA anticoagulant. In the clinical laboratory, we measured the values of leukocytes (LEU; Targeted (SEG and lymphocytes (LIN. The experimental design was a randomized block design using PROC GLM of SAS, considering the fixed effects of year and the age covariate in the statistical model and the averages compared by Tukey test at 5% probability. There was no significant difference (P>0,005 between variables leukocyte (LEU, SEG and LIN and class of RFI (table 1, indicating that there is no distinction between animals more efficient (low RFI and less efficient (high RFI, for inflammatory and immune responses to oxidative effects. Therefore the variables measured leukocytes not explain the differences

  11. Interaction of 18-residue peptides derived from amphipathic helical ...

    Indian Academy of Sciences (India)

    We investigated the interaction of six 18-residue peptides derived from amphipathic helical segments of globular proteins with model membranes. The net charge of the peptides at neutral pH varies from –1 to +6. Circular dichroism spectra indicate that peptides with a high net positive charge tend to fold into a helical ...

  12. Interplay between symmetries and residual interactions in rotating nuclei

    International Nuclear Information System (INIS)

    Cwiok, S.; Kvasil, J.; Nazmitdinov, R.G.

    1990-01-01

    Using the space rotation and translation invariance of the nuclear Hamiltonian, the residual interactions for a rotating nucleus are constructed. The connection is found between the Goldstone modes of motion (spurious states) and the symmetries of equations of motion in Random Phase Approximation for states near the yrast line. (author). 18 figs

  13. Computational learning on specificity-determining residue-nucleotide interactions

    KAUST Repository

    Wong, Ka-Chun

    2015-11-02

    The protein–DNA interactions between transcription factors and transcription factor binding sites are essential activities in gene regulation. To decipher the binding codes, it is a long-standing challenge to understand the binding mechanism across different transcription factor DNA binding families. Past computational learning studies usually focus on learning and predicting the DNA binding residues on protein side. Taking into account both sides (protein and DNA), we propose and describe a computational study for learning the specificity-determining residue-nucleotide interactions of different known DNA-binding domain families. The proposed learning models are compared to state-of-the-art models comprehensively, demonstrating its competitive learning performance. In addition, we describe and propose two applications which demonstrate how the learnt models can provide meaningful insights into protein–DNA interactions across different DNA binding families.

  14. 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 .

  15. 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...

  16. Agrochemical residue-biota interactions in soil and aquatic ecosystems

    International Nuclear Information System (INIS)

    1980-01-01

    Two FAO/IAEA coordinated research programmes are concerned with isotopic tracer-aided studies of agrochemical residue-biota interactions in soils and aquatic ecosystems. They currently involve 18 studies in 14 countries: Brazil, Canada, Egypt, F.R. Germany, Hungary, India, Indonesia, Iraq, Israel, Malaysia, Thailand, Turkey, USA and USSR. The aim was to develop, standardize and apply labelled substrate techniques for comparative assays of primary autotrophic and microheterotrophic production and decay, and complementary tracer techniques to determine the fate, persistence and bioconcentration of trace contaminants. Comparable data were studied concerning the current status of water bodies and likely changes due to contaminants. Soil capacity to decompose undesirable contaminants and residues, and to promote desirable transformations were studied. The techniques were also applied as a diagnostic and prognostic tool, with priority given to rice ecosystems

  17. Scoring protein interaction decoys using exposed residues (SPIDER): a novel multibody interaction scoring function based on frequent geometric patterns of interfacial residues.

    Science.gov (United States)

    Khashan, Raed; Zheng, Weifan; Tropsha, Alexander

    2012-08-01

    Accurate prediction of the structure of protein-protein complexes in computational docking experiments remains a formidable challenge. It has been recognized that identifying native or native-like poses among multiple decoys is the major bottleneck of the current scoring functions used in docking. We have developed a novel multibody pose-scoring function that has no theoretical limit on the number of residues contributing to the individual interaction terms. We use a coarse-grain representation of a protein-protein complex where each residue is represented by its side chain centroid. We apply a computational geometry approach called Almost-Delaunay tessellation that transforms protein-protein complexes into a residue contact network, or an undirectional graph where vertex-residues are nodes connected by edges. This treatment forms a family of interfacial graphs representing a dataset of protein-protein complexes. We then employ frequent subgraph mining approach to identify common interfacial residue patterns that appear in at least a subset of native protein-protein interfaces. The geometrical parameters and frequency of occurrence of each "native" pattern in the training set are used to develop the new SPIDER scoring function. SPIDER was validated using standard "ZDOCK" benchmark dataset that was not used in the development of SPIDER. We demonstrate that SPIDER scoring function ranks native and native-like poses above geometrical decoys and that it exceeds in performance a popular ZRANK scoring function. SPIDER was ranked among the top scoring functions in a recent round of CAPRI (Critical Assessment of PRedicted Interactions) blind test of protein-protein docking methods. Copyright © 2012 Wiley Periodicals, Inc.

  18. Milk quality parameters associated with the occurrence of veterinary drug residues in bulk tank milk

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    Lidia Cristina Almeida Picinin

    Full Text Available ABSTRACT Veterinary drug residues in bulk tank milk are important to all sectors of the dairy chain because they are one of the major factors which determine the safety of the final product. This study attempted to identify milk quality parameters that are associated with the occurrence of veterinary drug residues using multivariate principal component analysis (PCA. A total of 132 raw milk samples were collected from 45 dairy farms in the state of Minas Gerais - Brazil and analyzed for 42 analytes, including pyrethroids, macrocyclic lactones and antibacterials, using liquid chromatography coupled with mass spectrometry in tandem mode and gas chromatography with electron capture detection. Out of the 132 milk samples, 40 samples tested positive for at least one analyte (above the detection limit. The milk parameters associated with the antimicrobial residues by confirmatory tests were lactose and nonfat concentrations, as revealed by PCA. This analysis showed that fat and total solid concentrations, as well as the somatic cell and total bacteria counts were associated with macrocyclic lactone residues in bulk tank milk. A PCA assessing pyrethroid residues in bulk tank milk revealed that the lactose and nonfat solid concentrations and titratable acidity were inversely associated with these residues. Thus, the data analysis indicated that the veterinary drug residues were associated with certain milk quality parameters that can be used to target farms at higher risk of veterinary drug residue contamination for testing programs in combination with incentives, education and training programs to improve mammary health, milk hygiene and safety.

  19. Modeling the Influence of Process Parameters and Additional Heat Sources on Residual Stresses in Laser Cladding

    Science.gov (United States)

    Brückner, F.; Lepski, D.; Beyer, E.

    2007-09-01

    In laser cladding thermal contraction of the initially liquid coating during cooling causes residual stresses and possibly cracks. Preweld or postweld heating using inductors can reduce the thermal strain difference between coating and substrate and thus reduce the resulting stress. The aim of this work is to better understand the influence of various thermometallurgical and mechanical phenomena on stress evolution and to optimize the induction-assisted laser cladding process to get crack-free coatings of hard materials at high feed rates. First, an analytical one-dimensional model is used to visualize the most important features of stress evolution for a Stellite coating on a steel substrate. For more accurate studies, laser cladding is simulated including the powder-beam interaction, the powder catchment by the melt pool, and the self-consistent calculation of temperature field and bead shape. A three-dimensional finite element model and the required equivalent heat sources are derived from the results and used for the transient thermomechanical analysis, taking into account phase transformations and the elastic-plastic material behavior with strain hardening. Results are presented for the influence of process parameters such as feed rate, heat input, and inductor size on the residual stresses at a single bead of Stellite coatings on steel.

  20. Determination of antibiotic residues and their interaction in milk with lactate biosensor.

    Science.gov (United States)

    Rinken, T; Riik, H

    2006-03-31

    Milk and dairy products are among the most important foodstuffs and the quality of raw milk is of significant importance from the point of view of human health. For rapid determination of chloramphenicol and penicillin residues in raw milk, lactate oxidase-based amperometric biosensor was used. The concentration of antibiotic residuals was determined by two characteristic reaction parameters, calculated from the biosensor transient response with the dynamic biosensor model. Both chloramphenicol and penicillin caused the decrease of the value of the kinetic parameter, but they changed the total signal change parameter in different ways. The shift of the combined total signal change parameter at the simultaneous presence of these antibiotics indicated their antagonistic effect. Due to the respiration process of bacteria in raw milk, the dynamics of the biosensor signal was different in warm and cold seasons. The respiration characteristics were added to the biosensor model as a negative linear time-depending factor. The reaction characteristic parameters, obtained with this complemented model, showed excellent alignment in different conditions and allowed to detect antibiotic residues and their interaction in raw milk.

  1. THE LATTICE PARAMETERS AND RESIDUAL STRESSES IN BULK NANOCRYSTALLINE AND ULTRAFINE-GRAINED TITANIUM

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    Yu. M. Plotnikova

    2017-05-01

    Full Text Available Lattice parameters and residual stresses in the bulk nanocrystalline/ultrafine-grained titanium were studied by X-ray diffraction methods. The investigated samples were prepared using the method of the cryomechanical grain structure fragmentation with multiple rolling at the temperature of liquid nitrogen to the true strain value |e| = 3. Phasic change of the a and c parameters has been found with increasing degree of cryoreduction. This change was stronger for the parameter a. The observed change parameters associated with a relative slip and twinning activity (initial cryo-reduction stage as well as the formation of the nanocrystalline state (at higher degree of deformation. The most likely source of residual stresses arising in titanium at cryorolling is heterogeneous plastic deformation. The production of nanocrystalline / ultrafine-grained titanium using cryomechanical grain fragmentation method is accompanied by the formation of uniform compressive residual stresses in the informative deformable layer of billet.

  2. A residue level protein-protein interaction model in electrolyte solutions

    Science.gov (United States)

    Song, Xueyu

    2014-03-01

    The osmotic second virial coefficients B2 are directly related to the solubility of protein molecules in electrolyte solutions and can be useful to narrow down the search parameter space of protein crystallization conditions. Using a residue level model of protein-protein interaction in electrolyte solutions B2 of bovine pancreatic trypsin inhibitor and lysozyme in various solution conditions such as salt concentration, pH and temperature are calculated using an extended Fast Multipole Methods in combination with the boundary element formulation. Overall, the calculated B2 are well correlated with the experimental observations for various solution conditions. In combination with our previous work on the binding affinity calculations of protein complexes it is demonstrated that our residue level model can be used as a reliable model to describe protein-protein interaction in solutions.

  3. Residue-based Coordinated Selection and Parameter Design of Multiple Power System Stabilizers (PSSs)

    DEFF Research Database (Denmark)

    Su, Chi; Hu, Weihao; Fang, Jiakun

    2013-01-01

    Residue method is a commonly used approach to design the parameters of a power system stabilizer (PSS). In this paper, a residue identification method is adopted to obtain the system residues for different input-output pairs, using the system identification toolbox in MATLAB with the measurement...... as the test system is built in DIgSIELNT PowerFactory 14.0, in which the proposed coordination method is validated by time domain simulations and modal analysis....... data from time domain simulations. Then a coordinated approach for multiple PSS selection and parameter design based on residue method is proposed and realized in MATLAB m-files. Particle swarm optimization (PSO) is adopted in the coordination process. The IEEE 39-bus New England system model...

  4. A physically-motivated model describing the dynamic interactions between residual limb and socket in lower limb prostheses

    Directory of Open Access Journals (Sweden)

    Noll Veronika

    2017-03-01

    Full Text Available The amputee’s well-being and mobility are distinclty related to socket fit and resulting biomechanical interaction between residual limb and prosthetic socket. Understanding the dynamic interactions at the interface may lead to new socket standards. This paper introduces a physically-motivated reduced model of the interface, describing the dynamic interactions between residual limb and prosthetic socket. The model allows to investigate the sensitivity to changes of specific parameters in an isolated matter. A simulation study shows how stress distribution changes if friction coefficients are varied which might advance liner design.

  5. Estimating parameter and predictive uncertainty when model residuals are correlated, heteroscedastic, and non-Gaussian

    Science.gov (United States)

    Schoups, Gerrit; Vrugt, Jasper A.

    2010-05-01

    Estimation of parameter and predictive uncertainty of hydrologic models usually relies on the assumption of additive residual errors that are independent and identically distributed according to a normal distribution with a mean of zero and a constant variance. Here, we investigate to what extent estimates of parameter and predictive uncertainty are affected when these assumptions are relaxed. Parameter and predictive uncertainty are estimated by Monte Carlo Markov Chain sampling from a generalized likelihood function that accounts for correlation, heteroscedasticity, and non-normality of residual errors. Application to rainfall-runoff modeling using daily data from a humid basin reveals that: (i) residual errors are much better described by a heteroscedastic, first-order auto-correlated error model with a Laplacian density characterized by heavier tails than a Gaussian density, and (ii) proper representation of the statistical distribution of residual errors yields tighter predictive uncertainty bands and more physically realistic parameter estimates that are less sensitive to the particular time period used for inference. The latter is especially useful for regionalization and extrapolation of parameter values to ungauged basins. Application to daily rainfall-runoff data from a semi-arid basin shows that allowing skew in the error distribution yields improved estimates of predictive uncertainty when flows are close to zero.

  6. Hubungan Parameter Sifat Magnetik Dan Sifat Keteknikan Tanah Pada Tanah Residual Vulkanik

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    Mela Faridlah

    2017-10-01

    Full Text Available Penelitian mengenai karakteristik tanah residual vulkanik menggunakan metode magnetik dan metode geoteknik telah dilakukan pada lereng stabil dan lereng longsor yang berada di Desa Langensari Kecamatan Lembang Kabupaten Bandung Barat Provinsi Jawa Barat. Penelitian ini dimaksudkan untuk mengetahui gambaran karakteristik suseptibilitas magnetik dan parameter keteknikan tanah residual vulkanik. Karakteristik geoteknik ditentukan melalui uji fisik berupa uji bobot isi, berat isi tanah basah, berat isi tanah kering, kadar air, derajat kejenuhan dan porositas, uji batas atterberg serta uji ukuran butir tanah.. Karakteristik magnetik ditentukan melalui uji suseptibilitas magnetik menggunakan Bartington MS2B (Magnetic Suseptibility System sensor B dual frekuensi yaitu 470 Hz dan 4,7 kHz. Hasil penelitian ini menunjukkan peningkatan nilai-nilai χLF (suseptibilitas frekuensi rendah dan χFD% (suseptibilitas bergantung frekuensi kearah horizon bagian atas profil tanah residual. Peningkatan nilai-nilai χLF dan χFD% ke arah horizon bagian atas merupakan karakteristik dari suseptibilitas magnetik.Dari hasil penelitian geoteknik dan magnetik didapatkan hasil jenis tanah residual vulkanik tersebut merupakan tanah lempung dengan mineral dominan yaitu Ilmenit. Hubungan antara parameter magnetik dan keteknikan tanah yaitu beberapa parameter keteknikan yang mempengaruhi sifat kemagnetan diantaranya berat isi tanah basah dan kadar air. Research on volcanic residual soil characteristics using magnetic methods and geotechnic methods was carried out on a stable slope and landslide slope are located in Langensari Lembang west Bandung, West Java Province. This study are intended to describe the characteristics of the magnetic susceptibility and residual volcanic soil engineering parameters. Geotechnical characteristics were determined by physical properties tests such as bulk density test, wet density, dry density, water content, degree of saturation and porosity

  7. Prediction of residue-residue contact matrix for protein-protein interaction with Fisher score features and deep learning.

    Science.gov (United States)

    Du, Tianchuan; Liao, Li; Wu, Cathy H; Sun, Bilin

    2016-11-01

    Protein-protein interactions play essential roles in many biological processes. Acquiring knowledge of the residue-residue contact information of two interacting proteins is not only helpful in annotating functions for proteins, but also critical for structure-based drug design. The prediction of the protein residue-residue contact matrix of the interfacial regions is challenging. In this work, we introduced deep learning techniques (specifically, stacked autoencoders) to build deep neural network models to tackled the residue-residue contact prediction problem. In tandem with interaction profile Hidden Markov Models, which was used first to extract Fisher score features from protein sequences, stacked autoencoders were deployed to extract and learn hidden abstract features. The deep learning model showed significant improvement over the traditional machine learning model, Support Vector Machines (SVM), with the overall accuracy increased by 15% from 65.40% to 80.82%. We showed that the stacked autoencoders could extract novel features, which can be utilized by deep neural networks and other classifiers to enhance learning, out of the Fisher score features. It is further shown that deep neural networks have significant advantages over SVM in making use of the newly extracted features. Copyright © 2016. Published by Elsevier Inc.

  8. Evaluation of self-interaction parameters from binary phase diagrams

    International Nuclear Information System (INIS)

    Ellison, T.L.

    1977-10-01

    The feasibility of calculating Wagner self-interaction parameters from binary phase diagrams was examined. The self-interaction parameters of 22 non-ferrous liquid solutions were calculated utilizing an equation based on the equality of the chemical potentials of a component in two equilibrium phases. Utilization of the equation requires the evaluation of the first and second derivatives of various liquidus and solidus data at infinite dilution of the solute component. Several numerical methods for evaluating the derivatives of tabular data were examined. A method involving power series curve fitting and subsequent differentiation of the power series was found to be the most suitable for the interaction parameter calculations. Comparison of the calculated self-interaction parameters with values obtained from thermodynamic measurements indicates that the Wagner self-interaction parameter can be successfully calculated from binary phase diagrams

  9. Effects of different ratios of pig manure to fungus residue on physicochemical parameters during composting.

    Science.gov (United States)

    Zhou, Jiangming; Wang, Litong; Wang, Houming; Jiang, Long; Jiang, Xinyou

    2016-05-01

    This study examined physicochemical parameters to assess their effectiveness as stability and maturity indicators during the process of composting pig manure and fungus residue at different ratios. The results showed that composting mixtures with all ratios of pig manure to fungus residue maintained a temperature exceeding 50 °C for more than 10 days during composting and met the requirement for pathogen destruction. The treatment containing mainly pig manure showed higher nitrogen loss and a shorter thermophilic phase and maturity time than the treatment containing mainly fungus residue. The germination index (GI) values indicated that compost maturity was achieved in the final compost with initial ratios of pig manure to fungus residue of 9:1-7:3 (GIs of 101.4%, 91.2%, and 81.3%); the ratio of 6:4 did not reach compost maturity (GI of 63.8%) and had an inhibitory effect on seed germination. The results of this study suggest that a ratio of pig manure to fungus residue of approximately 8:2 can be considered suitable for the efficient and quality composting of pig manure and fungus residue. Co-composting of pig manure and edible fungi residue with appropriate proportion can effectively reduce the risk of environmental pollution caused by agricultural wastes, as well as achieve a safer and high-quality organic fertilizer, which can be used to improve physical and chemical properties of the soil, increase crop yields, and promote agricultural sustainable development. Therefore, technique of co-composting of pig manure and edible fungi residue has a wide prospect of application in practical production all over the world.

  10. Organomineral interactions as an important mechanism for stabilisation of bacterial residues in soil

    Science.gov (United States)

    Miltner, Anja; Achtenhagen, Jan; Kästner, Matthias

    2017-04-01

    Although plant material is the original input of organic matter to soils, microbial residues have been identified to contribute to a large extent to soil organic matter. However, until now it is unclear how microbial residues are stabilised in soil and protected from degradation. We hypothesised that organomineral interactions, in particular encrustation by oxides, may play an important role, which might vary depending on environmental conditions, e.g. redox potential. Therefore we produced 14C-labelled Escherichia coli cells and cell envelope fragments and coprecipitated these materials with Fe oxide or Al oxide. Mineral-free (control) and mineral-encrusted bacterial residues were incubated for 345 days at 20˚ C under either oxic or oxygen-limited conditions, and mineralisation was quantified by scintillation counting of the CO2 produced during incubation. Oxygen limitation was achieved by first exchanging the atmosphere in the incubation vessels with dinitrogen gas. After 100 days of incubation, the anoxic treatments were waterlogged to further decrease the redox potential, and after 290 days, glucose and nutrients were supplied to all treatments in order to foster microbial activity and consumption of electron acceptors. The mineralisation curves were fitted by double-exponential (0-100 days), first-order kinetic (100-290 days) and linear (290-345 days) models. The model parameters were tested for significant differences between the treatments by three-way ANOVA with post-hoc Bonferroni t-test. We found that encrustation by the oxides significantly reduced mineralisation of the bacterial residues. This effect was inversed by reductive dissolution of Fe oxides after substrate and nutrient addition to the oxygen-limited treatments, suggesting a significant role of the encrustation in stabilisation of the bacterial residues. We also observed that bacterial cell envelope fragments were generally slightly more resistant to mineralisation than whole cells. The

  11. The Association between Nutritional Markers and Biochemical Parameters and Residual Renal Function in Peritoneal Dialysis Patients.

    Directory of Open Access Journals (Sweden)

    Li Li

    Full Text Available Residual renal function (RRF is an important prognostic factor for peritoneal dialysis patients as it influences the quality of life and mortality. This study was conducted to explore the potential factors correlated with RRF. A cross-sectional study was conducted by recruiting 155 patients with residual GFR more than 1mL/min per 1.73m2 at the initiation of peritoneal dialysis. We collected the demographic characteristics, nutritional markers and biochemical parameters of all participants, and analyzed the correlation between these variables and residual GFR as well. The odds ratio of RRF loss associated with each of the nutritional markers and biochemical parameters were estimated by logistic regression model. The residual GFR was negatively correlated with serum phosphate (ORQ3 = 2.67, 95%CI: 1.03-6.92; ORQ4 = 3.45, 95%CI: 1.35-9.04, magnesium (ORQ4 = 3.77, 95%CI: 1.48-3.63, and creatinine (ORQ3 = 2.93, 95%CI: 1.09-7.88; ORQ4 = 8.64 95%CI: 2.79-26.78, while positively associated with normalized protein catabolic rate (ORQ3 = 0.24, 95%CI: 0.09-0.65; ORQ4 = 0.11, 95%CI: 0.03-0.35, 24 hours urine volume(ORQ1 = 22.87, 95%CI: 2.76-189.24; ORQ3 = 0.08, 95%CI: 0.02-0.28 and serum chlorine concentrations (ORQ1 = 5.34, 95%CI: 1.94-14.68; ORQ4 = 0.28, 95%CI: 0.09-0.85, respectively. Our study suggested that the nutritional markers and biochemical parameters, though not all, but at least in part were closely correlated with RRF in peritoneal dialysis patients.

  12. A study of photon interaction parameters in lung tissue substitutes

    Directory of Open Access Journals (Sweden)

    H C Manjunatha

    2014-01-01

    Full Text Available The study of photon interaction with different composite materials has become a topic of prime importance for radiation physicists. Some parameters of dosimetric interest are the mass attenuation coefficient, effective atomic number, and electron density; these help in the basic understanding of photon interactions with composite materials. The photon interaction parameters such as mass attenuation coefficient (μ/ρ, effective atomic number (Z eff , and effective electron density (N el must be identical for the phantom material and their tissue. In the present study, we have evaluated the photon interaction parameters such as (μ/ρ, Z eff and N el of 13 lung tissue substitutes. The variations of these parameters of lung tissue substitutes with photon energy are graphically represented. The photon interaction parameters of lung tissue substitutes are compared with that of lung tissue. The variation of photon interaction parameters of the studied lung tissue substitutes is similar that of the lung. Logically, it can be shown that Alderson lung is good substitute for lung than the other substitutes.

  13. A study of photon interaction parameters in lung tissue substitutes.

    Science.gov (United States)

    Manjunatha, H C

    2014-04-01

    The study of photon interaction with different composite materials has become a topic of prime importance for radiation physicists. Some parameters of dosimetric interest are the mass attenuation coefficient, effective atomic number, and electron density; these help in the basic understanding of photon interactions with composite materials. The photon interaction parameters such as mass attenuation coefficient (μ/ρ), effective atomic number (Zeff), and effective electron density (N el) must be identical for the phantom material and their tissue. In the present study, we have evaluated the photon interaction parameters such as (μ/ρ), Z eff and N el of 13 lung tissue substitutes. The variations of these parameters of lung tissue substitutes with photon energy are graphically represented. The photon interaction parameters of lung tissue substitutes are compared with that of lung tissue. The variation of photon interaction parameters of the studied lung tissue substitutes is similar that of the lung. Logically, it can be shown that Alderson lung is good substitute for lung than the other substitutes.

  14. Residual frying oil in the diets of sheep: intake, digestibility, nitrogen balance and ruminal parameters

    Science.gov (United States)

    Peixoto, Eduardo Lucas Terra; Mizubuti, Ivone Yurika; de Azambuja Ribeiro, Edson Luiz; dos Santos Moura, Elizabeth; Pereira, Elzânia Sales; do Prado, Odimari Pricila Pires; de Carvalho, Larissa Nóbrega; Pires, Kássia Amariz

    2017-01-01

    Objective The objective of this study was to evaluate the intake and nutrient digestibility, nitrogen balance and ruminal ammonia nitrogen in lambs of diets containing different levels of residual frying oil. Methods Levels of 0, 20, 40, 60, and 80 g/kg dry matter (DM) base of residual frying oil in the diets of lambs were evaluated. Five castrated lambs with initial body weights of 36.8±3.3 kg, distributed in a Latin square (5×5) design, were used. Results There was a decreasing linear effect on the intake of DM, organic matter (OM), crude protein (CP), neutral detergent fiber (NDF), total carbohydrates (TCH), and nonfibrous carbohydrates (NFC). There was an increased linear intake of ether extract (EE). The apparent digestibility of DM, OM, CP, NDF, TCH, and NFC, as well as urine nitrogen excretion, nitrogen balance and ruminal parameters, were not influenced by different levels of residual frying oil in the diet. EE digestibility presented a crescent linear effect. Conclusion It can be concluded that the addition of residual frying oil to the diets of sheep can affect nutrient intake without affecting the digestibility of most nutrients (with the exception of EE), nitrogen balance and ruminal ammonia nitrogen concentration. PMID:26954203

  15. NUMERICAL SIMULATION OF RESIDUAL STRESSES GENERATED IN THE WIRE DRAWING PROCESS FOR DIFFERENT PROCESS PARAMETERS

    Directory of Open Access Journals (Sweden)

    Juliana Zottis

    2014-03-01

    Full Text Available The drawing process of steel bars is usually used to check better dimensional accuracy and mechanical properties to the material. In the other hand, the major concern found in manufacturing axes through this process is the appearance of distortion of shape. Such distortions are directly linked to the accumulation of residual stresses generated during the processes. As a result, this paper aims to study the influence of process parameters such as shape of puller, speed and lubrication used in wire drawing analyzing the accumulation of residual stress after the process. The stress analysis was performed by FEM being used two simulation software: Simufact.formingGP and DeformTM. Through these analyzes, it was found that the shape of how the bar is pulled causes a reduction of up to 100 MPa in residual stresses in the center of the bar, which represents an important factor in the study of the possible causes of the distortion. As well as factors speed and homogeneity of lubrication significantly altered the profile of residual stresses in the bar.

  16. The Effect of Stochastically Varying Creep Parameters on Residual Stresses in Ceramic Matrix Composites

    Science.gov (United States)

    Pineda, Evan J.; Mital, Subodh K.; Bednarcyk, Brett A.; Arnold, Steven M.

    2015-01-01

    Constituent properties, along with volume fraction, have a first order effect on the microscale fields within a composite material and influence the macroscopic response. Therefore, there is a need to assess the significance of stochastic variation in the constituent properties of composites at the higher scales. The effect of variability in the parameters controlling the time-dependent behavior, in a unidirectional SCS-6 SiC fiber-reinforced RBSN matrix composite lamina, on the residual stresses induced during processing is investigated numerically. The generalized method of cells micromechanics theory is utilized to model the ceramic matrix composite lamina using a repeating unit cell. The primary creep phases of the constituents are approximated using a Norton-Bailey, steady state, power law creep model. The effect of residual stresses on the proportional limit stress and strain to failure of the composite is demonstrated. Monte Carlo simulations were conducted using a normal distribution for the power law parameters and the resulting residual stress distributions were predicted.

  17. Optimisation of process parameters in friction stir welding based on residual stress analysis: a feasibility study

    DEFF Research Database (Denmark)

    Tutum, Cem Celal; Hattel, Jesper Henri

    2010-01-01

    The present paper considers the optimisation of process parameters in friction stir welding (FSW). More specifically, the choices of rotational speed and traverse welding speed have been investigated using genetic algorithms. The welding process is simulated in a transient, two......-dimensional sequentially coupled thermomechanical model in ANSYS. This model is then used in an optimisation case where the two objectives are the minimisation of the peak residual stresses and the maximisation of the welding speed. The results indicate that the objectives for the considered case are conflicting......, and this is presented as a Pareto optimal front. Moreover, a higher welding speed for a fixed rotational speed results, in general, in slightly higher stress levels in the tension zone, whereas a higher rotational speed for a fixed welding speed yields somewhat lower peak residual stress, however, a wider tension zone...

  18. Maximising municipal solid waste--legume trimming residue mixture degradation in composting by control parameters optimization.

    Science.gov (United States)

    Cabeza, I O; López, R; Ruiz-Montoya, M; Díaz, M J

    2013-10-15

    Composting is one of the most successful biological processes for the treatment of the residues enriched in putrescible materials. The optimization of parameters which have an influence on the stability of the products is necessary in order to maximize recycling and recovery of waste components. The influence of the composting process parameters (aeration, moisture, C/N ratio, and time) on the stability parameters (organic matter, N-losses, chemical oxygen demand, nitrate, biodegradability coefficient) of the compost was studied. The composting experiment was carried out using Municipal Solid Waste (MSW) and Legume Trimming Residues (LTR) in 200 L isolated acrylic barrels following a Box-Behnken central composite experimental design. Second-order polynomial models were found for each of the studied compost stability parameter, which accurately described the relationship between the parameters. The differences among the experimental values and those estimated by using the equations never exceeded 10% of the former. Results of the modelling showed that excluding the time, the C/N ratio is the strongest variable influencing almost all the stability parameters studied in this case, with the exception of N-losses which is strongly dependent on moisture. Moreover, an optimized ratio MSW/LTR of 1/1 (w/w), moisture content in the range of 40-55% and moderate to low aeration rate (0.05-0.175 Lair kg(-)(1) min(-1)) is recommended to maximise degradation and to obtain a stable product during co-composting of MSW and LTR. Copyright © 2013 Elsevier Ltd. All rights reserved.

  19. A critical analysis of computational protein design with sparse residue interaction graphs.

    Science.gov (United States)

    Jain, Swati; Jou, Jonathan D; Georgiev, Ivelin S; Donald, Bruce R

    2017-03-01

    Protein design algorithms enumerate a combinatorial number of candidate structures to compute the Global Minimum Energy Conformation (GMEC). To efficiently find the GMEC, protein design algorithms must methodically reduce the conformational search space. By applying distance and energy cutoffs, the protein system to be designed can thus be represented using a sparse residue interaction graph, where the number of interacting residue pairs is less than all pairs of mutable residues, and the corresponding GMEC is called the sparse GMEC. However, ignoring some pairwise residue interactions can lead to a change in the energy, conformation, or sequence of the sparse GMEC vs. the original or the full GMEC. Despite the widespread use of sparse residue interaction graphs in protein design, the above mentioned effects of their use have not been previously analyzed. To analyze the costs and benefits of designing with sparse residue interaction graphs, we computed the GMECs for 136 different protein design problems both with and without distance and energy cutoffs, and compared their energies, conformations, and sequences. Our analysis shows that the differences between the GMECs depend critically on whether or not the design includes core, boundary, or surface residues. Moreover, neglecting long-range interactions can alter local interactions and introduce large sequence differences, both of which can result in significant structural and functional changes. Designs on proteins with experimentally measured thermostability show it is beneficial to compute both the full and the sparse GMEC accurately and efficiently. To this end, we show that a provable, ensemble-based algorithm can efficiently compute both GMECs by enumerating a small number of conformations, usually fewer than 1000. This provides a novel way to combine sparse residue interaction graphs with provable, ensemble-based algorithms to reap the benefits of sparse residue interaction graphs while avoiding their

  20. Optimization of the Process Parameters for Controlling Residual Stress and Distortion in Friction Stir Welding

    DEFF Research Database (Denmark)

    Tutum, Cem Celal; Schmidt, Henrik Nikolaj Blicher; Hattel, Jesper Henri

    2008-01-01

    In the present paper, numerical optimization of the process parameters, i.e. tool rotation speed and traverse speed, aiming minimization of the two conflicting objectives, i.e. the residual stresses and welding time, subjected to process-specific thermal constraints in friction stir welding......, is investigated. The welding process is simulated in 2-dimensions with a sequentially coupled transient thermo-mechanical model using ANSYS. The numerical optimization problem is implemented in modeFRONTIER and solved using the Multi-Objective Genetic Algorithm (MOGA-II). An engineering-wise evaluation or ranking...

  1. The effects of machine parameters on residual stress determined using micro-Raman spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

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

    1988-12-01

    The effects of machine parameters on residual stresses in single point diamond turned silicon and germanium have been investigated using micro-Raman spectroscopy. Residual stresses were sampled across ductile feed cuts in < 100 > silicon and germanium which were single point diamond turned using a variety of feed rates, rake angles and clearance angles. High spatial resolution micro-Raman spectra (1{mu}m spot) were obtained in regions of ductile cutting where no visible surface damage was present. The use of both 514-5nm and 488.0nm excitation wavelengths, by virtue of their differing characteristic penetration depths in the materials, allowed determinations of stress profiles as a function of depth into the sample. Previous discussions have demonstrated that such Raman spectra will exhibit asymmetrically broadened peaks which are characteristic of the superposition of a continuum of Raman scatterers from the various depths probed. Depth profiles of residual stress were obtained using computer deconvolution of the resulting asymmetrically broadened raman spectra.

  2. Solute-solvent interaction parameters by gas chromatography.

    Science.gov (United States)

    Kováts, Ervin sz; Fóti, György; Dallos, András

    2004-08-13

    Gas-liquid distribution coefficients at ideal dilution in non-volatile solvents can be measured by gas chromatography. The numerical value of a coefficient depends on the choice of the concentration unit in the solvent and in the gas phase. The relationships between different coefficients characterizing gas-liquid equilibria are discussed and summarized. Coefficients determined at several temperatures permit calculation of the standard chemical potential difference of the solute with the ideal gas phase as reference as a function of temperature, the g-SPOT. Following the proposal of Kirchhoff the latter can be formulated as an equation with three constants. As in the gas phase the molecules of the solute have no interacting partners, the three constants, deltaH, deltaS and deltaC, characterize the interaction between solvent and solute molecules. They will be called the "solute-solvent interaction parameters". In the same system the values of these parameters depend on the choice of the distribution coefficient. Five different distribution coefficients result five sets of interaction parameters. It is shown that conversion of a parameter set to another implies additive corrections independent of the nature of the solute. If g-SPOT-s are measured in a series of solvents, the data may be used to calculate the corresponding liquid-liquid partition coefficients by electing one of the solvents as reference (l-SPOT). The corresponding "relative interaction parameters" can be calculated by simple substraction. In a second chapter the precautions are summarized, necessary for gas chromatographic determination of distribution coefficients and examples are given for interaction parameters in different systems. It is concluded that there are significant differences between g-SPOT-s related to different distribution coefficients. On the other hand, differences between l-SPOT-s are negligible.

  3. 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.

  4. Molecular Determinants Underlying Binding Specificities of the ABL Kinase Inhibitors: Combining Alanine Scanning of Binding Hot Spots with Network Analysis of Residue Interactions and Coevolution

    Science.gov (United States)

    Tse, Amanda; Verkhivker, Gennady M.

    2015-01-01

    Quantifying binding specificity and drug resistance of protein kinase inhibitors is of fundamental importance and remains highly challenging due to complex interplay of structural and thermodynamic factors. In this work, molecular simulations and computational alanine scanning are combined with the network-based approaches to characterize molecular determinants underlying binding specificities of the ABL kinase inhibitors. The proposed theoretical framework unveiled a relationship between ligand binding and inhibitor-mediated changes in the residue interaction networks. By using topological parameters, we have described the organization of the residue interaction networks and networks of coevolving residues in the ABL kinase structures. This analysis has shown that functionally critical regulatory residues can simultaneously embody strong coevolutionary signal and high network centrality with a propensity to be energetic hot spots for drug binding. We have found that selective (Nilotinib) and promiscuous (Bosutinib, Dasatinib) kinase inhibitors can use their energetic hot spots to differentially modulate stability of the residue interaction networks, thus inhibiting or promoting conformational equilibrium between inactive and active states. According to our results, Nilotinib binding may induce a significant network-bridging effect and enhance centrality of the hot spot residues that stabilize structural environment favored by the specific kinase form. In contrast, Bosutinib and Dasatinib can incur modest changes in the residue interaction network in which ligand binding is primarily coupled only with the identity of the gate-keeper residue. These factors may promote structural adaptability of the active kinase states in binding with these promiscuous inhibitors. Our results have related ligand-induced changes in the residue interaction networks with drug resistance effects, showing that network robustness may be compromised by targeted mutations of key mediating

  5. 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.

  6. Interaction of 18-residue peptides derived from amphipathic helical ...

    Indian Academy of Sciences (India)

    Madhsudhan

    amphipathic peptides having potent antimicrobial activities;. Biochemistry 31 12688–12694. Cornell R B and Taneva S G 2006 Amphipathic helices as mediators of the membrane interaction of amphitropic proteins, and as modulators of bilayer physical properties; Curr. Protein. Pept. Sci. 6 539–552. Dathe M, Schumann M, ...

  7. Effect of fermented biogas residue on growth performance, serum biochemical parameters, and meat quality in pigs

    Directory of Open Access Journals (Sweden)

    Xiang Xu

    2017-10-01

    Full Text Available Objective This study investigated the effect of fermented biogas residue (FBR of wheat on the performance, serum biochemical parameters, and meat quality in pigs. Methods We selected 128 pigs (the mean initial body weight was 40.24±3.08 kg and randomly allocated them to 4 groups (1 control group and 3 treatment groups with 4 replicates per group and 8 pigs per pen in a randomized complete block design based on initial body weight and sex. The control group received a corn-soybean meal-based diet, the treatment group fed diets containing 5%, 10%, and 15% FBR, respectively (abbreviated as FBR5, FBR10, and FBR15, respectively. Every group received equivalent-energy and nitrogen diets. The test lasted 60 days and was divided into early and late stages. Blood and carcass samples were obtained on 60 d. Meat quality was collected from two pigs per pen. Results During the late stage, the average daily feed intake and average daily gain of the treatment groups was greater than that of the control group (p<0.05. During the entire experiment, the average daily gain of the treatment groups was higher than that of the control group (p<0.05. Fermented biomass residue did not significantly affect serum biochemical parameters or meat quality, but did affect amino acid profiles in pork. The contents of Asp, Arg, Tyr, Phe, Leu, Thr, Ser, Lys, Pro, Ala, essential amino acids, non-essential amino acids, and total amino acids in pork of FBR5 and FBR10 were greater than those of the control group (p<0.05. Conclusion These combined results suggest that feeding FBR could increase the average daily gain and average daily feed intake in pigs and the content of several flavor-promoting amino acids.

  8. Identification of Critical Paraoxonase 1 Residues Involved in High Density Lipoprotein Interaction*

    Science.gov (United States)

    Gu, Xiaodong; Huang, Ying; Levison, Bruce S.; Gerstenecker, Gary; DiDonato, Anthony J.; Hazen, Leah B.; Lee, Joonsue; Gogonea, Valentin; DiDonato, Joseph A.; Hazen, Stanley L.

    2016-01-01

    Paraoxonase 1 (PON1) is a high density lipoprotein (HDL)-associated protein with atherosclerosis-protective and systemic anti-oxidant functions. We recently showed that PON1, myeloperoxidase, and HDL bind to one another in vivo forming a functional ternary complex (Huang, Y., Wu, Z., Riwanto, M., Gao, S., Levison, B. S., Gu, X., Fu, X., Wagner, M. A., Besler, C., Gerstenecker, G., Zhang, R., Li, X. M., Didonato, A. J., Gogonea, V., Tang, W. H., et al. (2013) J. Clin. Invest. 123, 3815–3828). However, specific residues on PON1 involved in the HDL-PON1 interaction remain unclear. Unambiguous identification of protein residues involved in docking interactions to lipid surfaces poses considerable methodological challenges. Here we describe a new strategy that uses a novel synthetic photoactivatable and click chemistry-taggable phospholipid probe, which, when incorporated into HDL, was used to identify amino acid residues on PON1 that directly interact with the lipoprotein phospholipid surface. Several specific PON1 residues (Leu-9, Tyr-185, and Tyr-293) were identified through covalent cross-links with the lipid probes using affinity isolation coupled to liquid chromatography with on-line tandem mass spectrometry. Based upon the crystal structure for PON1, the identified residues are all localized in relatively close proximity on the surface of PON1, defining a domain that binds to the HDL lipid surface. Site-specific mutagenesis of the identified PON1 residues (Leu-9, Tyr-185, and Tyr-293), coupled with functional studies, reveals their importance in PON1 binding to HDL and both PON1 catalytic activity and stability. Specifically, the residues identified on PON1 provide important structural insights into the PON1-HDL interaction. More generally, the new photoactivatable and affinity-tagged lipid probe developed herein should prove to be a valuable tool for identifying contact sites supporting protein interactions with lipid interfaces such as found on cell membranes

  9. Interaction parameters of oxygen and deoxidants in liquid iron

    Directory of Open Access Journals (Sweden)

    Costa e Silva A.

    2016-01-01

    Full Text Available During decades before the evolution of more powerful computational tools, simplified formalisms such as the Wagner dilute solution formalism, have been successfully used in the study of deoxidation reactions of steel. This formalism relies on the introduction of interaction coefficients to account from deviations from Henry’s Law. With the evolution of thermodynamic modeling and of the CALPHAD method, the fact that thermodynamic descriptions using these parameters were derived to be used at relatively dilute solution has been sometimes overlooked and the formalism has been criticized for deviating from reality in non-dilute solutions. In this work, it is shown that the interaction parameters used in this formalism correlate with properties of the solutes and of the solvent. The work focuses on the interactions in systems Fe-M-O, where M is a deoxidant. Correlations between interaction coefficients and heats of formation of the corresponding oxides and with the atomic number of the deoxidants are demonstrated. This not only helps supporting the physicochemical soundness of the formalism but also provides a way of checking the consistency of data presented in this formalism.

  10. Standard test method for determining the effective elastic parameter for X-ray diffraction measurements of residual stress

    CERN Document Server

    American Society for Testing and Materials. Philadelphia

    1998-01-01

    1.1 This test method covers a procedure for experimentally determining the effective elastic parameter, Eeff, for the evaluation of residual and applied stresses by X-ray diffraction techniques. The effective elastic parameter relates macroscopic stress to the strain measured in a particular crystallographic direction in polycrystalline samples. Eeff should not be confused with E, the modulus of elasticity. Rather, it is nominally equivalent to E/(1 + ν) for the particular crystallographic direction, where ν is Poisson's ratio. The effective elastic parameter is influenced by elastic anisotropy and preferred orientation of the sample material. 1.2 This test method is applicable to all X-ray diffraction instruments intended for measurements of macroscopic residual stress that use measurements of the positions of the diffraction peaks in the high back-reflection region to determine changes in lattice spacing. 1.3 This test method is applicable to all X-ray diffraction techniques for residual stress measurem...

  11. Interaction between subdaily Earth rotation parameters and GPS orbits

    Science.gov (United States)

    Panafidina, Natalia; Seitz, Manuela; Hugentobler, Urs

    2013-04-01

    In processing GPS observations the geodetic parameters like station coordinates and ERPs (Earth rotation parameters) are estimated w.r.t. the celestial reference system realized by the satellite orbits. The interactions/correlations between estimated GPS orbis and other parameters may lead to numerical problems with the solution and introduce systematic errors in the computed values: the well known correlations comprise 1) the correlation between the orbital parameters determining the orientation of the orbital plane in inertial space and the nutation and 2) in the case of estimating ERPs with subdaily resolution the correlation between retrograde diurnal polar motion and nutation (and so the respective orbital elements). In this contribution we study the interaction between the GPS orbits and subdaily model for the ERPs. Existing subdaily ERP model recommended by the IERS comprises ~100 terms in polar motion and ~70 terms in Universal Time at diurnal and semidiurnal tidal periods. We use a long time series of daily normal equation systems (NEQ) obtaine from GPS observations from 1994 till 2007 where the ERPs with 1-hour resolution are transformed into tidal terms and the influence of the tidal terms with different frequencies on the estimated orbital parameters is considered. We found that although there is no algebraic correlation in the NEQ between the individual orbital parameters and the tidal terms, the changes in the amplitudes of tidal terms with periods close to 24 hours can be better accmodated by systematic changes in the orbital parameters than for tidal terms with other periods. Since the variation in Earth rotation with the period of siderial day (23.93h, tide K1) in terrestrial frame has in inertial space the same period as the period of revolution of GPS satellites, the K1 tidal term in polar motion is seen by the satellites as a permanent shift. The tidal terms with close periods (from ~24.13h to ~23.80h) are seen as a slow rotation of the

  12. Interactive effects of rice residue and water stress on growth and metabolism of wheat seedlings

    Directory of Open Access Journals (Sweden)

    Nimisha Amist

    2014-08-01

    Full Text Available In the present study effects of rice residue with and without water stress were studied on Triticum aestivum L. cv. Shatabadi. The mixture of residue and garden soil in 1:1 ratio was considered as 50% (R1 and only decomposed residue as 100% (R2. Garden soil was taken as control. Twenty five seeds were sown in each experimental trays filled with soil mixture according to the treatments. Trays were arranged in two groups. After 15 days one set was subjected to water stress (WS by withholding water supply for 3 days. Morphological and biochemical parameters of 18 days old seedlings were recorded. Seedling height decreased in all treatments. A gradual decrease in relative water content, pigment and protein contents of wheat seedlings were observed. Sugar and proline contents increased in treatments. An increase in malondialdehyde (MDA content and antioxidative enzyme activities was recorded. Elevation in catalase activity was observed in all treatments except in plants with water deficit. Ascorbate peroxidase (APX and guaiacol peroxidase (GPX activities increased when residue mixed with soil but decreased in seedlings under the combined influence of the residue and water stress. Higher amount of MDA and lower activities of APX and GPX reflected the oxidative damage in seedlings under combined treatments. Rice residue inhibited growth of wheat seedlings. Water stress intensified the effects of residue.

  13. Effect of fermented biogas residue on growth performance, serum biochemical parameters, and meat quality in pigs.

    Science.gov (United States)

    Xu, Xiang; Li, Lv-Mu; Li, Bin; Guo, Wen-Jie; Ding, Xiao-Ling; Xu, Fa-Zhi

    2017-10-01

    This study investigated the effect of fermented biogas residue (FBR) of wheat on the performance, serum biochemical parameters, and meat quality in pigs. We selected 128 pigs (the mean initial body weight was 40.24±3.08 kg) and randomly allocated them to 4 groups (1 control group and 3 treatment groups) with 4 replicates per group and 8 pigs per pen in a randomized complete block design based on initial body weight and sex. The control group received a corn-soybean meal-based diet, the treatment group fed diets containing 5%, 10%, and 15% FBR, respectively (abbreviated as FBR5, FBR10, and FBR15, respectively). Every group received equivalent-energy and nitrogen diets. The test lasted 60 days and was divided into early and late stages. Blood and carcass samples were obtained on 60 d. Meat quality was collected from two pigs per pen. During the late stage, the average daily feed intake and average daily gain of the treatment groups was greater than that of the control group (presidue did not significantly affect serum biochemical parameters or meat quality, but did affect amino acid profiles in pork. The contents of Asp, Arg, Tyr, Phe, Leu, Thr, Ser, Lys, Pro, Ala, essential amino acids, non-essential amino acids, and total amino acids in pork of FBR5 and FBR10 were greater than those of the control group (pfeeding FBR could increase the average daily gain and average daily feed intake in pigs and the content of several flavor-promoting amino acids.

  14. Predictive modeling and multi-objective optimization of machining-induced residual stresses: Investigation of machining parameter effects

    Science.gov (United States)

    Ulutan, Durul

    2013-01-01

    In the aerospace industry, titanium and nickel-based alloys are frequently used for critical structural components, especially due to their higher strength at both low and high temperatures, and higher wear and chemical degradation resistance. However, because of their unfavorable thermal properties, deformation and friction-induced microstructural changes prevent the end products from having good surface integrity properties. In addition to surface roughness, microhardness changes, and microstructural alterations, the machining-induced residual stress profiles of titanium and nickel-based alloys contribute in the surface integrity of these products. Therefore, it is essential to create a comprehensive method that predicts the residual stress outcomes of machining processes, and understand how machining parameters (cutting speed, uncut chip thickness, depth of cut, etc.) or tool parameters (tool rake angle, cutting edge radius, tool material/coating, etc.) affect the machining-induced residual stresses. Since experiments involve a certain amount of error in measurements, physics-based simulation experiments should also involve an uncertainty in the predicted values, and a rich set of simulation experiments are utilized to create expected value and variance for predictions. As the first part of this research, a method to determine the friction coefficients during machining from practical experiments was introduced. Using these friction coefficients, finite element-based simulation experiments were utilized to determine flow stress characteristics of materials and then to predict the machining-induced forces and residual stresses, and the results were validated using the experimental findings. A sensitivity analysis on the numerical parameters was conducted to understand the effect of changing physical and numerical parameters, increasing the confidence on the selected parameters, and the effect of machining parameters on machining-induced forces and residual

  15. Structural interface parameters are discriminatory in recognising near-native poses of protein-protein interactions.

    Directory of Open Access Journals (Sweden)

    Sony Malhotra

    Full Text Available Interactions at the molecular level in the cellular environment play a very crucial role in maintaining the physiological functioning of the cell. These molecular interactions exist at varied levels viz. protein-protein interactions, protein-nucleic acid interactions or protein-small molecules interactions. Presently in the field, these interactions and their mechanisms mark intensively studied areas. Molecular interactions can also be studied computationally using the approach named as Molecular Docking. Molecular docking employs search algorithms to predict the possible conformations for interacting partners and then calculates interaction energies. However, docking proposes number of solutions as different docked poses and hence offers a serious challenge to identify the native (or near native structures from the pool of these docked poses. Here, we propose a rigorous scoring scheme called DockScore which can be used to rank the docked poses and identify the best docked pose out of many as proposed by docking algorithm employed. The scoring identifies the optimal interactions between the two protein partners utilising various features of the putative interface like area, short contacts, conservation, spatial clustering and the presence of positively charged and hydrophobic residues. DockScore was first trained on a set of 30 protein-protein complexes to determine the weights for different parameters. Subsequently, we tested the scoring scheme on 30 different protein-protein complexes and native or near-native structure were assigned the top rank from a pool of docked poses in 26 of the tested cases. We tested the ability of DockScore to discriminate likely dimer interactions that differ substantially within a homologous family and also demonstrate that DOCKSCORE can distinguish correct pose for all 10 recent CAPRI targets.

  16. Power Saving Optimization for Linear Collider Interaction Region Parameters

    International Nuclear Information System (INIS)

    Seryi, Andrei

    2009-01-01

    Optimization of Interaction Region parameters of a TeV energy scale linear collider has to take into account constraints defined by phenomena such as beam-beam focusing forces, beamstrahlung radiation, and hour-glass effect. With those constraints, achieving a desired luminosity of about 2E34 would require use of e + e - beams with about 10 MW average power. Application of the 'travelling focus' regime may allow the required beam power to be reduced by at least a factor of two, helping reduce the cost of the collider, while keeping the beamstrahlung energy loss reasonably low. The technique is illustrated for the 500 GeV CM parameters of the International Linear Collider. This technique may also in principle allow recycling the e + e - beams and/or recuperation of their energy.

  17. A Database of Transition-Metal-Coordinated Peptide Cross-Sections: Selective Interaction with Specific Amino Acid Residues

    Science.gov (United States)

    Dilger, Jonathan M.; Glover, Matthew S.; Clemmer, David E.

    2017-07-01

    Ion mobility mass spectrometry (IMS-MS) techniques were used to generate a database of 2288 collision cross sections of transition-metal-coordinated tryptic peptide ions. This database consists of cross sections for 1253 [Pep + X]2+ and 1035 [Pep + X + H]3+, where X2+ corresponds to Mn2+, Co2+, Ni2+, Cu2+, or Zn2+. This number of measurements enables the extraction of structural trends for transition-metal-coordinated peptide ions. The range of structures and changes in collision cross sections for X2+-coordinated species (compared with protonated species of the same charge state) is similar to Mg2+-coordinated species. This suggests that the structures are largely determined by similarities in cation size with differences among the cross section distributions presumably caused by X2+ interactions with specific functional groups offered by the residue R-groups or the peptide backbone. Cross section contributions for individual residues upon X2+ solvation are assessed with the derivation of intrinsic size parameters (ISPs). The comparison of the [Pep + X]2+ ISPs with those previously reported for [Pep + Mg]2+ ions displays a lower contribution to the cross section for His, carboxyamidomethylated Cys, and Met, and is consistent with specific metal-residue interactions identified within protein X-ray crystallography databases.

  18. A method for computing the inter-residue interaction potentials for ...

    Indian Academy of Sciences (India)

    PRAKASH KUMAR

    2007-06-16

    Jun 16, 2007 ... [Luthra A, Jha A N, Ananthasuresh G K and Vishveswara S 2007 A method for computing the inter-residue interaction potentials for reduced amino acid alphabet; J. ... Therefore, a systematic approach to this problem is warranted so ... chemical and biological or quantitative measures are used. Dayhoff et al ...

  19. Viscosity is not a parameter of postdeglutitive pharyngeal residue: quantification and analysis with scintigraphy

    NARCIS (Netherlands)

    Bogaardt, H. C. A.; Burger, J. J.; Fokkens, W. J.; Bennink, R. J.

    2007-01-01

    The aim of this study was to explore the influence of viscosity on pharyngeal residue in normal healthy volunteers. Scintigraphy was used to measure pharyngeal residue in 11 healthy volunteers after swallowing three different substances (age = 20.2-48.3 years). The first substance was a 10-ml

  20. Genetic parameters for residual feed intake in a random population of Pekin duck

    Directory of Open Access Journals (Sweden)

    Yunsheng Zhang

    2017-02-01

    Full Text Available Objective The feed intake (FI and feed efficiency are economically important traits in ducks. To obtain insight into this economically important trait, we designed an experiment based on the residual feed intake (RFI and feed conversion ratio (FCR of a random population Pekin duck. Methods Two thousand and twenty pedigreed random population Pekin ducks were established from 90 males mated to 450 females in two hatches. Traits analyzed in the study were body weight at the 42th day (BW42, 15 to 42 days average daily gain (ADG, 15 to 42 days FI, 15 to 42 days FCR, and 15 to 42 days RFI to assess their genetic inter-relationships. The genetic parameters for feed efficiency traits were estimated using restricted maximum likelihood (REML methodology applied to a sire-dam model for all traits using the ASREML software. Results Estimates heritability of BW42, ADG, FI, FCR, and RFI were 0.39, 0.38, 0.33, 0.38, and 0.41, respectively. The genetic correlation was high between RFI and FI (0.77 and moderate between RFI and FCR (0.54. The genetic correlation was high and moderate between FCR and ADG (−0.80, and between FCR and BW42 (−0.64, and between FCR and FI (0.49, respectively. Conclusion Thus, selection on RFI was expected to improve feed efficiency, and reduce FI. Selection on RFI thus improves the feed efficiency of animals without impairing their FI and increase growth rate.

  1. Identification of Critical Paraoxonase 1 Residues Involved in High Density Lipoprotein Interaction.

    Science.gov (United States)

    Gu, Xiaodong; Huang, Ying; Levison, Bruce S; Gerstenecker, Gary; DiDonato, Anthony J; Hazen, Leah B; Lee, Joonsue; Gogonea, Valentin; DiDonato, Joseph A; Hazen, Stanley L

    2016-01-22

    Paraoxonase 1 (PON1) is a high density lipoprotein (HDL)-associated protein with atherosclerosis-protective and systemic anti-oxidant functions. We recently showed that PON1, myeloperoxidase, and HDL bind to one another in vivo forming a functional ternary complex (Huang, Y., Wu, Z., Riwanto, M., Gao, S., Levison, B. S., Gu, X., Fu, X., Wagner, M. A., Besler, C., Gerstenecker, G., Zhang, R., Li, X. M., Didonato, A. J., Gogonea, V., Tang, W. H., et al. (2013) J. Clin. Invest. 123, 3815-3828). However, specific residues on PON1 involved in the HDL-PON1 interaction remain unclear. Unambiguous identification of protein residues involved in docking interactions to lipid surfaces poses considerable methodological challenges. Here we describe a new strategy that uses a novel synthetic photoactivatable and click chemistry-taggable phospholipid probe, which, when incorporated into HDL, was used to identify amino acid residues on PON1 that directly interact with the lipoprotein phospholipid surface. Several specific PON1 residues (Leu-9, Tyr-185, and Tyr-293) were identified through covalent cross-links with the lipid probes using affinity isolation coupled to liquid chromatography with on-line tandem mass spectrometry. Based upon the crystal structure for PON1, the identified residues are all localized in relatively close proximity on the surface of PON1, defining a domain that binds to the HDL lipid surface. Site-specific mutagenesis of the identified PON1 residues (Leu-9, Tyr-185, and Tyr-293), coupled with functional studies, reveals their importance in PON1 binding to HDL and both PON1 catalytic activity and stability. Specifically, the residues identified on PON1 provide important structural insights into the PON1-HDL interaction. More generally, the new photoactivatable and affinity-tagged lipid probe developed herein should prove to be a valuable tool for identifying contact sites supporting protein interactions with lipid interfaces such as found on cell membranes

  2. Effects of flow forming parameters on the development of residual stresses in Cr–Mo–V steel tubes

    International Nuclear Information System (INIS)

    Tsivoulas, D.; Quinta da Fonseca, J.; Tuffs, M.; Preuss, M.

    2015-01-01

    Residual stress generation during flow forming tubular components of Cr–Mo–V ferritic steel has been studied in detail using laboratory X-ray and neutron diffraction. In the present work, flow formed tubes were available for a detailed parameter study including level of wall thickness reduction, starting hardness of the preform material, feed rate, and roller geometry. The high sensitivity of the residual stress distributions to the process parameters is showcased by selecting values within relatively short ranges. In general, low wall thickness reduction, low preform hardness, high feed rate, and rollers with a low contact angle were preferable for keeping stresses at a low level. Mohr's circle analysis was employed in order to determine the magnitude and direction of the principal stress, which were found to change depending on the combination of parameters. Finally, the level of stress mitigation by post-processing heat treatments was also characterised for selected samples

  3. Sulphur Atoms from Methionines Interacting with Aromatic Residues Are Less Prone to Oxidation

    Science.gov (United States)

    Aledo, Juan C.; Cantón, Francisco R.; Veredas, Francisco J.

    2015-01-01

    Methionine residues exhibit different degrees of susceptibility to oxidation. Although solvent accessibility is a relevant factor, oxidation at particular sites cannot be unequivocally explained by accessibility alone. To explore other possible structural determinants, we assembled different sets of oxidation-sensitive and oxidation-resistant methionines contained in human proteins. Comparisons of the proteins containing oxidized methionines with all proteins in the human proteome led to the conclusion that the former exhibit a significantly higher mean value of methionine content than the latter. Within a given protein, an examination of the sequence surrounding the non-oxidized methionine revealed a preference for neighbouring tyrosine and tryptophan residues, but not for phenylalanine residues. However, because the interaction between sulphur atoms and aromatic residues has been reported to be important for the stabilization of protein structure, we carried out an analysis of the spatial interatomic distances between methionines and aromatic residues, including phenylalanine. The results of these analyses uncovered a new determinant for methionine oxidation: the S-aromatic motif, which decreases the reactivity of the involved sulphur towards oxidants. PMID:26597773

  4. Energy dependence of radiation interaction parameters of some organic compounds

    Science.gov (United States)

    Singh, Mohinder; Tondon, Akash; Sandhu, B. S.; Singh, Bhajan

    2018-04-01

    Gamma rays interact with a material through photoelectric absorption, Compton scattering, Rayleigh scattering and Pair production in the intermediate energy range. The probability of occurrence of a particular type of process depends on the energy of incident gamma rays, atomic number of the material, scattering angle and geometrical conditions. Various radiological parameters for organic compounds, namely ethylene glycol (C2H6O2), propylene glycol (C3H8O2), glycerin (C3H8O3), isoamyl alcohol (C5H12O), butanone (C4H8O), acetophenone (C8H8O2), cyclohexanone (C6H10O), furfural (C5H4O2), benzaldehyde (C7H6O), cinnamaldehyde (C9H8O), glutaraldehyde (C5H8O2), aniline (C6H7N), benzyl amine (C6H7N), nitrobenzene (C6H5NO2), ethyl benzene (C8H10), ethyl formate (C3H6O2) and water (H2O) are presented at 81, 122, 356 and 511 keV energies employing NaI(Tl) scintillation detector in narrow-beam transmission geometry. The radiation interaction parameters such as mass attenuation, molar extinction and mass energy absorption coefficients, half value layer, total atomic and effective electronic cross-sections and CT number have been evaluated for these organic compounds. The general trend of values of mass attenuation coefficients, half value layer, molar extinction coefficients, total atomic and effective electronic cross-sections and mass energy absorption coefficients shows a decrease with increase in incident gamma photon energy. The values of CT number are found to increases linearly with increase of effective atomic number (Zeff). The variation in CT number around Zeff ≈ 3.3 shows the peak like structure with respect to water and the correlation between CT number and linear attenuation coefficient is about 0.99. Appropriate equations are fitted to these experimentally determined parameters for the organic compounds at incident photon energy ranging from 81 keV to 511 keV used in the present study. Experimental values are compared with the theoretical data obtained using Win

  5. Optimization of therapeutic proteins to delete T-cell epitopes while maintaining beneficial residue interactions.

    Science.gov (United States)

    Parker, Andrew S; Griswold, Karl E; Bailey-Kellogg, Chris

    2011-04-01

    Exogenous enzymes, signaling peptides, and other classes of nonhuman proteins represent a potentially massive but largely untapped pool of biotherapeutic agents. Adapting a foreign protein for therapeutic use poses numerous design challenges. We focus here on one significant problem: modifying the protein to mitigate the immune response mounted against "non-self" proteins, while not adversely affecting the protein's stability or therapeutic activity. In order to propose such variants suitable for experimental evaluation, this paper develops a computational method to select sets of mutations predicted to delete immunogenic T-cell epitopes, as evaluated by a 9-mer potential, while simultaneously maintaining important residues and residue interactions, as evaluated by one- and two-body potentials. While this design problem is NP-hard, we develop an integer programming approach that works very well in practice. We demonstrate the effectiveness of our approach by developing plans for biotherapeutic proteins that, in previous studies, have been partially deimmunized via extensive experimental characterization and modification of limited segments. In contrast, our global optimization technique considers an entire protein and accounts for all residues, residue interactions, and epitopes in proposing candidates worth subjecting to experimental evaluation.

  6. PAIRpred: partner-specific prediction of interacting residues from sequence and structure.

    Science.gov (United States)

    Minhas, Fayyaz ul Amir Afsar; Geiss, Brian J; Ben-Hur, Asa

    2014-07-01

    We present a novel partner-specific protein-protein interaction site prediction method called PAIRpred. Unlike most existing machine learning binding site prediction methods, PAIRpred uses information from both proteins in a protein complex to predict pairs of interacting residues from the two proteins. PAIRpred captures sequence and structure information about residue pairs through pairwise kernels that are used for training a support vector machine classifier. As a result, PAIRpred presents a more detailed model of protein binding, and offers state of the art accuracy in predicting binding sites at the protein level as well as inter-protein residue contacts at the complex level. We demonstrate PAIRpred's performance on Docking Benchmark 4.0 and recent CAPRI targets. We present a detailed performance analysis outlining the contribution of different sequence and structure features, together with a comparison to a variety of existing interface prediction techniques. We have also studied the impact of binding-associated conformational change on prediction accuracy and found PAIRpred to be more robust to such structural changes than existing schemes. As an illustration of the potential applications of PAIRpred, we provide a case study in which PAIRpred is used to analyze the nature and specificity of the interface in the interaction of human ISG15 protein with NS1 protein from influenza A virus. Python code for PAIRpred is available at http://combi.cs.colostate.edu/supplements/pairpred/. © 2013 Wiley Periodicals, Inc.

  7. Sequence-based discrimination of protein-RNA interacting residues using a probabilistic approach.

    Science.gov (United States)

    Pai, Priyadarshini P; Dash, Tirtharaj; Mondal, Sukanta

    2017-04-07

    Protein interactions with ribonucleic acids (RNA) are well-known to be crucial for a wide range of cellular processes such as transcriptional regulation, protein synthesis or translation, and post-translational modifications. Identification of the RNA-interacting residues can provide insights into these processes and aid in relevant biotechnological manipulations. Owing to their eventual potential in combating diseases and industrial production, several computational attempts have been made over years using sequence- and structure-based information. Recent comparative studies suggest that despite these developments, many problems are faced with respect to the usability, prerequisites, and accessibility of various tools, thereby calling for an alternative approach and perspective supplementation in the prediction scenario. With this motivation, in this paper, we propose the use of a simple-yet-efficient conditional probabilistic approach based on the application of local occurrence of amino acids in the interacting region in a non-numeric sequence feature space, for discriminating between RNA interacting and non-interacting residues. The proposed method has been meticulously tested for robustness using a cross-estimation method showing MCC of 0.341 and F- measure of 66.84%. Upon exploring large scale applications using benchmark datasets available to date, this approach showed an encouraging performance comparable with the state-of-art. The software is available at https://github.com/ABCgrp/DORAEMON. Copyright © 2017 Elsevier Ltd. All rights reserved.

  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

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

  9. Development of computer program ENMASK for prediction of residual environmental masking-noise spectra, from any three independent environmental parameters

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Y.-S.; Liebich, R. E.; Chun, K. C.

    2000-03-31

    Residual environmental sound can mask intrusive4 (unwanted) sound. It is a factor that can affect noise impacts and must be considered both in noise-impact studies and in noise-mitigation designs. Models for quantitative prediction of sensation level (audibility) and psychological effects of intrusive noise require an input with 1/3 octave-band spectral resolution of environmental masking noise. However, the majority of published residual environmental masking-noise data are given with either octave-band frequency resolution or only single A-weighted decibel values. A model has been developed that enables estimation of 1/3 octave-band residual environmental masking-noise spectra and relates certain environmental parameters to A-weighted sound level. This model provides a correlation among three environmental conditions: measured residual A-weighted sound-pressure level, proximity to a major roadway, and population density. Cited field-study data were used to compute the most probable 1/3 octave-band sound-pressure spectrum corresponding to any selected one of these three inputs. In turn, such spectra can be used as an input to models for prediction of noise impacts. This paper discusses specific algorithms included in the newly developed computer program ENMASK. In addition, the relative audibility of the environmental masking-noise spectra at different A-weighted sound levels is discussed, which is determined by using the methodology of program ENAUDIBL.

  10. Computational Analysis of the Interaction Energies between Amino Acid Residues of the Measles Virus Hemagglutinin and Its Receptors

    Directory of Open Access Journals (Sweden)

    Fengqi Xu

    2018-05-01

    Full Text Available Measles virus (MV causes an acute and highly devastating contagious disease in humans. Employing the crystal structures of three human receptors, signaling lymphocyte-activation molecule (SLAM, CD46, and Nectin-4, in complex with the measles virus hemagglutinin (MVH, we elucidated computationally the details of binding energies between the amino acid residues of MVH and those of the receptors with an ab initio fragment molecular orbital (FMO method. The calculated inter-fragment interaction energies (IFIEs revealed a number of significantly interacting amino acid residues of MVH that played essential roles in binding to the receptors. As predicted from previously reported experiments, some important amino-acid residues of MVH were shown to be common but others were specific to interactions with the three receptors. Particularly, some of the (non-polar hydrophobic residues of MVH were found to be attractively interacting with multiple receptors, thus indicating the importance of the hydrophobic pocket for intermolecular interactions (especially in the case of Nectin-4. In contrast, the electrostatic interactions tended to be used for specific molecular recognition. Furthermore, we carried out FMO calculations for in silico experiments of amino acid mutations, finding reasonable agreements with virological experiments concerning the substitution effect of residues. Thus, the present study demonstrates that the electron-correlated FMO method is a powerful tool to search exhaustively for amino acid residues that contribute to interactions with receptor molecules. It is also applicable for designing inhibitors of MVH and engineered MVs for cancer therapy.

  11. Interaction of residue tetracycline hydrochloride in milk with β-galactosidase protein by multi-spectrum methods and molecular docking

    Science.gov (United States)

    Gao, Xin; Bi, Hongna; Zuo, Huijun; Jia, Jingjing; Tang, Lin

    2017-08-01

    The purpose of this study was to explore the effect of residue tetracycline hydrochloride (TCH) in milk on molecular structure and activity of β-Gal. Inhibition kinetics assay showed the TCH inhibited β-Gal activity reversibly in a competitive manner. In addition, differences in the activity of β-Gal in the absence and presence of TCH as a function of pH and temperature were found although the optimum pH and temperature of β-Gal remained similar. Fluorescence experiment results showed that TCH effectively quenched the intrinsic fluorescence of β-Gal via static quenching. Thermodynamic parameters delineated the major roles of electrostatic forces played between β-Gal and TCH. Additionally, synchronous fluorescence and circular dichroism spectra (CD spectra) results indicated the secondary structure of β-Gal was changed due to the formation of β-Gal-TCH complexes. The molecular docking further revealed that TCH interacted with some amino acid residues of β-Gal, affecting the active site of the enzyme and thus leading to change in enzyme activity. These alterations in conformation and activity of β-Gal should be taken into consideration while using β-Gal for producing oligosaccharide prebiotics on dairy industries.

  12. Conserved cysteine residues provide a protein-protein interaction surface in dual oxidase (DUOX) proteins.

    Science.gov (United States)

    Meitzler, Jennifer L; Hinde, Sara; Bánfi, Botond; Nauseef, William M; Ortiz de Montellano, Paul R

    2013-03-08

    Intramolecular disulfide bond formation is promoted in oxidizing extracellular and endoplasmic reticulum compartments and often contributes to protein stability and function. DUOX1 and DUOX2 are distinguished from other members of the NOX protein family by the presence of a unique extracellular N-terminal region. These peroxidase-like domains lack the conserved cysteines that confer structural stability to mammalian peroxidases. Sequence-based structure predictions suggest that the thiol groups present are solvent-exposed on a single protein surface and are too distant to support intramolecular disulfide bond formation. To investigate the role of these thiol residues, we introduced four individual cysteine to glycine mutations in the peroxidase-like domains of both human DUOXs and purified the recombinant proteins. The mutations caused little change in the stabilities of the monomeric proteins, supporting the hypothesis that the thiol residues are solvent-exposed and not involved in disulfide bonds that are critical for structural integrity. However, the ability of the isolated hDUOX1 peroxidase-like domain to dimerize was altered, suggesting a role for these cysteines in protein-protein interactions that could facilitate homodimerization of the peroxidase-like domain or, in the full-length protein, heterodimeric interactions with a maturation protein. When full-length hDUOX1 was expressed in HEK293 cells, the mutations resulted in decreased H2O2 production that correlated with a decreased amount of the enzyme localized to the membrane surface rather than with a loss of activity or with a failure to synthesize the mutant proteins. These results support a role for the cysteine residues in intermolecular disulfide bond formation with the DUOX maturation factor DUOXA1.

  13. Intragenic suppressor of Osiaa23 revealed a conserved tryptophan residue crucial for protein-protein interactions.

    Directory of Open Access Journals (Sweden)

    Jun Ni

    Full Text Available The Auxin/Indole-3-Acetic Acid (Aux/IAA and Auxin Response Factor (ARF are two important families that play key roles in auxin signal transduction. Both of the families contain a similar carboxyl-terminal domain (Domain III/IV that facilitates interactions between these two families. In spite of the importance of protein-protein interactions among these transcription factors, the mechanisms involved in these interactions are largely unknown. In this study, we isolated six intragenic suppressors of an auxin insensitive mutant, Osiaa23. Among these suppressors, Osiaa23-R5 successfully rescued all the defects of the mutant. Sequence analysis revealed that an amino acid substitution occurred in the Tryptophan (W residue in Domain IV of Osiaa23. Yeast two-hybrid experiments showed that the mutation in Domain IV prevents the protein-protein interactions between Osiaa23 and OsARFs. Phylogenetic analysis revealed that the W residue is conserved in both OsIAAs and OsARFs. Next, we performed site-specific amino acid substitutions within Domain IV of OsARFs, and the conserved W in Domain IV was exchanged by Serine (S. The mutated OsARF(WSs can be released from the inhibition of Osiaa23 and maintain the transcriptional activities. Expression of OsARF(WSs in Osiaa23 mutant rescued different defects of the mutant. Our results suggest a previously unknown importance of Domain IV in both families and provide an indirect way to investigate functions of OsARFs.

  14. Interaction of arginine, lysine, and guanidine with surface residues of lysozyme: implication to protein stability.

    Science.gov (United States)

    Shah, Dhawal; Shaikh, Abdul Rajjak

    2016-01-01

    Additives are widely used to suppress aggregation of therapeutic proteins. However, the molecular mechanisms of effect of additives to stabilize proteins are still unclear. To understand this, we herein perform molecular dynamics simulations of lysozyme in the presence of three commonly used additives: arginine, lysine, and guanidine. These additives have different effects on stability of proteins and have different structures with some similarities; arginine and lysine have aliphatic side chain, while arginine has a guanidinium group. We analyze atomic contact frequencies to study the interactions of the additives with individual residues of lysozyme. Contact coefficient, quantified from contact frequencies, is helpful in analyzing the interactions with the guanidine groups as well as aliphatic side chains of arginine and lysine. Strong preference for contacts to the additives (over water) is seen for the acidic followed by polar and the aromatic residues. Further analysis suggests that the hydration layer around the protein surface is depleted more in the presence of arginine, followed by lysine and guanidine. Molecular dynamics simulations also reveal that the internal dynamics of protein, as indicated by the lifetimes of the hydrogen bonds within the protein, changes depending on the additives. Particularly, we note that the side-chain hydrogen-bonding patterns within the protein differ with the additives, with several side-chain hydrogen bonds missing in the presence of guanidine. These results collectively indicate that the aliphatic chain of arginine and lysine plays a critical role in the stabilization of the protein.

  15. Reexploration of interacting holographic dark energy model: cases of interaction term excluding the Hubble parameter

    Science.gov (United States)

    Li, Hai-Li; Zhang, Jing-Fei; Feng, Lu; Zhang, Xin

    2017-12-01

    In this paper, we make a deep analysis for the five typical interacting holographic dark energy models with the interaction terms Q=3β H0ρ _{de}, Q=3β H0ρ c, Q=3β H0(ρ _{de}+ρ _c), Q=3β H0√{ρ _{de}ρ _c}, and Q=3β H0ρ _{de}ρ c/ρ _{de+ρ _c}, respectively. We obtain observational constraints on these models by using the type Ia supernova data (the Joint Light-Curve Analysis sample), the cosmic microwave background data (Planck 2015 distance priors), the baryon acoustic oscillations data, and the direct measurement of the Hubble constant. We find that the values of χ _min^2 for all the five models are almost equal (around 699), indicating that the current observational data equally favor these IHDE models. In addition, a comparison with the cases of an interaction term involving the Hubble parameter H is also made.

  16. Emergent Learning and Interactive Media Artworks: Parameters of Interaction for Novice Groups

    Directory of Open Access Journals (Sweden)

    Marta Kawka

    2011-11-01

    Full Text Available Emergent learning describes learning that occurs when participants interact and distribute knowledge, where learning is self-directed, and where the learning destination of the participants is largely unpredictable (Williams, Karousou, & Mackness, 2011. These notions of learning arise from the topologies of social networks and can be applied to the learning that occurs in educational institutions. However, the question remains whether institutional frameworks can accommodate the opposing notion of “cooperative systems” (Shirky, 2005, systems that facilitate the creation of user-generated content, particularly as first-year education cohorts are novice groups in the sense of not yet having developed university-level knowledge.This paper theorizes an emergent learning assessment item (Flickr photo-narratives within a first-year media arts undergraduate education course. It challenges the conventional models of student–lecturer interaction by outlining a methodology of teaching for emergence that will facilitate student-directed and open-ended learning. The paper applies a matrix with four parameters (teacher-directed content/student-directed content; non-interactive learning task/interactive learning framework. This matrix is used as a conceptual space within which to investigate how a learning task might be constructed to afford the best opportunities for emergent learning. It explores the strategies that interactive artists utilize for participant engagement (particularly the relationship between the artist and the audience in the creation of interactive artworks and suggests how these strategies might be applied to emergent generative outcomes with first-year education students.We build upon Williams et al.’s framework of emergent learning, where “content will not be delivered to learners but co-constructed with them” (De Freitas & Conole, as cited in Williams et al., 2011, p. 40, and the notion that in constructing emergent

  17. Parameter Recovery for the 1-P HGLLM with Non-Normally Distributed Level-3 Residuals

    Science.gov (United States)

    Kara, Yusuf; Kamata, Akihito

    2017-01-01

    A multilevel Rasch model using a hierarchical generalized linear model is one approach to multilevel item response theory (IRT) modeling and is referred to as a one-parameter hierarchical generalized linear logistic model (1-P HGLLM). Although it has the flexibility to model nested structure of data with covariates, the model assumes the normality…

  18. Residual waters treatment by heterogeneous photocatalysis: a study of experimental parameters applied to the photoelectrocatalysis

    Directory of Open Access Journals (Sweden)

    Henrique de Santana

    2006-02-01

    Full Text Available In this paper, the use of electrochemically-assisted heterogeneous photo-catalysis will be discussed. Several operational parameters will also be discussed, in order to achieve optimum efficiency of this photo-degradation system, such as: the influence of variables as support electrolyte, applied potential, dye initial concentration, pH and choice of a UV source on dye degradation.

  19. Model parameter estimations from residual gravity anomalies due to simple-shaped sources using Differential Evolution Algorithm

    Science.gov (United States)

    Ekinci, Yunus Levent; Balkaya, Çağlayan; Göktürkler, Gökhan; Turan, Seçil

    2016-06-01

    An efficient approach to estimate model parameters from residual gravity data based on differential evolution (DE), a stochastic vector-based metaheuristic algorithm, has been presented. We have showed the applicability and effectiveness of this algorithm on both synthetic and field anomalies. According to our knowledge, this is a first attempt of applying DE for the parameter estimations of residual gravity anomalies due to isolated causative sources embedded in the subsurface. The model parameters dealt with here are the amplitude coefficient (A), the depth and exact origin of causative source (zo and xo, respectively) and the shape factors (q and ƞ). The error energy maps generated for some parameter pairs have successfully revealed the nature of the parameter estimation problem under consideration. Noise-free and noisy synthetic single gravity anomalies have been evaluated with success via DE/best/1/bin, which is a widely used strategy in DE. Additionally some complicated gravity anomalies caused by multiple source bodies have been considered, and the results obtained have showed the efficiency of the algorithm. Then using the strategy applied in synthetic examples some field anomalies observed for various mineral explorations such as a chromite deposit (Camaguey district, Cuba), a manganese deposit (Nagpur, India) and a base metal sulphide deposit (Quebec, Canada) have been considered to estimate the model parameters of the ore bodies. Applications have exhibited that the obtained results such as the depths and shapes of the ore bodies are quite consistent with those published in the literature. Uncertainty in the solutions obtained from DE algorithm has been also investigated by Metropolis-Hastings (M-H) sampling algorithm based on simulated annealing without cooling schedule. Based on the resulting histogram reconstructions of both synthetic and field data examples the algorithm has provided reliable parameter estimations being within the sampling limits of

  20. Considerations on the choice of experimental parameters in residual stress measurements by hole-drilling and ESPI

    Directory of Open Access Journals (Sweden)

    C. Barile

    2014-10-01

    Full Text Available Residual stresses occur in many manufactured structures and components. Great number of investigations have been carried out to study this phenomenon. Over the years, different techniques have been developed to measure residual stresses; nowadays the combination of Hole Drilling method (HD with Electronic Speckle Pattern Interferometry (ESPI has encountered great interest. The use of a high sensitivity optical technique instead of the strain gage rosette has the advantage to provide full field information without any contact with the sample by consequently reducing the cost and the time required for the measurement. The accuracy of the measurement, however, is influenced by the proper choice of several parameters: geometrical, analysis and experimental. In this paper, in particular, the effects of some of those parameters are investigated: misknowledgment in illumination and detection angles, the influence of the relative angle between the sensitivity vector of the system and the principal stress directions, the extension of the area of analysis and the adopted drilling rotation speed. In conclusion indications are provided to the scope of optimizing the measurement process together with the identification of the major sources of errors that can arise during the measuring and the analysis stages.

  1. Measurement of strong interaction parameters in antiprotonic hydrogen and deuterium

    CERN Document Server

    Augsburger, M A; Borchert, G L; Chatellard, D; Egger, J P; El-Khoury, P; Gorke, H; Gotta, D; Hauser, P R; Indelicato, P J; Kirch, K; Lenz, S; Siems, T; Simons, L M

    1999-01-01

    In the PS207 experiment at CERN, X-rays from antiprotonic hydrogen and deuterium have been measured at low pressure. The strong interaction shift and the broadening of the K/sub alpha / transition in antiprotonic hydrogen were $9 determined. Evidence was found for the individual hyperfine components of the protonium ground state. (7 refs).

  2. Pharmacokinetics of cefpodoxime proxetil with special reference to biochemical parameters, tissue residue, and spermatozoa motility in rats.

    Science.gov (United States)

    Mujeeb, Momin A; Pardeshi, Milind L

    2011-02-01

    Cefpodoxime is a semisynthetic third generation cephalosporin analogue with a relatively broader spectrum of antimicrobial activity against gram negative and gram positive organisms. This is attributed to their somewhat increased resistance to degradation by the betalactamase. Cefpodoxime shows good activity against Klebsiella pneumonia, many members of enterobactericeae and almost all strains of Escherichia coli. It is extensively used in human beings against infections caused by susceptible organisms for a prolonged period and even without its judicious indication. Though various researchers have worked on the pharmacokinetic aspects of the drug, its effects on biochemical parameters and spermatozoa activity are scarcely available in literature. To determine the oral kinetic ( blood and tissue) after single therapeutic dose of cefpodoxime proxetil (20mg/kg oral bid 7 days) in rats of either sex on tissue half life and certain biochemical parameters such as glucose, hemoglobin, protein, ALT, AST and other parameters like tissue residue, sperm count and spermatozoa motility in male rats. For kinetic studies,24 Wister rats of either sex, 3 months of age, (180-210 gm) were used.(Group I-IV; n=6) Blood samples collected from each animal of Group IV through heart puncture at 0 hour to serve as predrug control. All the group (I-IV) received cefpodoxime proxetil 20 mg/kg once orally as a single dose. At the end of 1,4,12 and 24 hour post oral administration, GroupI,II,III and IVwere utilized for kinetic studies. Blood samples were collected from each animal and vital organs viz brain, lung, liver, spleen, kidney and heart were dissected out for drug analysis and determination of weight. For biochemical parameters, tissue residue and spermatozoa motility, twelve male rats were randomly divided into Groups A and B (n=6) Group B received cefpodoxime (20mg/kg orally bid 7 days) while Group A served as control. Biochemical parameters [Blood glucose, protein, Aspartate

  3. Chemical Interaction of Protein Cysteine Residues with Reactive Metabolites of Methyleugenol.

    Science.gov (United States)

    Feng, Yukun; Wang, Hui; Wang, Qian; Huang, Wenlin; Peng, Ying; Zheng, Jiang

    2017-02-20

    Methyleugenol (ME), an alkenylbenzene compound, is a natural ingredient of several herbs and is used as flavoring agent in foodstuffs and fragrance in cosmetics. The hepatotoxicity, cytotoxicity, and carcinogenesis of ME have been well documented, and metabolic activation has been suggested to involve in ME-induced toxicities. The objective of this study was to identify chemical identity of interactions of protein with reactive metabolites of ME. Modification of cysteine residues of protein was observed in microsomal incubations and mice after exposure to ME. Three types of protein modification derived from the corresponding epoxide, α,β-unsaturated aldehyde, and carbonium ion of ME were detected in vitro and in vivo. The protein adduction took place in time- and dose-dependent manners. Dexamethasone, ketoconazole, and l-buthionine sulfoximine increased the protein modification induced by ME, which was proportional to the hepatotoxicity of ME. The findings facilitate the understanding of mechanism action of ME toxicities.

  4. Virtual Instruments for the Circuit Analysis with Interactive Parameter Modification

    Directory of Open Access Journals (Sweden)

    Eberhard Stefan Brenner

    2006-08-01

    Full Text Available Abstract—The contribution presents the possibilities of LabVIEW in the special application as formula interpreter by using of the formula node. The main advantage is the immediate presentation of results in case of a parameter modification. The presentation of the time behaviour, the calculation of characteristic values and curves for typical examples of power electronics and control engineering are shown. Index Terms—Education; Formula Interpretation; LabVIEW; Power Electronics; Virtual Instruments

  5. Ruminal parameters analyzed in remaining digestion residue of roughages in the in vitro/gas system

    Directory of Open Access Journals (Sweden)

    Campos Fábio Prudêncio de

    2002-01-01

    Full Text Available Animal performance is the most direct measure in the evaluation of feed quality. However, performance data are often insufficient to determine possible interactions that may take place in the ruminal environment. The purpose of the present trial was to evaluate the possible associative effects on the concentrations of volatile fatty acids (VFAs, ammoniacal nitrogen (N-NH3 and pH in the remaining liquid fraction from the dry matter (DM digestion for exclusive roughages: sugarcane (SC, 60- (EG60 and 180-day elephantgrass (EG180, and corn silage (SIL, as well as for combined roughages: sugarcane+corn silage (SCSIL, sugarcane+60-day elephantgrass (SCEG60, sugarcane+180-day elephantgrass (SCEG180, corn silage+60-day elephantgrass (SILEG60, corn silage+180-day elephantgrass (SILEG180 associated at equal DM proportions (50%. These associative effects present positive or negative effects on bovine performance. Concentrations of VFAs and N-NH3, as well as pH for the treatments were, respectively: SC= 56.9 mmol L-1, 50.1 mg dL-1, 5.7; SCSIL= 61.4 mmol L-1, 50.7 mg dL-1, 5.8; SCEG60= 54.7 mmol L-1, 47.6 mg dL-1, 5.8; SCEG180= 45.4 mmol L-1, 49.4 mg dL-1, 6.0; SIL= 57.2 mmol L-1, 54.0 mg dL-1, 5.8; SILEG60= 57.1 mmol L-1, 53.1 mg dL-1, 5.9; SILEG180= 55.9 mmol L-1, 52.3 mg dL-1, 6.0; EG60= 58.1 mmol L-1, 49.4 mg dL-1, 5.9; and EG180= 44.0 mmol L-1, 46.4 mg dL-1, 6.1. Nonstructural carbohydrates and starch, associated with fiber and protein, contributed to positive associative effect on the 50:50 sugarcane/corn silage mixtures. The high fermentative aspect of such mixture may have promoted the best results in bovine performance.

  6. Influence of process parameters and biomass characteristics on the durability of pellets from the pruning residues of Olea europaea L.

    Energy Technology Data Exchange (ETDEWEB)

    Carone, Maria Teresa; Pantaleo, Antonio; Pellerano, Achille [Department of Engineering and Management of the Agricultural, Livestock and Forest Systems, Faculty of Agriculture, University of Bari, Via Amendola, 165/A, 70126 Bari (Italy)

    2011-01-15

    The present work aims to investigate the influence of the main process parameters (pressure and temperature) and biomass characteristics (moisture content and particle size) on some mechanical properties (density and durability) of olive tree pruning residues pellets. By means of a lab scale pellet press, able to control process parameters, the biomass, ground with three different hammer mill screen sizes (1, 2 and 4 mm) and conditioned at different moisture contents (5, 10, 15 and 20% w.b.), was pelletized at various process temperatures (60, 90, 120 and 150 C) and pressures (71, 106, 141 and 176 MPa). Compressed sample dimensions and mass were measured in order to calculate pellet density, while compressive strength tests were carried out to estimate the durability of the final biofuel. The relationships between the factor settings and the responses (density, compression strength and modulus of elasticity) were examined by univariate and multivariate statistical analysis. Temperature resulted the most important variable influencing pellet mechanical properties, followed by the initial moisture content and the particle size of the raw material. In particular, high process temperature, low moisture contents and reduced particle sizes allowed obtaining good quality pellets. The effect of compression force resulted scarcely relevant. (author)

  7. Spring Chinook Salmon Interactions Indices and Residual/Precocial Monitoring in the Upper Yakima Basin, Annual Report 1998

    International Nuclear Information System (INIS)

    James, Brenda B.; Pearsons, Todd N.; McMichael, Geoffrey A.

    1999-01-01

    Select ecological interactions and spring chinook salmon residual/precocial abundance were monitored in 1998 as part of the Yakima/Klickitat Fisheries Project's supplementation monitoring program. Monitoring these variables is part of an effort to help evaluate the factors that contribute to, or limit supplementation success. The ecological interactions that were monitored were prey consumption, competition for food, and competition for space. The abundance of spring chinook salmon life-history forms that have the potential to be influenced by supplementation and that have important ecological and genetic roles were monitored (residuals and precocials). Residual spring chinook salmon do not migrate to the ocean during the normal emigration period and continue to rear in freshwater. Precocials are those salmon that precocially mature in freshwater. The purpose of sampling during 1998 was to collect baseline data one year prior to the release of hatchery spring chinook salmon which occurred during the spring of 1999. All sampling that the authors report on here was conducted in upper Yakima River during summer and fall 1998. The stomach fullness of juvenile spring chinook salmon during the summer and fall averaged 12%. The food competition index suggested that mountain whitefish (0.59), rainbow trout (0.55), and redside shiner (0.55) were competing for food with spring chinook salmon. The space competition index suggested that rainbow trout (0.31) and redside shiner (0.39) were competing for space with spring chinook salmon but mountain whitefish (0.05) were not. Age-0 spring chinook salmon selected a fairly narrow range of microhabitat parameters in the summer and fall relative to what was available. Mean focal depths and velocities for age 0 spring chinook salmon during the summer were 0.5 m ± 0.2 m and 0.26 m/s ± 0.19 m/s, and during the fall 0.5 m ± 0.2 m and 0.24 m/s ± 0.18 m/s. Among potential competitors, age 1+ rainbow trout exhibited the greatest degree

  8. 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.

  9. Treatment of waste incinerator air-pollution-control residues with FeSO4: Laboratory investigation of design parameters

    DEFF Research Database (Denmark)

    Jensen, Dorthe Lærke; Christensen, Thomas Højlund; Lundtorp, Kasper

    2002-01-01

    The key design parameters of a new process for treatment of air-pollution-control (APC) residues (the Ferroxprocess) were investigated in the laboratory. The optimisation involved two different APC-residues from actual incinerator plants. The design parameters considered were: amount of iron oxide...... that an optimum process configuration could be obtained yielding a stabilised solid product with low leaching of heavy metals and a dischargable wastewater with high contents of salts (in order to remove salts from the solid product) and low concentrations of heavy metals. The amount of iron added to the APC...

  10. Effect of deuteration on some structural parameters of methyl groups in proteins as evaluated by residual dipolar couplings

    International Nuclear Information System (INIS)

    Mittermaier, Anthony; Kay, Lewis E.

    2002-01-01

    One bond methyl 1 H- 13 C and 13 C methyl - 13 C scalar and residual dipolar couplings have been measured at sites in an 15 N, 13 C, ∼ 50% 2 H labeled sample of the B1 immunoglobulin binding domain of peptostreptococcal protein L to investigate changes in the structure of methyl groups in response to deuterium substitution. Both one bond methyl 1 H- 13 C and 13 C methyl - 13 C scalar coupling constants have been found to decrease slightly with increasing deuterium content. Previous studies have shown that 1 H- 13 C couplings in methyl groups are exquisitely sensitive to electronic structure, with decreases in coupling values as a function of deuteration consistent with a slight lengthening of the remaining H-C bonds. Changes in the H methyl C methyl C angle are found to be small, with average differences on the order of 0.3 ± 0.1 deg. and 0.4 ± 0.2 deg. between CH 3 , CH 2 D and CH 3 , CHD 2 isotopomers, respectively. Knowledge of methyl geometry is a prerequisite for the extraction of accurate dynamics parameters from spin relaxation studies involving these groups

  11. Isoscalar giant resonances and Landau parameters with density-dependent effective interactions

    International Nuclear Information System (INIS)

    Kohno, Michio; Ando, Kazuhiko

    1979-01-01

    Discussion is given on the relations between the Landau parameters and the isoscalar giant (quadrupole- and monopole-) resonance energies by using general density-dependent interactions. In the limit of infinite nuclear matter, the isoscalar giant quadrupole energy is shown to depend not only on the effective mass but also on the Landau parameter F 2 . Collective energies of the isoscalar giant resonances are calculated for 16 O and 40 Ca with four different effective interactions, G-0, B1, SII and SV, by using the scaling- and constrained Hartree-Fock-methods. It is shown that the dependence of the collective energies on the effective interactions is essentially determined by the Landau parameters. The G-0 force is found to be most successful in reproducing the giant resonance energies. Validity of the RPA-moment theorems is examined for the case of local density-dependent interactions. (author)

  12. Reconstituting Protein Interaction Networks Using Parameter-Dependent Domain-Domain Interactions

    Science.gov (United States)

    2013-05-07

    that approximately 80% of eukaryotic proteins and 67% of prokaryotic proteins have multiple domains [13,14]. Most annotation databases characterize...domain annotations, Domain-domain interactions, Protein-protein interaction networks Background The living cell is a dynamic, interconnected system...detailed in Methods. Here, we illustrate its application on a well- annotated single- cell organism. We created a merged set of protein-domain annotations

  13. Genotype x environment interactions in pig breeding programmes. V. Genetic parameters and sire x herd interaction in commercial fattening.

    NARCIS (Netherlands)

    Merks, J.W.M.; Kemenade, van P.G.M.

    1989-01-01

    An experimental progeny test of 107 Dutch Yorkshire AI boars was designed under commercial fattening conditions to estimate genetic parameters and to examine sire x herd interactions under these conditions. Individual records of 8148 crossbred fattening pigs, born on 27 sow herds and fattened on 35

  14. Millisecond and binary pulsars as nature's frequency standards - II. The effects of low-frequency timing noise on residuals and measured parameters

    Science.gov (United States)

    Kopeikin, Sergei M.

    1999-05-01

    Millisecond and binary pulsars are the most stable natural frequency standards. They can be applied to a number of principal problems in modern astronomy and time-keeping metrology, including the search for a stochastic gravitational wave background in the early Universe, testing general relativity and establishing a new ephemeris time-scale. The full exploration of pulsar properties requires that proper unbiased estimates of the spin and orbital parameters be obtained, a problem which deserves special investigation. These estimates depend essentially on the random noise component being revealed in the residuals of time of arrival (TOA) and having various physical origins. In the present paper, the influence of low-frequency (`red') timing noise with spectral indices from 1 to 6 on TOA residuals, variances, and covariances of the estimates of measured parameters of single and binary pulsars is studied. In order to determine the functional dependence of these quantities on time, an analytical technique for processing observational data in the time domain is developed. Data processing in the time domain is more informative, because it takes into account both the stationary and non-stationary components of noise. Data processing in the frequency domain is valid if and only if the noise is stationary. Our analysis includes a simplified timing model of a binary pulsar in a circular orbit and a procedure for estimating pulsar parameters and residuals under the influence of red noise. We reconfirm, in accordance with the results of previous authors, that uncorrelated white noise in the errors of measurements of TOA causes gradually decreasing residuals, variances and covariances of all parameters. On the other hand, we show that any low-frequency, correlated noise of terrestrial or/and astrophysical origin that is present causes the residuals, variances and covariances of certain parameters to increase with time. Hence, the low-frequency noise corrupts our observations

  15. Key residues involved in the interaction between Cydia pomonella pheromone binding protein 1 (CpomPBP1) and Codlemone.

    Science.gov (United States)

    Tian, Zhen; Liu, Jiyuan; Zhang, Ya-Lin

    2016-10-06

    Codlemone exhibited high affinity to CpomPBP1, studying their binding mode can provide insights into the rational design of active semiochemicals. Our findings suggested that residues including Phe12, Phe36, Trp37, Ile52, Ile 94, Ala115 and Phe118 were favorable to the binding of Codlemone to CpomPBP1, whereas residues providing unfavorable contributions like Ser56 were negative to the binding. Van der waals energy and electrostatic energy, mainly derived from the sidechains of favorable residues, contributed most in the formation and stability keeping of CpomPBP1-Codlemone complex. Of the residues involved in the interaction between CpomPBP1 and Codlemone, Phe12 and Trp37, whose mutation into Ala caused significant decrease of CpomPBP1 binding ability, were two key residues in determining the binding affinity of Codlemone to CpomPBP1. This study shed lights on discovering novel active semiochemicals as well as facilitating chemical modification of lead semiochemicals.

  16. Emergent Learning and Interactive Media Artworks: Parameters of Interaction for Novice Groups

    Science.gov (United States)

    Kawka, Marta; Larkin, Kevin; Danaher, P. A.

    2011-01-01

    Emergent learning describes learning that occurs when participants interact and distribute knowledge, where learning is self-directed, and where the learning destination of the participants is largely unpredictable (Williams, Karousou, & Mackness, 2011). These notions of learning arise from the topologies of social networks and can be applied to…

  17. Characterization of residual stress as a function of friction stir welding parameters in oxide dispersion strengthened (ODS) steel MA956

    Energy Technology Data Exchange (ETDEWEB)

    Brewer, L.N., E-mail: lnbrewer1@eng.ua.edu [Naval Postgraduate School (United States); Bennett, M.S.; Baker, B.W. [Naval Postgraduate School (United States); Payzant, E.A.; Sochalski-Kolbus, L.M. [Oak Ridge National Laboratory (United States)

    2015-10-28

    Friction stir welding (FSW) can generate large residual stresses during solid state joining of oxide dispersion strengthened steels. In this work, a plate of MA956 steel was friction stir welded at three conditions: 500 rpm/25 mm per minute (mmpm), 400 rpm/50 mmpm and 400 rpm/100 mmpm. The residual stresses across these welds were measured using both x-ray and neutron diffraction techniques. The distribution and magnitude of the residual stresses agreed well between the two techniques. Longitudinal residual stresses up to eighty percent of the yield strength were observed for the 400 rpm/100 mmpm condition. The surface residual stresses were somewhat larger on the root side of the weld than on the crown side. Increases in the relative heat input during FSW decreased the measured residual stresses in the stir zone and the thermomechanically affected zone (TMAZ). Increasing the traverse rate while holding the rotational speed fixed increased the residual stress levels. The fatigue strength of the material is predicted to decrease by at least twenty percent with cracking most likely in the TMAZ.

  18. Characterization of residual stress as a function of friction stir welding parameters in oxide dispersion strengthened (ODS) steel MA956

    International Nuclear Information System (INIS)

    Brewer, L.N.; Bennett, M.S.; Baker, B.W.; Payzant, E.A.; Sochalski-Kolbus, L.M.

    2015-01-01

    Friction stir welding (FSW) can generate large residual stresses during solid state joining of oxide dispersion strengthened steels. In this work, a plate of MA956 steel was friction stir welded at three conditions: 500 rpm/25 mm per minute (mmpm), 400 rpm/50 mmpm and 400 rpm/100 mmpm. The residual stresses across these welds were measured using both x-ray and neutron diffraction techniques. The distribution and magnitude of the residual stresses agreed well between the two techniques. Longitudinal residual stresses up to eighty percent of the yield strength were observed for the 400 rpm/100 mmpm condition. The surface residual stresses were somewhat larger on the root side of the weld than on the crown side. Increases in the relative heat input during FSW decreased the measured residual stresses in the stir zone and the thermomechanically affected zone (TMAZ). Increasing the traverse rate while holding the rotational speed fixed increased the residual stress levels. The fatigue strength of the material is predicted to decrease by at least twenty percent with cracking most likely in the TMAZ.

  19. Insight into the interactions, residue snorkeling, and membrane disordering potency of a single antimicrobial peptide into different lipid bilayers.

    Directory of Open Access Journals (Sweden)

    Majid Jafari

    Full Text Available Pardaxin, with a bend-helix-bend-helix structure, is a membrane-active antimicrobial peptide that its membrane activity depends on the lipid bilayer composition. Herein, all-atom molecular dynamics (MD simulations were performed to provide further molecular insight into the interactions, structural dynamics, orientation behavior, and cationic residues snorkeling of pardaxin in the DMPC, DPPC, POPC, POPG, POPG/POPE (3:1, and POPG/POPE (1:3 lipid bilayers. The results showed that the C-terminal helix of the peptide was maintained in all six types of the model-bilayers and pardaxin was tilted into the DMPC, DPPC, and POPG/POPE mixed bilayers more than the POPC and POPG bilayers. As well as, the structure of zwitterionic membranes was more affected by the peptide than the anionic bilayers. Taken together, the study demonstrated that the cationic residues of pardaxin snorkeled toward the interface of lipid bilayers and all phenylalanine residues of the peptide played important roles in the peptide-membrane interactions. We hope that this work will provide a better understanding of the interactions of antimicrobial peptides with the membranes.

  20. A cation-pi interaction in the binding site of the glycine receptor is mediated by a phenylalanine residue

    DEFF Research Database (Denmark)

    Pless, Stephan Alexander; Millen, Kat S; Hanek, Ariele P

    2008-01-01

    Cys-loop receptor binding sites characteristically contain many aromatic amino acids. In nicotinic ACh and 5-HT3 receptors, a Trp residue forms a cation-pi interaction with the agonist, whereas in GABA(A) receptors, a Tyr performs this role. The glycine receptor binding site, however, contains...... of fluorinated Phe derivatives using unnatural amino acid mutagenesis. The data reveal a clear correlation between the glycine EC(50) value and the cation-pi binding ability of the fluorinated Phe derivatives at position 159, but not at positions 207 or 63, indicating a single cation-pi interaction between...

  1. UNIQUAC interaction parameters for alkane/amine systems determined by Molecular Mechanics

    DEFF Research Database (Denmark)

    Jonsdottir, Svava Osk; Klein, R. A.; Rasmussen, Kjeld

    1996-01-01

    UNIQUAC interaction parameters have been successfully determined for three alkane/primary amine systems using a Molecular Mechanics method called the Consistent Force Field. Interaction parameters for alkane/alkane and alkane/ketone systems had been determined previously using this method...... and in this contribution the method has been extended to polar systems with extensive hydrogen bonding. It is thus possible to predict reliable vapor liquid equilibrium data using pure component data only. A method for finding the global minimum on the potential energy surface of a pair of molecules was developed. Good...

  2. HIGH TEMPERATURE INTERACTIONS BETWEEN RESIDUAL OIL ASH AND DISPERSED KAOLINITE POWDERS

    Science.gov (United States)

    The potential use of sorbents to manage ultrafine ash aerosol emissions from residual oil combustion was investigated using a downfired 82-kW-rated laboratory-scale refractory-lined combustor. The major constituents were vanadium (V), iron (Fe), nickel, (Ni) and zinc (Zn). Of the...

  3. GROUP CONTRIBUTIONS TO COSPHERE COSPHERE INTERACTION PARAMETERS - ESTER HYDROLYSIS IN AQUEOUS-SOLUTIONS CONTAINING CARBOXAMIDES

    NARCIS (Netherlands)

    Engberts, Jan B F N; Kerstholt, R; Blandamer, Michael J

    1991-01-01

    Rate constants for the hydrolysis of p-methoxyphenyl dichloroethanoate in dilute aqueous solutions of carboxamides can be quantitatively accounted for using cosphere interaction parameters G(c) which are linear functions of the number of methylene groups in an added carboxamide.

  4. Coiled-coil destabilizing residues in the group A Streptococcus M1 protein are required for functional interaction.

    Science.gov (United States)

    Stewart, Chelsea M; Buffalo, Cosmo Z; Valderrama, J Andrés; Henningham, Anna; Cole, Jason N; Nizet, Victor; Ghosh, Partho

    2016-08-23

    The sequences of M proteins, the major surface-associated virulence factors of the widespread bacterial pathogen group A Streptococcus, are antigenically variable but have in common a strong propensity to form coiled coils. Paradoxically, these sequences are also replete with coiled-coil destabilizing residues. These features are evident in the irregular coiled-coil structure and thermal instability of M proteins. We present an explanation for this paradox through studies of the B repeats of the medically important M1 protein. The B repeats are required for interaction of M1 with fibrinogen (Fg) and consequent proinflammatory activation. The B repeats sample multiple conformations, including intrinsically disordered, dissociated, as well as two alternate coiled-coil conformations: a Fg-nonbinding register 1 and a Fg-binding register 2. Stabilization of M1 in the Fg-nonbinding register 1 resulted in attenuation of Fg binding as expected, but counterintuitively, so did stabilization in the Fg-binding register 2. Strikingly, these register-stabilized M1 proteins gained the ability to bind Fg when they were destabilized by a chaotrope. These results indicate that M1 stability is antithetical to Fg interaction and that M1 conformational dynamics, as specified by destabilizing residues, are essential for interaction. A "capture-and-collapse" model of association accounts for these observations, in which M1 captures Fg through a dynamic conformation and then collapses into a register 2-coiled coil as a result of stabilization provided by binding energy. Our results support the general conclusion that destabilizing residues are evolutionarily conserved in M proteins to enable functional interactions necessary for pathogenesis.

  5. [Equilibrium and kinetic parameters of interaction between peroxidase conjugates of strophanthin and anti-peroxidase antibodies].

    Science.gov (United States)

    Tarun, E I; Karaseva, E I; Metelitsa, D I

    1997-01-01

    Interactions of three horseradish peroxidase (HRP)-strophanthin conjugates containing one, two, or three glycoside molecules (HRP-Str1, 2, or 3, respectively) with polyclonal anti-HRP antibodies were studied by homogeneous enzyme immunoassay. The total peroxidase activity of free conjugates and their immune complexes was estimated from the oxidation of o-phenylenediamine. The dissociation constants of the immune complexes and the rate constants of their dissociation and formation were determined. The equilibrium and kinetic parameters were determined for the interactions of the HRP-Str2 immune complex with anti-strophanthin and anti-HRP antibodies. The determined equilibrium and kinetic parameters of the HRP-Str interactions with anti-HRP antibodies depended on the molecular weights, sizes, and structures of the antigens studied.

  6. IRBIT Interacts with the Catalytic Core of Phosphatidylinositol Phosphate Kinase Type Iα and IIα through Conserved Catalytic Aspartate Residues.

    Directory of Open Access Journals (Sweden)

    Hideaki Ando

    Full Text Available Phosphatidylinositol phosphate kinases (PIPKs are lipid kinases that generate phosphatidylinositol 4,5-bisphosphate (PI(4,5P2, a critical lipid signaling molecule that regulates diverse cellular functions, including the activities of membrane channels and transporters. IRBIT (IP3R-binding protein released with inositol 1,4,5-trisphosphate is a multifunctional protein that regulates diverse target proteins. Here, we report that IRBIT forms signaling complexes with members of the PIPK family. IRBIT bound to all PIPK isoforms in heterologous expression systems and specifically interacted with PIPK type Iα (PIPKIα and type IIα (PIPKIIα in mouse cerebellum. Site-directed mutagenesis revealed that two conserved catalytic aspartate residues of PIPKIα and PIPKIIα are involved in the interaction with IRBIT. Furthermore, phosphatidylinositol 4-phosphate, Mg2+, and/or ATP interfered with the interaction, suggesting that IRBIT interacts with catalytic cores of PIPKs. Mutations of phosphorylation sites in the serine-rich region of IRBIT affected the selectivity of its interaction with PIPKIα and PIPKIIα. The structural flexibility of the serine-rich region, located in the intrinsically disordered protein region, is assumed to underlie the mechanism of this interaction. Furthermore, in vitro binding experiments and immunocytochemistry suggest that IRBIT and PIPKIα interact with the Na+/HCO3- cotransporter NBCe1-B. These results suggest that IRBIT forms signaling complexes with PIPKIα and NBCe1-B, whose activity is regulated by PI(4,5P2.

  7. Contribution of factor VIII light-chain residues 2007-2016 to an activated protein C-interactive site.

    Science.gov (United States)

    Takeyama, Masahiro; Wakabayashi, Hironao; Fay, Philip J

    2013-02-01

    Although factor (F) VIIIa is inactivated by activated protein C (APC) through cleavages in the FVIII heavy chain-derived A1 (Arg(336)) and A2 subunits (Arg(562), the FVIII light chain (LC) contributes to catalysis by binding the enzyme. ELISA-based binding assays showed that FVIII and FVIII LC bound to immobilised active site-modified APC (DEGR-APC) (apparent K(d) ~270 nM and 1.0 μM, respectively). Fluid-phase binding studies using fluorescence indicated an estimated K(d) of ~590 nM for acrylodan-labelled LC binding to DEGR-APC. Furthermore, FVIII LC effectively competed with FVIIIa in blocking APC-catalysed cleavage at Arg(336) (K(i) = 709 nM). A binding site previously identified near the C-terminal end of the A3 domain (residues 2007-2016) of FVIII LC was subjected to Ala-scanning mutagenesis. FXa generation assays and western and dot blotting were employed to assess the contribution of these residues to FVIIIa interactions with APC. Virtually all variants tested showed reductions in the rates of APC-catalysed inactivation of the cofactor and cleavage at the primary inactivation site (Arg(336)), with maximal reductions in inactivation rates (~3-fold relative to WT) and cleavage rates (~3 to ~9-fold relative to WT) observed for the Met2010Ala, Ser2011Ala, and Leu2013Ala variants. Titration of FVIIIa substrate concentration monitoring cleavage by a dot blot assay indicated that these variants also showed ~3-fold increases relative to WT while a double mutant (Met2010Ala/Ser2011Ala) showed a >4-fold increase in K(m). These results show a contribution of a number of residues within the 2007-2016 sequence, and in particular residues Met2010, Ser2011, and Leu2013 to an APC-interactive site.

  8. Mass-based hygroscopicity parameter interaction model and measurement of atmospheric aerosol water uptake

    Science.gov (United States)

    Mikhailov, E.; Vlasenko, S.; Rose, D.; Pöschl, U.

    2013-01-01

    In this study we derive and apply a mass-based hygroscopicity parameter interaction model for efficient description of concentration-dependent water uptake by atmospheric aerosol particles with complex chemical composition. The model approach builds on the single hygroscopicity parameter model of Petters and Kreidenweis (2007). We introduce an observable mass-based hygroscopicity parameter κm which can be deconvoluted into a dilute hygroscopicity parameter (κm0) and additional self- and cross-interaction parameters describing non-ideal solution behavior and concentration dependencies of single- and multi-component systems. For reference aerosol samples of sodium chloride and ammonium sulfate, the κm-interaction model (KIM) captures the experimentally observed concentration and humidity dependence of the hygroscopicity parameter and is in good agreement with an accurate reference model based on the Pitzer ion-interaction approach (Aerosol Inorganic Model, AIM). Experimental results for pure organic particles (malonic acid, levoglucosan) and for mixed organic-inorganic particles (malonic acid - ammonium sulfate) are also well reproduced by KIM, taking into account apparent or equilibrium solubilities for stepwise or gradual deliquescence and efflorescence transitions. The mixed organic-inorganic particles as well as atmospheric aerosol samples exhibit three distinctly different regimes of hygroscopicity: (I) a quasi-eutonic deliquescence & efflorescence regime at low-humidity where substances are just partly dissolved and exist also in a non-dissolved phase, (II) a gradual deliquescence & efflorescence regime at intermediate humidity where different solutes undergo gradual dissolution or solidification in the aqueous phase; and (III) a dilute regime at high humidity where the solutes are fully dissolved approaching their dilute hygroscopicity. For atmospheric aerosol samples collected from boreal rural air and from pristine tropical rainforest air (secondary

  9. Mass-based hygroscopicity parameter interaction model and measurement of atmospheric aerosol water uptake

    Directory of Open Access Journals (Sweden)

    E. Mikhailov

    2013-01-01

    Full Text Available In this study we derive and apply a mass-based hygroscopicity parameter interaction model for efficient description of concentration-dependent water uptake by atmospheric aerosol particles with complex chemical composition. The model approach builds on the single hygroscopicity parameter model of Petters and Kreidenweis (2007. We introduce an observable mass-based hygroscopicity parameter κm which can be deconvoluted into a dilute hygroscopicity parameterm0 and additional self- and cross-interaction parameters describing non-ideal solution behavior and concentration dependencies of single- and multi-component systems.

    For reference aerosol samples of sodium chloride and ammonium sulfate, the κm-interaction model (KIM captures the experimentally observed concentration and humidity dependence of the hygroscopicity parameter and is in good agreement with an accurate reference model based on the Pitzer ion-interaction approach (Aerosol Inorganic Model, AIM. Experimental results for pure organic particles (malonic acid, levoglucosan and for mixed organic-inorganic particles (malonic acid – ammonium sulfate are also well reproduced by KIM, taking into account apparent or equilibrium solubilities for stepwise or gradual deliquescence and efflorescence transitions.

    The mixed organic-inorganic particles as well as atmospheric aerosol samples exhibit three distinctly different regimes of hygroscopicity: (I a quasi-eutonic deliquescence & efflorescence regime at low-humidity where substances are just partly dissolved and exist also in a non-dissolved phase, (II a gradual deliquescence & efflorescence regime at intermediate humidity where different solutes undergo gradual dissolution or solidification in the aqueous phase; and (III a dilute regime at high humidity where the solutes are fully dissolved approaching their dilute hygroscopicity.

    For atmospheric aerosol samples

  10. Role of deceleration parameter and interacting dark energy in singularity avoidance

    Science.gov (United States)

    Abdussattar; Prajapati, S. R.

    2011-02-01

    A class of non-singular bouncing FRW models are obtained by constraining the deceleration parameter in the presence of an interacting dark energy represented by a time-varying cosmological constant. The models being geometrically closed, initially accelerate for a certain period of time and decelerate thereafter and are also free from the entropy and cosmological constant problems. Taking a constant of integration equal to zero one particular model is discussed in some detail and the variation of different cosmological parameters are shown graphically for specific values of the parameters of the model. For some specific choice of the parameters of the model the ever expanding models of Ozer & Taha and Abdel-Rahman and the decelerating models of Berman and also the Einstein de-Sitter model may be obtained as special cases of this particular model.

  11. Feasibility of Using Electrocochleography for Objective Estimation of Electro-Acoustic Interactions in Cochlear Implant Recipients with Residual Hearing.

    Science.gov (United States)

    Koka, Kanthaiah; Litvak, Leonid M

    2017-01-01

    Although cochlear implants (CI) traditionally have been used to treat individuals with bilateral profound sensorineural hearing loss, a recent trend is to implant individuals with residual low-frequency hearing. Patients who retain some residual acoustic hearing after surgery often can benefit from electro-acoustic stimulation (EAS) technologies, which combine conventional acoustic amplification with electrical stimulation. However, interactions between acoustic and electrical stimulation may affect outcomes adversely and are time-consuming and difficult to assess behaviorally. This study demonstrated the feasibility of using the Advanced Bionics HiRes90K Advantage implant electronics and HiFocus Mid Scala/1j electrode to measure electrocochleography (ECochG) responses in the presence of electrical stimulation to provide an objective estimate of peripheral physiologic EAS interactions. In general, electrical stimulation reduced ECochG response amplitudes to acoustic stimulation. The degree of peripheral EAS interaction varied as a function of acoustic pure tone frequency and the intra-cochlear location of the electrically stimulated electrode. Further development of this technique may serve to guide and optimize clinical EAS system fittings in the future.

  12. Acute and residual interactive effects of repeated administrations of oral methamphetamine and alcohol in humans

    Science.gov (United States)

    Kirkpatrick, Matthew G.; Gunderson, Erik W.; Levin, Frances R.; Foltin, Richard W.; Hart, Carl L.

    2011-01-01

    Although methamphetamine and alcohol are commonly used together in a binge-like pattern, there is a dearth of empirical data investigating the repeated effects of this drug combination. The current study examined acute and residual mood, performance, and physiological effects of methamphetamine alone, alcohol alone, and the combination. Nine adult male volunteers completed this 20-day within-participant, residential laboratory study. During four 5-day blocks of sessions, participants were administered oral methamphetamine (0, 10 mg) combined with alcohol (0, 0.375, 0.75 g/kg) three times (day 2: AM, day 2: PM, and day 3: PM). Breath alcohol concentrations, cardiovascular, subjective, and cognitive/psychomotor performance effects were assessed before drug administration and repeatedly thereafter. Subjective and objective sleep measures were also assessed; residual effects were assessed on days 3–5 of each block. Following the first drug administration, the methamphetamine–alcohol combination produced greater elevations of heart rate and ratings of “good drug effect” compared to either drug alone. Methamphetamine attenuated alcohol-related performance decrements and feelings of intoxication, whereas alcohol attenuated methamphetamine-related sleep disruptions. By the third administration, many of these effects were significantly diminished, suggesting that participants developed tolerance. Few residual effects were observed. These data show that methamphetamine combined with alcohol produced a profile of effects that was different from the effects of either drug alone. The largely positive effects of the drug combination (i.e., greater euphoria, and fewer performance and sleep disruptions) might explain why these drugs are often used in combination. PMID:21748253

  13. Non-Abelian monopole in the parameter space of point-like interactions

    International Nuclear Information System (INIS)

    Ohya, Satoshi

    2014-01-01

    We study non-Abelian geometric phase in N=2 supersymmetric quantum mechanics for a free particle on a circle with two point-like interactions at antipodal points. We show that non-Abelian Berry’s connection is that of SU(2) magnetic monopole discovered by Moody, Shapere and Wilczek in the context of adiabatic decoupling limit of diatomic molecule. - Highlights: • Supersymmetric quantum mechanics is an ideal playground for studying geometric phase. • We determine the parameter space of supersymmetric point-like interactions. • Berry’s connection is given by a Wu–Yang-like magnetic monopole in SU(2) Yang–Mills

  14. Calculation of parameters of the interaction potential between excited alkali atoms and mercury atoms: The Cs*, Pr*-Hg interaction

    International Nuclear Information System (INIS)

    Glushkov, A.V.

    1994-01-01

    Based on the method of effective potential involving the new polarization interaction potential calculated from polarization diagrams of the perturbation theory in the Thomas-Fermi approximation, the main parameters of the interatomic potentials (equilibrium distances, potential well depth) are evaluated for a system consisting of an alkali atom in the ground and excited states and of a mercury atom. The results of calculations of quasi-molecular terms for the A-Hg system, where A = Na, Cs, Fr, are reported, some of which are obtained for the first time. A comparison is made with available experimental and theoretical data. 29 refs., 2 figs., 1 tab

  15. The interactive effect of fungicide residues and yeast assimilable nitrogen on fermentation kinetics and hydrogen sulfide production during cider fermentation.

    Science.gov (United States)

    Boudreau, Thomas F; Peck, Gregory M; O'Keefe, Sean F; Stewart, Amanda C

    2017-01-01

    Fungicide residues on fruit may adversely affect yeast during cider fermentation, leading to sluggish or stuck fermentation or the production of hydrogen sulfide (H 2 S), which is an undesirable aroma compound. This phenomenon has been studied in grape fermentation but not in apple fermentation. Low nitrogen availability, which is characteristic of apples, may further exacerbate the effects of fungicides on yeast during fermentation. The present study explored the effects of three fungicides: elemental sulfur (S 0 ) (known to result in increased H 2 S in wine); fenbuconazole (used in orchards but not vineyards); and fludioxonil (used in post-harvest storage of apples). Only S 0 led to increased H 2 S production. Fenbuconazole (≥0.2 mg L -1 ) resulted in a decreased fermentation rate and increased residual sugar. An interactive effect of yeast assimilable nitrogen (YAN) concentration and fenbuconazole was observed such that increasing the YAN concentration alleviated the negative effects of fenbuconazole on fermentation kinetics. Cidermakers should be aware that residual fenbuconazole (as low as 0.2 mg L -1 ) in apple juice may lead to stuck fermentation, especially when the YAN concentration is below 250 mg L -1 . These results indicate that fermentation problems attributed to low YAN may be caused or exacerbated by additional factors such as fungicide residues, which have a greater impact on fermentation performance under low YAN conditions. © 2016 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. © 2016 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

  16. Effect of gamma radiation on the microbiological and physicochemical parameters and on the phenolic compounds of a fruit residue flour during storage

    International Nuclear Information System (INIS)

    Aranha, Jessica Bomtorin; Negri, Talita Costa; Martin, José Guilherme Prado; Spoto, Marta Helena Fillet

    2017-01-01

    Agroindustrial residues have high levels of nutrients, but are little exploited for consumption because they require prior treatment to ensure microbiological safety. Irradiation is an effective process for the reduction of microbial counts with maintenance of the product characteristics. The objective of this study was to evaluate the effect of irradiation on the microbiological quality, physicochemical properties and phenolic compounds of a fruit residue flour during storage. The flour was obtained from dehydrated residues of pineapple, melon, papaya and apple, which were submitted to irradiation doses of (0, 1, 2 and 3 kGy). The microbiological (coliforms, moulds, yeast and Salmonella sp. counts) and physicochemical (pH, titratable acidity, soluble solids, water activity, colour parameters L⁎, a⁎ and b⁎ and phenolic compounds) parameters were evaluated after 0, 7, 14 and 21 days of storage. All the irradiation treatments reduced the microbial count, and the presence of Salmonella sp was not detected in any of the samples. The acidity and pH showed changes during storage. The soluble solids and water activity showed no significant differences between the doses during storage. The phenolic compounds were preserved by the application of irradiation. The colour of the flour samples darkened slightly with irradiation. It was concluded that the most effective doses for the maintenance of the microbiological quality and physicochemical characteristics of the flour were 2 and 3 kGy. (author)

  17. The method of adaptation under the parameters of the subject of the information interaction

    Directory of Open Access Journals (Sweden)

    Инесса Анатольевна Воробьёва

    2014-12-01

    Full Text Available To ensure the effectiveness of settings (adaptation created software and hardware on the particular subject of the method was developed for adaptation under the parameters of the subject of information interaction in the form of a set of operations to build a network dialog procedures on the basis of accounting for entry-level qualification of the subject, assessment of the current level of skills and operational restructuring of the network in accordance with the assessment of his level.

  18. Residual-interaction renormalization effect on the spherical-nuclei α-decay absolute widths

    International Nuclear Information System (INIS)

    Dumitresku, T.; Kadmenskij, S.G.; Lomachenkov, I.A.; Kholan, S.; Furman, V.I.

    1978-01-01

    In the framework of the shell model approximation for the probabilities of alpha-decay the exact formulas (for alpha-widths) taking into account the contribution of density dependent effective interaction between nucleons forming the emitted alpha-particle are obtained. In agreement with previous estimations the numerical calculation reveals that the inclusion of the above-mentioned interaction is followed by some decrease of absolute alpha-widths

  19. Residues of E. coli topoisomerase I conserved for interaction with a specific cytosine base to facilitate DNA cleavage

    Science.gov (United States)

    Narula, Gagandeep; Tse-Dinh, Yuk-Ching

    2012-01-01

    Bacterial and archaeal topoisomerase I display selectivity for a cytosine base 4 nt upstream from the DNA cleavage site. Recently, the solved crystal structure of Escherichia coli topoisomerase I covalently linked to a single-stranded oligonucleotide revealed that R169 and R173 interact with the cytosine base at the −4 position via hydrogen bonds while the phenol ring of Y177 wedges between the bases at the −4 and the −5 position. Substituting R169 to alanine changed the selectivity of the enzyme for the base at the −4 position from a cytosine to an adenine. The R173A mutant displayed similar sequence selectivity as the wild-type enzyme, but weaker cleavage and relaxation activity. Mutation of Y177 to serine or alanine rendered the enzyme inactive. Although mutation of each of these residues led to different outcomes, R169, R173 and Y177 work together to interact with a cytosine base at the −4 position to facilitate DNA cleavage. These strictly conserved residues might act after initial substrate binding as a Molecular Ruler to form a protein–DNA complex with the scissile phosphate positioned at the active site for optimal DNA cleavage by the tyrosine hydroxyl nucleophile to facilitate DNA cleavage in the reaction pathway. PMID:22833607

  20. Soil Parameter Identification and Driving Force Prediction for Wheel-Terrain Interaction

    Directory of Open Access Journals (Sweden)

    Suksun Hutangkabodee

    2008-11-01

    Full Text Available This paper considers wheeled vehicles traversing unknown terrain, and proposes an approach for identifying the unknown soil parameters required for vehicle driving force prediction (drawbar pull prediction. The predicted drawbar pull can potentially be employed for traversability prediction, traction control, and trajectory following which, in turn, improve overall performance of off-road wheeled vehicles. The proposed algorithm uses an approximated form of the wheel-terrain interaction model and the Generalized Newton Raphson method to identify terrain parameters in real-time. With few measurements of wheel slip, i, vehicle sinkage, z, and drawbar pull, DP, samples, the algorithm is capable of identifying all the soil parameters required to predict vehicle driving forces over an entire range of wheel slip. The algorithm is validated with experimental data from a wheel-terrain interaction test rig. The identified soil parameters are used to predict the drawbar pull with good accuracy. The technique presented in this paper can be applied to any vehicle with rigid wheels or deformable wheels with relatively high inflation pressure, to predict driving forces in unknown environments.

  1. Bottom-up modeling approach for the quantitative estimation of parameters in pathogen-host interactions

    Directory of Open Access Journals (Sweden)

    Teresa eLehnert

    2015-06-01

    Full Text Available Opportunistic fungal pathogens can cause bloodstream infection and severe sepsis upon entering the blood stream of the host. The early immune response in human blood comprises the elimination of pathogens by antimicrobial peptides and innate immune cells, such as neutrophils or monocytes. Mathematical modeling is a predictive method to examine these complex processes and to quantify the dynamics of pathogen-host interactions. Since model parameters are often not directly accessible from experiment, their estimation is required by calibrating model predictions with experimental data. Depending on the complexity of the mathematical model, parameter estimation can be associated with excessively high computational costs in terms of run time and memory. We apply a strategy for reliable parameter estimation where different modeling approaches with increasing complexity are used that build on one another. This bottom-up modeling approach is applied to an experimental human whole-blood infection assay for Candida albicans. Aiming for the quantification of the relative impact of different routes of the immune response against this human-pathogenic fungus, we start from a non-spatial state-based model (SBM, because this level of model complexity allows estimating textit{a priori} unknown transition rates between various system states by the global optimization method simulated annealing. Building on the non-spatial SBM, an agent-based model (ABM is implemented that incorporates the migration of interacting cells in three-dimensional space. The ABM takes advantage of estimated parameters from the non-spatial SBM, leading to a decreased dimensionality of the parameter space. This space can be scanned using a local optimization approach, i.e. least-squares error estimation based on an adaptive regular grid search, to predict cell migration parameters that are not accessible in experiment.

  2. Nematode succession and microfauna-microorganism interactions during root residue decomposition

    DEFF Research Database (Denmark)

    Georgieva, Slavka; Christensen, Søren; Andersen, Karen Stevnbak

    2005-01-01

    The quality of plant material affects the vigor of the decomposition process and composition of the decomposer biota. Root residues from hairy vetch (Vicia villosa Roth), rye (Secale cereale L.) and vetch+rye, packed in litterbags were placed in pots of soil at 15 C and the content of the bags...... assemblages (composed of 25 taxa) showed a clear relationship to initial plant resource quality as well as decomposition phase. Early successional microbivorous nematodes vary according to resource quality with demanding bacterivores+predators (Neodiplogasteridae) dominating in vetch and less demanding...... in rye. At week 12 no species dominated the nematode assemblages that were similar between the resources. The differences between nematode assemblages among plant resources at 2 week were similar to the results of a field study sampled after 6 weeks with the same soil and plant resources. This lends...

  3. Interactive Approach for Multi-Level Multi-Objective Fractional Programming Problems with Fuzzy Parameters

    Directory of Open Access Journals (Sweden)

    M.S. Osman

    2018-03-01

    Full Text Available In this paper, an interactive approach for solving multi-level multi-objective fractional programming (ML-MOFP problems with fuzzy parameters is presented. The proposed interactive approach makes an extended work of Shi and Xia (1997. In the first phase, the numerical crisp model of the ML-MOFP problem has been developed at a confidence level without changing the fuzzy gist of the problem. Then, the linear model for the ML-MOFP problem is formulated. In the second phase, the interactive approach simplifies the linear multi-level multi-objective model by converting it into separate multi-objective programming problems. Also, each separate multi-objective programming problem of the linear model is solved by the ∊-constraint method and the concept of satisfactoriness. Finally, illustrative examples and comparisons with the previous approaches are utilized to evince the feasibility of the proposed approach.

  4. Application of multivariate heavy-tailed distributions to residuals in the estimation of genetic parameters of growth traits in beef cattle.

    Science.gov (United States)

    Peters, S O; Kizilkaya, K; Garrick, D J; Fernando, R L; Pollak, E J; De Donato, M; Hussain, T; Imumorin, I G

    2013-04-01

    Assumptions of normality in most animal breeding applications may make inferences vulnerable to the presence of outliers. Heavy-tail densities are viable alternatives to normal distributions and provide robustness against unusual or outlying observations when used to model the densities of residual effects. Our objective is to compare estimates of genetic parameters by fitting multivariate normal (MN) or heavy-tail distributions [multivariate Student's t (MSt) and multivariate slash (MS)] for residuals in data of body birth weight (BBW), weaning (WW), and yearling (YW) weight traits in beef cattle. A total of 17,019 weight records for BBW, WW, and YW from 1998 through 2010 from a large commercial cow/calf operation in the sand hills of Nebraska were analyzed. Models included fixed effects of contemporary group and sire breed whereas animal and maternal effects were random and the degrees of freedom (v) was treated as unknown for MSt and MS. Model comparisons using deviance information criteria (DIC) favored MSt over MS and MN models, respectively. The posterior means [and 95% posterior probability intervals (PPI)] of v for the MSt and MS models were 5.28 (4.80, 5.85) and 1.88 (1.76, 2.00), respectively. Smaller values of posterior densities of v for MSt and MS models confirm that the assumption of normally distributed residuals is not adequate for the analysis of BBW, WW, and YW datasets. Posterior mean (PM) and posterior median (PD) estimates of direct and maternal genetic variances were the same and posterior densities of these parameters were found to be symmetric. The 95% PPI estimates from MN and MSt models for BBW did not overlap, which indicates significant difference between PM estimates from MN or MSt models. The observed antagonistic relationship between additive direct and additive maternal effects indicated that genetic evaluation and selection strategies will be sensitive to the assumed model for residuals.

  5. Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels.

    Science.gov (United States)

    Yip, Kevin Y; Kim, Philip M; McDermott, Drew; Gerstein, Mark

    2009-08-05

    Proteins interact through specific binding interfaces that contain many residues in domains. Protein interactions thus occur on three different levels of a concept hierarchy: whole-proteins, domains, and residues. Each level offers a distinct and complementary set of features for computationally predicting interactions, including functional genomic features of whole proteins, evolutionary features of domain families and physical-chemical features of individual residues. The predictions at each level could benefit from using the features at all three levels. However, it is not trivial as the features are provided at different granularity. To link up the predictions at the three levels, we propose a multi-level machine-learning framework that allows for explicit information flow between the levels. We demonstrate, using representative yeast interaction networks, that our algorithm is able to utilize complementary feature sets to make more accurate predictions at the three levels than when the three problems are approached independently. To facilitate application of our multi-level learning framework, we discuss three key aspects of multi-level learning and the corresponding design choices that we have made in the implementation of a concrete learning algorithm. 1) Architecture of information flow: we show the greater flexibility of bidirectional flow over independent levels and unidirectional flow; 2) Coupling mechanism of the different levels: We show how this can be accomplished via augmenting the training sets at each level, and discuss the prevention of error propagation between different levels by means of soft coupling; 3) Sparseness of data: We show that the multi-level framework compounds data sparsity issues, and discuss how this can be dealt with by building local models in information-rich parts of the data. Our proof-of-concept learning algorithm demonstrates the advantage of combining levels, and opens up opportunities for further research. The software

  6. Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels

    Directory of Open Access Journals (Sweden)

    McDermott Drew

    2009-08-01

    Full Text Available Abstract Background Proteins interact through specific binding interfaces that contain many residues in domains. Protein interactions thus occur on three different levels of a concept hierarchy: whole-proteins, domains, and residues. Each level offers a distinct and complementary set of features for computationally predicting interactions, including functional genomic features of whole proteins, evolutionary features of domain families and physical-chemical features of individual residues. The predictions at each level could benefit from using the features at all three levels. However, it is not trivial as the features are provided at different granularity. Results To link up the predictions at the three levels, we propose a multi-level machine-learning framework that allows for explicit information flow between the levels. We demonstrate, using representative yeast interaction networks, that our algorithm is able to utilize complementary feature sets to make more accurate predictions at the three levels than when the three problems are approached independently. To facilitate application of our multi-level learning framework, we discuss three key aspects of multi-level learning and the corresponding design choices that we have made in the implementation of a concrete learning algorithm. 1 Architecture of information flow: we show the greater flexibility of bidirectional flow over independent levels and unidirectional flow; 2 Coupling mechanism of the different levels: We show how this can be accomplished via augmenting the training sets at each level, and discuss the prevention of error propagation between different levels by means of soft coupling; 3 Sparseness of data: We show that the multi-level framework compounds data sparsity issues, and discuss how this can be dealt with by building local models in information-rich parts of the data. Our proof-of-concept learning algorithm demonstrates the advantage of combining levels, and opens up

  7. Outcomes and biochemical parameters following cardiac surgery: effects of transfusion of residual blood using centrifugation and multiple-pass hemoconcentration.

    Science.gov (United States)

    McNair, Erick; McKay, William; Qureshi, Abdul Mohamed; Rosin, Mark; Gamble, Jon; Dalshaug, Greg; Mycyk, Taras; Prasad, Kailash

    2013-12-01

    To determine whether or not there was a significant difference between the methods of centrifugation (CF) and multiple-pass hemoconcentration (MPH) of the residual cardiopulmonary-bypass volume in relation to biochemical measurements and patient outcomes. Prospective, randomized, and controlled. Conducted at a western Canadian tertiary care hospital. Consisted of 61 consecutive male and female patients from ages 40 to 80 who were scheduled for cardiac surgery with cardiopulmonary bypass. Either the centrifugation or multiple-pass hemoconcentration method was used to process the residual blood from the cardiopulmonary bypass circuit. The 12-hour postoperative levels of serum hemoglobin were not significantly different in the centrifugation group as compared to the multiple-pass hemoconcentration group. However, the serum levels of total protein and albumin were significantly higher in the multiple-pass hemoconcentration group as compared to the centrifugation group. Additionally, after 12-hours postoperatively, the serum fibrinogen and platelet counts were significantly higher in the multiple-pass hemoconcentration group as compared to those of the centrifugation group. The allogeneic product transfusion index and the chest-tube blood drainage indices were lower in the multiple-pass hemoconcentration group as compared to the centrifugation group. Although the CF method provided a product in a shorter turnaround time, with consistent clearance of heparin, the MPH method trended towards enhanced biochemical and clinical patient outcomes over the 12-hour postoperative period. Copyright © 2013 Elsevier Inc. All rights reserved.

  8. Microbiological parameters and maturity degree during composting of Posidonia oceanica residues mixed with vegetable wastes in semi-arid pedo-climatic condition.

    Science.gov (United States)

    Saidi, Neyla; Kouki, Soulwene; M'hiri, Fadhel; Jedidi, Naceur; Mahrouk, Meriam; Hassen, Abdennaceur; Ouzari, Hadda

    2009-01-01

    The aim of this study was to characterize the biological stability and maturity degree of compost during a controlled pile-composting trial of mixed vegetable residues (VR) collected from markets of Tunis City with residues of Posidonia oceanica (PoR), collected from Tunis beaches. The accumulation in beaches (as well as their removal) constitutes a serious environmental problem in all Mediterranean countries particularly in Tunisia. Aerobic-thermophilic composting is the most reasonable way to profit highly-valuable content of organic matter in these wastes for agricultural purposes. The physical, chemical, and biological parameters were monitored during composting over 150 d. The most appropriate parameters were selected to establish the maturity degree. The main result of this research was the deduction of the following maturity criterion: (a) C/N ratio 80%. These five parameters, considered jointly are indicative of a high maturity degree and thus of a high-quality organic amendment which employed in a rational way, may improve soil fertility and soil quality. The mature compost was relatively rich in N (13.0 g/kg), P (4.74 g/kg) and MgO (15.80 g/kg). Thus composting definitively constitutes the most optimal option to exploit these wastes.

  9. Weak Interactions Govern the Viscosity of Concentrated Antibody Solutions: High-Throughput Analysis Using the Diffusion Interaction Parameter

    Science.gov (United States)

    Connolly, Brian D.; Petry, Chris; Yadav, Sandeep; Demeule, Barthélemy; Ciaccio, Natalie; Moore, Jamie M.R.; Shire, Steven J.; Gokarn, Yatin R.

    2012-01-01

    Weak protein-protein interactions are thought to modulate the viscoelastic properties of concentrated antibody solutions. Predicting the viscoelastic behavior of concentrated antibodies from their dilute solution behavior is of significant interest and remains a challenge. Here, we show that the diffusion interaction parameter (kD), a component of the osmotic second virial coefficient (B2) that is amenable to high-throughput measurement in dilute solutions, correlates well with the viscosity of concentrated monoclonal antibody (mAb) solutions. We measured the kD of 29 different mAbs (IgG1 and IgG4) in four different solvent conditions (low and high ion normality) and found a linear dependence between kD and the exponential coefficient that describes the viscosity concentration profiles (|R| ≥ 0.9). Through experimentally measured effective charge measurements, under low ion normality where the electroviscous effect can dominate, we show that the mAb solution viscosity is poorly correlated with the mAb net charge (|R| ≤ 0.6). With this large data set, our results provide compelling evidence in support of weak intermolecular interactions, in contrast to the notion that the electroviscous effect is important in governing the viscoelastic behavior of concentrated mAb solutions. Our approach is particularly applicable as a screening tool for selecting mAbs with desirable viscosity properties early during lead candidate selection. PMID:22828333

  10. ShinyKGode: an Interactive Application for ODE Parameter Inference Using Gradient Matching.

    Science.gov (United States)

    Wandy, Joe; Niu, Mu; Giurghita, Diana; Daly, Rónán; Rogers, Simon; Husmeier, Dirk

    2018-02-27

    Mathematical modelling based on ordinary differential equations (ODEs) is widely used to describe the dynamics of biological systems, particularly in systems and pathway biology. Often the kinetic parameters of these ODE systems are unknown and have to be inferred from the data. Approximate parameter inference methods based on gradient matching (which do not require performing computationally expensive numerical integration of the ODEs) have been getting popular in recent years, but many implementations are difficult to run without expert knowledge. Here we introduce ShinyKGode, an interactive web application to perform fast parameter inference on ODEs using gradient matching. ShinyKGode can be used to infer ODE parameters on simulated and observed data using gradient matching. Users can easily load their own models in Systems Biology Markup Language format, and a set of pre-defined ODE benchmark models are provided in the application. Inferred parameters are visualised alongside diagnostic plots to assess convergence. The R package for ShinyKGode can be installed through the Comprehensive R Archive Network (CRAN). Installation instructions, as well as tutorial videos and source code are available at https://joewandy.github.io/shinyKGode. dirk.husmeier@glasgow.ac.uk. None.

  11. Structural polymorphism of human islet amyloid polypeptide (hIAPP) oligomers highlights the importance of interfacial residue interactions.

    Science.gov (United States)

    Zhao, Jun; Yu, Xiang; Liang, Guizhao; Zheng, Jie

    2011-01-10

    A 37-residue of human islet amyloid polypeptide (hIAPP or amylin) is a main component of amyloid plaques found in the pancreas of ∼90% of type II diabetes patients. It is reported that hIAPP oligomers, rather than mature fibrils, are major toxic species responsible for pancreatic islet β-cell dysfunction and even cell death, but molecular structures of these oligomers remain elusive. In this work, on the basis of recent solid-state NMR and mass-per-length (MPL) data, we model a series of hIAPP oligomers with different β-layers (one, two, and three layers), symmetries (symmetry and asymmetry), and associated interfaces using molecular dynamics simulations. Three distinct interfaces formed by C-terminal β-sheet and C-terminal β-sheet (CC), N-terminal β-sheet and N-terminal β-sheet (NN), and C-terminal β-sheet and N-terminal β-sheet (CN) are identified to drive multiple cross-β-layers laterally associated together to form different amyloid organizations via different intermolecular interactions, in which the CC interface is dominated by polar interactions, the NN interface is dominated by hydrophobic interactions, and the CN interface is dominated by mixed polar and hydrophobic interactions. Overall, the structural stability of the proposed hIAPP oligomers is a result of delicate balance between maximization of favorable peptide-peptide interactions at the interfaces and optimization of solvation energy with globular structure. Different hIAPP oligomeric models indicate a general and intrinsic nature of amyloid polymorphism, driven by different interfacial side-chain interactions. The proposed models are compatible with recent experimental data in overall size, cross-section area, and molecular weight. A general hIAPP aggregation mechanism is proposed on the basis of our simulated models and experimental data.

  12. Determination of the interaction parameter and topological scaling features of symmetric star polymers in dilute solution.

    Science.gov (United States)

    Rai, Durgesh K; Beaucage, Gregory; Ratkanthwar, Kedar; Beaucage, Peter; Ramachandran, Ramnath; Hadjichristidis, Nikos

    2015-07-01

    Star polymers provide model architectures to understand the dynamic and rheological effects of chain confinement for a range of complex topological structures like branched polymers, colloids, and micelles. It is important to describe the structure of such macromolecular topologies using small-angle neutron and x-ray scattering to facilitate understanding of their structure-property relationships. Modeling of scattering from linear, Gaussian polymers, such as in the melt, has applied the random phase approximation using the Debye polymer scattering function. The Flory-Huggins interaction parameter can be obtained using neutron scattering by this method. Gaussian scaling no longer applies for more complicated chain topologies or when chains are in good solvents. For symmetric star polymers, chain scaling can differ from ν=0.5(d(f)=2) due to excluded volume, steric interaction between arms, and enhanced density due to branching. Further, correlation between arms in a symmetric star leads to an interference term in the scattering function first described by Benoit for Gaussian chains. In this work, a scattering function is derived which accounts for interarm correlations in symmetric star polymers as well as the polymer-solvent interaction parameter for chains of arbitrary scaling dimension using a hybrid Unified scattering function. The approach is demonstrated for linear, four-arm and eight-arm polyisoprene stars in deuterated p-xylene.

  13. Determination of the interaction parameter and topological scaling features of symmetric star polymers in dilute solution

    KAUST Repository

    Rai, Durgesh K.

    2015-07-15

    Star polymers provide model architectures to understand the dynamic and rheological effects of chain confinement for a range of complex topological structures like branched polymers, colloids, and micelles. It is important to describe the structure of such macromolecular topologies using small-angle neutron and x-ray scattering to facilitate understanding of their structure-property relationships. Modeling of scattering from linear, Gaussian polymers, such as in the melt, has applied the random phase approximation using the Debye polymer scattering function. The Flory-Huggins interaction parameter can be obtained using neutron scattering by this method. Gaussian scaling no longer applies for more complicated chain topologies or when chains are in good solvents. For symmetric star polymers, chain scaling can differ from ν=0.5(df=2) due to excluded volume, steric interaction between arms, and enhanced density due to branching. Further, correlation between arms in a symmetric star leads to an interference term in the scattering function first described by Benoit for Gaussian chains. In this work, a scattering function is derived which accounts for interarm correlations in symmetric star polymers as well as the polymer-solvent interaction parameter for chains of arbitrary scaling dimension using a hybrid Unified scattering function. The approach is demonstrated for linear, four-arm and eight-arm polyisoprene stars in deuterated p-xylene.

  14. Experimental Investigations to evaluate the effects of cutting parameters on cutting temperature and residual stresses during milling process of the AISI 1045

    Science.gov (United States)

    Abdelkrim, M.; Brabie, G.; Belloufi, A.; Catalin, T.; Chirita, B.

    2017-08-01

    Today major metal cutting companies in industrial countries, looking to gain time and reduce manufacturing costs while respecting the environment. There are many phenomena which affect the quality and production costs of the product, including cutting efforts, cutting temperature, residual stresses, etc. A better understanding of these phenomena will reduce production costs and maximize productivity. The aim of this work is to analyze the effect of machining conditions (cutting speed, feed speed and cutting depth) on cutting temperature and residual stresses, during the milling operations using the response surface method. A good accuracy between predicted and measured values of the cutting temperature was found, the cutting speed and the depth of cut are parameters whose effect is most sensitive to the residual stresses and the cutting temperature.However, little influence has been registered in the case of an increase of the feed rate. The percentage of error is 4.57%, indicating that the numerical approach can accurately predict the cutting temperature of the AISI 1045.

  15. Interaction between local parameters of two-phase flow and random forces on a cylinder

    International Nuclear Information System (INIS)

    Sylviane Pascal-Ribot; Yves Blanchet; Franck Baj; Phillippe Piteau

    2005-01-01

    Full text of publication follows: In the frame of assessments of steam generator tube bundle vibrations, a study was conducted in order to investigate the effects of an air/water flow on turbulent buffeting forces induced on a cylinder. The main purpose is to relate the physical parameters characterizing an air/water two-phase crossflow with the structural loading of a fixed cylindrical tube. In this first approach, the experiments are carried out in a rectangular acrylic test section supplied with a vertical upward bubbly flow. This flow is transversally impeded by a fixed rigid 12,15 mm diameter cylinder. Different turbulence grids are used in order to modify two-phase characteristics such as bubble diameter, void fraction profile, fluctuation parameters. Preliminarily, a dimensional analysis of fluid-structure interaction under two-phase turbulent solicitations has enabled to identify a list of physically relevant variables which must be measured to evaluate the random forces. The meaning of these relevant parameters as well as the effect of flow patterns are discussed. Direct measurements of two-phase flow parameters are performed simultaneously with measurements of forces exerted on the cylinder. The main descriptive parameters of a two-phase flow are measured using a bi-optical probe, in particular void fraction profiles, interfacial velocities, bubble diameters, void fraction fluctuations. In the same time, the magnitude of random forces caused by two-phase flow is measured with a force transducer. A thorough analysis of the experimental data is then undertaken in order to correlate physical two-phase mechanisms with the random forces exerted on the cylinder. The hypotheses made while applying the dimensional analysis are verified and their pertinence is discussed. Finally, physical parameters involved in random buffeting forces applied on a transverse tube are proposed to scale the spectral magnitude of these forces and comparisons with other authors

  16. Residues of the UL25 Protein of Herpes Simplex Virus That Are Required for Its Stable Interaction with Capsids ▿

    Science.gov (United States)

    Cockrell, Shelley K.; Huffman, Jamie B.; Toropova, Katerina; Conway, James F.; Homa, Fred L.

    2011-01-01

    The herpes simplex virus 1 (HSV-1) UL25 gene product is a minor capsid component that is required for encapsidation, but not cleavage, of replicated viral DNA. UL25 is located on the capsid surface in a proposed heterodimer with UL17, where five copies of the heterodimer are found at each of the capsid vertices. Previously, we demonstrated that amino acids 1 to 50 of UL25 are essential for its stable interaction with capsids. To further define the UL25 capsid binding domain, we generated recombinant viruses with either small truncations or amino acid substitutions in the UL25 N terminus. Studies of these mutants demonstrated that there are two important regions within the capsid binding domain. The first 27 amino acids are essential for capsid binding of UL25, while residues 26 to 39, which are highly conserved in the UL25 homologues of other alphaherpesviruses, were found to be critical for stable capsid binding. Cryo-electron microscopy reconstructions of capsids containing either a small tag on the N terminus of UL25 or the green fluorescent protein (GFP) fused between amino acids 50 and 51 of UL25 demonstrate that residues 1 to 27 of UL25 contact the hexon adjacent to the penton. A second region, most likely centered on amino acids 26 to 39, contacts the triplex that is one removed from the penton. Importantly, both of these UL25 capsid binding regions are essential for the stable packaging of full-length viral genomes. PMID:21411517

  17. Fast and accurate multivariate Gaussian modeling of protein families: predicting residue contacts and protein-interaction partners.

    Directory of Open Access Journals (Sweden)

    Carlo Baldassi

    Full Text Available In the course of evolution, proteins show a remarkable conservation of their three-dimensional structure and their biological function, leading to strong evolutionary constraints on the sequence variability between homologous proteins. Our method aims at extracting such constraints from rapidly accumulating sequence data, and thereby at inferring protein structure and function from sequence information alone. Recently, global statistical inference methods (e.g. direct-coupling analysis, sparse inverse covariance estimation have achieved a breakthrough towards this aim, and their predictions have been successfully implemented into tertiary and quaternary protein structure prediction methods. However, due to the discrete nature of the underlying variable (amino-acids, exact inference requires exponential time in the protein length, and efficient approximations are needed for practical applicability. Here we propose a very efficient multivariate Gaussian modeling approach as a variant of direct-coupling analysis: the discrete amino-acid variables are replaced by continuous Gaussian random variables. The resulting statistical inference problem is efficiently and exactly solvable. We show that the quality of inference is comparable or superior to the one achieved by mean-field approximations to inference with discrete variables, as done by direct-coupling analysis. This is true for (i the prediction of residue-residue contacts in proteins, and (ii the identification of protein-protein interaction partner in bacterial signal transduction. An implementation of our multivariate Gaussian approach is available at the website http://areeweb.polito.it/ricerca/cmp/code.

  18. Fast and accurate multivariate Gaussian modeling of protein families: predicting residue contacts and protein-interaction partners.

    Science.gov (United States)

    Baldassi, Carlo; Zamparo, Marco; Feinauer, Christoph; Procaccini, Andrea; Zecchina, Riccardo; Weigt, Martin; Pagnani, Andrea

    2014-01-01

    In the course of evolution, proteins show a remarkable conservation of their three-dimensional structure and their biological function, leading to strong evolutionary constraints on the sequence variability between homologous proteins. Our method aims at extracting such constraints from rapidly accumulating sequence data, and thereby at inferring protein structure and function from sequence information alone. Recently, global statistical inference methods (e.g. direct-coupling analysis, sparse inverse covariance estimation) have achieved a breakthrough towards this aim, and their predictions have been successfully implemented into tertiary and quaternary protein structure prediction methods. However, due to the discrete nature of the underlying variable (amino-acids), exact inference requires exponential time in the protein length, and efficient approximations are needed for practical applicability. Here we propose a very efficient multivariate Gaussian modeling approach as a variant of direct-coupling analysis: the discrete amino-acid variables are replaced by continuous Gaussian random variables. The resulting statistical inference problem is efficiently and exactly solvable. We show that the quality of inference is comparable or superior to the one achieved by mean-field approximations to inference with discrete variables, as done by direct-coupling analysis. This is true for (i) the prediction of residue-residue contacts in proteins, and (ii) the identification of protein-protein interaction partner in bacterial signal transduction. An implementation of our multivariate Gaussian approach is available at the website http://areeweb.polito.it/ricerca/cmp/code.

  19. Control Parameters for Boundary-Layer Instabilities in Unsteady Shock Interactions

    Directory of Open Access Journals (Sweden)

    LaVar King Isaacson

    2012-01-01

    Full Text Available This article presents the computation of a set of control parameters for the deterministic prediction of laminar boundary-layer instabilities induced by an imposed unsteady shock interaction. The objective of the study is exploratory in nature by computing a supersonic flight environment for flow over a blunt body and the deterministic prediction of the spectral entropy rates for the boundary layer subjected to an unsteady pressure disturbance. The deterministic values for the spectral entropy rate within the instabilities are determined for each control parameter. Computational results imply that the instabilities are of a span-wise vortex form, that the maximum vertical velocity wave vector components are produced in the region nearest the wall and that extended transient coherent structures are produced in the boundary layer at a vertical location slightly below the mid-point of the boundary layer.

  20. Shifts of neutrino oscillation parameters in reactor antineutrino experiments with non-standard interactions

    Directory of Open Access Journals (Sweden)

    Yu-Feng Li

    2014-11-01

    Full Text Available We discuss reactor antineutrino oscillations with non-standard interactions (NSIs at the neutrino production and detection processes. The neutrino oscillation probability is calculated with a parametrization of the NSI parameters by splitting them into the averages and differences of the production and detection processes respectively. The average parts induce constant shifts of the neutrino mixing angles from their true values, and the difference parts can generate the energy (and baseline dependent corrections to the initial mass-squared differences. We stress that only the shifts of mass-squared differences are measurable in reactor antineutrino experiments. Taking Jiangmen Underground Neutrino Observatory (JUNO as an example, we analyze how NSIs influence the standard neutrino measurements and to what extent we can constrain the NSI parameters.

  1. Identification of key amino acid residues in the hTGR5-nomilin interaction and construction of its binding model.

    Science.gov (United States)

    Sasaki, Takashi; Mita, Moeko; Ikari, Naho; Kuboyama, Ayane; Hashimoto, Shuzo; Kaneko, Tatsuya; Ishiguro, Masaji; Shimizu, Makoto; Inoue, Jun; Sato, Ryuichiro

    2017-01-01

    TGR5, a member of the G protein-coupled receptor (GPCR) family, is activated by bile acids. Because TGR5 promotes energy expenditure and improves glucose homeostasis, it is recognized as a key target in treating metabolic diseases. We previously showed that nomilin, a citrus limonoid, activates TGR5 and confers anti-obesity and anti-hyperglycemic effects in mice. Information on the TGR5-nomilin interaction regarding molecular structure, however, has not been reported. In the present study, we found that human TGR5 (hTGR5) shows higher nomilin responsiveness than does mouse TGR5 (mTGR5). Using mouse-human chimeric TGR5, we also found that three amino acid residues (Q77ECL1, R80ECL1, and Y893.29) are important in the hTGR5-nomilin interaction. Based on these results, an hTGR5-nomilin binding model was constructed using in silico docking simulation, demonstrating that four hydrophilic hydrogen-bonding interactions occur between nomilin and hTGR5. The binding mode of hTGR5-nomilin is vastly different from those of other TGR5 agonists previously reported, suggesting that TGR5 forms various binding patterns depending on the type of agonist. Our study promotes a better understanding of the structure of TGR5, and it may be useful in developing and screening new TGR5 agonists.

  2. The same number of optimized parameters scheme for determining intermolecular interaction energies

    DEFF Research Database (Denmark)

    Kristensen, Kasper; Ettenhuber, Patrick; Eriksen, Janus Juul

    2015-01-01

    We propose the Same Number Of Optimized Parameters (SNOOP) scheme as an alternative to the counterpoise method for treating basis set superposition errors in calculations of intermolecular interaction energies. The key point of the SNOOP scheme is to enforce that the number of optimized wave...... as numerically. Numerical results for second-order Møller-Plesset perturbation theory (MP2) and coupled-cluster with single, double, and approximate triple excitations (CCSD(T)) show that the SNOOP scheme in general outperforms the uncorrected and counterpoise approaches. Furthermore, we show that SNOOP...

  3. Asymmetric dark matter: residual annihilations and self-interactions arXiv

    CERN Document Server

    Baldes, Iason; Panci, Paolo; Petraki, Kalliopi; Sala, Filippo; Taoso, Marco

    Dark matter (DM) coupled to light mediators has been invoked to resolve the putative discrepancies between collisionless cold DM and galactic structure observations. However, $\\gamma$-ray searches and the CMB strongly constrain such scenarios. To ease the tension, we consider asymmetric DM. We show that, contrary to the common lore, detectable annihilations occur even for large asymmetries, and derive bounds from the CMB, $\\gamma$-ray, neutrino and antiproton searches. We then identify the viable space for self-interacting DM. Direct detection does not exclude this scenario, but provides a way to test it.

  4. Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication.

    Directory of Open Access Journals (Sweden)

    Gabrielle Stetz

    2017-01-01

    Full Text Available Allosteric interactions in the Hsp70 proteins are linked with their regulatory mechanisms and cellular functions. Despite significant progress in structural and functional characterization of the Hsp70 proteins fundamental questions concerning modularity of the allosteric interaction networks and hierarchy of signaling pathways in the Hsp70 chaperones remained largely unexplored and poorly understood. In this work, we proposed an integrated computational strategy that combined atomistic and coarse-grained simulations with coevolutionary analysis and network modeling of the residue interactions. A novel aspect of this work is the incorporation of dynamic residue correlations and coevolutionary residue dependencies in the construction of allosteric interaction networks and signaling pathways. We found that functional sites involved in allosteric regulation of Hsp70 may be characterized by structural stability, proximity to global hinge centers and local structural environment that is enriched by highly coevolving flexible residues. These specific characteristics may be necessary for regulation of allosteric structural transitions and could distinguish regulatory sites from nonfunctional conserved residues. The observed confluence of dynamics correlations and coevolutionary residue couplings with global networking features may determine modular organization of allosteric interactions and dictate localization of key mediating sites. Community analysis of the residue interaction networks revealed that concerted rearrangements of local interacting modules at the inter-domain interface may be responsible for global structural changes and a population shift in the DnaK chaperone. The inter-domain communities in the Hsp70 structures harbor the majority of regulatory residues involved in allosteric signaling, suggesting that these sites could be integral to the network organization and coordination of structural changes. Using a network-based formalism of

  5. Observational Data Analysis and Numerical Model Assessment of the Seafloor Interaction and Mobility of Sand and Weathered Oil Agglomerates (Surface Residual Balls) in the Surf Zone

    Science.gov (United States)

    Dalyander, S.; Long, J.; Plant, N. G.; Penko, A.; Calantoni, J.; Thompson, D.; Mclaughlin, M. K.

    2014-12-01

    When weathered oil is transported ashore, such as during the Deepwater Horizon oil spill, it can mix with suspended sediment in the surf zone to create heavier-than-water sand and oil agglomerates in the form of mats several centimeters thick and tens of meters long. Broken off pieces of these mats and smaller agglomerates formed in situ (called Surface Residual Balls, SRBs) can cause beach re-oiling months to years after the initial spill. The physical dynamics of these SRBs in the nearshore, where they are larger (cm-scale) and less dense than natural sediment, are poorly understood. In the current study, SRB mobility and seafloor interaction is investigated through a combination of laboratory and field experiments with pseudo-SRBs developed to be physically stable proxies for genuine agglomerates. Formulations for mobility prediction based on comparing estimated shear stress to the critical Shields and modified Shields parameters developed for mixed sediment beds are assessed against observations. Processes such as burial, exhumation, and interaction with bedforms (e.g., migrating ripples) are also explored. The observations suggest that incipient motion estimates based on a modified Shields parameter have some skill in predicting SRB movement, but that other forcing mechanisms such as pressure gradients may be important under some conditions. Additionally, burial and exhumation due to the relatively high mobility of sand grains are confirmed as key processes controlling SRB dynamics in the surf zone. This work has broad implications for understanding surf zone sediment transport at the short timescale associated with mobilizing sand grains and SRBs as well as at the longer timescales associated with net transport patterns, sediment budgets, and bed elevation changes.

  6. Parameter validation of analytical methods of insecticide residue analyses in foods of animal origin, feed and water.

    Science.gov (United States)

    Debebe, Amsalu; Kuttalam, S

    2011-06-01

    The study was conducted to examine the interrelationship and coherence of analytical parameters in method validation. Recovery, sensitivity, linearity, precision and limits of detection (LOD) were tested in six methods for organochlorine and organophosphate insecticides. Compounds that fell out of the stipulated recovery, 70-120%, in a matrix have concurrently failed to meet the requirements for sensitivity (≥ 0.7), linearity (R² > 0.99) and precision (< 0.2) in the same matrix. Highest LOD was recorded in those compounds and matrices. Different from the conventional point estimate, a new approach was introduced for setting upper and lower confidence limits of the LOD in quantitative analyses.

  7. Interacting Effects Induced by Two Neighboring Pits Considering Relative Position Parameters and Pit Depth

    Directory of Open Access Journals (Sweden)

    Yongfang Huang

    2017-04-01

    Full Text Available For pre-corroded aluminum alloy 7075-T6, the interacting effects of two neighboring pits on the stress concentration are comprehensively analyzed by considering various relative position parameters (inclination angle θ and dimensionless spacing parameter λ and pit depth (d with the finite element method. According to the severity of the stress concentration, the critical corrosion regions, bearing high susceptibility to fatigue damage, are determined for intersecting and adjacent pits, respectively. A straightforward approach is accordingly proposed to conservatively estimate the combined stress concentration factor induced by two neighboring pits, and a concrete application example is presented. It is found that for intersecting pits, the normalized stress concentration factor Ktnor increases with the increase of θ and λ and always reaches its maximum at θ = 90°, yet for adjacent pits, Ktnor decreases with the increase of λ and the maximum value appears at a slight asymmetric location. The simulations reveal that Ktnor follows a linear and an exponential relationship with the dimensionless depth parameter Rd for intersecting and adjacent cases, respectively.

  8. Comparison of volumetric and functional parameters in simultaneous cardiac PET/MR: feasibility of volumetric assessment with residual activity from prior PET/CT

    Energy Technology Data Exchange (ETDEWEB)

    Luecke, C.; Brenneis, B.; Grothoff, M.; Gutberlet, M. [University Leipzig - Heart Center, Department of Diagnostic and Interventional Radiology, Leipzig (Germany); Oppolzer, B.; Werner, P.; Jochimsen, T.; Sattler, B.; Barthel, H.; Sabri, O. [University Hospital Leipzig, Department of Nuclear Medicine, Leipzig (Germany); Foldyna, B. [University Leipzig - Heart Center, Department of Diagnostic and Interventional Radiology, Leipzig (Germany); Massachusetts General Hospital - Harvard Medical School, Cardiac MR PET CT Program, Boston, MA (United States); Lurz, P. [University Leipzig - Heart Center, Clinic for Internal Medicine/Cardiology, Leipzig (Germany); Lehmkuhl, L. [Herz- und Gefaess-Klinik GmbH, Radiologische Klinik, Bad Neustadt (Germany)

    2017-12-15

    To compare cardiac left ventricular (LV) parameters in simultaneously acquired hybrid fluorine-18-fluorodeoxyglucose ([18F] FDG) positron emission tomography/magnetic resonance imaging (PET/MRI) in patients with residual tracer activity of upstream PET/CT. Twenty-nine patients (23 men, age 58±17 years) underwent cardiac PET/MRI either directly after a non-cardiac PET/CT with homogenous cardiac [18F] FDG uptake (n=20) or for viability assessment (n=9). Gated cardiac [18F] FDG PET and cine MR sequences were acquired simultaneously and evaluated blinded to the cross-imaging results. Image quality (IQ), end-diastolic (LVEDV), end-systolic volume (LVESV), ejection fraction (LVEF) and myocardial mass (LVMM) were measured. Pearson correlation and intraclass correlation coefficient (ICC), regression and a Bland-Altman analysis were assessed. Except LVMM, volumetric and functional LV parameters demonstrated high correlations (LVESV: r=0.97, LVEDV: r=0.95, LVEF: r=0.91, LVMM: r=0.87, each p<0.05), but wide limits of agreement (LOA) for LVEDV (-25.3-82.5ml); LVESV (-33.1-72.7ml); LVEF (-18.9-14.8%) and LVMM (-78.2-43.2g). Intra- and interobserver reliability were very high (ICC≥0.95) for all parameters, except for MR-LVEF (ICC=0.87). PET-IQ (0-3) was high (mean: 2.2±0.9) with significant influence on LVMM calculations only. In simultaneously acquired cardiac PET/MRI data, LVEDV, LVESV and LVEF show good agreement. However, the agreement seems to be limited if cardiac PET/MRI follows PET/CT and only the residual activity is used. (orig.)

  9. Developing a high-quality scoring function for membrane protein structures based on specific inter-residue interactions

    Science.gov (United States)

    Heim, Andrew J.; Li, Zhijun

    2012-03-01

    Membrane proteins are of particular biological and pharmaceutical importance, and computational modeling and structure prediction approaches play an important role in studies of membrane proteins. Developing an accurate model quality assessment program is of significance to the structure prediction of membrane proteins. Few such programs are proposed that can be applied to a broad range of membrane protein classes and perform with high accuracy. We developed a new model scoring function Interaction-based Quality assessment (IQ), based on the analysis of four types of inter-residue interactions within the transmembrane domains of helical membrane proteins. This function was tested using three high-quality model sets: all 206 models of GPCR Dock 2008, all 284 models of GPCR Dock 2010, and all 92 helical membrane protein models of the HOMEP set. For all three sets, the scoring function can select the native structures among all of the models with the success rates of 93, 85, and 100% respectively. For comparison, these three model sets were also adopted for a recently published model assessment program for membrane protein structures, ProQM, which gave the success rates of 85, 79, and 92% separately. These results suggested that IQ outperforms ProQM when only the transmembrane regions of the models are considered. This scoring function should be useful for the computational modeling of membrane proteins.

  10. Quantitative relations between interaction parameter, miscibility and function in organic solar cells

    KAUST Repository

    Ye, Long

    2018-02-02

    Although it is known that molecular interactions govern morphology formation and purity of mixed domains of conjugated polymer donors and small-molecule acceptors, and thus largely control the achievable performance of organic solar cells, quantifying interaction-function relations has remained elusive. Here, we first determine the temperature-dependent effective amorphous-amorphous interaction parameter, χaa(T), by mapping out the phase diagram of a model amorphous polymer:fullerene material system. We then establish a quantitative \\'constant-kink-saturation\\' relation between χaa and the fill factor in organic solar cells that is verified in detail in a model system and delineated across numerous high- and low-performing materials systems, including fullerene and non-fullerene acceptors. Our experimental and computational data reveal that a high fill factor is obtained only when χaa is large enough to lead to strong phase separation. Our work outlines a basis for using various miscibility tests and future simulation methods that will significantly reduce or eliminate trial-and-error approaches to material synthesis and device fabrication of functional semiconducting blends and organic blends in general.

  11. Optimal conditions and operational parameters for conversion of Robusta coffee residues in a continuous stirred tank reactor

    Energy Technology Data Exchange (ETDEWEB)

    Msambichaka, B.L.; Kivaisi, A.K.; Rubindamayugi, M.S.T. [Univ. of Dar es Salaam, Applied Microbiology Unit (Tanzania, United Republic of)

    1997-12-31

    This experiment studied the possibility of optimizing anaerobic degradation, developing microbial adaptation and establishing long term process stability in a Continuous Stirred Tank Reactor (CSTR) running on Robusta coffee hulls as feed substrate. Decrease in lag phase and increase in methane production rate in batch culture experiment conducted before and after process stabilization of each operational phase in the CSTR clearly suggested that microbial adaptation to increasing coffee percentage composition was attained. Through gradual increase of coffee percentage composition, from 10% coffee, 2% VS, 20 days HRT and a 1 g VS/1/day loading rate to 80% coffee, 4.5% VS, 12 days HRT and a loading rate of 3 g VS/1/day the CSTR system was optimized at a maximum methane yield of 535 ml/g VS. Again it was possible to attain long term process stability at the above mentioned optimal operational parameters for a further 3 month period. (au)

  12. Conserved surface residues on the feline calicivirus (FCV) capsid are essential for interaction with its receptor feline junctional adhesion molecule A (fJAM-A).

    Science.gov (United States)

    Lu, Zhengchun; Ledgerwood, Emily D; Hinchman, Meleana M; Dick, Robert; Parker, John S L

    2018-01-31

    Host cell surface receptors are required for attachment, binding, entry and infection by nonenveloped viruses. Receptor binding can induce conformational changes in the viral capsid and/or the receptor that couple binding with downstream events in the viral life cycle (intracellular signaling, endocytosis and trafficking, and membrane penetration). Virus-receptor interactions also influence viral spread and pathogenicity. The interaction between feline calicivirus (FCV) and its receptor feline Junctional Adhesion Molecule A (fJAM-A) on host cells is required for infection and induces irreversible, inactivating conformational changes in the capsid of some viral strains. Cryo-EM structures of FCV bound to fJAM-A showed several possible virus-receptor interactions. However, the specific residues on the viral capsid required for binding are not known. Capsid residues that may be involved in post-binding events have been implicated by isolation of soluble receptor-resistant (srr) mutants in which changes in the capsid protein sequence change the capacity of such srr mutants to be inactivated upon incubation with soluble fJAM-A. To clarify which residues on the surface of FCV are required for its interaction with fJAM-A, and to potentially identify residues required for post-receptor binding events, we used the existing atomic resolution structures of FCV and the FCV-fJAM-A cryo-EM structures to select 14 capsid residues for mutation and preparation of recombinant viral capsids. Using this approach, we identified residues on the FCV capsid that are required for fJAM-A binding and other residues not required for binding, but required for infection that are likely important for subsequent post-binding events. IMPORTANCE Feline calicivirus (FCV) is a common cause of mild upper respiratory disease in cats. Some FCV isolates can cause virulent systemic disease. The genetic determinants of virulence for FCV are unknown. We previously found that virulent FCV isolates have

  13. The equivalent of a thallium binding residue from an archeal homolog controls cation interactions in brain glutamate transporters.

    Science.gov (United States)

    Teichman, Shlomit; Qu, Shaogang; Kanner, Baruch I

    2009-08-25

    Glutamate transporters maintain low synaptic concentrations of neurotransmitter by coupling uptake to flux of other ions. Their transport cycle consists of two separate translocation steps, namely cotransport of glutamic acid with three Na(+) followed by countertransport of K(+). Two Tl(+) binding sites, presumed to serve as sodium sites, were observed in the crystal structure of a related archeal homolog and the side chain of a conserved aspartate residue contributed to one of these sites. We have mutated the corresponding residue of the eukaryotic glutamate transporters GLT-1 and EAAC1 to asparagine, serine, and cysteine. Remarkably, these mutants exhibited significant sodium-dependent radioactive acidic amino acid uptake when expressed in HeLa cells. Reconstitution experiments revealed that net uptake by the mutants in K(+)-loaded liposomes was impaired. However, with Na(+) and unlabeled L-aspartate inside the liposomes, exchange levels were around 50-90% of those by wild-type. In further contrast to wild-type, where either substrate or K(+) stimulated the anion conductance by the transporter, substrate but not K(+) modulated the anion conductance of the mutants expressed in oocytes. Both with wild-type EAAC1 and EAAC1-D455N, not only sodium but also lithium could support radioactive acidic amino acid uptake. In contrast, with D455S and D455C, radioactive uptake was only observed in the presence of sodium. Thus the conserved aspartate is required for transporter-cation interactions in each of the two separate translocation steps and likely participates in an overlapping sodium and potassium binding site.

  14. Self-contacts in Asx and Glx residues of high-resolution protein structures: role of local environment and tertiary interactions.

    Science.gov (United States)

    Pal, Tuhin Kumar; Sankararamakrishnan, Ramasubbu

    2008-08-01

    In protein structures, side-chains of asparagine and aspartic acid (Asx) and glutamine and glutamic acid (Glx) can approach their own backbone nitrogen or carbonyl group. We have systematically analyzed intra-residue contacts in Asx and Glx residues and their secondary structure preferences in two different datasets consisting of 500 and 1506 high-resolution structures. Intra-residue contact in an Asx/Glx residue between the heavy atoms of side-chain and main-chain functional groups of the same residue was investigated irrespective of whether such contacts are due to hydrogen bonding or not. Our search yielded 563 and 1462 cases of self-contacting Asx and Glx residues from the two datasets. Two important observations have been made in this analysis. First, self-contacts involving side-chain oxygen and backbone nitrogen atoms in majority of Asx residues are not due to hydrogen bonds. In the second instance, surprisingly, side-chain and backbone carbonyl oxygens of a significant number of Asx and Glx residues approach each other. For a wide-range of accessible surface areas, self-contacting residues are surrounded by less number of polar groups compared to all other Asx/Glx residues. In buried and partially buried regions, side-chain and main-chain functional groups of these residues together participate in simultaneous interactions with the available polar groups or water molecules. Asx/Glx residues with self-contacts are rarely observed in the middle of an alpha-helix or a beta-strand. Asx/Glx side-chain having contact with its own backbone nitrogen shows different capping preferences compared to those having contact with its backbone oxygen. Examples of proteins with multiple self-contacting Asx/Glx residues are found. We speculate that mutation of a self-contacting residue in the buried or partially buried region of a protein will destabilize the structure. The results of this analysis will help in engineering protein structures and site-directed mutagenesis

  15. Importance of the character and configuration of residues B24, B25, and B26 in insulin-receptor interactions

    International Nuclear Information System (INIS)

    Mirmira, R.G.; Nakagawa, S.H.; Tager, H.S.

    1991-01-01

    By use of isolated canine hepatocytes and insulin analogs prepared by trypsin-catalyzed semisynthesis, we have investigated the importance of the aromatic triplet PheB24-PheB25-TyrB26 of the COOH-terminal B-chain domain of insulin in directing the affinity of insulin-receptor interactions. Analysis of the receptor binding potencies of analogs bearing transpositions or replacements (by Tyr, D-Tyr or their corresponding 3,5-diiodo derivatives) in this region demonstrates a wide divergence in the acceptance both of configurational change (with [D-TyrB24,PheB26]insulin and [D-TyrB25,PheB26]insulin exhibiting 160 and 0.1% of the receptor binding potency of insulin, respectively) and of detailed side chain structure (with [TyrB24,PheB26]insulin and [TyrB25,PheB26]insulin exhibiting 2 and 80% of the receptor binding potency of insulin, respectively). Additional experiments addressed the solvent accessibilities of the 4 tyrosine residues of insulin and the insulin analogs at selected peptide concentrations by use of analytical radioiodination. Whereas two analogs ([TyrB25,PheB26]insulin and [D-TyrB24,PheB26]insulin) were found to undergo self aggregation, no strict correlation was found between the ability of an analog to aggregate and its potency for interaction with the insulin receptor. Related findings are discussed in terms of the interplay between side chain and main chain structure in the COOH-terminal domain of the insulin B-chain and the structural attributes of insulin that determine the affinity of insulin-receptor interactions

  16. Influence of excitons interaction with charge carriers on photovoltaic parameters in organic solar cells

    Science.gov (United States)

    Głowienka, Damian; Szmytkowski, Jędrzej

    2018-03-01

    We report on theoretical analysis of excitons annihilation on charge carriers in organic solar cells. Numerical calculations based on transient one-dimensional drift-diffusion model have been carried out. An impact of three quantities (an annihilation rate constant, an exciton mobility and a recombination reduction factor) on current density and concentrations of charge carriers and excitons is investigated. Finally, we discuss the influence of excitons interaction with electrons and holes on four photovoltaic parameters (a short-circuit current, an open-circuit voltage, a fill factor and a power conversion efficiency). The conclusion is that the annihilation process visibly decreases the efficiency of organic photocells, if the annihilation rate constant is greater than 10-15m3s-1 .

  17. Interactions between somatometric parameters and endogenous hormone levels as well as hormonal induced events in females.

    Science.gov (United States)

    Kirchengast, S

    1998-09-01

    The present paper contains the results of a five year research project focusing on the complex interaction between body build and endogenous hormone levels as well as on hormonal induced events in 1095 healthy adult females from Austria. It could be demonstrated that even long after termination of the pubertal growth phase significant associations exist between body dimensions as well as body composition compartments and endogenous hormone levels. Beside positive associations between length and height dimensions as well as traits of robustness and those hormonal parameters which are essential for an undisturbed linear growth, i.e. growth hormone, thyroid hormones and testosterone, the complex interaction between body fat development and the sex hormones as well as the lipolytic active growth could be proved. These association patterns were observed independently of the menopausal status. Furthermore marked associations between female body build, above all body fat development, and hormonal induced events such as menarche, menstrual cycle patterns, fertility and menopause were observed. A more feminine type of body build combined with moderate development of body fat was associated with earlier menarche, more regular menstrual cycles, higher reproductive success and a delayed menopause. Moderate fatness and a gynoid kind of fat distribution may be stated as indicators of potential female reproductive success.

  18. Experimental parameter estimation of a visuo-vestibular interaction model in humans.

    Science.gov (United States)

    Laurens, Jean; Valko, Yulia; Straumann, Dominik

    2011-01-01

    Visuo-vestibular interactions in monkeys can be accurately modelled using the classical Raphan and Cohen's model. This model is composed of direct vestibular and visual contributions to the vestibulo-ocular reflex (VOR) and of a velocity storage. We applied this model to humans and estimated its parameters in a series of experiments: yaw rotations at moderate (60°/s) and high velocities (240°/s), suppression of the VOR by a head-fixed wide-field visual stimulus, and optokinetic stimulation with measurements of optokinetic nystagmus (OKN) and optokinetic afternystagmus (OKAN). We found the velocity storage time constant to be 13 s, which decreased to 8 s during visual suppression. OKAN initial velocity was 12% of the OKN stimulus velocity. The gain of the direct visual pathway was 0.75 during both visual suppression and OKN; however, the visual input to the velocity storage was higher during visual suppression than during OKN. We could not estimate the time constant of the semicircular canals accurately. Finally, we inferred from high-velocity rotations that the velocity storage saturates around 20-30°/s. Our results indicate that the dynamics of visuo-vestibular interactions in humans is similar as in monkeys. The central integration of visual cues, however, is weaker in humans.

  19. Conserved residues in the coiled-coil pocket of human immunodeficiency virus type 1 gp41 are essential for viral replication and interhelical interaction

    International Nuclear Information System (INIS)

    Mo Hongmei; Konstantinidis, Alex K.; Stewart, Kent D.; Dekhtyar, Tatyana; Ng, Teresa; Swift, Kerry; Matayoshi, Edmund D.; Kati, Warren; Kohlbrenner, William; Molla, Akhteruzzaman

    2004-01-01

    The human immunodeficiency virus type 1 (HIV-1) gp41 plays an important role in mediating the fusion of HIV with host cells. During the fusion process, three N-terminal helices and three C-terminal helices pack in an anti-parallel direction to form a six-helix bundle. X-ray crystallographic analysis of the gp41 core demonstrated that within each coiled-coil interface, there is a deep and large pocket, formed by a cluster of residues in the N-helix coiled-coil. In this report, we systematically analyzed the role of seven conserved residues that are either lining or packing this pocket on the infectivity and interhelical interaction using novel approaches. Our results show that residues L568, V570, W571, and K574 of the N-helix that are lining the side chain and right wall of the pocket are important for establishing a productive infection. Mutations V570A and W571A completely abolished replication, while replication of the L568A and K574A mutants was significantly attenuated relative to wild type. Similarly, residues W628, W631, and I635 of the C-helix that insert into the pocket are essential for infectivity. The impaired infectivity of these seven mutants is in part attributed to the loss in binding affinity of the interhelical interaction. Molecular modeling of the crystal structure of the coiled-coil further shows that alanine substitution of those residues disrupts the hydrophobic interaction between the N- and C-helix. These results suggest that the conserved residues in the coiled-coil domain play a key role in HIV infection and this coiled-coil pocket is a good target for development of inhibitors against HIV. In addition, our data indicate that the novel fluorescence polarization assay described in this study could be valuable in screening for inhibitors that block the interhelical interaction and HIV entry

  20. Extending the GERG-2008 equation of state: Improved departure function and interaction parameters for (methane + butane)

    International Nuclear Information System (INIS)

    Rowland, Darren; Hughes, Thomas J.; May, Eric F.

    2016-01-01

    Highlights: • The GERG-2008 EOS was tested against recently published low temperature data for (methane + butane). • A simpler departure function reduced the maximum c p deviation at T = 120 K from (110 to 7) %. • Improved BIPs for (methane + butane) were determined by re-fitting to an extended data set. • Deviations for high pressure VLE data at T = 244 K were reduced from (9 to 1.4) %. - Abstract: The Groupe Européen de Recherches Gazières (GERG) 2008 multi-parameter equation of state (EOS) is considered the reference model for the prediction of natural gas mixture properties. However, the limited quality of thermodynamic property data available for many key binary mixtures at the time of its development constrained both its range of validity and achievable uncertainty. The data situation for the binary system (CH 4 + C 4 H 10 ) in particular was identified previously as limiting the ability of the GERG-EOS to describe rich natural gases at low temperatures. Recently, new vapour-liquid equilibrium (VLE) and liquid mixture heat capacity data measured at low temperatures and high pressures have been published that significantly improve the data situation for this crucial binary, allowing erroneous literature data to be identified and the predictive behaviour of the GERG-EOS when extrapolated to be tested. The 10 basis functions in the generalised departure function used by the GERG-EOS for several binaries including (CH 4 + C 4 H 10 ) were examined to eliminate the term causing a divergence between measured and predicted liquid mixture isobaric heat capacities at T < 150 K. With a simplified nine-term departure function, the maximum relative deviation between the measured and predicted heat capacities was reduced from nearly (110 to 7) %. The interaction parameters in the GERG equation were also re-determined by including, for the first time for this binary, reliable low temperature VLE data together with most of the other high temperature data used in

  1. Interaction of the protein transduction domain of HIV-1 TAT with heparan sulfate: binding mechanism and thermodynamic parameters.

    Science.gov (United States)

    Ziegler, André; Seelig, Joachim

    2004-01-01

    The positively charged protein transduction domain of the HIV-1 TAT protein (TAT-PTD; residues 47-57 of TAT) rapidly translocates across the plasma membrane of living cells. This property is exploited for the delivery of proteins, drugs, and genes into cells. The mechanism of this translocation is, however, not yet understood. Recent theories for translocation suggest binding of the protein transduction domain (PTD) to extracellular glycosaminoglycans as a possible mechanism. We have studied the binding equilibrium between TAT-PTD and three different glycosaminoglycans with high sensitivity isothermal titration calorimetry and provide the first quantitative thermodynamic description. The polysulfonated macromolecules were found to exhibit multiple identical binding sites for TAT-PTD with only small differences between the three species as far as the thermodynamic parameters are concerned. Heparan sulfate (HS, molecular weight, 14.2 +/- 2 kDa) has 6.3 +/- 1.0 independent binding sites for TAT-PTD which are characterized by a binding constant K0 = (6.0 +/- 0.6) x 10(5) M(-1) and a reaction enthalpy deltaHpep0 = -4.6 +/- 1.0 kcal/mol at 28 degrees C. The binding affinity, deltaGpep0, is determined to equal extent by enthalpic and entropic contributions. The HS-TAT-PTD complex formation entails a positive heat capacity change of deltaCp0 = +135 cal/mol peptide, which is characteristic of a charge neutralization reaction. This is in contrast to hydrophobic binding reactions which display a large negative heat capacity change. The stoichiometry of 6-7 TAT-PTD molecules per HS corresponds to an electric charge neutralization. Light scattering data demonstrate a maximum scattering intensity at this stoichiometric ratio, the intensity of which depends on the order of mixing of the two components. The data suggest cross-linking and/or aggregation of HS-TAT-PTD complexes. Two other glycosaminoglycans, namely heparin and chondroitin sulfate B, were also studied with isothermal

  2. Low-energy structure studies of odd-odd deformed nuclei and the coriolis and residual interactions

    Energy Technology Data Exchange (ETDEWEB)

    Dewberry, R.A.

    1980-08-01

    The nuclear level structure of /sup 176/Lu, /sup 170/Tm, /sup 166/Ho, and /sup 160/Tb have been studied by means of the /sup 177/Hf(t,..cap alpha..)/sup 176/Lu, /sup 171/Yb(t,..cap alpha..)/sup 170/Tm, /sup 167/Er(t,..cap alpha..)/sup 166/Ho, and /sup 161/Dy(t,..cap alpha..)/sup 160/Tb reactions and with the use of previously published (d,p) spectroscopy and gamma transitions from the (n,..gamma..) reactions. The (t,..cap alpha..) reactions have been performed and analyzed with 17 MeV tritons and the Los Alamos Q3D spectrometer. Eighty-one new rotational states in excited proton configurations or vibrational excited states are proposed. An independent parameterization of the Coriolis interaction is presented, which leads to satisfactory results in reproducing experimental single-particle transfer reaction cross-sections by theoretical calculations. The anomalous population of the excited neutron configurations (404 reduces to -624 up arrow) in /sup 176/Lu and (411 reduces to +- 512 up arrow) in /sup 170/Tm, and the anomalously low (t,..cap alpha..) cross-sections of the (411 up arrow +- 633 up arrow) configuration in /sup 166/Ho are observed. Qualitative explanation of the anomalies is presented in terms of the mixing of states which satisfy the requirement delta/sub I'/,/sub I/delta/sub K'/,/sub K/. Off-diagonal H/sub INT/ matrix elements are calculated, which show that the residual interaction cannot be used to account for the magnitude of the cross-sections observed.

  3. Contribution to the study of the interactions between residual stresses and oxygen dissolution in a reactive deformable solid

    International Nuclear Information System (INIS)

    Raceanu, Laura

    2011-01-01

    The aim of this PhD work is to highlight the interactions between the mechanical stress and the chemical composition within diffusion of matter process for a reactive solid. The chronological evolution of our work goes from a parametric numerical study to an experimental study and reveals the role of mechanical stresses on the oxygen diffusion process. Different origins of mechanical stress were first numerically analysed from the point of view of their impacts on the process of oxygen diffusion into a metal (Zr) or a ceramic (UO 2 ) subjected to an oxidizing environment. This approach allowed us: - to identify a surface treatment (shot-peening) able to generate a residual specific stress field, as a starting point for an experimental study implementation in order to validate the numerical study conclusions; - to highlight the ability of the stress field on the stabilisation of the morphology of an undulated metal/oxide interface (case of Zr). In the experimental approach, different techniques were used to characterize the material (GDOS, SEM, TGA, hole-drilling method, micro-hardness tests). They permitted the detection of a strong influence of shot-peening on the oxidation rate. The comparison of experimental and numerical simulation results reveals strong interactions between stress and compositions fields induced by the different treatments (shot-peening and/or pre-oxidation). This study opens up many opportunities in the understanding of multi-physics coupling effects being very useful for the optimization of mechanical and chemical surface-treatments, able furthermore to favour the diffusion (nitriding, cementation) or to slow it down (corrosion). (author) [fr

  4. Inhibition by etomoxir of rat liver carnitine octanoyltransferase is produced through the co-ordinate interaction with two histidine residues.

    Science.gov (United States)

    Morillas, M; Clotet, J; Rubí, B; Serra, D; Ariño, J; Hegardt, F G; Asins, G

    2000-10-15

    Rat peroxisomal carnitine octanoyltransferase (COT), which facilitates the transport of medium-chain fatty acids through the peroxisomal membrane, is irreversibly inhibited by the hypoglycaemia-inducing drug etomoxir. To identify the molecular basis of this inhibition, cDNAs encoding full-length wild-type COT, two different variant point mutants and one variant double mutant from rat peroxisomal COT were expressed in Saccharomyces cerevisiae, an organism devoid of endogenous COT activity. The recombinant mutated enzymes showed activity towards both carnitine and decanoyl-CoA in the same range as the wild type. Whereas the wild-type version expressed in yeast was inhibited by etomoxir in an identical manner to COT from rat liver peroxisomes, the activity of the enzyme containing the double mutation H131A/H340A was completely insensitive to etomoxir. Individual point mutations H131A and H340A also drastically reduced sensitivity to etomoxir. Taken together, these results indicate that the two histidine residues, H131 and H340, are the sites responsible for inhibition by etomoxir and that the full inhibitory properties of the drug will be shown only if both histidines are intact at the same time. Our data demonstrate that both etomoxir and malonyl-CoA inhibit COT by interacting with the same sites.

  5. Effects of dietary supplementation of fermented Ginkgo biloba L. residues on growth performance, nutrient digestibility, serum biochemical parameters and immune function in weaned piglets.

    Science.gov (United States)

    Zhou, Hao; Wang, Chengzhang; Ye, Jianzhong; Chen, Hongxia; Tao, Ran

    2015-08-01

    This study evaluated the effects of fermented Ginkgo biloba L. residues (FGBLR) on growth performance, nutrient digestibility, serum biochemical parameters and immune function in weaned piglets. Pigs were allotted to five dietary treatments, including negative control (NC: antibiotic free basal diet), positive control (PC) (NC + 30 mg apramycin/kg) and FGBLR-50, 100, 150 (NC + 50, 100, 150 g FGBLR/kg). Pigs in FGBLR-100 and PC treatments showed increased final body weight, average daily gain, gain:feed and apparent total tract digestibility of dry matter, N and gross energy (P alkaline phosphatase, glucose, hemoglobin, total iron, total iron binding capacity, superoxide dismutase and glutathione superoxide dismutase levels, and lower serum blood urea nitrogen, malondialdehyde, glutamic-pyruvic transaminase, glutamic-oxalacetic transaminase, triglyceride and total cholesterol levels than those fed with PC and NC diets (P dietary supplementation with 10% of FGBLR showed greatest beneficial effects on growth performance, nutrient digestibility, serum biochemical parameters and immune function in weaned piglets, which were superior to antibiotic supplemental diets. © 2015 Japanese Society of Animal Science.

  6. Residual blood processing by centrifugation, cell salvage or ultrafiltration in cardiac surgery: effects on clinical hemostatic and ex-vivo rheological parameters.

    Science.gov (United States)

    Vonk, Alexander B; Muntajit, Warayouth; Bhagirath, Pranav; van Barneveld, Laurentius J; Romijn, Johannes W; de Vroege, Roel; Boer, Christa

    2012-10-01

    The study compared the effects of three blood concentration techniques after cardiopulmonary bypass on clinical hemostatic and ex-vivo rheological parameters. Residual blood of patients undergoing elective cardiac surgery was processed by centrifugation, cell salvage or ultrafiltration, and retransfused (n = 17 per group). Study parameters included blood loss, (free) hemoglobin, hematocrit, fibrinogen and erythrocyte aggregation, deformability and 2,3-diphosphoglycerate content. Patient characteristics were similar between groups. Ultrafiltration was associated with the highest weight of the transfusion bag [649 ± 261 vs. 320 ± 134 g (centrifugation) and 391 ± 158 g (cell salvage); P blood induced the largest gain in postoperative patient hemoglobin levels when compared to centrifugation and ultrafiltration, and was associated with the largest increase in 2,3-diphosphoglycerate when compared to ultrafiltration (Δ2,3-diphosphoglycerate 1.34 ± 1.92 vs. -0.77 ± 1.56 mmol/l; P = 0.03). Cell salvage is superior with respect to postoperative hemoglobin gain and washout of free hemoglobin when compared to centrifugation or ultrafiltration.

  7. Development of non-bonded interaction parameters between graphene and water using particle swarm optimization.

    Science.gov (United States)

    Bejagam, Karteek K; Singh, Samrendra; Deshmukh, Sanket A

    2018-05-05

    New Lennard-Jones parameters have been developed to describe the interactions between atomistic model of graphene, represented by REBO potential, and five commonly used all-atom water models, namely SPC, SPC/E, SPC/Fw, SPC/Fd, and TIP3P/Fs by employing particle swarm optimization (PSO) method. These new parameters were optimized to reproduce the macroscopic contact angle of water on a graphene sheet. The calculated line tension was in the order of 10 -11 J/m for the droplets of all water models. Our molecular dynamics simulations indicate the preferential orientation of water molecules near graphene-water interface with one OH bond pointing toward the graphene surface. Detailed analysis of simulation trajectories reveals the presence of water molecules with ≤∼1, ∼2, and ∼4 hydrogen bonds at the surface of air-water interface, graphene-water interface, and bulk region of the water droplet, respectively. Presence of water molecules with ≤∼1 and ∼2 hydrogen bonds suggest the existence of water clusters of different sizes at these interfaces. The trends observed in the libration, bending, and stretching bands of the vibrational spectra are closely associated with these structural features of water. The inhomogeneity in hydrogen bond network of water at the air-water and graphene-water interface is manifested by broadening of the peaks in the libration band for water present at these interfaces. The stretching band for the molecules in water droplet shows a blue shift as compared to the pure bulk water, which conjecture the presence of weaker hydrogen bond network in a droplet. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  8. The method of extraction of subspectra with appreciably different values of hyperfine interaction parameters from Moessbauer spectra

    International Nuclear Information System (INIS)

    Nemtsova, O.M.

    2006-01-01

    The task of Moessbauer spectra processing of complex locally inhomogeneous or multi-phase systems is to reveal subspectral contributions with appreciably different values of hyperfine interaction parameters (HFI) in them. A universal method of processing such spectra is suggested which allows to extract the probability density distribution (PDD) of HFI parameters corresponding to the subspectra with essentially different parameters values. The basis of the method is Tikhonov's regularization method with selection for each subspectrum its own value of the regularization parameter. The universal application of the method is demonstrated in the examples of processing real spectra with different sets of subspectral contributions

  9. Sequence analysis and structure prediction of enoyl-CoA hydratase from Avicennia marina: implication of various amino acid residues on substrate-enzyme interactions.

    Science.gov (United States)

    Jabeen, Uzma; Salim, Asmat

    2013-10-01

    Enoyl-CoA hydratase catalyzes the hydration of 2-trans-enoyl-CoA into 3-hydroxyacyl-CoA. The present study focuses on the correlation between the functional and structural aspects of enoyl-CoA hydratase from Avicennia marina. We have used bioinformatics tools to construct and analyze 3D homology models of A. marina enoyl-CoA hydratase (AMECH) bound to different substrates and inhibitors and studied the residues involved in the ligand-enzyme interaction. Structural information obtained from the models was compared with those of the reported crystal structures. We observed that the overall folds were similar; however, AMECH showed few distinct structural changes which include structural variation in the mobile loop, formation and loss of certain interactions between the active site residues and substrates. Some changes were also observed within specific regions of the enzyme. Glu106 is almost completely conserved in sequences of the isomerases/hydratases including AMECH while Glu86 which is the other catalytic residue in most of the isomerases/hydratases is replaced by Gly and shows no interaction with the substrate. Asp114 is located within 4Å distance of the catalytic water which makes it a probable candidate for the second catalytic residue in AMECH. Another prominent feature of AMECH is the presence of structurally distinct mobile loop having a completely different coordination with the hydrophobic binding pocket of acyl portion of the substrate. Copyright © 2013 Elsevier Ltd. All rights reserved.

  10. Nonlinear Interaction of Zero Sound with the Order Parameter Collective Modes in Superfluid HELIUM-3-BORON.

    Science.gov (United States)

    McKenzie, Ross Hugh

    A brief overview of past experimental and theoretical investigations of the linear and nonlinear interaction of zero sound with the order parameter collective modes in superfluid ^3He-B is given before introducing the quasiclassical (QC) theory of superfluid ^3He. A new approach to calculating the linear and nonlinear response is presented. The QC propagator is calculated by expanding the low energy Dyson's equation in powers of the nonequilibrium self energy. The expression given for the expansion coefficients, involving products of pairs of equilibrium Green's functions, has a simple diagrammatic representation, and establishes a connection between the QC theory and other theoretical formalisms which have been used to investigate the collective modes. It is shown that the expansion coefficients satisfy Onsager-like relations and some identities required by gauge and galilean invariance. Consequently, this new approach to deriving dynamical equations for the collective modes is more efficient and transparent than solving the QC transport equations. This new approach is used to investigate the linear coupling of zero sound to the order parameter collective modes in weakly inhomogeneous superfluid ^3 He. It makes tractable the treatment of (nonlinear) parametric processes involving zero sound and the collective modes. It is shown that the approximate particle-hole symmetry of the ^3He Fermi liquid determines important selection rules for nonlinear acoustic processes, just as it is well known to do for linear processes. Analogues with nonlinear optics guide the derivation, solution and interpretation of the dynamical equations for a three-wave resonance between two zero sound waves and the J = 2 ^+ order parameter collective mode. It is shown that stimulated Raman scattering and two phonon absorption of zero sound by the J = 2^+ collective mode should be observable when the pump sound wave has energy density larger than about one percent of the superfluid

  11. Interaction between Soil Physicochemical Parameters and Earthworm Communities in Irrigated Areas with Natural Water and Wastewaters

    Directory of Open Access Journals (Sweden)

    Kourtel Ghanem Nadra

    2017-01-01

    Full Text Available Our objective is to study interaction between physical and chemical properties of soils and their earthworm community characteristics in different areas irrigated by wastewaters and well waters. The fields have different topography and agricultural practices conditions and are located in two regions of Batna department (Eastern Algeria. Both regions are characterized by a semiarid climate with cold winters and Calcisol soils. Nine fields were subject of this study. Three of these fields are located in Ouled Si Slimane region whose irrigation is effectuated by natural waters of Kochbi effluent. The other six fields are located at edges of Wed El Gourzi, effluent from Batna city, and partially treated through water treatment station. The best rates of water saturation and infiltration as well as abundance of earthworms were recorded at sites characterized by irrigation with wastewaters downstream of El Gourzi effluent. PCA characterizes two major groups: a group of hydrodynamic infiltration parameters and structural index stability of soil, explained by fields irrigated with wastewaters downstream of El Gourzi effluent. This group includes chemical characteristics: pH and electric conductivity. The second group is the characteristics of earthworms and includes organic matter content, active limestone levels, and Shannon Biodiversity Index.

  12. Solubility of Methane, Ethane, and Propane in Pure Water Using New Binary Interaction Parameters

    Directory of Open Access Journals (Sweden)

    Masoud Behrouz

    2015-07-01

    Full Text Available Solubility of hydrocarbons in water is important due to ecological concerns and new restrictions on the existence of organic pollutants in water streams. Also, the creation of a thermodynamic model has required an advanced study of the phase equilibrium between water (as a basis for the widest spread muds and amines and gas hydrocarbon phases in wide temperature and pressure ranges. Therefore, it is of great interest to develop semi-empirical correlations, charts, or thermodynamic models for estimating the solubility of hydrocarbons in liquid water. In this work, a thermodynamic model based on Mathias modification of Sova-Redlich-Kwong (SRK equation of state is suggested using classical mixing rules with new binary interaction parameters which were used for two-component systems of hydrocarbons and water. Finally, the model results and their deviations in comparison with the experimental data are presented; these deviations were equal to 5.27, 6.06, and 4.1% for methane, ethane, and propane respectively.

  13. Research of interaction between technological and material parameters during densification of sunflower hulls

    Science.gov (United States)

    Križan, Peter; Matúš, Miloš; Beniak, Juraj; Šooš, Ľubomír

    2018-01-01

    During the biomass densification can be recognized various technological variables and also material parameters which significantly influences the final solid biofuels (pellets) quality. In this paper, we will present the research findings concerning relationships between technological and material variables during densification of sunflower hulls. Sunflower hulls as an unused source is a typical product of agricultural industry in Slovakia and belongs to the group of herbaceous biomass. The main goal of presented experimental research is to determine the impact of compression pressure, compression temperature and material particle size distribution on final biofuels quality. Experimental research described in this paper was realized by single-axis densification, which was represented by experimental pressing stand. The impact of mentioned investigated variables on the final briquettes density and briquettes dilatation was determined. Mutual interactions of these variables on final briquettes quality are showing the importance of mentioned variables during the densification process. Impact of raw material particle size distribution on final biofuels quality was also proven by experimental research on semi-production pelleting plant.

  14. Electroweak oblique parameters as a probe of the trilinear Higgs boson self-interaction

    DEFF Research Database (Denmark)

    Kribs, Graham D.; Maier, Andreas; Rzehak, Heidi

    2017-01-01

    We calculate the two-loop contributions from a modified trilinear Higgs self-interaction, κλλSMvh3, to the electroweak oblique parameters S and T. Using the current bounds on S and T from electroweak measurements, we find the 95% C.L. constraint on the modified trilinear coupling to be -14.0≤κλ≤17.......4. The largest effects on S and T arise from two insertions of the modified trilinear coupling that result in T/S≃-3/2; remarkably, this is nearly parallel to the axis of the tightest experimental constraint in the S-T plane. No contributions to S and T arise from a modified Higgs quartic coupling at two......-loop order. These calculations utilized a gauge-invariant parametrization of the trilinear Higgs coupling in terms of higher-dimensional operators (H†H)n with n≥3. Interestingly, the bounds on κλ that we obtain are comparable to constraints from di-Higgs production at the LHC as well as recent bounds from...

  15. On the Physics of Machining Titanium Alloys: Interactions between Cutting Parameters, Microstructure and Tool Wear

    Directory of Open Access Journals (Sweden)

    Mohammed Nouari

    2014-07-01

    Full Text Available The current work deals with the analysis of mechanisms involved during the machining process of titanium alloys. Two different materials were chosen for the study: Ti-6Al-4V and Ti-55531. The objective was to understand the effect of all cutting parameters on the tool wear behavior and stability of the cutting process. The investigations were focused on the mechanisms of the chip formation process and their interaction with tool wear. At the microstructure scale, the analysis confirms the intense deformation of the machined surface and shows a texture modification. As the cutting speed increases, cutting forces and temperature show different progressions depending on the considered microstructure (Ti-6Al-4V or Ti-55531 alloy. Results show for both materials that the wear process is facilitated by the high cutting temperature and the generation of high stresses. The analysis at the chip-tool interface of friction and contact nature (sliding or sticking contact shows that machining Ti55531 often exhibits an abrasion wear process on the tool surface, while the adhesion and diffusion modes followed by the coating delamination process are the main wear modes when machining the usual Ti-6Al-4V alloy.

  16. Biological activities and molecular interactions of the C-terminal residue of thrombospondin-4, an epitome of acidic amphipathic peptides.

    Science.gov (United States)

    Congote, Luis F; Sadvakassova, Gulzhakhan; Dobocan, Monica C; Difalco, Marcos R; Kriazhev, Leonid

    2010-04-01

    C21, the C-terminal residue of thrombospondin-4 (TSP-4), was identified as a peptide growth factor during an investigation concerning erythropoietin-dependent, erythroid stimulating factors of endothelial origin. It is active in cultures of several human hematopoietic stem cells, skin fibroblasts and kidney epithelial cells and stimulates red cell formation in anemic mice. A method of affinity chromatography in the presence of high concentrations of Triton X-100, previously developed for identifying proteins associated with the TSP-1 receptor CD47, was utilized for the detection of C21 binding molecules and their detergent-resistant, associated partners. These experiments helped to delineate two different mechanisms of C21 action, which are compatible with its cell proliferating activity. As a cell matrix peptide, C21 binds to the osteopontin receptor CD44 and could act as an osteopontin antagonist, preventing the inhibition of primitive hematopoietic stem cell proliferation. TSP-1, another matrix protein, binds to C21 and could indirectly act as an antagonist, by shunting C21-CD44 interactions. The second mechanism is a direct effect of C21 on cell proliferation. The extremely rapid internalization and nuclear localization of the peptide could be explained by CD44-mediated internalization, followed by a microtubule-mediated transport towards the nucleus, or, eventually, direct membrane insertion. These alternative hypotheses are supported by previously observed membrane insertion of similar synthetic and viral acidic amphipathic peptides, the presence of microtubule-associated protein 1B (MAP1B) and dynactin in the triton-soluble complexes associated with C21 and the presence in such complexes of dual compartment proteins for nuclei and plasma membranes, such as MAP1B, AHNAK and CD44. Copyright (c) 2009 Elsevier Inc. All rights reserved.

  17. Elicitin-induced distal systemic resistance in plants is mediated through the protein-protein interactions influenced by selected lysine residues

    Directory of Open Access Journals (Sweden)

    Hana eUhlíková

    2016-02-01

    Full Text Available Elicitins are a family of small proteins with sterol-binding activity that are secreted by Phytophthora and Pythium spp. classified as oomycete PAMPs. Although alfa- and beta-elicitins bind with the same affinity to one high affinity binding site on the plasma membrane, beta-elicitins (possessing 6-7 lysine residues are generally 50- to 100-fold more active at inducing distal HR and systemic resistance than the alfa-isoforms (with only 1-3 lysine residues.To examine the role of lysine residues in elicitin biological activity, we employed site-directed mutagenesis to prepare a series of beta-elicitin cryptogein variants with mutations on specific lysine residues. In contrast to direct infiltration of protein into leaves, application to the stem revealed a rough correlation between protein’s charge and biological activity, resulting in protection against Phytophthora parasitica. A detailed analysis of proteins’ movement in plants showed no substantial differences in distribution through phloem indicating differences in consequent apoplastic or symplastic transport. In this process, an important role of homodimer formation together with the ability to form a heterodimer with potential partner represented by endogenous plants LTPs is suggested. Our work demonstrates a key role of selected lysine residues in these interactions and stresses the importance of processes preceding elicitin recognition responsible for induction of distal systemic resistance.

  18. The presence of modifiable residues in the core peptide part of precursor nisin is not crucial for precursor nisin interactions with NisB- and NisC.

    Directory of Open Access Journals (Sweden)

    Rustem Khusainov

    Full Text Available Precursor nisin is a model posttranslationally modified precursor lantibiotic that can be structurally divided into a leader peptide sequence and a modifiable core peptide part. The nisin core peptide clearly plays an important role in the precursor nisin-nisin modification enzymes interactions, since it has previously been shown that the construct containing only the nisin leader sequence is not sufficient to pull-down the nisin modification enzymes NisB and NisC. Serines and threonines in the core peptide part are the residues that NisB specifically dehydrates, and cysteines are the residues that NisC stereospecifically couples to the dehydrated amino acids. Here, we demonstrate that increasing the number of negatively charged residues in the core peptide part of precursor nisin, which are absent in wild-type nisin, does not abolish binding of precursor nisin to the modification enzymes NisB and NisC, but dramatically decreases the antimicrobial potency of these nisin mutants. An unnatural precursor nisin variant lacking all serines and threonines in the core peptide part and an unnatural precursor nisin variant lacking all cysteines in the core peptide part still bind the nisin modification enzymes NisB and NisC, suggesting that these residues are not essential for direct interactions with the nisin modification enzymes NisB and NisC. These results are important for lantibiotic engineering studies.

  19. Effects of the Manufacturing Process on the Reliability of the Multilayer Structure in MetalMUMPs Actuators: Residual Stresses and Variation of Design Parameters

    Directory of Open Access Journals (Sweden)

    Jianbin Guo

    2017-11-01

    Full Text Available Potential problems induced by the multilayered manufacturing process pose a serious threat to the long-term reliability of MEMSCAP® actuators under in-service thermal cycling. Damage would initiate and propagate in different material layers because of a large mismatch of their thermal expansions. In this research, residual stresses and variations of design parameters induced by metal multi-user micro electromechanical system processes (MetalMUMPs were examined to evaluate their effects on the thermal fatigue lifetime of the multilayer structure and, thus, to improve MEMSCAP® design. Since testing in such micro internal structure is difficult to conduct and traditional testing schemes are destructive, a numerical subdomain method based on a finite element technique was employed. Thermomechanical deformation from metal to insulator layers under in-service temperature cycling (obtained from the multiphysics model of the entire actuator, which was validated by experimental and specified analytical solutions was accurately estimated to define failures with a significant efficiency and feasibility. Simulation results showed that critical failure modes included interface delamination, plastic deformation, micro cracking, and thermal fatigue, similarly to what was concluded in the MEMSCAP® technical report.

  20. Role of enthalpy-entropy compensation interactions in determining the conformational propensities of amino acid residues in unfolded peptides.

    Science.gov (United States)

    Toal, Siobhan E; Verbaro, Daniel J; Schweitzer-Stenner, Reinhard

    2014-02-06

    The driving forces governing the unique and restricted conformational preferences of amino acid residues in the unfolded state are still not well understood. In this study, we experimentally determine the individual thermodynamic components underlying intrinsic conformational propensities of these residues. Thermodynamic analysis of ultraviolet-circular dichroism (UV-CD) and (1)H NMR data for a series of glycine capped amino acid residues (i.e., G-x-G peptides) reveals the existence of a nearly exact enthalpy-entropy compensation for the polyproline II-β strand equilibrium for all investigated residues. The respective ΔHβ, ΔSβ values exhibit a nearly perfect linear relationship with an apparent compensation temperature of 295 ± 2 K. Moreover, we identified iso-equilibrium points for two subsets of residues at 297 and 305 K. Thus, our data suggest that within this temperature regime, which is only slightly below physiological temperatures, the conformational ensembles of amino acid residues in the unfolded state differ solely with respect to their capability to adopt turn-like conformations. Such iso-equilibria are rarely observed, and their existence herein indicates a common physical origin behind conformational preferences, which we are able to assign to side-chain dependent backbone solvation. Conformational effects such as differences between the number of sterically allowed side chain rotamers can contribute to enthalpy and entropy but not to the Gibbs energy associated with conformational preferences. Interestingly, we found that alanine, aspartic acid, and threonine are the only residues which do not share these iso-equilbiria. The enthalpy-entropy compensation discovered as well as the iso-equilbrium and thermodynamics obtained for each amino acid residue provide a new and informative way of identifying the determinants of amino acid propensities in unfolded and disordered states.

  1. Interaction between anxiety, depression, quality of life and clinical parameters in chronic tension-type headache.

    Science.gov (United States)

    Peñacoba-Puente, Cecilia; Fernández-de-Las-Peñas, César; González-Gutierrez, Jose L; Miangolarra-Page, Juan C; Pareja, Juan A

    2008-10-01

    Our aim was to investigate the mediating or moderating role of anxiety and depression in the relationship between headache clinical parameters and quality of life in Chronic Tension-Type Headache (CTTH). Twenty-five patients diagnosed with CTTH according to the criteria of the International Headache Society were studied. A headache diary was kept for 4 weeks in order to substantiate the diagnosis and record the pain history. Quality of life was assessed by means of the Medical Outcome Study (MOS) 36-Item Short-Form (SF-36) questionnaire. The Beck Depression Inventory (BDI-II) was used to assess depression, and the Trait Anxiety Scale (TA) from the State-Trait Anxiety Inventory was administered in order to assess anxiety. Moderating and mediating analyses were conducted with ordinary least squares multiple regression analysis using the SPSS General Linear Model procedure. Anxiety mediated the effect between headache frequency and quality of life, but not the effect of either headache intensity or duration. Anxiety totally mediated the effects of headache frequency on vitality, social functioning and mental health. On the other hand, depression modulated the effect in the mental health domain. The effect in the mental health domain was a function of the interaction between headache duration and depression (beta=-0.34, p<0.05), after controlling for age, gender, the main effects of headache duration, and depression. We did not find anxiety to be a moderating factor between intensity, frequency or duration of headache and perceived quality of life. Anxiety exerts a mediating effect, conditioning the relationship between headache frequency and some quality of life domains; depression seems to play an inherent role in the reduced quality of life of these patients, that is, it has a moderating effect.

  2. Residual deposits (residual soil)

    International Nuclear Information System (INIS)

    Khasanov, A.Kh.

    1988-01-01

    Residual soil deposits is accumulation of new formate ore minerals on the earth surface, arise as a result of chemical decomposition of rocks. As is well known, at the hyper genes zone under the influence of different factors (water, carbonic acid, organic acids, oxygen, microorganism activity) passes chemical weathering of rocks. Residual soil deposits forming depends from complex of geologic and climatic factors and also from composition and physical and chemical properties of initial rocks

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

    Science.gov (United States)

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

    2013-01-01

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

  4. β{sup -} transitions of {sub 7}{sup 16}N{sub 9} → {sub 8}{sup 16}O{sub 8} with optimized SDI residual interaction using pnTDA and TDA approximations

    Energy Technology Data Exchange (ETDEWEB)

    Pahlavani, M.R.; Firoozi, B. [University of Mazandaran, Department of Nuclear Physics, Faculty of Basic Science, P.O. Box 47415-416, Babolsar (Iran, Islamic Republic of)

    2015-11-15

    Within a developed particle-hole approach, a systematic study of the β{sup -} transition from the ground state of the {sup 16}N nucleus to the ground and some exited states of the {sup 16}O nucleus has been carried out. The energy spectrum and the wave functions of pure configuration of the {sup 16}N and {sup 16}O nuclei are numerically obtained using the mean-field shell model with respect to the Woods-Saxon nuclear potential accompanying spin-orbit and Coulomb interaction. Considering SDI residual interaction, mixed configuration of ground and excited pnTDA and TDA states are extracted for the aforementioned nucleus. These energy spectra and corresponding eigenstates are highly correspondent to the experimental energy spectrum and eigenstates after adjusting the residual potential parameters using the Nelder-Mead (NM) algorithm. In this approach, the endpoint energy, log ft and the partial half-lives of some possible transitions are calculated. The obtained results using the optimized SDI approach are reasonably close to the available experimental data. (orig.)

  5. Interactive 3-D Immersive Visualization for Analysis of Large Multi-Parameter Atmospheric Data Sets

    Science.gov (United States)

    Frenzer, J. B.; Hoell, J. M.; Holdzkom, J. J.; Jacob, D.; Fuelberg, H.; Avery, M.; Carmichael, G.; Hopkins, D. L.

    2001-12-01

    Significant improvements in the ability of atmospheric chemistry models to predict the transport and production of atmospheric constituents on regional and global scales have been realized over the past decade. Concurrent with the model improvements, has been an increase in the size and complexity of atmospheric observational data sets. As a result, the challenge to provide efficient and realistic visualization of atmospheric data "products" has increased dramatically. Over the past several years, personnel from the Atmospheric Sciences Data Center (ASDC) at NASA's Langley Research Center have explored the merits of visualizing atmospheric data products using interactive, immersive visualization hardware and software. As part of this activity, the Virtual Global Explorer and Observatory (vGeo) software, developed by VRCO, Inc., has been utilized to support the visual analysis of large multivariate data sets. The vGeo software provides an environment in which the user can create, view, navigate, and interact with data, models, and images in an immersive 3-D environment. The vGeo visualization capability was employed during the March/April 2001, NASA Global Tropospheric Experiment Transport and Chemical Evolution over the Pacific (TRACE-P) mission [(GTE) http://www-gte.larc.nasa.gov] to support day-to-day flight-planning activities through the creation of virtual 3-D worlds containing modeled data and proposed aircraft flight paths. The GTE, a major activity within NASA's Earth Science Enterprise, is primarily an aircraft-based measurement program, supplemented by ground-based measurements and satellite observations, focused on understanding the impact of human activity on the global troposphere. The TRACE-P is the most recent campaign conducted by GTE and was deployed to Hong Kong and then to the Yokota Airbase, Japan. TRACE-P is the third in a series of GTE field campaigns in the northwestern Pacific region to understand the chemical composition of air masses

  6. Needle parameter variation of mature black spruce families displaying a genetic x environment interaction in growth

    Science.gov (United States)

    John E. Major; Kurt H. Johnsen; Debby C. Barsi; Moira Campbell

    2013-01-01

    To examine soil moisture stress, light, and genetic effects on individual needle parameters and investigate total needle contribution to productivity, individual and total needle parameter variation were quantified in 32-year-old black spruce from five crown positions from four full-sib families studied previously for drought tolerance and differential productivity on...

  7. Residues essential for Panton-Valentine leukocidin S component binding to its cell receptor suggest both plasticity and adaptability in its interaction surface.

    Directory of Open Access Journals (Sweden)

    Benoit-Joseph Laventie

    Full Text Available Panton-Valentine leukocidin (PVL, a bicomponent staphylococcal leukotoxin, is involved in the poor prognosis of necrotizing pneumonia. The present study aimed to elucidate the binding mechanism of PVL and in particular its cell-binding domain. The class S component of PVL, LukS-PV, is known to ensure cell targeting and exhibits the highest affinity for the neutrophil membrane (Kd∼10(-10 M compared to the class F component of PVL, LukF-PV (Kd∼10(-9 M. Alanine scanning mutagenesis was used to identify the residues involved in LukS-PV binding to the neutrophil surface. Nineteen single alanine mutations were performed in the rim domain previously described as implicated in cell membrane interactions. Positions were chosen in order to replace polar or exposed charged residues and according to conservation between leukotoxin class S components. Characterization studies enabled to identify a cluster of residues essential for LukS-PV binding, localized on two loops of the rim domain. The mutations R73A, Y184A, T244A, H245A and Y250A led to dramatically reduced binding affinities for both human leukocytes and undifferentiated U937 cells expressing the C5a receptor. The three-dimensional structure of five of the mutants was determined using X-ray crystallography. Structure analysis identified residues Y184 and Y250 as crucial in providing structural flexibility in the receptor-binding domain of LukS-PV.

  8. A modified Leslie-Gower predator-prey interaction model and parameter identifiability

    Science.gov (United States)

    Tripathi, Jai Prakash; Meghwani, Suraj S.; Thakur, Manoj; Abbas, Syed

    2018-01-01

    In this work, bifurcation and a systematic approach for estimation of identifiable parameters of a modified Leslie-Gower predator-prey system with Crowley-Martin functional response and prey refuge is discussed. Global asymptotic stability is discussed by applying fluctuation lemma. The system undergoes into Hopf bifurcation with respect to parameters intrinsic growth rate of predators (s) and prey reserve (m). The stability of Hopf bifurcation is also discussed by calculating Lyapunov number. The sensitivity analysis of the considered model system with respect to all variables is performed which also supports our theoretical study. To estimate the unknown parameter from the data, an optimization procedure (pseudo-random search algorithm) is adopted. System responses and phase plots for estimated parameters are also compared with true noise free data. It is found that the system dynamics with true set of parametric values is similar to the estimated parametric values. Numerical simulations are presented to substantiate the analytical findings.

  9. Estimation of kinetic parameters related to biochemical interactions between hydrogen peroxide and signal transduction proteins

    OpenAIRE

    Brito, Paula M.; Antunes, Fernando

    2014-01-01

    The lack of kinetic data concerning the biological effects of reactive oxygen species is slowing down the development of the field of redox signaling. Herein, we deduced and applied equations to estimate kinetic parameters from typical redox signaling experiments. H2O2-sensing mediated by the oxidation of a protein target and the switch-off of this sensor, by being converted back to its reduced form, are the two processes for which kinetic parameters are determined. The experimental data requ...

  10. Uncovering the local inelastic interactions during manufacture of ductile cast iron: How the substructure of the graphite particles can induce residual stress concentrations in the matrix

    DEFF Research Database (Denmark)

    Andriollo, Tito; Hellström, Kristina; Sonne, Mads Rostgaard

    2018-01-01

    Recent X-ray diffraction (XRD) measurements have revealed that plastic deformation and a residual elastic strain field can be present around the graphite particles in ductile cast iron after manufacturing, probably due to some local mismatch in thermal contraction. However, as only one component...... of the elastic strain tensor could be obtained from the XRD data, the shape and magnitude of the associated residual stress field have remained unknown. To compensate for this and to provide theoretical insight into this unexplored topic, a combined experimental-numerical approach is presented in this paper....... First, a ma terial equivalent to the ductile cast iron matrix is manufactured and subjected to dilato- metric and high-temperature tensile tests. Subsequently, a two-scale hierarchical top-down model is devised, calibrated on the basis of the collected data and used to simulate the interaction between...

  11. Influenza human monoclonal antibody 1F1 interacts with three major antigenic sites and residues mediating human receptor specificity in H1N1 viruses.

    Directory of Open Access Journals (Sweden)

    Tshidi Tsibane

    Full Text Available Most monoclonal antibodies (mAbs to the influenza A virus hemagglutinin (HA head domain exhibit very limited breadth of inhibitory activity due to antigenic drift in field strains. However, mAb 1F1, isolated from a 1918 influenza pandemic survivor, inhibits select human H1 viruses (1918, 1943, 1947, and 1977 isolates. The crystal structure of 1F1 in complex with the 1918 HA shows that 1F1 contacts residues that are classically defined as belonging to three distinct antigenic sites, Sa, Sb and Ca(2. The 1F1 heavy chain also reaches into the receptor binding site (RBS and interacts with residues that contact sialoglycan receptors and determine HA receptor specificity. The 1F1 epitope is remarkably similar to the previously described murine HC63 H3 epitope, despite significant sequence differences between H1 and H3 HAs. Both antibodies potently inhibit receptor binding, but only HC63 can block the pH-induced conformational changes in HA that drive membrane fusion. Contacts within the RBS suggested that 1F1 may be sensitive to changes that alter HA receptor binding activity. Affinity assays confirmed that sequence changes that switch the HA to avian receptor specificity affect binding of 1F1 and a mAb possessing a closely related heavy chain, 1I20. To characterize 1F1 cross-reactivity, additional escape mutant selection and site-directed mutagenesis were performed. Residues 190 and 227 in the 1F1 epitope were found to be critical for 1F1 reactivity towards 1918, 1943 and 1977 HAs, as well as for 1I20 reactivity towards the 1918 HA. Therefore, 1F1 heavy-chain interactions with conserved RBS residues likely contribute to its ability to inhibit divergent HAs.

  12. Optimization of long range potential interaction parameters in ion mobility spectrometry

    Science.gov (United States)

    Wu, Tianyang; Derrick, Joseph; Nahin, Minal; Chen, Xi; Larriba-Andaluz, Carlos

    2018-02-01

    The problem of optimizing Lennard-Jones (L-J) potential parameters to perform collision cross section (CCS) calculations in ion mobility spectrometry has been undertaken. The experimental CCS of 16 small organic molecules containing carbon, hydrogen, oxygen, nitrogen, and fluoride in N2 was compared to numerical calculations using Density Functional Theory (DFT). CCS calculations were performed using the momentum transfer algorithm IMoS and a 4-6-12 potential without incorporating the ion-quadrupole potential. A ceteris paribus optimization method was used to optimize the intercept σ and potential well-depth ɛ for the given atoms. This method yields important information that otherwise would remain concealed. Results show that the optimized L-J parameters are not necessarily unique with intercept and well-depth following an exponential relation at an existing line of minimums. Similarly, the method shows that some molecules containing atoms of interest may be ill-conditioned candidates to perform optimizations of the L-J parameters. The final calculated CCSs for the chosen parameters differ 1% on average from their experimental counterparts. This result conveys the notion that DFT calculations can indeed be used as potential candidates for CCS calculations and that effects, such as the ion-quadrupole potential or diffuse scattering, can be embedded into the L-J parameters without loss of accuracy but with a large increase in computational efficiency.

  13. The interactive effect of fungicide residues and yeast assimilable nitrogen on fermentation kinetics and hydrogen sulfide production during cider fermentation

    OpenAIRE

    Boudreau, Thomas F; Peck, Gregory M; O'Keefe, Sean F; Stewart, Amanda C

    2016-01-01

    Abstract BACKGROUND Fungicide residues on fruit may adversely affect yeast during cider fermentation, leading to sluggish or stuck fermentation or the production of hydrogen sulfide (H2S), which is an undesirable aroma compound. This phenomenon has been studied in grape fermentation but not in apple fermentation. Low nitrogen availability, which is characteristic of apples, may further exacerbate the effects of fungicides on yeast during fermentation. The present study explored the effects of...

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

    Science.gov (United States)

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

    2013-01-28

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

  15. A novel method to survey parameters of an ion beam and its interaction with a target

    Science.gov (United States)

    Long, J. D.; Yang, Z.; Li, J.; Wang, X. H.; Wang, T.; Lan, C. H.; Dong, P.; Li, X.; He, J. L.; Zheng, L.; Liu, P.

    2017-09-01

    Beam profile and composition of the pulsed ion beam from a vacuum arc source are valuable information for designing a high-intensity deuterium-tritium neutron generator. Traditional methods are notoriously difficult to obtain the information at the same time. A novel off-line diagnostic method is presented, which can obtain the transverse beam profile with high resolution as well as species of the ions in the beam. The method is using a silicon target with high purity to interact with the ion beam, and then use secondary ion mass spectrometry (SIMS) to analyze the interaction zone of the target to get the beam information. More information on beam-target interaction could get simultaneously. Proof-of-principle simulation and experimental works have demonstrated this method is practical.

  16. Identification of dominant interactions between climatic seasonality, catchment characteristics and agricultural activities on Budyko-type equation parameter estimation

    Science.gov (United States)

    Xing, Wanqiu; Wang, Weiguang; Shao, Quanxi; Yong, Bin

    2018-01-01

    Quantifying precipitation (P) partition into evapotranspiration (E) and runoff (Q) is of great importance for global and regional water availability assessment. Budyko framework serves as a powerful tool to make simple and transparent estimation for the partition, using a single parameter, to characterize the shape of the Budyko curve for a "specific basin", where the single parameter reflects the overall effect by not only climatic seasonality, catchment characteristics (e.g., soil, topography and vegetation) but also agricultural activities (e.g., cultivation and irrigation). At the regional scale, these influencing factors are interconnected, and the interactions between them can also affect the single parameter of Budyko-type equations' estimating. Here we employ the multivariate adaptive regression splines (MARS) model to estimate the Budyko curve shape parameter (n in the Choudhury's equation, one form of the Budyko framework) of the selected 96 catchments across China using a data set of long-term averages for climatic seasonality, catchment characteristics and agricultural activities. Results show average storm depth (ASD), vegetation coverage (M), and seasonality index of precipitation (SI) are three statistically significant factors affecting the Budyko parameter. More importantly, four pairs of interactions are recognized by the MARS model as: The interaction between CA (percentage of cultivated land area to total catchment area) and ASD shows that the cultivation can weaken the reducing effect of high ASD (>46.78 mm) on the Budyko parameter estimating. Drought (represented by the value of Palmer drought severity index 0.23) tend to enhance the Budyko parameter reduction by large SI (>0.797). Low vegetation coverage (34.56%) is likely to intensify the rising effect on evapotranspiration ratio by IA (percentage of irrigation area to total catchment area). The Budyko n values estimated by the MARS model reproduce the calculated ones by the observation well

  17. Generation of a residual current by interaction between the coastal boundary-layer and the ekman layer in a tidal motion

    OpenAIRE

    Aelbrecht, D; Dhieres, Gc; Zhang, Xz

    1993-01-01

    Some experiments have been made with the large rotating tank at the Institut de Mecanique de Grenoble to reproduce a sinusoidal flow along a vertical wall, over a flat bottom, with or without slope, in a homogeneous fluid. The objective of these experiments was to simulate a tidal motion, restricted to its main harmonic component M2, parallel to a vertical coast; and to demonstrate a particular mode of generation of residual circulation near the coast as a result of the interaction between fr...

  18. Creating and Exploring Huge Parameter Spaces: Interactive Evolution as a Tool for Sound Generation

    DEFF Research Database (Denmark)

    Dahlstedt, Palle

    2001-01-01

    In this paper, a program is presented that applies interactive evolution to sound generation, i.e., preferred individuals are repeatedly selected from a population of genetically bred sound objects, created with various synthesis and pattern generation algorithms. This simplifies aural exploratio...

  19. Impact parameter analysis of proton-proton elastic and inelastic interactions at 360 GeV/c

    International Nuclear Information System (INIS)

    Banerjee, S.; Ragavan, R.; Bailly, J

    1987-01-01

    Data obtained with the European Hybrid Spectrometer on the proton-proton elastic scattering at 360 GeV/c are presented. The differential cross sections of elastic and inelastic pp-interactions are studied as a function of the impact parameter. The results are compared to those obtained at other energies. They are interpreted in the framework of a simple geometrical Monte-Carlo model of inelastic collisions considering protons as composite particles having a definite effective radius with valence quarks inside. The shape of the inelastic overlap function is well reproduced for both pp- and π + p-interactions. The effective radii of the proton and pion as well as of the valence quarks are estimated for inelastic interactions. The model calculations indicate an increase of the effective radii both of protons and valence quarks and an increase of the proton opacity with increasing energy

  20. Strip footing - retaining wall interaction : Parameters of influence : Numerical and physical modelling

    OpenAIRE

    POPA, H; THOREL, L; GAUDIN, C; GARNIER, J

    2005-01-01

    Diaphragms walls are often used for supporting deep excavations, especially in urban areas. The correct estimation of their behaviour is very important considering the impact on the neighbouring buildings.The paper presents some of the numerical results using FEM for an embedded wall nearby a strip footing. Different parameters have been investigated : soil characteristics, distance between the retaining wall and the strip footing, foundation embedment and width. The finite element model and ...

  1. Creating and Exploring Huge Parameter Spaces: Interactive Evolution as a Tool for Sound Generation

    DEFF Research Database (Denmark)

    Dahlstedt, Palle

    2001-01-01

    of huge synthesis parameter spaces, and presents a possibility for the sound artist to create new sound engines customized for this kind of creation and exploration – sound engines too complex to control in any other way. Different sound engines are presented, together with a discussion of compositional...... applications. It is also shown how this technique can be used to simplify sound design in standard hardware synthesizers, a task normally avoided by most musicians, due to the required amount of technical understanding....

  2. Intake of Fruits and Vegetables with Low-to-Moderate Pesticide Residues Is Positively Associated with Semen-Quality Parameters among Young Healthy Men123

    Science.gov (United States)

    Gaskins, Audrey J; Williams, Paige L; Mendiola, Jaime; Levine, Hagai; Hauser, Russ; Swan, Shanna H; Chavarro, Jorge E

    2016-01-01

    Background: Numerous studies have shown that occupational or environmental pesticide exposure can affect male fertility. There is less evidence, however, regarding any potentially adverse effects of pesticide residues in foods on markers of male fertility potential. Objectives: We examined the relations between fruit and vegetable intake, considering pesticide residue status, and semen quality and serum concentrations of reproductive hormones in healthy young men. Methods: The Rochester Young Men's Study is a cross-sectional study that recruited men aged 18–22 y (n = 189) in Rochester, New York. Participants completed a questionnaire, provided a semen sample, had a blood sample drawn, and underwent a physical examination at enrollment. Semen samples were analyzed for total sperm count, sperm concentration, morphology, motility, ejaculate volume, total motile count, and total normal count. Dietary intake during the previous year was assessed by a validated food-frequency questionnaire. Fruit and vegetables were categorized as having high [Pesticide Residue Burden Score (PRBS) ≥4] or low-to-moderate (PRBS vegetable intake with semen variables and reproductive hormones while adjusting for potential confounding factors. Results: The total intake of fruit and vegetables was unrelated to semen quality. However, the intake of fruit and vegetables with low-to-moderate pesticide residues was associated with a higher total sperm count and sperm concentration, whereas the intake of fruit and vegetables with high pesticide residues was unrelated to semen quality. On average, men in the highest quartile of low-to-moderate-pesticide fruit and vegetable intake (≥2.8 servings/d) had a 169% (95% CI: 45%, 400%) higher total sperm count and a 173% (95% CI: 57%, 375%) higher sperm concentration than did men in the lowest quartile (vegetables, regardless of pesticide-residue status, was not associated with reproductive hormone concentrations. Conclusions: The consumption of fruit

  3. Intake of Fruits and Vegetables with Low-to-Moderate Pesticide Residues Is Positively Associated with Semen-Quality Parameters among Young Healthy Men.

    Science.gov (United States)

    Chiu, Yu-Han; Gaskins, Audrey J; Williams, Paige L; Mendiola, Jaime; Jørgensen, Niels; Levine, Hagai; Hauser, Russ; Swan, Shanna H; Chavarro, Jorge E

    2016-05-01

    Numerous studies have shown that occupational or environmental pesticide exposure can affect male fertility. There is less evidence, however, regarding any potentially adverse effects of pesticide residues in foods on markers of male fertility potential. We examined the relations between fruit and vegetable intake, considering pesticide residue status, and semen quality and serum concentrations of reproductive hormones in healthy young men. The Rochester Young Men's Study is a cross-sectional study that recruited men aged 18-22 y (n = 189) in Rochester, New York. Participants completed a questionnaire, provided a semen sample, had a blood sample drawn, and underwent a physical examination at enrollment. Semen samples were analyzed for total sperm count, sperm concentration, morphology, motility, ejaculate volume, total motile count, and total normal count. Dietary intake during the previous year was assessed by a validated food-frequency questionnaire. Fruit and vegetables were categorized as having high [Pesticide Residue Burden Score (PRBS) ≥4] or low-to-moderate (PRBS vegetable intake with semen variables and reproductive hormones while adjusting for potential confounding factors. The total intake of fruit and vegetables was unrelated to semen quality. However, the intake of fruit and vegetables with low-to-moderate pesticide residues was associated with a higher total sperm count and sperm concentration, whereas the intake of fruit and vegetables with high pesticide residues was unrelated to semen quality. On average, men in the highest quartile of low-to-moderate-pesticide fruit and vegetable intake (≥2.8 servings/d) had a 169% (95% CI: 45%, 400%) higher total sperm count and a 173% (95% CI: 57%, 375%) higher sperm concentration than did men in the lowest quartile (vegetables, regardless of pesticide-residue status, was not associated with reproductive hormone concentrations. The consumption of fruit and vegetables with low-to-moderate pesticide residues

  4. Study of the experimental parameters associated to the determination of residual macro stresses in stainless steel tubes through x-rays diffraction method

    International Nuclear Information System (INIS)

    Guimaraes, L.R.

    1990-01-01

    The basic principles related to the determination of residual macro stresses by X-rays diffractometry are present, whereas different techniques associated with the respective experimental errors are discussed. The residual stresses in two 304 L stainless steel tubes were measured using three models of diffractometers, Rigaku SG-8, Jeol JDX-11PA and Rigaku Strainflex. The measured values of stresses as well as the reproducibilities are examined. The suitability of peak location method, by fitting three data points to the parabolic function, is discussed through values of position and intensity obtained by two of the above diffractometers. (author)

  5. Study of the experimental parameters associated to the determination of residual macro stresses in stainless steel tubes, through x-ray diffraction method

    International Nuclear Information System (INIS)

    Guimaraes, L.R.

    1990-01-01

    The basic principles related to the determination of residual macro stresses by X-rays diffractometry are present, whereas different techniques associated with the respective experimental errors are discussed. The residual stresses in two 304 L stainless steel tubes were measured using three models of diffractometers, Rigaku SG-8, Jeol JDX-11PA and Rigaku Strainflex. The measured values of stresses as well as the reproducibilities are examined. The suitability of peak location method, by fitting three data points to the parabolic function, is discussed through values of position and intensity obtained by two of the above diffractometers. (author)

  6. Assessing the relative importance of parameter and forcing uncertainty and their interactions in conceptual hydrological model simulations

    Science.gov (United States)

    Mockler, E. M.; Chun, K. P.; Sapriza-Azuri, G.; Bruen, M.; Wheater, H. S.

    2016-11-01

    Predictions of river flow dynamics provide vital information for many aspects of water management including water resource planning, climate adaptation, and flood and drought assessments. Many of the subjective choices that modellers make including model and criteria selection can have a significant impact on the magnitude and distribution of the output uncertainty. Hydrological modellers are tasked with understanding and minimising the uncertainty surrounding streamflow predictions before communicating the overall uncertainty to decision makers. Parameter uncertainty in conceptual rainfall-runoff models has been widely investigated, and model structural uncertainty and forcing data have been receiving increasing attention. This study aimed to assess uncertainties in streamflow predictions due to forcing data and the identification of behavioural parameter sets in 31 Irish catchments. By combining stochastic rainfall ensembles and multiple parameter sets for three conceptual rainfall-runoff models, an analysis of variance model was used to decompose the total uncertainty in streamflow simulations into contributions from (i) forcing data, (ii) identification of model parameters and (iii) interactions between the two. The analysis illustrates that, for our subjective choices, hydrological model selection had a greater contribution to overall uncertainty, while performance criteria selection influenced the relative intra-annual uncertainties in streamflow predictions. Uncertainties in streamflow predictions due to the method of determining parameters were relatively lower for wetter catchments, and more evenly distributed throughout the year when the Nash-Sutcliffe Efficiency of logarithmic values of flow (lnNSE) was the evaluation criterion.

  7. Optimal definition of inter-residual contact in globular proteins based on pairwise interaction energy calculations, its robustness, and applications.

    Science.gov (United States)

    Fačkovec, Boris; Vondrášek, Jiří

    2012-10-25

    Although a contact is an essential measurement for the topology as well as strength of non-covalent interactions in biomolecules and their complexes, there is no general agreement in the definition of this feature. Most of the definitions work with simple geometric criteria which do not fully reflect the energy content or ability of the biomolecular building blocks to arrange their environment. We offer a reasonable solution to this problem by distinguishing between "productive" and "non-productive" contacts based on their interaction energy strength and properties. We have proposed a method which converts the protein topology into a contact map that represents interactions with statistically significant high interaction energies. We do not prove that these contacts are exclusively stabilizing, but they represent a gateway to thermodynamically important rather than geometry-based contacts. The process is based on protein fragmentation and calculation of interaction energies using the OPLS force field and relies on pairwise additivity of amino acid interactions. Our approach integrates the treatment of different types of interactions, avoiding the problems resulting from different contributions to the overall stability and the different effect of the environment. The first applications on a set of homologous proteins have shown the usefulness of this classification for a sound estimate of protein stability.

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

    DEFF Research Database (Denmark)

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

    2016-01-01

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

  9. Calculation of Coulomb-interaction parameters for La2CuO4 using a constrained-density-functional approach

    Science.gov (United States)

    Hybertsen, Mark S.; Schlüter, Michael; Christensen, Niels E.

    1989-05-01

    The constrained-density-functional approach is used to calculate the energy surface as a function of local charge fluctuations in La2CuO4. This energy surface is then mapped onto a self-consistent mean-field solution of the Hubbard model which allows extraction of the Coulomb interaction parameters when combined with one-electron parameters derived from band-structure results. Variations in the local Cu d charges and in-plane O p charge are considered for the prototypical high-Tc parent oxide La2CuO4. To isolate the charge fluctuations, the calculations are done in a supercell of size up to 2×2 in the basal plane. The local density-functional calculations are done using the linear muffin-tin orbital approach with the atomic sphere approximation. In the Hubbard Hamiltonian, the Cu d(x2-y2) and O p(x,y) orbitals are included in the pdσ configuration. The one-electron parameters consist of bare on-site energies (ɛp,ɛd) and first-neighbor hopping from Cu to O (tpd) and from O to O (tpp) while the Coulomb-interaction parameters include on-site (Ud,Up) and intersite (Upd,Upp) terms. Results of the present calculation indicate that La2CuO4 is intermediate between the extreme spin or charge fluctuation regimes. This places strong constraints on the available parameter space for theories of high-Tc superconductivity based on the extended Hubbard model.

  10. A cation-π interaction at a phenylalanine residue in the glycine receptor binding site is conserved for different agonists

    DEFF Research Database (Denmark)

    Pless, Stephan Alexander; Hanek, Ariele P; Price, Kerry L

    2011-01-01

    . In the current study, we investigated whether the lower efficacy agonists of the human GlyR β-alanine and taurine also form cation-π interactions with Phe159. By incorporating a series of unnatural amino acids, we found cation-π interactions between Phe159 and the amino groups of β-alanine and taurine....... The strengths of these interactions were significantly weaker than for glycine. Modeling studies suggest that β-alanine and taurine are orientated subtly differently in the binding pocket, with their amino groups further from Phe159 than that of glycine. These data therefore show that similar agonists can have...... similar but not identical orientations and interactions in the binding pocket and provide a possible explanation for the lower potencies of β-alanine and taurine....

  11. DUAL PARAMETER FLOW-CYTOMETRY FOR DEOXYRIBONUCLEIC-ACID AND INTERMEDIATE FILAMENT PROTEINS OF RESIDUAL MATURE TERATOMA - ALL TUMOR-CELLS ARE ANEUPLOID

    NARCIS (Netherlands)

    LOOIJENGA, LHJ; OOSTERHUIS, JW; RAMAEKERS, FCS; DEJONG, B; BECK, JLM; SLEIJFER, DT; KOOPS, HS; Dam, A.

    Most testicular germ cell tumors of adults are presumably derived from polyploid carcinoma in situ. Thus, one would expect that even highly differentiated teratoma components are aneuploid and that it is unlikely to find diploid tumor cell (sub)populations. We studied 10 residual mature teratomas

  12. Critical parameters of Quark-Hadron phase transition with interacting and massive quarks

    International Nuclear Information System (INIS)

    Singh, C.P.; Patra, B.K.

    1994-06-01

    Current techniques to simulate the dynamical behaviour of Quark-Gluon Plasma (QGP) reveal that the order of the phase transition as well as the values of the critical parameters depend on the number of quark flavours as well as on the quark-masses included in the simulation. We attempt to show here the effects of the number of quark flavours and quark-masses on critical parameters by using the perturbative, finite temperature field theory to g 3 s order in the strong coupling g s . We treat the hadrons as particles with finite size and its implications on the equation of state for hadron gas are studied. We find that the critical temperature T c is lowered by 9 MeV as we move from two to three quark flavours. The nature of the phase transition always remains as first order. However, the inclusion of quark-masses in our calculation does not affect the result much. (author). 14 refs, 3 figs

  13. Dynamical vanishing of the order parameter in a confined Bardeen-Cooper-Schrieffer Fermi gas after an interaction quench

    Science.gov (United States)

    Hannibal, S.; Kettmann, P.; Croitoru, M. D.; Axt, V. M.; Kuhn, T.

    2018-01-01

    We present a numerical study of the Higgs mode in an ultracold confined Fermi gas after an interaction quench and find a dynamical vanishing of the superfluid order parameter. Our calculations are done within a microscopic density-matrix approach in the Bogoliubov-de Gennes framework which takes the three-dimensional cigar-shaped confinement explicitly into account. In this framework, we study the amplitude mode of the order parameter after interaction quenches starting on the BCS side of the BEC-BCS crossover close to the transition and ending in the BCS regime. We demonstrate the emergence of a dynamically vanishing superfluid order parameter in the spatiotemporal dynamics in a three-dimensional trap. Further, we show that the signal averaged over the whole trap mirrors the spatiotemporal behavior and allows us to systematically study the effects of the system size and aspect ratio on the observed dynamics. Our analysis enables us to connect the confinement-induced modifications of the dynamics to the pairing properties of the system. Finally, we demonstrate that the signature of the Higgs mode is contained in the dynamical signal of the condensate fraction, which, therefore, might provide a new experimental access to the nonadiabatic regime of the Higgs mode.

  14. Study of parameters important to soil-structure interaction in seismic analyses of nuclear power plants

    International Nuclear Information System (INIS)

    Nelson, T.A.

    1983-12-01

    The development of state-of-the-art techniques for analyzing the effects of soil-structure interaction (SSI) on structures during earthquakes is outlined. Emphasis is placed on methods to account for energy dissipation as a result of both wave propagation away from the structure's foundation and hysteretic soil response. Solution techniques are grouped into two major types: substructure methods, which break the problem into a series of steps; and direct methods, which analyze the soil-structure model in one step. In addition to theoretical and historical development of SSI methodology, case studies are presented illustrating the application of these solution techniques. 94 references

  15. Relativistic effects in the intermolecular interaction-induced nuclear magnetic resonance parameters of xenon dimer

    DEFF Research Database (Denmark)

    Hanni, Matti; Lantto, Perttu; Ilias, Miroslav

    2007-01-01

    leading-order one-electron Breit-Pauli perturbation theory (BPPT) is applied using a common gauge origin. Electron correlation effects are studied at the nonrelativistic (NR) coupled-cluster singles and doubles with perturbational triples [CCSD(T)] level of theory. The fully relativistic second...... interaction-induced binary chemical shift d, the anisotropy of the shielding tensor ?s, and the NQC constant along the internuclear axis ?ll are calculated as a function of the internuclear distance. DHF shielding calculations are carried out using gauge-including atomic orbitals. For comparison, the full...

  16. Spin-wave excitations in the SDW state of iron pnictides: A comparison between the roles of interaction parameters

    Science.gov (United States)

    Singh, Dheeraj Kumar

    2017-08-01

    We investigate the roles of interaction parameters in the spin-wave excitations of the ( π,0 ) ordered magnetic state within a five-orbital tight-binding model for iron pnictides. To differentiate between the roles of intraorbital Coulomb interaction (U) and Hund's coupling (J), we focus on the self-consistently obtained mean-field spin-density wave state with a fixed magnetic moment obtained by using different combinations of interaction parameters. We find that J is crucial for the description of various experimentally observed characteristics of the spin-wave excitations including energy-dependent behavior, spin-wave spectral weight distribution, and anisotropy. In particular, J at the higher end of the range of various theoretical and experimental estimates ( J ˜U /4 ) is required to explain the sharp and well-defined spin-wave dispersion in most part of the high-symmetry directions. Moreover, a similar value is also needed for the spectral weight to be concentrated near energy ≳ 200 meV.

  17. Chemical Control of Black Flies in Large Rivers as an Impact in Agrochemical Residue-Biota Interactions in Water Ecosystems

    International Nuclear Information System (INIS)

    Haufe, W.O.

    1981-01-01

    Livestock losses have been an obstacle to economic development of the farming and livestock industry in more northerly areas of Canada until two species of black fly, Simulium arcticum and S. luggeri, outbreaks are controlled effectively. The problem is complicated by its association with an abundance of large rivers and streams. Since effective control of black flies is presently limited to reduction of their breeding sources in flowing water, the managers of Canadian inland waters have been concerned about any major practice of using pesticides as black fly larvicides. Consequently, Canadian inland waters have been subject to continuous monitoring of major drainage systems with special attention to the chlorinated hydrocarbon insecticides. The latest status of residues was published from a Canadian Survey of 333 sampling locations between 1972 and 1975

  18. A flexible, interactive software tool for fitting the parameters of neuronal models

    Directory of Open Access Journals (Sweden)

    Péter eFriedrich

    2014-07-01

    Full Text Available The construction of biologically relevant neuronal models as well as model-based analysis of experimental data often requires the simultaneous fitting of multiple model parameters, so that the behavior of the model in a certain paradigm matches (as closely as possible the corresponding output of a real neuron according to some predefined criterion. Although the task of model optimization is often computationally hard, and the quality of the results depends heavily on technical issues such as the appropriate choice (and implementation of cost functions and optimization algorithms, no existing program provides access to the best available methods while also guiding the user through the process effectively. Our software, called Optimizer, implements a modular and extensible framework for the optimization of neuronal models, and also features a graphical interface which makes it easy for even non-expert users to handle many commonly occurring scenarios. Meanwhile, educated users can extend the capabilities of the program and customize it according to their needs with relatively little effort. Optimizer has been developed in Python, takes advantage of open-source Python modules for nonlinear optimization, and interfaces directly with the NEURON simulator to run the models. Other simulators are supported through an external interface. We have tested the program on several different types of problem of varying complexity, using different model classes. As targets, we used simulated traces from the same or a more complex model class, as well as experimental data. We successfully used Optimizer to determine passive parameters and conductance densities in compartmental models, and to fit simple (adaptive exponential integrate-and-fire neuronal models to complex biological data. Our detailed comparisons show that Optimizer can handle a wider range of problems, and delivers equally good or better performance than any other existing neuronal model fitting

  19. Selection and Validation of Charge and Lennard-Jones Parameters for QM/MM Simulations of Hydrocarbon Interactions with Zeolites.

    Science.gov (United States)

    Zimmerman, Paul M; Head-Gordon, Martin; Bell, Alexis T

    2011-06-14

    Quantum mechanics/molecular mechanics (QM/MM) models are an appealing method for performing zeolite simulations. In QM/MM, a small cluster chosen to encompass the active center is described by QM, while the rest of the zeolite is described by MM. In the present study, we demonstrate that the charges and Lennard-Jones parameters on Si and O must be chosen properly for QM/MM calculations of adsorption energies and activation energies to agree closely with full QM calculations. The selection of parameters for Si and O is based on using the ωB97X-D functional for DFT calculations of the QM region, which is effective in capturing the effects of van der Waals interactions. A comparison of the heats of adsorption for a variety of adsorbates and activation energies for the cracking of propane and butane reveals that energies derived from QM/MM calculation carried out with appropriately selected MM parameters agree to within an rms error of ∼1.5 kcal/mol with QM calculations. To avoid reparametrization for new substrates, Lennard-Jones zeolite parameters are chosen to be compatible with existing CHARMM parameters. Transferability of these parameters is demonstrated by tests utilizing the B3LYP density functional and simulations of MFI and FAU zeolites. Moreover, the computational time for QM/MM calculations is considerably lower than that for QM calculations, and the ratio of computational times decreases rapidly with increasing size of the cluster used to represent the zeolite.

  20. TWIST- The TRIUMF weak interaction symmetry test the Michel parameters from {mu}{sup +} decay

    Energy Technology Data Exchange (ETDEWEB)

    Rodning, N.L.; Andersson, W.; Davydov, Y.; Depommier, P.; Doornbos, J.; Faszer, W.; Gagliardi, C.A.; Gaponenko, A.; Gill, D.R.; Green, P.W.; Gumplinger, P.; Hardy, J.C.; Hasinoff, M.; Helmer, R.; Henderson, R.; Kitching, P.; Koetke, D.D.; Korkmaz, E.; Khruchinsky, A.; Maas, D.; Macdonald, J.A.; MacDonald, R.; Manweiler, R.; Marshall, G.; Mathie, T.; Musser, J.R.; Nord, P.; Olin, A.; Openshaw, R.; Ottewell, D.; Porcelli, T.; Poutissou, J-M.; Poutissou, R.; Price, G.; Quraan, M.; Schaapman, J.; Selivanov, V.; Sheffer, G.; Shin, B.; Sobratee, F.; Soukup, J.; Stanislaus, T.D.S.; Stinson, G.; Tacik, R.; Torokhov, V.; Tribble, R.E.; Vasiliev, M.A.; Walter, H-C.; Wang, S-C.; Wright, D

    2001-04-01

    We propose to make the first high precision measurements of nearly the entire differential spectrum (in energy and angle) of positrons from the decay of polarized muons. The main goal of the experiment is the precise testing of the (V - A) structure of electroweak interactions in the framework of the SU(2){sub L} x U(1) model. Highly polarized 'surface' {mu}{sup +} from the TRIUMF M13 beamline will enter a large volume, high field superconducting magnet on axis and will stop in a thin target at its center. The e{sup +} from the muon decay will be precisely tracked in the magnetic field using small-cell planar drift chambers. This spectrometer has been simulated with GEANT and EGS4 and has been demonstrated to meet the precision requirements.

  1. Estimation of the solubility parameters of model plant surfaces and agrochemicals: a valuable tool for understanding plant surface interactions.

    Science.gov (United States)

    Khayet, Mohamed; Fernández, Victoria

    2012-11-14

    Most aerial plant parts are covered with a hydrophobic lipid-rich cuticle, which is the interface between the plant organs and the surrounding environment. Plant surfaces may have a high degree of hydrophobicity because of the combined effects of surface chemistry and roughness. The physical and chemical complexity of the plant cuticle limits the development of models that explain its internal structure and interactions with surface-applied agrochemicals. In this article we introduce a thermodynamic method for estimating the solubilities of model plant surface constituents and relating them to the effects of agrochemicals. Following the van Krevelen and Hoftyzer method, we calculated the solubility parameters of three model plant species and eight compounds that differ in hydrophobicity and polarity. In addition, intact tissues were examined by scanning electron microscopy and the surface free energy, polarity, solubility parameter and work of adhesion of each were calculated from contact angle measurements of three liquids with different polarities. By comparing the affinities between plant surface constituents and agrochemicals derived from (a) theoretical calculations and (b) contact angle measurements we were able to distinguish the physical effect of surface roughness from the effect of the chemical nature of the epicuticular waxes. A solubility parameter model for plant surfaces is proposed on the basis of an increasing gradient from the cuticular surface towards the underlying cell wall. The procedure enabled us to predict the interactions among agrochemicals, plant surfaces, and cuticular and cell wall components, and promises to be a useful tool for improving our understanding of biological surface interactions.

  2. Estimation of the solubility parameters of model plant surfaces and agrochemicals: a valuable tool for understanding plant surface interactions

    Science.gov (United States)

    2012-01-01

    Background Most aerial plant parts are covered with a hydrophobic lipid-rich cuticle, which is the interface between the plant organs and the surrounding environment. Plant surfaces may have a high degree of hydrophobicity because of the combined effects of surface chemistry and roughness. The physical and chemical complexity of the plant cuticle limits the development of models that explain its internal structure and interactions with surface-applied agrochemicals. In this article we introduce a thermodynamic method for estimating the solubilities of model plant surface constituents and relating them to the effects of agrochemicals. Results Following the van Krevelen and Hoftyzer method, we calculated the solubility parameters of three model plant species and eight compounds that differ in hydrophobicity and polarity. In addition, intact tissues were examined by scanning electron microscopy and the surface free energy, polarity, solubility parameter and work of adhesion of each were calculated from contact angle measurements of three liquids with different polarities. By comparing the affinities between plant surface constituents and agrochemicals derived from (a) theoretical calculations and (b) contact angle measurements we were able to distinguish the physical effect of surface roughness from the effect of the chemical nature of the epicuticular waxes. A solubility parameter model for plant surfaces is proposed on the basis of an increasing gradient from the cuticular surface towards the underlying cell wall. Conclusions The procedure enabled us to predict the interactions among agrochemicals, plant surfaces, and cuticular and cell wall components, and promises to be a useful tool for improving our understanding of biological surface interactions. PMID:23151272

  3. Structure effect on the interaction of phenylurea herbicides with model biomembrane as an environmental mobility parameter.

    Science.gov (United States)

    Librando, Vito; Forte, Stefano; Sarpietro, Maria G

    2004-01-15

    During recent years, intensive use of herbicides has raised increasing concern mainly due to their massive pollution of the environment. As these herbicides are directly or indirectly toxic to a wide range of organisms, their potential for contaminating soil, surface water, and groundwater makes these xenobiotics of special interest from a health and environmental point of view. Knowledge of the mechanisms by which they exert their toxic effects is becoming a need. Because of the herbicides' lipophilicity, a possible site of interaction in the cell is represented by biomembranes. The interaction of four herbicides, difenoxuron, diuron, linuron, and metoxuron, with model membranes constituted of dimyristoylphosphatidylcholine multilamellar vesicles was investigated by the differential scanning calorimetry technique. The aim was to study the effects exerted by an increasing amount of the examined compounds on thermotropic behavior of the model phospholipid membranes and to correlate the obtained results with structural features of the herbicides due to their environmental mobility. Among the herbicides studied, linuron is the most effective in perturbing the ordinate structure of vesicles forming phospholipids, whereas metoxuron is the least effective and the others exert an intermediate effect. Linuron exerts its effect both on the transition temperature of the gel to the liquid crystalline phase and on the enthalpy change. Difenoxuron, diuron, and metoxuron cause a change in the transition temperature but have an insignificant effect on the enthalpy change. The calorimetric results, correlated with the structural features of the herbicides, are consistent with their partition coefficient, log K(ow), suggesting that the more hydrophobic compound character causes a greater liposolubility and consequential cellular absorption with more effectiveness on the membrane order.

  4. Biophysical parameters of erythrocyte membranes and mechanisms of interaction with non-opioid analgesics under acute pain syndrome

    Directory of Open Access Journals (Sweden)

    Yu. I. Gubskyi

    2014-06-01

    Full Text Available Methods of fluorescent probing, spectrophotometry and microcalorimetry were applied to investigate the alterations in biophysical parameters of erythrocytes membranes, and specifically microviscosity, surface charge, molecular organization of lipid bilayer and lipid-protein interactions under conditions of acute pain syndrome produced by experimental chemical lesion. The distinctive features of non-opiod analgesics interactions and binding to the erythrocytes membranes of rats subjected to acute nociceptive pain accompanied with oxidative stress development were investigated. The abilities of analgesics under research, and namely paracetamol, aspirin, phenazone, ketorolac, pyrodazole, ketoprofenum, natrium mefenaminate, indometacin, nimesulide to make up physico-chemical complexes with lipoperoxidation modified erythrocytes surface and protein-lipid bilayer showed marked changes. The significance of oxidative damage of biophase under conditions of acute pain syndrome for analgesics effective pharmacodynamics and pharmacokinetics realization is under consideration.

  5. Plasma parameters and electromagnetic forces induced by the magneto hydro dynamic interaction in a hypersonic argon flow experiment

    International Nuclear Information System (INIS)

    Cristofolini, Andrea; Neretti, Gabriele; Borghi, Carlo A.

    2012-01-01

    This work proposes an experimental analysis on the magneto hydro dynamic (MHD) interaction induced by a magnetic test body immersed into a hypersonic argon flow. The characteristic plasma parameters are measured. They are related to the voltages arising in the Hall direction and to the variation of the fluid dynamic properties induced by the interaction. The tests have been performed in a hypersonic wind tunnel at Mach 6 and Mach 15. The plasma parameters are measured in the stagnation region in front of the nozzle of the wind tunnel and in the free stream region at the nozzle exit. The test body has a conical shape with the cone axis in the gas flow direction and the cone vertex against the flow. It is placed at the nozzle exit and is equipped with three permanent magnets. In the configuration adopted, the Faraday current flows in a closed loop completely immersed into the plasma of the shock layer. The electric field and the pressure variation due to MHD interaction have been measured on the test body walls. Microwave adsorption measurements have been used for the determination of the electron number density and the electron collision frequency. Continuum recombination radiation and line radiation emissions have been detected. The electron temperature has been determined by means of the spectroscopic data by using different methods. The electron number density has been also determined by means of the Stark broadening of H α and the H β lines. Optical imaging has been utilized to visualize the pattern of the electric current distribution in the shock layer around the test body. The experiments show a considerable effect of the electromagnetic forces produced by the MHD interaction acting on the plasma flow around the test body. A comparison of the experimental data with simulation results shows a good agreement.

  6. Interaction of carbon nanoparticles to serum albumin: elucidation of the extent of perturbation of serum albumin conformations and thermodynamical parameters.

    Science.gov (United States)

    Mandal, Samir; Hossain, Maidul; Devi, P Sujatha; Kumar, Gopinatha Suresh; Chaudhuri, Keya

    2013-03-15

    Carbon nanoparticles continuously generated from industries and vehicles due to incomplete combustion of fuels is one of the potent causes of air pollution. The exposure of this polluted air with carbon nanoparticles, introduced into the bloodstream of animals in the course of respiration, motivated us to study their interaction with plasma proteins, bovine serum albumin and human serum albumin. Carbon nanoparticles with very small size and high purity were synthesized by dehydration of d-glucose using concentrated sulphuric acid as dehydrating agent. These were characterized by transmission electron microscopy, atomic force microscopy, X-ray diffraction, Raman spectroscopy, FTIR spectroscopy and UV-visible spectroscopy. Carbon nanoparticles-protein interactions were studied by fluorescence spectroscopy, circular dichroism spectroscopy and isothermal titration calorimetry. The fluorescence quenching constants and thermodynamic parameters such as enthalpy change (ΔH°), entropy change (ΔS°) and free energy change (ΔG°) were calculated, which indicated a strong static quenching and primary electrostatic interaction between the carbon nanoparticles and blood proteins. Circular dichroism spectra provided the information about the secondary structure alteration of the proteins in presence of carbon nanoparticles. These findings have shed light towards an understanding of the interactions between carbon nanoparticles and serum proteins which may clarify the potential risks and undesirable health effects of carbon nanoparticles, as well as the related cellular trafficking and systemic translocation. Copyright © 2013 Elsevier B.V. All rights reserved.

  7. Multi-parameter measurements in a blast furnace using interactions of neutrons and γ-rays

    International Nuclear Information System (INIS)

    Shirakawa, Yoshiyuki; Horikoshi, Kiyomi

    1998-01-01

    This paper describes the possibility of multi-parameter measurements to meet the requirements for more precise and stable control of a blast furnace. A basic concept of such measurements is to make use of multi-radiations of neutrons and γ-rays, and to obtain multi-types of information on conditions of materials (iron ore and coke) inside the blast furnace. A prototype gauge was assembled and examined which consisted of a radiation source of 252 Cf, a neutron moderator, a lead shield, a bismuth germanate detector, a stainless casing and a control unit. Laboratory experiments showed that the gauge could measure the quantities to be essential to estimate material conditions. In practice, it clearly distinguished between iron ore and coke layers, and at the same time measured bulk density of iron contained in iron ore by counting thermal neutron capture γ-rays from iron. It also gave the information on material bulk density by detecting Compton scattered γ-rays from material, i.e. iron ore and coke. Finally, reducibility of iron ore was calculated by using both bulk densities. Relative accuracy of measurements was reasonable in practical use. The possibility of realization of the gauge has been proved and the on-line trial will be expected in the near future. (author)

  8. Recognition of 5'-YpG-3' sequences by coupled stacking/hydrogen bonding interactions with amino acid residues.

    Science.gov (United States)

    Lamoureux, Jason S; Maynes, Jason T; Glover, J N Mark

    2004-01-09

    The combined biochemical and structural study of hundreds of protein-DNA complexes has indicated that sequence-specific interactions are mediated by two mechanisms termed direct and indirect readout. Direct readout involves direct interactions between the protein and base-specific atoms exposed in the major and minor grooves of DNA. For indirect readout, the protein recognizes DNA by sensing conformational variations in the structure dependent on nucleotide sequence, typically through interactions with the phosphodiester backbone. Based on our recent structure of Ndt80 bound to DNA in conjunction with a search of the existing PDB database, we propose a new method of sequence-specific recognition that utilizes both direct and indirect readout. In this mode, a single amino acid side-chain recognizes two consecutive base-pairs. The 3'-base is recognized by canonical direct readout, while the 5'-base is recognized through a variation of indirect readout, whereby the conformational flexibility of the particular dinucleotide step, namely a 5'-pyrimidine-purine-3' step, facilitates its recognition by the amino acid via cation-pi interactions. In most cases, this mode of DNA recognition helps explain the sequence specificity of the protein for its target DNA.

  9. Investigations of residue of veterinary medicines and environmental contaminants during production cycle of Petrovska klobasa as part of compulsory parameters for food safety

    Directory of Open Access Journals (Sweden)

    Janković Vesna

    2012-01-01

    Full Text Available A significant factor in the protection of consumer health is the systematic and constant implementation of control for the presence of residue of biologically active substances and their metabolites in raw materials and in primary products of animal origin. As regards meat, an essential aspect of security is definitely the control of possible residue of veterinary medicines and environmental contaminants. In that respect, the objective of the national project entitled „Development of technology for drying and fermentation of the sausage petrovačka kobasica (Petrovská klobása - registered geographic origin under controlled conditions“, Number TR - 20037, was to protect the product petrovačka kobasica (Petrovská klobása with the appropriate appellation. A part of the compulsory investigations also included the establishing of the presence of residue of veterinary medicines and environmental contaminants in raw materials and in the finished product, which was also the aim of this work. [Projekat Ministarstva nauke Republike Srbije, br. TR-20037: Petrovská klobása - oznaka geografskog porekla u kontrolisanim uslovima

  10. Kinetic parameters of polyreactive immunoglobulins interaction with antigens in the presence of protamine

    Directory of Open Access Journals (Sweden)

    S. A. Bobrovnik

    2016-06-01

    Full Text Available The discovered earlier phenomenon of the enhancment of polyreactive immunoglobulines (PRIGs binding to antigens in the presence of protamine and Tween 20 was investigated in more details. The comparative analysis of PRIGs reaction dynamics with immobilized antigen was provided. In addition, the rate constants for the reaction and the affinity constants of PRIGs-antigen binding in the presence or absence of optimal protamine concentration were determined. The rate constant of PRIGs-antigen reaction did not increase in the presence of protamine optimal concentration and was even reduced approximately twice. However, in the presence of protamine the concentration of reactive PRIGs molecules, that were able to interact with antigen, increased approximately 30 times, and this led to strong reaction rate increase. Protamine also influenced the affinity constant of PRIGs-antigen binding, which increased approximately three times. The suggestion was made that such protamine effect was due to its influence on the PRIGs molecules special structure, and, as a result of the conformational change PRIGs became able to bind more effectively to the antigens.

  11. Quantification of interaction and topological parameters of polyisoprene star polymers under good solvent conditions

    KAUST Repository

    Rai, Durgesh K.

    2016-05-05

    Mass fractal scaling, reflected in the mass fractal dimension df, is independently impacted by topology, reflected in the connectivity dimension c, and by tortuosity, reflected in the minimum dimension dmin. The mass fractal dimension is related to these other dimensions by df=cdmin. Branched fractal structures have a higher mass fractal dimension compared to linear structures due to a higher c, and extended structures have a lower dimension compared to convoluted self-avoiding and Gaussian walks due to a lower dmin. It is found, in this work, that macromolecules in thermodynamic equilibrium display a fixed mass fractal dimension df under good solvent conditions, regardless of chain topology. These equilibrium structures accommodate changes in chain topology such as branching c by a decrease in chain tortuosity dmin. Symmetric star polymers are used to understand the structure of complex macromolecular topologies. A recently published hybrid Unified scattering function accounts for interarm correlations in symmetric star polymers along with polymer-solvent interaction for chains of arbitrary scaling dimension. Dilute solutions of linear, three-arm and six-arm polyisoprene stars are studied under good solvent conditions in deuterated p-xylene. Reduced chain tortuosity can be viewed as steric straightening of the arms. Steric effects for star topologies are quantified, and it is found that steric straightening of arms is more significant for lower-molecular-weight arms. The observation of constant df is explained through a modification of Flory-Krigbaum theory for branched polymers.

  12. Spring Chinook Salmon Interactions Indices and Residual/Precocial Monitoring in the Upper Yakima Basin; Yakima/Klickitat Fisheries Project Monitoring and Evaluation, 2001-2002 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Pearsons, Todd N.; James, Brenda B.; Johnson, Christopher L. (Washington Department of Fish and Wildlife, Olympia, WA)

    2003-05-01

    This report examines some of the factors that can influence the success of supplementation, which is currently being tested in the Yakima Basin using upper Yakima stock of spring chinook salmon. Supplementation success in the Yakima Basin is defined relative to four topic areas: natural production, genetics, ecological interactions, and harvest (Busack et al. 1997). The success of spring chinook salmon supplementation in the Yakima Basin is dependent, in part, upon fish culture practices and favorable physical and biological conditions in the natural environment (Busack et al. 1997). Shortfalls in either of these two topics (i.e., failure in culturing many fish that have high long-term fitness or environmental conditions that constrain spring chinook salmon production) will cause supplementation success to be limited. For example, inadvertent selection or propagation of spring chinook that residualize or precocially mature may hinder supplementation success. Spring chinook salmon that residualize (do not migrate during the normal migration period) may have lower survival rates than migrants and, additionally, may interact with wild fish and cause unacceptable impacts to non-target taxa. Large numbers of precocials (nonanadromous spawners) may increase competition for females and significantly skew ratios of offspring sired by nonanadromous males, which could result in more nonanadromous spring chinook in future generations. Conditions in the natural environment may also limit the success of spring chinook supplementation. For example, intra or interspecific competition may constrain spring chinook salmon production. Spring chinook salmon juveniles may compete with each other for food or space or compete with other species that have similar ecological requirements. Monitoring of spring chinook salmon residuals, precocials, prey abundance, carrying capacity, and competition will help researchers interpret why supplementation is working or not working (Busack et al

  13. Quantification of interaction and topological parameters of polyisoprene star polymers under good solvent conditions.

    Science.gov (United States)

    Rai, Durgesh K; Beaucage, Gregory; Ratkanthwar, Kedar; Beaucage, Peter; Ramachandran, Ramnath; Hadjichristidis, Nikos

    2016-05-01

    Mass fractal scaling, reflected in the mass fractal dimension d_{f}, is independently impacted by topology, reflected in the connectivity dimension c, and by tortuosity, reflected in the minimum dimension d_{min}. The mass fractal dimension is related to these other dimensions by d_{f}=cd_{min}. Branched fractal structures have a higher mass fractal dimension compared to linear structures due to a higher c, and extended structures have a lower dimension compared to convoluted self-avoiding and Gaussian walks due to a lower d_{min}. It is found, in this work, that macromolecules in thermodynamic equilibrium display a fixed mass fractal dimension d_{f} under good solvent conditions, regardless of chain topology.  These equilibrium structures accommodate changes in chain topology such as branching c by a decrease in chain tortuosity d_{min}. Symmetric star polymers are used to understand the structure of complex macromolecular topologies. A recently published hybrid Unified scattering function accounts for interarm correlations in symmetric star polymers along with polymer-solvent interaction for chains of arbitrary scaling dimension. Dilute solutions of linear, three-arm and six-arm polyisoprene stars are studied under good solvent conditions in deuterated p-xylene. Reduced chain tortuosity can be viewed as steric straightening of the arms. Steric effects for star topologies are quantified, and it is found that steric straightening of arms is more significant for lower-molecular-weight arms. The observation of constant d_{f} is explained through a modification of Flory-Krigbaum theory for branched polymers.

  14. Exploring medical diagnostic performance using interactive, multi-parameter sourced receiver operating characteristic scatter plots.

    Science.gov (United States)

    Moore, Hyatt E; Andlauer, Olivier; Simon, Noah; Mignot, Emmanuel

    2014-04-01

    Determining diagnostic criteria for specific disorders is often a tedious task that involves determining optimal diagnostic thresholds for symptoms and biomarkers using receiver-operating characteristic (ROC) statistics. To help this endeavor, we developed softROC, a user-friendly graphic-based tool that lets users visually explore possible ROC tradeoffs. The software requires MATLAB installation and an Excel file containing threshold symptoms/biological measures, with corresponding gold standard diagnoses for a set of patients. The software scans the input file for diagnostic and symptom/biomarkers columns, and populates the graphical-user-interface (GUI). Users select symptoms/biomarkers of interest using Boolean algebra as potential inputs to create diagnostic criteria outputs. The software evaluates subtests across the user-established range of cut-points and compares them to a gold standard in order to generate ROC and quality ROC scatter plots. These plots can be examined interactively to find optimal cut-points of interest for a given application (e.g. sensitivity versus specificity needs). Split-set validation can also be used to set up criteria and validate these in independent samples. Bootstrapping is used to produce confidence intervals. Additional statistics and measures are provided, such as the area under the ROC curve (AUC). As a testing set, softROC is used to investigate nocturnal polysomnogram measures as diagnostic features for narcolepsy. All measures can be outputted to a text file for offline analysis. The softROC toolbox, with clinical training data and tutorial instruction manual, is provided as supplementary material and can be obtained online at http://www.stanford.edu/~hyatt4/software/softroc or from the open source repository at http://www.github.com/informaton/softroc. Copyright © 2014 Elsevier Ltd. All rights reserved.

  15. Evaluation of Interactive Visualization on Mobile Computing Platforms for Selection of Deep Brain Stimulation Parameters.

    Science.gov (United States)

    Butson, Christopher R; Tamm, Georg; Jain, Sanket; Fogal, Thomas; Krüger, Jens

    2013-01-01

    In recent years, there has been significant growth in the use of patient-specific models to predict the effects of neuromodulation therapies such as deep brain stimulation (DBS). However, translating these models from a research environment to the everyday clinical workflow has been a challenge, primarily due to the complexity of the models and the expertise required in specialized visualization software. In this paper, we deploy the interactive visualization system ImageVis3D Mobile, which has been designed for mobile computing devices such as the iPhone or iPad, in an evaluation environment to visualize models of Parkinson's disease patients who received DBS therapy. Selection of DBS settings is a significant clinical challenge that requires repeated revisions to achieve optimal therapeutic response, and is often performed without any visual representation of the stimulation system in the patient. We used ImageVis3D Mobile to provide models to movement disorders clinicians and asked them to use the software to determine: 1) which of the four DBS electrode contacts they would select for therapy; and 2) what stimulation settings they would choose. We compared the stimulation protocol chosen from the software versus the stimulation protocol that was chosen via clinical practice (independent of the study). Lastly, we compared the amount of time required to reach these settings using the software versus the time required through standard practice. We found that the stimulation settings chosen using ImageVis3D Mobile were similar to those used in standard of care, but were selected in drastically less time. We show how our visualization system, available directly at the point of care on a device familiar to the clinician, can be used to guide clinical decision making for selection of DBS settings. In our view, the positive impact of the system could also translate to areas other than DBS.

  16. Uncovering the local inelastic interactions during manufacture of ductile cast iron: How the substructure of the graphite particles can induce residual stress concentrations in the matrix

    Science.gov (United States)

    Andriollo, Tito; Hellström, Kristina; Sonne, Mads Rostgaard; Thorborg, Jesper; Tiedje, Niels; Hattel, Jesper

    2018-02-01

    Recent X-ray diffraction (XRD) measurements have revealed that plastic deformation and a residual elastic strain field can be present around the graphite particles in ductile cast iron after manufacturing, probably due to some local mismatch in thermal contraction. However, as only one component of the elastic strain tensor could be obtained from the XRD data, the shape and magnitude of the associated residual stress field have remained unknown. To compensate for this and to provide theoretical insight into this unexplored topic, a combined experimental-numerical approach is presented in this paper. First, a material equivalent to the ductile cast iron matrix is manufactured and subjected to dilatometric and high-temperature tensile tests. Subsequently, a two-scale hierarchical top-down model is devised, calibrated on the basis of the collected data and used to simulate the interaction between the graphite particles and the matrix during manufacturing of the industrial part considered in the XRD study. The model indicates that, besides the viscoplastic deformation of the matrix, the effect of the inelastic deformation of the graphite has to be considered to explain the magnitude of the XRD strain. Moreover, the model shows that the large elastic strain perturbations recorded with XRD close to the graphite-matrix interface are not artifacts due to e.g. sharp gradients in chemical composition, but correspond to residual stress concentrations induced by the conical sectors forming the internal structure of the graphite particles. In contrast to common belief, these results thus suggest that ductile cast iron parts cannot be considered, in general, as stress-free at the microstructural scale.

  17. Force spectroscopy unravels the role of ionic strength on DNA-cisplatin interaction: Modulating the binding parameters

    Science.gov (United States)

    Oliveira, L.; Rocha, M. S.

    2017-09-01

    In the present work we have gone a step forward in the understanding of the DNA-cisplatin interaction, investigating the role of the ionic strength on the complexes formation. To achieve this task, we use optical tweezers to perform force spectroscopy on the DNA-cisplatin complexes, determining their mechanical parameters as a function of the drug concentration in the sample for three different buffers. From such measurements, we determine the binding parameters and study their behavior as a function of the ionic strength. The equilibrium binding constant decreases with the counterion concentration ([Na]) and can be used to estimate the effective net charge of cisplatin in solution. The cooperativity degree of the binding reaction, on the other hand, increases with the ionic strength, as a result of the different conformational changes induced by the drug on the double-helix when binding under different buffer conditions. Such results can be used to modulate the drug binding to DNA, by appropriately setting the ionic strength of the surrounding buffer. The conclusions drawn provide significant new insights on the complex cooperative interactions between the DNA molecule and the class of platinum-based compounds, much used in chemotherapies.

  18. Interactive effects of salinity stress and nicotinamide on physiological and biochemical parameters of Faba bean plant

    International Nuclear Information System (INIS)

    Abdelhamid, Magdi T; Sadak, Mervat Sh; Schmidhalter, Urs; El Saady, Abdel Kareem M.

    2013-01-01

    percentage and solutes concentrations in seeds of salinity treated plants. Nicotinamide not only neutralized the effect of salinity stress but resulted in a significant improvement in physiological and biochemical parameters as well as the concentrations of soluble sugars, proline, amino acids, and total N and other mineral contents.

  19. Vacuum stability and residual gas density estimation for the vacuum chamber upgrade of the ATLAS interaction region of the Large Hadron Collider

    CERN Document Server

    Bregliozzi, G; Baglin, V; Jimenez, J M

    2012-01-01

    The CERN Large Hadron Collider (LHC) has 54 km of ultra-high vacuum (UHV) beam chambers out of which about 90% are at cryogenic temperature (1.9 K) and the rest at room temperature. During operation, the residual gas density in the beam pipes is dominated by beam induced effect such ion, electron and photon-stimulated gas desorption. Therefore, the computation of gas density profile is of great importance to confirm the vacuum stability, and to estimate the beam lifetime. Moreover, the gas density profiles are essential to determine the machine induced background in the experimental areas, and to define the pressure profile in the cryogenic sectors where there is no vacuum instrumentation available. In this paper, the vacuum stability is studied for a newly proposed upgrade of the vacuum chamber at the ATLAS interaction point, using the vacuum stability code called VASCO. The residual gas density profile along the ATLAS vacuum chambers and the effects of photon and electron flux hitting the vacuum chamber wal...

  20. Decomposição do resíduo de milho e variáveis relacionadas Corn crop residue decomposition and related parameters

    Directory of Open Access Journals (Sweden)

    I. Bertol

    2004-04-01

    Full Text Available A eficácia da semeadura direta na redução da erosão hídrica depende, em grande parte, da cobertura do solo ocasionada pelos resíduos das culturas. Objetivou-se determinar, entre agosto de 2001 e junho de 2002, em um Cambissolo Húmico alumínico léptico, situado entre 27 º 49 ' latitude Sul e 50 º 20 ' longitude Oeste de Greenwich, a decomposição do resíduo de milho. Os tratamentos, em três repetições, consistiram de: solo sem resíduo ou descoberto (SSR, solo com 8,77 Mg ha-1 de resíduo de milho (SR e solo com 8,77 Mg ha-1 de resíduo de milho mais 100 kg ha-1 de N (SR + N, avaliados em intervalos regulares de 30 dias. Determinou-se a quantidade do resíduo de milho, C orgânico e N total do referido resíduo. No solo, na camada de 0-0,03 m, foram avaliados C orgânico, N mineral, K trocável, pH em água, umidade e temperatura e, no ar, a temperatura a um metro acima da superfície do solo. O SR + N apresentou maior decomposição do resíduo de milho do que o SR, principalmente nos primeiros 120 dias, de tal modo que o tempo necessário para a quase que completa decomposição do resíduo (restando ainda cerca de 10 % da massa inicial seria de aproximadamente 1.300 dias, para o SR, e de aproximadamente 900 dias, para o SR + N.The efficacy of no-tillage systems in reducing water erosion depends largely on the soil cover by crop residues. The study was carried out in Santa Catarina State, Southern Brazil, from August 2001 to July 2002, aiming to evaluate the decay of corn residue on the surface of an Inseptisol and its influence on soil properties. The treatments, with three replicates, were: bare soil (BS, 8.77 Mg ha-1 of air dried corn residue (CR and 8.77 Mg ha-1 of air dried corn residue plus 100 kg ha-1 of nitrogen (CR + N. The remaining residue biomass on soil and its organic carbon and total nitrogen contents were evaluated every 30 days. It was also determined organic carbon, total nitrogen, potassium, pH, soil

  1. Electronic polarizability, optical basicity and interaction parameter for Nd2O3 doped lithium-zinc-phosphate glasses

    Science.gov (United States)

    Algradee, M. A.; Sultan, M.; Samir, O. M.; Alwany, A. Elwhab B.

    2017-08-01

    The Nd3+-doped lithium-zinc-phosphate glasses were prepared by means of conventional melt quenching method. X-ray diffraction results confirmed the glassy nature of the studied glasses. The physical parameters such as the density, molar volume, ion concentration, polaron radius, inter-ionic distance, field strength and oxygen packing density were calculated using different formulae. The transmittance and reflectance spectra of glasses were recorded in the wavelength range 190-1200 nm. The values of optical band gap and Urbach energy were determined based on Mott-Davis model. The refractive indices for the studied glasses were evaluated from optical band gap values using different methods. The average electronic polarizability of the oxide ions, optical basicity and an interaction parameter were investigated from the calculated values of the refractive index and the optical band gap for the studied glasses. The variations in the different physical and optical properties of glasses with Nd2O3 content were discussed in terms of different parameters such as non-bridging oxygen and different concentrations of Nd cation in glass system.

  2. Applications of Experimental Design to the Optimization of Microextraction Sample Preparation Parameters for the Analysis of Pesticide Residues in Fruits and Vegetables.

    Science.gov (United States)

    Abdulra'uf, Lukman Bola; Sirhan, Ala Yahya; Tan, Guan Huat

    2015-01-01

    Sample preparation has been identified as the most important step in analytical chemistry and has been tagged as the bottleneck of analytical methodology. The current trend is aimed at developing cost-effective, miniaturized, simplified, and environmentally friendly sample preparation techniques. The fundamentals and applications of multivariate statistical techniques for the optimization of microextraction sample preparation and chromatographic analysis of pesticide residues are described in this review. The use of Placket-Burman, Doehlert matrix, and Box-Behnken designs are discussed. As observed in this review, a number of analytical chemists have combined chemometrics and microextraction techniques, which has helped to streamline sample preparation and improve sample throughput.

  3. The Shigella flexneri OmpA amino acid residues 188EVQ190 are essential for the interaction with the virulence factor PhoN2.

    Science.gov (United States)

    Scribano, Daniela; Damico, Rosanna; Ambrosi, Cecilia; Superti, Fabiana; Marazzato, Massimiliano; Conte, Maria Pia; Longhi, Catia; Palamara, Anna Teresa; Zagaglia, Carlo; Nicoletti, Mauro

    2016-12-01

    Shigella flexneri is an intracellular pathogen that deploys an arsenal of virulence factors promoting host cell invasion, intracellular multiplication and intra- and inter-cellular dissemination. We have previously reported that the interaction between apyrase (PhoN2), a periplasmic ATP-diphosphohydrolase, and the C-terminal domain of the outer membrane (OM) protein OmpA is likely required for proper IcsA exposition at the old bacterial pole and thus for full virulence expression of Shigella flexneri (Scribano et al., 2014). OmpA, that is the major OM protein of Gram-negative bacteria, is a multifaceted protein that plays many different roles both in the OM structural integrity and in the virulence of several pathogens. Here, by using yeast two-hybrid technology and by constructing an in silico 3D model of OmpA from S. flexneri 5a strain M90T, we observed that the OmpA residues 188 EVQ 190 are likely essential for PhoN2-OmpA interaction. The 188 EVQ 190 amino acids are located within a flexible region of the OmpA protein that could represent a scaffold for protein-protein interaction.

  4. Non-Synonymous Single-Nucleotide Polymorphisms and Physical Activity Interactions on Adiposity Parameters in Malaysian Adolescents

    Directory of Open Access Journals (Sweden)

    Nur Lisa Zaharan

    2018-04-01

    Full Text Available BackgroundSeveral non-synonymous single-nucleotide polymorphisms (nsSNPs have been shown to be associated with obesity. Little is known about their associations and interactions with physical activity (PA in relation to adiposity parameters among adolescents in Malaysia.MethodsWe examined whether (a PA and (b selected nsSNPs are associated with adiposity parameters and whether PA interacts with these nsSNPs on these outcomes in adolescents from the Malaysian Health and Adolescents Longitudinal Research Team study (n = 1,151. Body mass indices, waist–hip ratio, and percentage body fat (% BF were obtained. PA was assessed using Physical Activity Questionnaire for Older Children (PAQ-C. Five nsSNPs were included: beta-3 adrenergic receptor (ADRB3 rs4994, FABP2 rs1799883, GHRL rs696217, MC3R rs3827103, and vitamin D receptor rs2228570, individually and as combined genetic risk score (GRS. Associations and interactions between nsSNPs and PAQ-C scores were examined using generalized linear model.ResultsPAQ-C scores were associated with % BF (β = −0.44 [95% confidence interval −0.72, −0.16], p = 0.002. The CC genotype of ADRB3 rs4994 (β = −0.16 [−0.28, −0.05], corrected p = 0.01 and AA genotype of MC3R rs3827103 (β = −0.06 [−0.12, −0.00], p = 0.02 were significantly associated with % BF compared to TT and GG genotypes, respectively. Significant interactions with PA were found between ADRB3 rs4994 (β = −0.05 [−0.10, −0.01], p = 0.02 and combined GRS (β = −0.03 [−0.04, −0.01], p = 0.01 for % BF.ConclusionHigher PA score was associated with reduced % BF in Malaysian adolescents. Of the nsSNPs, ADRB3 rs4994 and MC3R rs3827103 were associated with % BF. Significant interactions with PA were found for ADRB3 rs4994 and combined GRS on % BF but not on measurements of weight or circumferences. Targeting body fat represent prospects for molecular studies and lifestyle intervention

  5. Excitation functions for some evaporation residues identified in the interaction of 20Ne and 93Nb at moderate excitation energies

    International Nuclear Information System (INIS)

    Agarwal, Avinash; Rizvi, I.A.; Gupta, Meenal; Ahamad, Tauseef; Ghugre, S.S.; Sinha, A.K.; Chaubey, A.K.

    2008-01-01

    With the motivation of studying the complete and incomplete fusion reactions, excitation functions for the reactions 93 Nb(Ne, p2n) 110 Sn, 93 Nb(Ne, 2pn) 110 In, 93 Nb(Ne, 2p2n) 109 In, 93 Nb(Ne, αn) 108 In, 93 Nb(Neα2n) 107 In and 93 Nb(Ne, α p n) 107 Cd have been measured at the incident energy ranging from 91.4 MeV - 145 MeV. The well established activation technique followed by off line high purity gamma- ray spectroscopy was employed. The measured excitation functions were compared with the statistical model calculations by using the codes ALICE-91 and Pace-4. The effect of variation of different parameters including level density parameter involved in these codes has also been studied. Excellent agreement was found between theoretical and experimental values in some of the fusion evaporation reaction channels. However, significant enhancement of cross-section observed in α-emission channels may be due to incomplete fusion process. (author)

  6. Two-quasineutron states in 98248Cf and 98250Cf and the neutron-neutron residual interactions

    International Nuclear Information System (INIS)

    Katori, K.; Ahmad, I.; Friedman, A. M.

    2008-01-01

    Two-quasineutron states in 248 Cf and 250 Cf were investigated by single-neutron transfer reactions, 249 Cf(d,t) 248 Cf and 249 Cf(d,p) 250 Cf. The majority of levels observed were assigned to 12 bands in 248 Cf and six bands in 250 Cf, constructed from the single-particle states in neighboring Cf nuclei. The effective two-body interactions between two odd neutrons coupled outside a deformed core were deduced from the differences in the energies of the bandheads formed by the parallel and antiparallel coupling of the intrinsic spins of the two single-particle states

  7. /sup 13/C nuclear magnetic resonance study of the interaction of ligands with arginine residues in dihydrofolate reductase

    Energy Technology Data Exchange (ETDEWEB)

    Cocco, L. (Univ. of Iowa, Iowa City); Blakley, R.L.; Walker, T.E.; London, R.E.

    1977-01-01

    /sup 13/C NMR spectra of Streptococcus faecium dihydrofolate reductase containing (/sup 13/C-guanidino) arginine and ligand complexes with the labeled enzyme are reported. The spectrum of the native enzyme shows 5 well-resolved resonances (the enzyme contains 8 Arg) with a chemical shift range of 1.2 ppM. Addition of ligands to the enzyme produces distinct changes in the enzyme spectrum, and demonstrates that /sup 13/C NMR of labeled protein can be used in studies of protein-ligand interactions. An example of the use of /sup 13/C-depleted material is also presented.

  8. Interaction of acid mine drainage with Ordinary Portland Cement blended solid residues generated from active treatment of acid mine drainage with coal fly ash.

    Science.gov (United States)

    Gitari, Wilson M; Petrik, Leslie F; Key, David L; Okujeni, Charles

    2011-01-01

    Fly ash (FA) has been investigated as a possible treatment agent for Acid mine drainage (AMD) and established to be an alternative, cheap and economically viable agent compared to the conventional alkaline agents. However, this treatment option also leads to generation of solid residues (SR) that require disposal and one of the proposed disposal method is a backfill in coal mine voids. In this study, the interaction of the SR with AMD that is likely to be present in such backfill scenario was simulated by draining columns packed with SR and SR + 6% Ordinary Portland Cement (OPC) unsaturated with simulated AMD over a 6 month period. The evolving geochemistry of the liquid/solid (L/S) system was evaluated in-terms of the mineral phases likely or controlling contaminants attenuation at the different pH regimes generated. Stepwise acidification of the percolates was observed as the drainage progressed. Two pH buffer zones were observed (7.5-9 and 3-4) for SR and (11.2-11.3 and 3.5-4) for SR + 6% OPC. The solid residue cores (SR) appeared to have a significant buffering capacity, maintaining a neutral to slightly alkaline pH in the leachates for an extended period of time (97 days: L/S 4.3) while SR + 6% OPC reduced this neutralization capacity to 22 days (L/S 1.9). Interaction of AMD with SR or SR + 6% OPC generated alkaline conditions that favored precipitation of Fe, Al, Mn-(oxy) hydroxides, Fe and Ca-Al hydroxysulphates that greatly contributed to the contaminants removal. However, precipitation of these phases was restricted to the pH of the leachates remaining at neutral to circum-neutral levels. Backfill of mine voids with SR promises to be a feasible technology for the disposal of the SR but its success will greatly depend on the disposal scenario, AMD generated and the alkalinity generating potential of the SR. A disadvantage would be the possible re-dissolution of the precipitated phases at pH water column. However extrapolation of this concept to a field

  9. Interaction of fisetin with human serum albumin by fluorescence, circular dichroism spectroscopy and DFT calculations: binding parameters and conformational changes

    Energy Technology Data Exchange (ETDEWEB)

    Matei, Iulia; Ionescu, Sorana [Department of Physical Chemistry, Faculty of Chemistry, University of Bucharest, Bd. Regina Elisabeta 4-12, 030018 Bucharest (Romania); Hillebrand, Mihaela, E-mail: mihh@gw-chimie.math.unibuc.ro [Department of Physical Chemistry, Faculty of Chemistry, University of Bucharest, Bd. Regina Elisabeta 4-12, 030018 Bucharest (Romania)

    2011-08-15

    The interaction between fisetin, an antioxidant and neuroprotective flavonoid, and human serum albumin (HSA) is investigated by means of fluorescence (steady-state, synchronous, time-resolved) and circular dichroism (CD) spectroscopy. The formation of a 1:1 complex with a constant of about 10{sup 5} M{sup -1} was evidenced. Foerster's resonance energy transfer and competitive binding with site markers warfarin and ibuprofen were considered and discussed. Changes in the CD band of HSA indicate a decrease in the {alpha}-helix content upon binding. An induced CD signal for bound fisetin was observed and rationalized in terms of density functional theory calculations. - Highlights: > Fisetin-BSA system was studied by fluorescence spectroscopy. > Binding parameters, association constant and number of sites were estimated. > Binding site of fisetin was identified by competitive experiments. > Conformational changes in HSA and fisetin were evidenced by circular dichroism. > TDDFT calculated CD spectra supported the experimental data.

  10. LEDGIN-mediated Inhibition of Integrase–LEDGF/p75 Interaction Reduces Reactivation of Residual Latent HIV

    Directory of Open Access Journals (Sweden)

    Lenard S. Vranckx

    2016-06-01

    Full Text Available Persistence of latent, replication-competent Human Immunodeficiency Virus type 1 (HIV-1 provirus is the main impediment towards a cure for HIV/AIDS (Acquired Immune Deficiency Syndrome. Therefore, different therapeutic strategies to eliminate the viral reservoirs are currently being explored. We here propose a novel strategy to reduce the replicating HIV reservoir during primary HIV infection by means of drug-induced retargeting of HIV integration. A novel class of integration inhibitors, referred to as LEDGINs, inhibit the interaction between HIV integrase and the LEDGF/p75 host cofactor, the main determinant of lentiviral integration site selection. We show for the first time that LEDGF/p75 depletion hampers HIV-1 reactivation in cell culture. Next we demonstrate that LEDGINs relocate and retarget HIV integration resulting in a HIV reservoir that is refractory to reactivation by different latency-reversing agents. Taken together, these results support the potential of integrase inhibitors that modulate integration site targeting to reduce the likeliness of viral rebound.

  11. LEDGIN-mediated Inhibition of Integrase-LEDGF/p75 Interaction Reduces Reactivation of Residual Latent HIV.

    Science.gov (United States)

    Vranckx, Lenard S; Demeulemeester, Jonas; Saleh, Suha; Boll, Annegret; Vansant, Gerlinde; Schrijvers, Rik; Weydert, Caroline; Battivelli, Emilie; Verdin, Eric; Cereseto, Anna; Christ, Frauke; Gijsbers, Rik; Debyser, Zeger

    2016-06-01

    Persistence of latent, replication-competent Human Immunodeficiency Virus type 1 (HIV-1) provirus is the main impediment towards a cure for HIV/AIDS (Acquired Immune Deficiency Syndrome). Therefore, different therapeutic strategies to eliminate the viral reservoirs are currently being explored. We here propose a novel strategy to reduce the replicating HIV reservoir during primary HIV infection by means of drug-induced retargeting of HIV integration. A novel class of integration inhibitors, referred to as LEDGINs, inhibit the interaction between HIV integrase and the LEDGF/p75 host cofactor, the main determinant of lentiviral integration site selection. We show for the first time that LEDGF/p75 depletion hampers HIV-1 reactivation in cell culture. Next we demonstrate that LEDGINs relocate and retarget HIV integration resulting in a HIV reservoir that is refractory to reactivation by different latency-reversing agents. Taken together, these results support the potential of integrase inhibitors that modulate integration site targeting to reduce the likeliness of viral rebound. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

  12. Evaluation of intensity and energy interaction parameters for the complexation of Pr(III) with selected nucleoside and nucleotide through absorption spectral studies

    Science.gov (United States)

    Bendangsenla, N.; Moaienla, T.; David Singh, Th.; Sumitra, Ch.; Rajmuhon Singh, N.; Indira Devi, M.

    2013-02-01

    The interactions of Pr(III) with nucleosides and nucleotides have been studied in different organic solvents employing absorption difference and comparative absorption spectrophotometry. The magnitudes of the variations in both energy and intensity interaction parameters were used to explore the degree of outer and inner sphere co-ordination, incidence of covalency and the extent of metal 4f-orbital involvement in chemical bonding. Various electronic spectral parameters like Slater-Condon (Fk), Racah (Ek), Lande parameter (ξ4f), Nephelauxatic ratio (β), bonding (b1/2), percentage covalency (δ) and intensity parameters like oscillator strength (P) and Judd Ofelt electronic dipole intensity parameter (Tλ, λ = 2, 4, 6) have been evaluated. The variation of these evaluated parameters were employed to interpret the nature of binding of Pr(III) with different ligands i.e. Adenosine/ATP in presence and absence of Ca2+.

  13. Social anxiety, acute social stress, and reward parameters interact to predict risky decision-making among adolescents.

    Science.gov (United States)

    Richards, Jessica M; Patel, Nilam; Daniele-Zegarelli, Teresa; MacPherson, Laura; Lejuez, C W; Ernst, Monique

    2015-01-01

    Risk-taking behavior increases during adolescence, leading to potentially disastrous consequences. Social anxiety emerges in adolescence and may compound risk-taking propensity, particularly during stress and when reward potential is high. However, the manner in which social anxiety, stress, and reward parameters interact to impact adolescent risk-taking is unclear. To clarify this question, a community sample of 35 adolescents (15-18yo), characterized as having high or low social anxiety, participated in a study over two separate days, during each of which they were exposed to either a social stress or a control condition, while performing a risky decision-making task. The task manipulated, orthogonally, reward magnitude and probability across trials. Three findings emerged. First, reward magnitude had a greater impact on the rate of risky decisions in high social anxiety (HSA) than low social anxiety (LSA) adolescents. Second, reaction times (RTs) were similar during the social stress and the control conditions for the HSA group, whereas the LSA group's RTs differed between conditions. Third, HSA adolescents showed the longest RTs on the most negative trials. These findings suggest that risk-taking in adolescents is modulated by context and reward parameters differentially as a function of social anxiety. Published by Elsevier Ltd.

  14. Residuation theory

    CERN Document Server

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

    1972-01-01

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

  15. The Effect of Cholesterol on the Long-Range Network of Interactions Established among Sea Anemone Sticholysin II Residues at the Water-Membrane Interface

    Directory of Open Access Journals (Sweden)

    Sara García-Linares

    2015-03-01

    Full Text Available Actinoporins are α-pore forming proteins with therapeutic potential, produced by sea anemones. Sticholysin II (StnII from Stichodactyla helianthus is one of its most extensively characterized members. These proteins remain stably folded in water, but upon interaction with lipid bilayers, they oligomerize to form a pore. This event is triggered by the presence of sphingomyelin (SM, but cholesterol (Chol facilitates pore formation. Membrane attachment and pore formation require changes involving long-distance rearrangements of residues located at the protein-membrane interface. The influence of Chol on membrane recognition, oligomerization, and/or pore formation is now studied using StnII variants, which are characterized in terms of their ability to interact with model membranes in the presence or absence of Chol. The results obtained frame Chol not only as an important partner for SM for functional membrane recognition but also as a molecule which significantly reduces the structural requirements for the mentioned conformational rearrangements to occur. However, given that the DOPC:SM:Chol vesicles employed display phase coexistence and have domain boundaries, the observed effects could be also due to the presence of these different phases on the membrane. In addition, it is also shown that the Arg51 guanidinium group is strictly required for membrane recognition, independently of the presence of Chol.

  16. Interaction between cadmium and iron. Accumulation and distribution of metals and changes in growth parameters of Phaseolus vulgaris L. seedlings

    Directory of Open Access Journals (Sweden)

    Anna Siedlecka

    2014-01-01

    Full Text Available The interaction between cadmium, one of the most toxic heavy metals, and iron, an essential plant nutritional element, was investigated in Phaseolus vulgaris L. (cv. Słowianka seedlings. The interaction was externally induced by changing the content of both metals in the nutrient medium. Under iron deficiency conditions (0 and 0.5 of normal dose of this element, the toxic effects of cadmium on plant growth parameters, like fresh and dry weight accumulation, primary leaves area, etc., were generally much more pronounced than under normal iron supply. At normal and excess iron supply (1, 2 and 4 doses cadmium diminished iron accumulation in roots and primary leaves, but on the other hand excess iron decreased cadmium level, preventing plants from extreme toxicity of very high cadmium concentrations in the growth environment. It is to be noted that iron is classified also as a heavy metal, and its excess may become toxic, e.g. decreasing root dry weight or diminishing leaf area, especially at the highest dose. The detoxication role of iron against cadmium, and possibly other toxic metals is, however, limited to concentrations of this element in the nutrient solution which themselves are not toxic for the organism.

  17. Consequences of dark matter-dark energy interaction on cosmological parameters derived from type Ia supernova data

    International Nuclear Information System (INIS)

    Amendola, Luca; Campos, Gabriela Camargo; Rosenfeld, Rogerio

    2007-01-01

    Models where the dark matter component of the Universe interacts with the dark energy field have been proposed as a solution to the cosmic coincidence problem, since in the attractor regime both dark energy and dark matter scale in the same way. In these models the mass of the cold dark matter particles is a function of the dark energy field responsible for the present acceleration of the Universe, and different scenarios can be parametrized by how the mass of the cold dark matter particles evolves with time. In this article we study the impact of a constant coupling δ between dark energy and dark matter on the determination of a redshift dependent dark energy equation of state w DE (z) and on the dark matter density today from SNIa data. We derive an analytical expression for the luminosity distance in this case. In particular, we show that the presence of such a coupling increases the tension between the cosmic microwave background data from the analysis of the shift parameter in models with constant w DE and SNIa data for realistic values of the present dark matter density fraction. Thus, an independent measurement of the present dark matter density can place constraints on models with interacting dark energy

  18. Screening of the most relevant parameters for method development in ultra-high performance hydrophilic interaction chromatography.

    Science.gov (United States)

    Periat, Aurélie; Debrus, Benjamin; Rudaz, Serge; Guillarme, Davy

    2013-03-22

    The goal of the present work was to provide some guidelines for method development in hydrophilic interaction chromatography (HILIC). For this purpose, a training set of 82 representative pharmaceutical compounds possessing diverse polarity and including acidic, basic and neutral properties was analyzed. All these drugs were injected on five short HILIC columns packed with sub-2μm particles and dedicated for UHPLC (ultra-high performance liquid chromatography) operation. Four different pH conditions ranging from pH 3 to 6 were tested at two ionic strengths (10 and 50mmol/L) and finally, the reference organic modifier in HILIC, namely acetonitrile was modified with small amounts of methanol or isopropanol. From these experiments and using multivariate data analysis, it is clear that the stationary phase was the most relevant parameters for tuning selectivity in HILIC, since the types of interactions (i.e. dipole-dipole, hydrogen bonding and ion exchange) with analytes strongly vary between columns. Among the selected phases, the diol phase was the less interesting one, in terms of selectivity and peak shape. The zwitterionic phase was attractive, as it allowed a better retention of acidic compounds. Finally, the bare silica phase was the most versatile HILIC column packed with sub-2μm particles in terms of retention, peak shape and selectivity. Mobile phase pH was the other important parameter to achieve an appropriate selectivity and retention, even if it remains always difficult to assess precisely the mobile phase pH, analyte pKa and silanols pKa, when working with more 70% acetonitrile. Finally, buffer ionic strength and organic modifier nature could be considered as secondary parameters for HILIC method development. In conclusion, screening four different columns packed with sub-2μm particles at two mobile phase pH, using a fast gradient seems to be a good generic approach for initial HILIC method development. The total time for such a screening was

  19. Trace metals, melanin-based pigmentation and their interaction influence immune parameters in feral pigeons (Columba livia).

    Science.gov (United States)

    Chatelain, M; Gasparini, J; Frantz, A

    2016-04-01

    Understanding the effects of trace metals emitted by anthropogenic activities on wildlife is of great concern in urban ecology; yet, information on how they affect individuals, populations, communities and ecosystems remains scarce. In particular, trace metals may impact survival by altering the immune system response to parasites. Plumage melanin is assumed to influence the effects of trace metals on immunity owing to its ability to bind metal ions in feathers and its synthesis being coded by a pleiotropic gene. We thus hypothesized that trace metal exposure would interact with plumage colouration in shaping immune response. We experimentally investigated the interactive effect between exposure to an environmentally relevant range of zinc and/or lead and melanin-based plumage colouration on components of the immune system in feral pigeons (Columba livia). We found that zinc increased anti-keyhole limpet hemocyanin (KLH) IgY primary response maintenance, buffered the negative effect of lead on anti-KLH IgY secondary response maintenance and tended to increase T-cell mediated phytohaemagglutinin (PHA) skin response. Lead decreased the peak of the anti-KLH IgY secondary response. In addition, pheomelanic pigeons exhibited a higher secondary anti-KLH IgY response than did eumelanic ones. Finally, T-cell mediated PHA skin response decreased with increasing plumage eumelanin level of birds exposed to lead. Neither treatments nor plumage colouration correlated with endoparasite intensity. Overall, our study points out the effects of trace metals on some parameters of birds' immunity, independently from other confounding urbanization factors, and underlines the need to investigate their impacts on other life history traits and their consequences in the ecology and evolution of host-parasite interactions.

  20. Effect of acute exposure to nonylphenol on biochemical, hormonal, and hematological parameters and muscle tissues residues of Nile tilapia; Oreochromis niloticus

    Directory of Open Access Journals (Sweden)

    Hager Tarek H. Ismail

    2016-06-01

    Full Text Available Aim: This study is aimed to evaluate some biochemical, hormonal, hematological, and histopathological changes in Nile tilapia, Oreochromis niloticus, after acute exposure to nonylphenol (NP. In addition to detection of NP residues in the fish, muscle tissues for human health concern. Materials and Methods: A total of 90 apparently healthy Nile tilapia, O. niloticus, were randomly divided into three equal groups; each containing 30 fish (three replicates. Groups 1 and 2 kept as a control and solvent control (acetone, respectively, and Group 3 exposed to NP at a dose level of 500 μg/L water for 7 successive days. Blood and tissue samples were collected 2 times randomly from each group after 7 days from fish exposure to NP and 10 days from exposure stopping. Results: Fish exposed to NP Group 3 showed anorexia, sluggish movement, erythema of the skin, areas of scales loss, and hemorrhagic ulcers in some areas of body region leading to exposing the viscera. Biochemical results revealed a significant increase in serum total proteins and globulins levels, a highly significant increase in serum alanine aminotransferase and aspartate aminotransferase activities, triglycerides, cholesterol, and creatinine levels, insignificant increase in serum uric acid level, and a highly significant decrease in serum testosterone and estradiol-β17 levels in Group 3 in compare with the control group. Histopathological finding confirms these results. While hematological results of the same group revealed a significant increase in red blood cells count and packed cell volume value, insignificant increase in hemoglobin concentration, leukopenia, lymphopenia, and monocytopenia in compared with the control group. All of these changes appeared after 7 days from fish exposure to NP. Most of these alterations returned toward the normal level after 10 days from stopping exposure to NP. NP residues detected in fish muscle tissues of Group 3 during exposure and after stopping

  1. Effect of acute exposure to nonylphenol on biochemical, hormonal, and hematological parameters and muscle tissues residues of Nile tilapia; Oreochromis niloticus.

    Science.gov (United States)

    Ismail, Hager Tarek H; Mahboub, Heba Hassan H

    2016-06-01

    This study was aimed to evaluate some biochemical, hormonal, hematological, and histopathological changes in Nile tilapia, Oreochromis niloticus, after acute exposure to nonylphenol (NP). In addition to detection of NP residues in the fish, muscle tissues for human health concern. A total of 90 apparently healthy Nile tilapia, O. niloticus, were randomly divided into three equal groups; each containing 30 fish (three replicates). Groups 1 and 2 kept as a control and solvent control (acetone), respectively, and Group 3 exposed to NP at a dose level of 500 µg/L water for 7 successive days. Blood and tissue samples were collected 2 times randomly from each group after 7 days from fish exposure to NP and 10 days from exposure stopping. Fish exposed to NP Group 3 showed anorexia, sluggish movement, erythema of the skin, areas of scales loss, and hemorrhagic ulcers in some areas of body region leading to exposing the viscera. Biochemical results revealed a significant increase in serum total proteins and globulins levels, a highly significant increase in serum alanine aminotransferase and aspartate aminotransferase activities, triglycerides, cholesterol, and creatinine levels, insignificant increase in serum uric acid level, and a highly significant decrease in serum testosterone and estradiol-β17 levels in Group 3 in compare with the control group. Histopathological finding confirms these results. While hematological results of the same group revealed a significant increase in red blood cells count and packed cell volume value, insignificant increase in hemoglobin concentration, leukopenia, lymphopenia, and monocytopenia in compared with the control group. All of these changes appeared after 7 days from fish exposure to NP. Most of these alterations returned toward the normal level after 10 days from stopping exposure to NP. NP residues detected in fish muscle tissues of Group 3 during exposure and after stopping exposure to it. It is concluded that NP is a toxic

  2. Potential of lignin from Canna edulis ker residue in the inhibition of α-d-glucosidase: Kinetics and interaction mechanism merging with docking simulation.

    Science.gov (United States)

    Xie, Fan; Gong, Shengxiang; Zhang, Wei; Wu, Jinhong; Wang, Zhengwu

    2017-02-01

    In this study, we extracted lignin from Canna edulis ker residue. Its chemical structure, inhibitory activity on α-d-glucosidase, and kinetics as well as interaction mechanism were investigated by using spectrum analysis and docking simulation. The isolated lignin was composed by guaiacyl and syringal units, and exhibited stronger inhibition on α-d-glucosidase than acarbose with the half maximal inhibitory concentration at 5.3±0.3μM. It was a non-competitive inhibitior with K m and K i values of 0.53±0.02mM and 0.92±0.12μM, respectively. It could quench the intrinsic fluorescence of α-d-glucosidase through a static quenching mode. The calculated values of enthalpy and entropy change were 20.8±2.5kJmol -1 and 172.7±0.8Jmol -1 K -1 , respectively. There was a single binding site on α-d-glucosidase for lignin, and the binding distance was 3.2nm. The molecular docking analysis exhibited that the hydrogen bonds, hydropholic interaction, and van der Waals forces were the main forces for lignin bind to α-d-glucosidase. This work provides a new insight into the interaction between the lignin and α-d-glucosidase, which might be beneficial to type 2 diabetes with the application of lignin in functional food and pharmacy fields. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Hydrophobic interaction between contiguous residues in the S6 transmembrane segment acts as a stimuli integration node in the BK channel

    Science.gov (United States)

    Carrasquel-Ursulaez, Willy; Contreras, Gustavo F.; Sepúlveda, Romina V.; Aguayo, Daniel; González-Nilo, Fernando

    2015-01-01

    Large-conductance Ca2+- and voltage-activated K+ channel (BK) open probability is enhanced by depolarization, increasing Ca2+ concentration, or both. These stimuli activate modular voltage and Ca2+ sensors that are allosterically coupled to channel gating. Here, we report a point mutation of a phenylalanine (F380A) in the S6 transmembrane helix that, in the absence of internal Ca2+, profoundly hinders channel opening while showing only minor effects on the voltage sensor active–resting equilibrium. Interpretation of these results using an allosteric model suggests that the F380A mutation greatly increases the free energy difference between open and closed states and uncouples Ca2+ binding from voltage sensor activation and voltage sensor activation from channel opening. However, the presence of a bulky and more hydrophobic amino acid in the F380 position (F380W) increases the intrinsic open–closed equilibrium, weakening the coupling between both sensors with the pore domain. Based on these functional experiments and molecular dynamics simulations, we propose that F380 interacts with another S6 hydrophobic residue (L377) in contiguous subunits. This pair forms a hydrophobic ring important in determining the open–closed equilibrium and, like an integration node, participates in the communication between sensors and between the sensors and pore. Moreover, because of its effects on open probabilities, the F380A mutant can be used for detailed voltage sensor experiments in the presence of permeant cations. PMID:25548136

  4. Fluid-structure interaction of patient-specific Circle of Willis with aneurysm: Investigation of hemodynamic parameters.

    Science.gov (United States)

    Jahed, Mahsa; Ghalichi, Farzan; Farhoudi, Mehdi

    2018-01-01

    Circle of Willis (COW) is a network of cerebral artery which continually supplies the brain with blood. Any disturbance in this supply will result in trauma or even death. One of these damages is known as brain Aneurysm. Clinical methods for diagnosing aneurysm can only measure blood velocity; while, in order to understand the causes of these occurrences it is necessary to have information about the amount of pressure and wall shear stress, which is possible through computational models. In this study purpose is achieving exact information of hemodynamic blood flow in COW with an aneurysm and investigation of effective factors on growth and rupture of aneurysm. Here, realistic three-dimensional models have been produced from angiography images. Considering fluid-structure interaction have been simulated by the ANSYS.CFX software. Hemodynamic Studying of the COW and intra-aneurysm showed that the WSS and wall tension in the neck of aneurysms for case A are 129.5 Pa, and 12.2 kPa and for case B they are 53.3 Pa and 56.2 kPa, and more than their fundus, thus neck of aneurysm is prone to rupture. This study showed that the distribution of parameters was dependent on the geometry of the COW, and maximum values are seen in areas prone to aneurysm formation.

  5. Investigations on the Phase Diagram and Interaction Parameter of Poly(styrene-b-1,3-cyclohexadiene) Copolymers

    KAUST Repository

    Misichronis, Konstantinos

    2017-03-15

    A series of linear diblock copolymers containing polystyrene (PS) and poly(1,3-cyclohexadiene) (PCHD) with high 1,4-microstructure (>87%) was synthesized by anionic polymerization and high vacuum techniques. Microphase separation in the bulk was examined by transmission electron microscopy (TEM) and small-angle X-ray scattering (SAXS) and compared to computational analysis of the predicted morphological phase diagram for this system. Because of the high conformational asymmetry between PS and PCHD, these materials self-assemble into typical morphologies expected for linear diblock copolymer systems and atypical structures. Rheological measurements were conducted and revealed order–disorder transition temperatures (TODT), for the first time for PS-b-PCHD copolymers, resulting in a working expression for the effective interaction parameter χeff = 32/T – 0.016. Furthermore, we performed computational studies that coincide with the experimental results. These copolymers exhibit well-ordered structures even at high temperatures (∼260 °C) therefore providing a better insight concerning their microphase separation at the nanoscale which is important for their potential use in nanotechnology and/or nanolithography applications.

  6. Measurement of the $\\beta$-asymmetry parameter of $^{67}$Cu in search for tensor type currents in the weak interaction

    CERN Document Server

    Soti, G.; Breitenfeldt, M.; Finlay, P.; Herzog, P.; Knecht, A.; Köster, U.; Kraev, I.S.; Porobic, T.; Prashanth, P.N.; Towner, I.S.; Tramm, C.; Zákoucký, D.; Severijns, N.

    2014-01-01

    Precision measurements at low energy search for physics beyond the Standard Model in a way complementary to searches for new particles at colliders. In the weak sector the most general $\\beta$ decay Hamiltonian contains, besides vector and axial-vector terms, also scalar, tensor and pseudoscalar terms. Current limits on the scalar and tensor coupling constants from neutron and nuclear $\\beta$ decay are on the level of several percent. The goal of this paper is extracting new information on tensor coupling constants by measuring the $\\beta$-asymmetry parameter in the pure Gamow-Teller decay of $^{67}$Cu, thereby testing the V-A structure of the weak interaction. An iron sample foil into which the radioactive nuclei were implanted was cooled down to milliKelvin temperatures in a $^3$He-$^4$He dilution refrigerator. An external magnetic field of 0.1 T, in combination with the internal hyperfine magnetic field, oriented the nuclei. The anisotropic $\\beta$ radiation was observed with planar high purity germanium d...

  7. Residue processing

    Energy Technology Data Exchange (ETDEWEB)

    Gieg, W.; Rank, V.

    1942-10-15

    In the first stage of coal hydrogenation, the liquid phase, light and heavy oils were produced; the latter containing the nonliquefied parts of the coal, the coal ash, and the catalyst substances. It was the problem of residue processing to extract from these so-called let-down oils that which could be used as pasting oils for the coal. The object was to obtain a maximum oil extraction and a complete removal of the solids, because of the latter were returned to the process they would needlessly burden the reaction space. Separation of solids in residue processing could be accomplished by filtration, centrifugation, extraction, distillation, or low-temperature carbonization (L.T.C.). Filtration or centrifugation was most suitable since a maximum oil yield could be expected from it, since only a small portion of the let-down oil contained in the filtration or centrifugation residue had to be thermally treated. The most satisfactory centrifuge at this time was the Laval, which delivered liquid centrifuge residue and centrifuge oil continuously. By comparison, the semi-continuous centrifuges delivered plastic residues which were difficult to handle. Various apparatus such as the spiral screw kiln and the ball kiln were used for low-temperature carbonization of centrifuge residues. Both were based on the idea of carbonization in thin layers. Efforts were also being made to produce electrode carbon and briquette binder as by-products of the liquid coal phase.

  8. 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

  9. 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

  10. The influence of soil organic carbon on interactions between microbial parameters and metal concentrations at a long-term contaminated site

    Energy Technology Data Exchange (ETDEWEB)

    Muhlbachova, G. [Crop Research Institute, Drnovska 507, 161 06 Prague 6, Ruzyne (Czech Republic); Sagova-Mareckova, M., E-mail: sagova@vurv.cz [Crop Research Institute, Drnovska 507, 161 06 Prague 6, Ruzyne (Czech Republic); Omelka, M. [Charles University, Faculty of Mathematics and Physics, Dept. of Probability and Mathematical Statistics, Prague 8, Karlin (Czech Republic); Szakova, J.; Tlustos, P. [Czech University of Life Sciences, Department of Agroenvironmental Chemistry and Plant Nutrition, Prague 6, Suchdol (Czech Republic)

    2015-01-01

    The effects of lead, zinc, cadmium, arsenic and copper deposits on soil microbial parameters were investigated at a site exposed to contamination for over 200 years. Soil samples were collected in triplicates at 121 sites differing in contamination and soil organic carbon (SOC). Microbial biomass, respiration, dehydrogenase activity and metabolic quotient were determined and correlated with total and extractable metal concentrations in soil. The goal was to analyze complex interactions between toxic metals and microbial parameters by assessing the effect of soil organic carbon in the relationships. The effect of SOC was significant in all interactions and changed the correlations between microbial parameters and metal fractions from negative to positive. In some cases, the effect of SOC was combined with that of clay and soil pH. In the final analysis, dehydrogenase activity was negatively correlated to total metal concentrations and acetic acid extractable metals, respiration and metabolic quotient were to ammonium nitrate extractable metals. Dehydrogenase activity was the most sensitive microbial parameter correlating most frequently with contamination. Total and extractable zinc was most often correlated with microbial parameters. The large data set enabled robust explanation of discrepancies in organic matter functioning occurring frequently in analyzing of contaminated soil processes. - Highlights: • Soil organic carbon affected all interactions between metals and microorganisms. • Soil organic carbon adjustment changed correlations from positive to negative. • Ammonium nitrate extractable metals were the most influencing fraction. • Dehydrogenase activity was the most affected soil parameter. • Zinc was the most toxic metal among studied metals.

  11. Opinions on Drug Interaction Sources in Anticancer Treatments and Parameters for an Oncology-Specific Database by Pharmacy Practitioners in Asia

    Directory of Open Access Journals (Sweden)

    2010-01-01

    Full Text Available Cancer patients undergoing chemotherapy are particularly susceptible to drug-drug interactions (DDIs. Practitioners should keep themselves updated with the most current DDI information, particularly involving new anticancer drugs (ACDs. Databases can be useful to obtain up-to-date DDI information in a timely and efficient manner. Our objective was to investigate the DDI information sources of pharmacy practitioners in Asia and their views on the usefulness of an oncology-specific database for ACD interactions. A qualitative, cross-sectional survey was done to collect information on the respondents' practice characteristics, sources of DDI information and parameters useful in an ACD interaction database. Response rate was 49%. Electronic databases (70%, drug interaction textbooks (69% and drug compendia (64% were most commonly used. Majority (93% indicated that a database catering towards ACD interactions was useful. Essential parameters that should be included in the database were the mechanism and severity of the detected interaction, and the presence of a management plan (98% each. This study has improved our understanding on the usefulness of various DDI information sources for ACD interactions among pharmacy practitioners in Asia. An oncology-specific DDI database targeting ACD interactions is definitely attractive for clinical practice.

  12. Residue-Ligand Interaction Energy (ReLIE on a Receptor-Dependent 3D-QSAR Analysis of S- and NH-DABOs as Non-Nucleoside Reverse Transcriptase Inhibitors

    Directory of Open Access Journals (Sweden)

    Monique Araújo de Brito

    2012-06-01

    Full Text Available A series of 74 dihydroalkoxybenzyloxopyrimidines (DABOs, a class of highly potent non-nucleoside reverse transcriptase inhibitors (NNRTIs, was retrieved from the literature and studied by receptor-dependent (RD three-dimensional quantitative structure-activity relationship (3D-QSAR analysis to derive RD-3D-QSAR models. The descriptors in this new method are the steric and electrostatic interaction energies of the protein-ligand complexes (per residue simulated by molecular dynamics, an approach named Residue-Ligand Interaction Energy (ReLIE. This study was performed using a training set of 59 compounds and the MKC-442/RT complex structure as reference. The ReLIE-3D-QSAR models were constructed and evaluated by genetic algorithm (GA and partial least squares (PLS. In the best equations, at least one term is related to one of the amino acid residues of the p51 subunit: Asn136, Asn137, Glu138, and Thr139. This fact implies the importance of interchain interaction (p66-p51 in the equations that best describe the structure-activity relationship for this class of compounds. The best equation shows q2 = 0.660, SEcv = 0.500, r2 = 0.930, and SEE = 0.226. The external predictive ability of this best model was evaluated using a test set of 15 compounds. In order to design more potent DABO analogues as anti-HIV/AIDS agents, substituents capable of interactions with residues like Ile94, Lys101, Tyr181, and Tyr188 should be selected. Also, given the importance of the conserved Asn136, this residue could become an attractive target for the design of novel NNRTIs with improved potency and increased ability to avoid the development of drug-resistant viruses.

  13. Positively charged residues at the five-fold symmetry axis of cell culture-adapted foot-and-mouth disease virus permit novel receptor interactions.

    Science.gov (United States)

    Berryman, Stephen; Clark, Stuart; Kakker, Naresh K; Silk, Rhiannon; Seago, Julian; Wadsworth, Jemma; Chamberlain, Kyle; Knowles, Nick J; Jackson, Terry

    2013-08-01

    Field isolates of foot-and-mouth disease virus (FMDV) have a restricted cell tropism which is limited by the need for certain RGD-dependent integrin receptors. In contrast, cell culture-adapted viruses use heparan sulfate (HS) or other unidentified molecules as receptors to initiate infection. Here, we report several novel findings resulting from cell culture adaptation of FMDV. In cell culture, a virus with the capsid of the A/Turkey/2/2006 field isolate gained the ability to infect CHO and HS-deficient CHO cells as a result of a single glutamine (Q)-to-lysine (K) substitution at VP1-110 (VP1-(Q)110(K)). Using site-directed mutagenesis, the introduction of lysine at this same site also resulted in an acquired ability to infect CHO cells by type O and Asia-1 FMDV. However, this ability appeared to require a second positively charged residue at VP1-109. CHO cells express two RGD-binding integrins (α5β1 and αvβ5) that, although not used by FMDV, have the potential to be used as receptors; however, viruses with the VP1-(Q)110(K) substitution did not use these integrins. In contrast, the VP1-(Q)110(K) substitution appeared to result in enhanced interactions with αvβ6, which allowed a virus with KGE in place of the normal RGD integrin-binding motif to use αvβ6 as a receptor. Thus, our results confirmed the existence of nonintegrin, non-HS receptors for FMDV on CHO cells and revealed a novel, non-RGD-dependent use of αvβ6 as a receptor. The introduction of lysine at VP1-110 may allow for cell culture adaptation of FMDV by design, which may prove useful for vaccine manufacture when cell culture adaptation proves intractable.

  14. Residual risk

    African Journals Online (AJOL)

    ing the residual risk of transmission of HIV by blood transfusion. An epidemiological approach assumed that all HIV infections detected serologically in first-time donors were pre-existing or prevalent infections, and that all infections detected in repeat blood donors were new or incident infections. During 1986 - 1987,0,012%.

  15. TRIP-ID: A tool for a smart and interactive identification of Magic Formula tyre model parameters from experimental data acquired on track or test rig

    Science.gov (United States)

    Farroni, Flavio; Lamberti, Raffaele; Mancinelli, Nicolò; Timpone, Francesco

    2018-03-01

    Tyres play a key role in ground vehicles' dynamics because they are responsible for traction, braking and cornering. A proper tyre-road interaction model is essential for a useful and reliable vehicle dynamics model. In the last two decades Pacejka's Magic Formula (MF) has become a standard in simulation field. This paper presents a Tool, called TRIP-ID (Tyre Road Interaction Parameters IDentification), developed to characterize and to identify with a high grade of accuracy and reliability MF micro-parameters from experimental data deriving from telemetry or from test rig. The tool guides interactively the user through the identification process on the basis of strong diagnostic considerations about the experimental data made evident by the tool itself. A motorsport application of the tool is shown as a case study.

  16. Physicochemical parameters and antibiotics residuals in Algerian ...

    African Journals Online (AJOL)

    The physicochemical analyses of the Algerian honeys show that 56% of samples correspond to Codex standards and 44% not in conformity with the standards required by the Codex Alimentarius and EU, because part of the samples had one or more defects. The percentage not in conformity was due to the high rates of ...

  17. Residual basins

    International Nuclear Information System (INIS)

    D'Elboux, C.V.; Paiva, I.B.

    1980-01-01

    Exploration for uranium carried out over a major portion of the Rio Grande do Sul Shield has revealed a number of small residual basins developed along glacially eroded channels of pre-Permian age. Mineralization of uranium occurs in two distinct sedimentary units. The lower unit consists of rhythmites overlain by a sequence of black shales, siltstones and coal seams, while the upper one is dominated by sandstones of probable fluvial origin. (Author) [pt

  18. [Equilibrium and kinetic parameters of the interaction of strophanthin K and its peroxidase conjugates with soluble and immobilized specific antibodies].

    Science.gov (United States)

    Tarun, E I; Savenkova, M I; Metelitsa, D I

    1995-07-01

    Using solid phase enzyme-linked immunoassay (ELISA), rate constants for the formation and dissociation as well as equilibrium dissociation constants for strophanthin complexes interaction with specific antibodies (both soluble and immobilized on activated polystyrene beads and polyamide membranes) have been determined. A satisfactory correlation was found between dissociation constants for immune complexes determined by ELISA (both soluble and immobilized ones) and associations constants for these complexes determined by the Scatchard method. The experimental values of kinetic and equilibrium constants for strophanthin K and its peroxidase complexes interaction reflect the difference in the nature of interacting particles and their environment. Strophanthin complexes with antibodies appeared to be more stable when formed on adsorbents (in comparison with those formed in solution). Strophanthin interaction with immobilized antibodies occurred at a slower rate than that with soluble antibodies. Strophanthin reacts with antibodies more readily than its complexes both in solution and on solid matrices of various polymeric nature.

  19. Features of parameters of gamma-ray families formed from AA-interactions at superhigh energies above 1016 eV

    International Nuclear Information System (INIS)

    Yuldashbaev, T S; Nuritdinov, Kh

    2013-01-01

    Different lateral and energetic characteristics of gamma-ray families produced in nucleus-nucleus (AA) interactions of primary cosmic rays (PCR) are studied. Primary mass composition analysis performed on the basis of 'Pamir' Collaboration X-ray emulsion chambers (XREC) data by using of selection criteria of gamma-ray families originating from AA-interactions above 10 PeV. Experimental data are compared with results of MC0 algorithm based on quark-gluon string model (QGSM). Among seven considered variables, only two lateral parameters, R 1E and ρ, are not described by the MC0 model.

  20. Computation of energy interaction parameters as well as electric dipole intensity parameters for the absorption spectral study of the interaction of Pr(III) with l-phenylalanine, l-glycine, l-alanine and l-aspartic acid in the presence and absence of Ca2+ in organic solvents.

    Science.gov (United States)

    Moaienla, T; Singh, Th David; Singh, N Rajmuhon; Devi, M Indira

    2009-10-01

    Studying the absorption difference and comparative absorption spectra of the interaction of Pr(III) and Nd(III) with l-phenylalanine, l-glycine, l-alanine and l-aspartic acid in the presence and absence of Ca(2+) in organic solvents, various energy interaction parameters like Slater-Condon (F(K)), Racah (E(k)), Lande factor (xi(4f)), nephelauxetic ratio (beta), bonding (b(1/2)), percentage-covalency (delta) have been evaluated applying partial and multiple regression analysis. The values of oscillator strength (P) and Judd-Ofelt electric dipole intensity parameter T(lambda) (lambda = 2, 4, 6) for different 4f-4f transitions have been computed. On analysis of the variation of the various energy interaction parameters as well as the changes in the oscillator strength (P) and T(lambda) values reveal the mode of binding with different ligands.

  1. Factorial experimental design for the culture of human embryonic stem cells as aggregates in stirred suspension bioreactors reveals the potential for interaction effects between bioprocess parameters.

    Science.gov (United States)

    Hunt, Megan M; Meng, Guoliang; Rancourt, Derrick E; Gates, Ian D; Kallos, Michael S

    2014-01-01

    Traditional optimization of culture parameters for the large-scale culture of human embryonic stem cells (ESCs) as aggregates is carried out in a stepwise manner whereby the effect of varying each culture parameter is investigated individually. However, as evidenced by the wide range of published protocols and culture performance indicators (growth rates, pluripotency marker expression, etc.), there is a lack of systematic investigation into the true effect of varying culture parameters especially with respect to potential interactions between culture variables. Here we describe the design and execution of a two-parameter, three-level (3(2)) factorial experiment resulting in nine conditions that were run in duplicate 125-mL stirred suspension bioreactors. The two parameters investigated here were inoculation density and agitation rate, which are easily controlled, but currently, poorly characterized. Cell readouts analyzed included fold expansion, maximum density, and exponential growth rate. Our results reveal that the choice of best case culture parameters was dependent on which cell property was chosen as the primary output variable. Subsequent statistical analyses via two-way analysis of variance indicated significant interaction effects between inoculation density and agitation rate specifically in the case of exponential growth rates. Results indicate that stepwise optimization has the potential to miss out on the true optimal case. In addition, choosing an optimum condition for a culture output of interest from the factorial design yielded similar results when repeated with the same cell line indicating reproducibility. We finally validated that human ESCs remain pluripotent in suspension culture as aggregates under our optimal conditions and maintain their differentiation capabilities as well as a stable karyotype and strong expression levels of specific human ESC markers over several passages in suspension bioreactors.

  2. Computation of methodology-independent single-ion solvation properties from molecular simulations. IV. Optimized Lennard-Jones interaction parameter sets for the alkali and halide ions in water

    Science.gov (United States)

    Reif, Maria M.; Hünenberger, Philippe H.

    2011-04-01

    The raw single-ion solvation free energies computed from atomistic (explicit-solvent) simulations are extremely sensitive to the boundary conditions and treatment of electrostatic interactions used during these simulations. However, as shown recently [M. A. Kastenholz and P. H. Hünenberger, J. Chem. Phys. 124, 224501 (2006), 10.1529/biophysj.106.083667; M. M. Reif and P. H. Hünenberger, J. Chem. Phys. 134, 144103 (2010)], the application of appropriate correction terms permits to obtain methodology-independent results. The corrected values are then exclusively characteristic of the underlying molecular model including in particular the ion-solvent van der Waals interaction parameters, determining the effective ion size and the magnitude of its dispersion interactions. In the present study, the comparison of calculated (corrected) hydration free energies with experimental data (along with the consideration of ionic polarizabilities) is used to calibrate new sets of ion-solvent van der Waals (Lennard-Jones) interaction parameters for the alkali (Li+, Na+, K+, Rb+, Cs+) and halide (F-, Cl-, Br-, I-) ions along with either the SPC or the SPC/E water models. The experimental dataset is defined by conventional single-ion hydration free energies [Tissandier et al., J. Phys. Chem. A 102, 7787 (1998), 10.1021/jp982638r; Fawcett, J. Phys. Chem. B 103, 11181] along with three plausible choices for the (experimentally elusive) value of the absolute (intrinsic) hydration free energy of the proton, namely, Δ G_hyd^{ominus }[H+] = -1100, -1075 or -1050 kJ mol-1, resulting in three sets L, M, and H for the SPC water model and three sets LE, ME, and HE for the SPC/E water model (alternative sets can easily be interpolated to intermediate Δ G_hyd^{ominus }[H+] values). The residual sensitivity of the calculated (corrected) hydration free energies on the volume-pressure boundary conditions and on the effective ionic radius entering into the calculation of the correction terms is

  3. Comparison of designs for estimating genetic parameters and obtaining response to selection for social interaction traits in aquaculture

    NARCIS (Netherlands)

    Sae-Lim, P.; Bijma, P.

    2016-01-01

    Social interactions among individuals may affect individual productivity and welfare in aquaculture. Since social effects may have a genetic component, known as an indirect genetic effect (IGE), genetic selection may be a promising tool to simultaneously improve welfare and productivity in

  4. A climatic atlas of the air-sea interaction parameters and fluxes of the oceans using satellite data

    Digital Repository Service at National Institute of Oceanography (India)

    RameshKumar, M.R.; Schulz, J.; Jost, V.

    . It is intended to provide a climatological data base for scientists in the field of climatology and air-sea interaction. It is hoped that this atlas will serve as a reference to the students as well as the scientists working in the fields of Climatology...

  5. RESIDUAL RISK ASSESSMENTS - RESIDUAL RISK ...

    Science.gov (United States)

    This source category previously subjected to a technology-based standard will be examined to determine if health or ecological risks are significant enough to warrant further regulation for Coke Ovens. These assesments utilize existing models and data bases to examine the multi-media and multi-pollutant impacts of air toxics emissions on human health and the environment. Details on the assessment process and methodologies can be found in EPA's Residual Risk Report to Congress issued in March of 1999 (see web site). To assess the health risks imposed by air toxics emissions from Coke Ovens to determine if control technology standards previously established are adequately protecting public health.

  6. Estimation of the solubility parameters of model plant surfaces and agrochemicals: a valuable tool for understanding plant surface interactions

    OpenAIRE

    Khayet, Mohamed; Fernandez Fernandez, Victoria

    2012-01-01

    Background Most aerial plant parts are covered with a hydrophobic lipid-rich cuticle, which is the interface between the plant organs and the surrounding environment. Plant surfaces may have a high degree of hydrophobicity because of the combined effects of surface chemistry and roughness. The physical and chemical complexity of the plant cuticle limits the development of models that explain its internal structure and interactions with surface-applied agrochemicals. In this article we int...

  7. Interactions in recovery and in residual injury from sequential treatments of mouse haemopoietic and stromal marrow cell populations, using X-rays, cyclophosphamide and busulphan

    International Nuclear Information System (INIS)

    Qi, D.Y.; Hendry, J.H.; Testa, N.G.

    1991-01-01

    The acute recovery of day 11 CFU-S, iv-CFC and CFU-F in mouse bone marrow, following a test dose of X-rays, cyclophosphamide (CP) or busulphan given to mice previously treated with repeated priming dose X-rays or CP, was in general predictable from the amount of residual injury after the priming doses. A marked exception was iv-CFC after X-rays, which although amplified to near normal levels during the residual injury phase, recovered after the test irradiation from low-levels of CFU-S. The amount of residual injury after sequential treatments of different agents was in general less than expected on the basis of the product of the effects of the individual agents. This was most marked for CP priming treatments, where the long-term recovery of day 11 CFU-S after the test dose remained persistently above control levels. Also, some correlation was found between improved stromal recovery (CFU-F) and the CFU-S content following the sequential treatment protocols. (author). 33 refs.; 3 figs.; 5 tabs

  8. Spectroscopic study of the interaction of Nd{sup +3} with amino acids: phenomenological 4f-4f intensity parameters

    Energy Technology Data Exchange (ETDEWEB)

    Jerico, Soraya; Carubelli, Celia R.; Massabni, Ana M.G.; Stucchi, Elizabeth B.; Leite, Sergio R. de A. [UNESP, Araraquara, SP (Brazil). Inst. de Quimica; Malta, Oscar [Pernambuco Univ., Recife, PE (Brazil). Dept. de Quimica Fundamental

    1998-10-01

    We have studied behaviour of the phenomenological 4f-4f intensity parameters in compounds of the Nd{sup 3+} ion with glycine, L-aspartic acid, L-glutamic acid, L-histidine, DL-malic acid and Aspartame{sup TM} in aqueous solution, as function of the pK values and partial charges on the oxygens of the carboxylate groups of these molecules. The results are discussed and qualitatively interpreted in terms of the forced electric dipole and dynamic coupling mechanisms of the 4f-4f intensities, thus indicating that the forced electric dipole mechanism is dominant. (author)

  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. Usefulness and limitations of dK random graph models to predict interactions and functional homogeneity in biological networks under a pseudo-likelihood parameter estimation approach

    Directory of Open Access Journals (Sweden)

    Luan Yihui

    2009-09-01

    Full Text Available Abstract Background Many aspects of biological functions can be modeled by biological networks, such as protein interaction networks, metabolic networks, and gene coexpression networks. Studying the statistical properties of these networks in turn allows us to infer biological function. Complex statistical network models can potentially more accurately describe the networks, but it is not clear whether such complex models are better suited to find biologically meaningful subnetworks. Results Recent studies have shown that the degree distribution of the nodes is not an adequate statistic in many molecular networks. We sought to extend this statistic with 2nd and 3rd order degree correlations and developed a pseudo-likelihood approach to estimate the parameters. The approach was used to analyze the MIPS and BIOGRID yeast protein interaction networks, and two yeast coexpression networks. We showed that 2nd order degree correlation information gave better predictions of gene interactions in both protein interaction and gene coexpression networks. However, in the biologically important task of predicting functionally homogeneous modules, degree correlation information performs marginally better in the case of the MIPS and BIOGRID protein interaction networks, but worse in the case of gene coexpression networks. Conclusion Our use of dK models showed that incorporation of degree correlations could increase predictive power in some contexts, albeit sometimes marginally, but, in all contexts, the use of third-order degree correlations decreased accuracy. However, it is possible that other parameter estimation methods, such as maximum likelihood, will show the usefulness of incorporating 2nd and 3rd degree correlations in predicting functionally homogeneous modules.

  11. Cubic Dresselhaus interaction parameter from quantum corrections to the conductivity in the presence of an in-plane magnetic field

    Science.gov (United States)

    Marinescu, D. C.

    2017-09-01

    We evaluate the quantum corrections to the conductivity of a two-dimensional electron system with competing Rashba (R) and linear and cubic Dresselhaus (D) spin-orbit interactions in the presence of an in-plane magnetic field B . Within a perturbative approximation, we investigate the interplay between the spin-orbit coupling and the magnetic field in determining the transport regime in two different limiting scenarios: when only one of the linear terms, either Rashba or Dresselhaus, dominates, and at equal linear couplings, when the cubic Dresselhaus breaks the spin symmetry. In each instance, we find that for B higher than a critical value, the antilocalization correction is suppressed and the effective dephasing time saturates to a constant value determined only by the spin-orbit interaction. At equal R-D linear couplings, this value is directly proportional with the cubic Dresselhaus contribution. In the same regime, the magnetoconductivity is expressed as a simple logarithmic function dependent only on the cubic Dresselhaus constant.

  12. A Mutational Analysis of Residues in Cholera Toxin A1 Necessary for Interaction with Its Substrate, the Stimulatory G Protein Gsα

    Directory of Open Access Journals (Sweden)

    Michael G. Jobling

    2015-03-01

    Full Text Available Pathogenesis of cholera diarrhea requires cholera toxin (CT-mediated adenosine diphosphate (ADP-ribosylation of stimulatory G protein (Gsα in enterocytes. CT is an AB5 toxin with an inactive CTA1 domain linked via CTA2 to a pentameric receptor-binding B subunit. Allosterically activated CTA1 fragment in complex with NAD+ and GTP-bound ADP-ribosylation factor 6 (ARF6-GTP differs conformationally from the CTA1 domain in holotoxin. A surface-exposed knob and a short α-helix (formed, respectively, by rearranging “active-site” and “activation” loops in inactive CTA1 and an ADP ribosylating turn-turn (ARTT motif, all located near the CTA1 catalytic site, were evaluated for possible roles in recognizing Gsα. CT variants with one, two or three alanine substitutions at surface-exposed residues within these CTA1 motifs were tested for assembly into holotoxin and ADP-ribosylating activity against Gsα and diethylamino-(benzylidineamino-guanidine (DEABAG, a small substrate predicted to fit into the CTA1 active site. Variants with single alanine substitutions at H55, R67, L71, S78, or D109 had nearly wild-type activity with DEABAG but significantly decreased activity with Gsα, suggesting that the corresponding residues in native CTA1 participate in recognizing Gsα. As several variants with multiple substitutions at these positions retained partial activity against Gsα, other residues in CTA1 likely also participate in recognizing Gsα.

  13. The Natural Aging Effect on Hardenability in Al-Mg-Si: A Complex Interaction between Composition and Heat Treatment Parameters

    Directory of Open Access Journals (Sweden)

    Alex Poznak

    2018-05-01

    Full Text Available The technological relevance of Al-Mg-Si alloys has been rapidly growing over the last decade. Of particular interest to current and future applications is the problematic negative effect of prior natural aging on subsequent artificial age hardening. The influence of natural aging is dependent on both processing and compositional variables and has origins that are far from well-understood. This work examines the hardenability of 6000 series alloys under a wide range of conditions, paying particular attention to the natural aging effect. Experimental variables include alloy composition (Mg + Si, Mg/Si, cooling rate after solutionization, and duration of prior natural aging. Hardenability was evaluated with full hardness and conductivity aging curves for each condition, as well as select Transmission Electron Microscopy (TEM. Results are discussed based on the actions of naturally aged solute clusters during artificial aging. In particular, a complex interaction between vacancy concentration, cluster stability, and precipitation driving force is suggested.

  14. UNIQUAC interaction parameters for molecules with -OH groups on adjacent carbon atoms in aqueous solution determined by molecular mechanics - glycols, glycerol and glucose

    DEFF Research Database (Denmark)

    Jonsdottir, Svava Osk; Klein, R. A.

    1997-01-01

    Procedure (BJP).The predicted vapor-liquid-equilibrium (VLE) data for the water/1,2-ethanediol system are in excellent agreement with the experimentalvalues and good results were obtained for the water/glycerol system by taking larger samples. This was not true for the other two systemsfor which there were...... difficulties in sampling conformational space in a statistically acceptable manner. As the parameters representinteractions per unit molecular surface area and all of the molecules consist of -CH2OH or -CH2O- units, the values obtained for thewater/1,2-ethanediol system were used to predict VLE data...... for the other systems. This gave results in good agreement with the experimental data.The possibility of transferring interaction parameters is very interesting,especially as it can be applied to systems for which the additivity principle of the UNIFAC method fails.Simulations were carried out for 1...

  15. A non-homogeneous dynamic Bayesian network with sequentially coupled interaction parameters for applications in systems and synthetic biology.

    Science.gov (United States)

    Grzegorczyk, Marco; Husmeier, Dirk

    2012-07-12

    An important and challenging problem in systems biology is the inference of gene regulatory networks from short non-stationary time series of transcriptional profiles. A popular approach that has been widely applied to this end is based on dynamic Bayesian networks (DBNs), although traditional homogeneous DBNs fail to model the non-stationarity and time-varying nature of the gene regulatory processes. Various authors have therefore recently proposed combining DBNs with multiple changepoint processes to obtain time varying dynamic Bayesian networks (TV-DBNs). However, TV-DBNs are not without problems. Gene expression time series are typically short, which leaves the model over-flexible, leading to over-fitting or inflated inference uncertainty. In the present paper, we introduce a Bayesian regularization scheme that addresses this difficulty. Our approach is based on the rationale that changes in gene regulatory processes appear gradually during an organism's life cycle or in response to a changing environment, and we have integrated this notion in the prior distribution of the TV-DBN parameters. We have extensively tested our regularized TV-DBN model on synthetic data, in which we have simulated short non-homogeneous time series produced from a system subject to gradual change. We have then applied our method to real-world gene expression time series, measured during the life cycle of Drosophila melanogaster, under artificially generated constant light condition in Arabidopsis thaliana, and from a synthetically designed strain of Saccharomyces cerevisiae exposed to a changing environment.

  16. Residual analysis for spatial point processes

    DEFF Research Database (Denmark)

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

    process. Residuals are ascribed to locations in the empty background, as well as to data points of the point pattern. We obtain variance formulae, and study standardised residuals. There is also an analogy between our spatial residuals and the usual residuals for (non-spatial) generalised linear models...... or covariate effects. Q-Q plots of the residuals are effective in diagnosing interpoint interaction. Some existing ad hoc statistics of point patterns (quadrat counts, scan statistic, kernel smoothed intensity, Berman's diagnostic) are recovered as special cases....

  17. INTERACT

    DEFF Research Database (Denmark)

    Jochum, Elizabeth; Borggreen, Gunhild; Murphey, TD

    This paper considers the impact of visual art and performance on robotics and human-computer interaction and outlines a research project that combines puppetry and live performance with robotics. Kinesics—communication through movement—is the foundation of many theatre and performance traditions...... including puppetry and dance. However, the aesthetics of these traditions vary across cultures and carry different associative and interpretive meanings. Puppetry offers a useful frame for understanding the relationship between abstract and imitative gestures and behavior, and instantiates the complex...... interaction between a human operator and an artificial actor or agent. We can apply insights from puppetry to develop culturally-aware robots. Here we describe the development of a robotic marionette theatre wherein robotic controllers assume the role of human puppeteers. The system has been built, tested...

  18. Interactions

    DEFF Research Database (Denmark)

    The main theme of this anthology is the unique interaction between mathematics, physics and philosophy during the beginning of the 20th century. Seminal theories of modern physics and new fundamental mathematical structures were discovered or formed in this period. Significant physicists such as ......The main theme of this anthology is the unique interaction between mathematics, physics and philosophy during the beginning of the 20th century. Seminal theories of modern physics and new fundamental mathematical structures were discovered or formed in this period. Significant physicists...... such as Lorentz and Einstein as well as mathematicians such as Poincare, Minkowski, Hilbert and Weyl contributed to this development. They created the new physical theories and the mathematical disciplines that play such paramount roles in their mathematical formulations. These physicists and mathematicians were...... also key figures in the philosophical discussions of nature and science - from philosophical tendencies like logical empiricism via critical rationalism to various neo-Kantian trends....

  19. Persistence of organophosphorus pesticides in aquatic environments. Coordinated programme on isotope-tracer-aided research and monitoring on agricultural residue - biological interactions in aquatic environment

    International Nuclear Information System (INIS)

    Horvath, L.

    1982-08-01

    A radiometric enzymic assay method was developed for quick measuring of organophosphorous insecticides in water samples. All steps of the assay procedure were carried out in scintillation vials. 50 μl enzyme solution (acetylcholinesterase of electric eel) and 50 μl buffer pH 7 were pipetted into the vial followed by 100 μl of water sample or aqueous solution of the insecticide and the mixture was incubated for 60 minutes. 50 μl 3 H-acetylcholine were added to the vial and the enzymic reaction stopped after 10 minutes by adding 200 μl buffer solution pH 2.5. 10 ml scintillation cocktail were then added and after shaking and 30 minutes standing the radioactivity was determined in a liquid scintillation spectrometer. Acetylcholine remained in the water phase while 3 H-acetic acid released in enzymic hydrolysis may be extracted by an organic solvent. By this method, not only the parent compound but also some of its degradation products, which possess some anticholinesteratic activity can be measured. The method is suitable for combination with thin-layer chromatography for identification purposes. Using this method, we studied the degradation of the organophosphorous insecticides malathion, parathion, DDVP and imidan. The degradation in distilled water and natural water was compared. For example, the half-time of malathion in distilled water at room temperature was 6 days while in natural water (Danube river) it was 4 hours. The degradation processes were also studied in model systems containing sediment and water. Degradation was faster in models containing solid particles than in filtered water. The radiometric enzymic method was tested as analytical procedure for residue monitoring. Since 1978 a residue monitoring programme was in progress in the Danube river near Budapest. Occasionally high residue levels were detected in spring and early summer. The radiometric enzymic method has proved to be a useful analytical method for anticholinesterase pesticides in

  20. Interactive effects of copper stress and arbuscular mycorrhizal fungi on photosynthetic characteristics and chlorphyl fluorescence parameters of elsholtzia splendens

    International Nuclear Information System (INIS)

    Li, Y.; Jin, Z.; Li, J.

    2017-01-01

    To determine interactive effects of added copper (Cu) and arbuscular mycorrhizal fungi (AMF) inoculation on the photosynthesis of Elsholtzia splendens, a greenhouse pot experiment was conducted. Four treatments were used, including -Cu-AMF (no Cu addition and no AMF inoculation), +Cu-AMF (Cu addition but no AMF inoculation), -Cu+AMF (no Cu addition and AMF inoculation), and +Cu+AMF (Cu addition and AMF inoculation). Cu addition did not change diurnal variation curves of the net photosynthetic rate(PN), the intercellular CO/sub 2/ concentration (Ci), the stomatal conductance (gs), or the transpiration rate (E); however, it significantly decreased the daily mean PN, gs, E, light-use efficiency (LUE), and carboxylation efficiency (CE). Furthermore, AMF inoculation significantly increased the daily mean PN, gs, LUE, and CE of E. splendens. In response to light, Cu addition significantly decreased the light-saturated net photosynthetic rate (PNmax), the light saturation point (LSP), the light compensation point (LCP), and the apparent quantum yield (AQY), while AMF inoculation significantly increased PNmax and AQY. In response to the CO/sub 2/ concentration, Cu addition significantly decreased PNmax and the CO/sub 2/ saturation point (CSP), while AMF inoculation significantly increased PNmax. Both Cu addition and AMF inoculation significantly decreased the relative chlorophyll content. Compared to the negative control treatment (-Cu-AMF), Cu addition significantly increased the minimal fluorescence, but significantly decreased maximal fluorescence, variable fluorescence,and maximum photochemical efficiency of PSII. These results suggest that AMF inoculations alleviate the inhibitory effect of copper stress on E. splendens plants by weakening its toxic effects on the photosynthetic apparatus and pigments. (author)

  1. Spring Chinook Salmon Interactions Indices and Residual/Precocious Male Monitoring in the Upper Yakima Basin; Yakima/Klickitat Fisheries Project Monitoring and Evaluation, 2004-2005 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Pearsons, Todd N.; Johnson, Christopher L. (Washington Department of Fish and Wildlife, Olympia, WA); James, Brenda B. (Cascade Aquatics, Ellensburg, WA)

    2005-05-01

    This report examines some of the factors that can influence the success of supplementation, which is currently being tested in the Yakima Basin using upper Yakima stock of spring chinook salmon. Supplementation success in the Yakima Basin is defined relative to four topic areas: natural production, genetics, ecological interactions, and harvest (Busack et al. 1997). The success of spring chinook salmon supplementation in the Yakima Basin is dependent, in part, upon fish culture practices and favorable physical and biological conditions in the natural environment (Busack et al. 1997; James et al. 1999; Pearsons et al., 2003; Pearsons et al. 2004). Shortfalls in either of these two topics (i.e., failure in culturing many fish that have high long-term fitness or environmental conditions that constrain spring chinook salmon production) will cause supplementation success to be limited. For example, inadvertent selection or propagation of spring chinook that residualize or precocially mature may hinder supplementation success. Spring chinook salmon that residualize (do not migrate during the normal migration period) may have lower survival rates than migrants and, additionally, may interact with wild fish and cause unacceptable impacts to non-target taxa. Large numbers of precocials (nonanadromous spawners) may increase competition for females and significantly skew ratios of offspring sired by nonanadromous males, which could result in more nonanadromous spring chinook in future generations. Conditions in the natural environment may also limit the success of spring chinook supplementation. For example, intra or interspecific competition may constrain spring chinook salmon production. Spring chinook salmon juveniles may compete with each other for food or space or compete with other species that have similar ecological requirements. Monitoring of spring chinook salmon residuals, precocials, prey abundance, carrying capacity, and competition will help researchers

  2. Accounting for Genotype-by-Environment Interactions and Residual Genetic Variation in Genomic Selection for Water-Soluble Carbohydrate Concentration in Wheat.

    Science.gov (United States)

    Ovenden, Ben; Milgate, Andrew; Wade, Len J; Rebetzke, Greg J; Holland, James B

    2018-04-16

    Abiotic stress tolerance traits are often complex and recalcitrant targets for conventional breeding improvement in many crop species. This study evaluated the potential of genomic selection to predict water-soluble carbohydrate concentration (WSCC), an important drought tolerance trait, in wheat under field conditions. A panel of 358 varieties and breeding lines constrained for maturity was evaluated under rainfed and irrigated treatments across two locations and two years. Whole-genome marker profiles and factor analytic mixed models were used to generate genomic estimated breeding values (GEBVs) for specific environments and environment groups. Additive genetic variance was smaller than residual genetic variance for WSCC, such that genotypic values were dominated by residual genetic effects rather than additive breeding values. As a result, GEBVs were not accurate predictors of genotypic values of the extant lines, but GEBVs should be reliable selection criteria to choose parents for intermating to produce new populations. The accuracy of GEBVs for untested lines was sufficient to increase predicted genetic gain from genomic selection per unit time compared to phenotypic selection if the breeding cycle is reduced by half by the use of GEBVs in off-season generations. Further, genomic prediction accuracy depended on having phenotypic data from environments with strong correlations with target production environments to build prediction models. By combining high-density marker genotypes, stress-managed field evaluations, and mixed models that model simultaneously covariances among genotypes and covariances of complex trait performance between pairs of environments, we were able to train models with good accuracy to facilitate genetic gain from genomic selection. Copyright © 2018, G3: Genes, Genomes, Genetics.

  3. Numerical simulation of residual stresses at holes near edges and corners in tempered glass: A parametric study

    DEFF Research Database (Denmark)

    Pourmoghaddam, Navid; Nielsen, Jens Henrik; Schneider, Jens

    2016-01-01

    This work presents 3D results of the thermal tempering simulation by the Finite Element Method in order to calculate the residual stresses in the area of the holes near edges and corners of a tem-pered glass plate. A viscoelastic material behavior of the glass is considered for the tempering...... the influence of the hole and edge distances on the minimal residual compressive stress-es at holes after the tempering process. The residual stresses in the area of the holes are calculat-ed varying the following parameters: the hole diameter, the plate thickness and the interaction between holes and edges...

  4. INTERACT

    DEFF Research Database (Denmark)

    Jochum, Elizabeth; Borggreen, Gunhild; Murphey, TD

    This paper considers the impact of visual art and performance on robotics and human-computer interaction and outlines a research project that combines puppetry and live performance with robotics. Kinesics—communication through movement—is the foundation of many theatre and performance traditions...... including puppetry and dance. However, the aesthetics of these traditions vary across cultures and carry different associative and interpretive meanings. Puppetry offers a useful frame for understanding the relationship between abstract and imitative gestures and behavior, and instantiates the complex...

  5. Electronic polarizability, optical basicity and interaction parameter for Nd{sub 2}O{sub 3} doped lithium-zinc-phosphate glasses

    Energy Technology Data Exchange (ETDEWEB)

    Algradee, M.A.; Sultan, M.; Samir, O.M.; Alwany, A.E.B. [Ibb University, Department of Physics, Faculty of Science, Ibb (Yemen)

    2017-08-15

    The Nd{sup 3+}-doped lithium-zinc-phosphate glasses were prepared by means of conventional melt quenching method. X-ray diffraction results confirmed the glassy nature of the studied glasses. The physical parameters such as the density, molar volume, ion concentration, polaron radius, inter-ionic distance, field strength and oxygen packing density were calculated using different formulae. The transmittance and reflectance spectra of glasses were recorded in the wavelength range 190-1200 nm. The values of optical band gap and Urbach energy were determined based on Mott-Davis model. The refractive indices for the studied glasses were evaluated from optical band gap values using different methods. The average electronic polarizability of the oxide ions, optical basicity and an interaction parameter were investigated from the calculated values of the refractive index and the optical band gap for the studied glasses. The variations in the different physical and optical properties of glasses with Nd{sub 2}O{sub 3} content were discussed in terms of different parameters such as non-bridging oxygen and different concentrations of Nd cation in glass system. (orig.)

  6. Distinct iris gene expression profiles of primary angle closure glaucoma and primary open angle glaucoma and their interaction with ocular biometric parameters.

    Science.gov (United States)

    Seet, Li-Fong; Narayanaswamy, Arun; Finger, Sharon N; Htoon, Hla M; Nongpiur, Monisha E; Toh, Li Zhen; Ho, Henrietta; Perera, Shamira A; Wong, Tina T

    2016-11-01

    This study aimed to evaluate differences in iris gene expression profiles between primary angle closure glaucoma (PACG) and primary open angle glaucoma (POAG) and their interaction with biometric characteristics. Prospective study. Thirty-five subjects with PACG and thirty-three subjects with POAG who required trabeculectomy were enrolled at the Singapore National Eye Centre, Singapore. Iris specimens, obtained by iridectomy, were analysed by real-time polymerase chain reaction for expression of type I collagen, vascular endothelial growth factor (VEGF)-A, -B and -C, as well as VEGF receptors (VEGFRs) 1 and 2. Anterior segment optical coherence tomography (ASOCT) imaging for biometric parameters, including anterior chamber depth (ACD), anterior chamber volume (ACV) and lens vault (LV), was also performed pre-operatively. Relative mRNA levels between PACG and POAG irises, biometric measurements, discriminant analyses using genes and biometric parameters. COL1A1, VEGFB, VEGFC and VEGFR2 mRNA expression was higher in PACG compared to POAG irises. LV, ACD and ACV were significantly different between the two subgroups. Discriminant analyses based on gene expression, biometric parameters or a combination of both gene expression and biometrics (LV and ACV), correctly classified 94.1%, 85.3% and 94.1% of the original PACG and POAG cases, respectively. The discriminant function combining genes and biometrics demonstrated the highest accuracy in cross-validated classification of the two glaucoma subtypes. Distinct iris gene expression supports the pathophysiological differences that exist between PACG and POAG. Biometric parameters can combine with iris gene expression to more accurately define PACG from POAG. © 2016 The Authors. Clinical & Experimental Ophthalmology published by John Wiley & Sons Australia, Ltd on behalf of Royal Australian and New Zealand College of Ophthalmologists.

  7. A Virtual Reality avatar interaction (VRai) platform to assess residual executive dysfunction in active military personnel with previous mild traumatic brain injury: proof of concept.

    Science.gov (United States)

    Robitaille, Nicolas; Jackson, Philip L; Hébert, Luc J; Mercier, Catherine; Bouyer, Laurent J; Fecteau, Shirley; Richards, Carol L; McFadyen, Bradford J

    2017-10-01

    This proof of concept study tested the ability of a dual task walking protocol using a recently developed avatar-based virtual reality (VR) platform to detect differences between military personnel post mild traumatic brain injury (mTBI) and healthy controls. The VR platform coordinated motion capture, an interaction and rendering system, and a projection system to present first (participant-controlled) and third person avatars within the context of a specific military patrol scene. A divided attention task was also added. A healthy control group was compared to a group with previous mTBI (both groups comprised of six military personnel) and a repeated measures ANOVA tested for differences between conditions and groups based on recognition errors, walking speed and fluidity and obstacle clearance. The VR platform was well tolerated by both groups. Walking fluidity was degraded for the control group within the more complex navigational dual tasking involving avatars, and appeared greatest in the dual tasking with the interacting avatar. This navigational behaviour was not seen in the mTBI group. The present findings show proof of concept for using avatars, particularly more interactive avatars, to expose differences in executive functioning when applying context-specific protocols (here for the military). Implications for rehabilitation Virtual reality provides a means to control context-specific factors for assessment and intervention. Adding human interaction and agency through avatars increases the ecologic nature of the virtual environment. Avatars in the present application of the Virtual Reality avatar interaction platform appear to provide a better ability to reveal differences between trained, military personal with and without mTBI.

  8. Lumped-parameter models

    Energy Technology Data Exchange (ETDEWEB)

    Ibsen, Lars Bo; Liingaard, M.

    2006-12-15

    A lumped-parameter model represents the frequency dependent soil-structure interaction of a massless foundation placed on or embedded into an unbounded soil domain. In this technical report the steps of establishing a lumped-parameter model are presented. Following sections are included in this report: Static and dynamic formulation, Simple lumped-parameter models and Advanced lumped-parameter models. (au)

  9. Fate and persistence of 14C pesticide residues in different soils: effects of 14C pesticide contaminated run-off soil water on biological systems. Part of a coordinated programme on isotopic-tracer-aided studies of agrochemical residue - soil biota interactions

    International Nuclear Information System (INIS)

    Lichtenstein, E.

    1982-09-01

    The interaction of selected fungicides, herbicides and N-fertilizers with microorganisms in cranberry soils and their effects on the degradation of 14 C-phenyl-parathion were investigated. Incubation of soils with parathion of p-nitrophenol for 4 days, followed by the addition of 14 C-parathion resulted after 24 h in an enhanced degradation of the insecticide to 14 CO 2 (34-39% of the applied radiocarbon as opposed to 2% in controls) and also in an increased binding of 14 C to the soil. The fungicide captafol inhibited the degradation of soil-applied 14 C-parathion as evidenced by a reduction of both 14 CO 2 evolution and 14 C-bound residues. Maneb and benomyl suppressed the degradation of 14 C-parathion to 14 CO 2 but not the formation of bound residues. Addition of 2,4-D to 14 C-parathion treated soil also resulted in an increased persistence of the insecticide. Studies conducted with the insecticide and (NH 4 ) 2 SO 4 , NH 4 NO 3 , KNO 3 or urea showed that under all experimental conditions the total amounts of 14 C recovered were similar, yet the distribution of 14 C-compounds into benzene-soluble, water-soluble and bound residues was not. This possibly indicated a change in the pathway of 14 C-parathion degradation. The insecticide was most persistent in soils containing (NH 4 ) 2 SO 4 , as demonstrated by a recovery of 29% of the applied radiocarbon in benzene-soluble form. Analyses by TIC of this benzene extraction phase revealed the presence of 14 C-parathion, 14 C-p-aminophenol and 14 C-aminoparathion

  10. Enhanced Retention of Chelating Reagents in Octadecylsilyl Silica Phase by Interaction with Residual Silanol Groups in Solid Phase Extraction of Divalent Metal Ions.

    Science.gov (United States)

    Ohmuro, Satoshi; Fujii, Kan; Yasui, Takashi; Takada, Kazutake; Yuchi, Akio; Kokusen, Hisao

    2016-01-01

    Solid-phase extraction (SPE) of divalent metal ions with a lipophilic and potentially divalent hexadentate chelating reagent (H2L), with which octadecylsilyl silica (ODS), was impregnated with was studied to gain more insight into and develop the potential of this methodology. This is the first time to demonstrate that this reagent as well as other common nitrogen-containing reagents were retained both by adsorption due to hydrogen bonding between nitrogen atoms of the reagent and residual silanol groups in the ODS phase and by simple distribution into the hydrophobic space. An appreciably large amount of this reagent could be retained by the adsorption mechanism even with a relatively thin loading solution. The divalent metal ions of Mn(2+), Co(2+) and Zn(2+) were extracted as 1:1 neutral complexes ([ML]), while Ni(2+) and Cu(2+) as ion-pairs of 1:1 cationic complex ([MHL](+)) with anion in SPE with H2L. The extractability and selectivity were substantially the same as that in liquid-liquid extraction.

  11. Spring Chinook Salmon Interactions Indices and Residual/Precocial Monitoring in the Upper Yakima Basin; Yakima/Klickitat Fisheries Project Monitoring and Evaluation Report 5 of 7, 2003-2004 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Pearsons, Todd N.; Johnson, Christopher L.; James, Brenda B. (Washington Department of Fish and Wildlife, Olympia, WA)

    2004-05-01

    This report examines some of the factors that can influence the success of supplementation, which is currently being tested in the Yakima Basin using upper Yakima stock of spring chinook salmon. Supplementation success in the Yakima Basin is defined relative to four topic areas: natural production, genetics, ecological interactions, and harvest (Busack et al. 1997). The success of spring chinook salmon supplementation in the Yakima Basin is dependent, in part, upon fish culture practices and favorable physical and biological conditions in the natural environment (Busack et al. 1997; James et al. 1999; Pearsons et al., 2003). Shortfalls in either of these two topics (i.e., failure in culturing many fish that have high long-term fitness or environmental conditions that constrain spring chinook salmon production) will cause supplementation success to be limited. For example, inadvertent selection or propagation of spring chinook that residualize or precocially mature may hinder supplementation success. Spring chinook salmon that residualize (do not migrate during the normal migration period) may have lower survival rates than migrants and, additionally, may interact with wild fish and cause unacceptable impacts to non-target taxa. Large numbers of precocials (nonanadromous spawners) may increase competition for females and significantly skew ratios of offspring sired by nonanadromous males, which could result in more nonanadromous spring chinook in future generations. Conditions in the natural environment may also limit the success of spring chinook supplementation. For example, intra or interspecific competition may constrain spring chinook salmon production. Spring chinook salmon juveniles may compete with each other for food or space or compete with other species that have similar ecological requirements. Monitoring of spring chinook salmon residuals, precocials, prey abundance, carrying capacity, and competition will help researchers interpret why supplementation

  12. The 3.2 Å resolution structure of a receptor: CheA:CheW signaling complex defines overlapping binding sites and key residue interactions within bacterial chemosensory arrays.

    Science.gov (United States)

    Li, Xiaoxiao; Fleetwood, Aaron D; Bayas, Camille; Bilwes, Alexandrine M; Ortega, Davi R; Falke, Joseph J; Zhulin, Igor B; Crane, Brian R

    2013-06-04

    Bacterial chemosensory arrays are composed of extended networks of chemoreceptors (also known as methyl-accepting chemotaxis proteins, MCPs), the histidine kinase CheA, and the adaptor protein CheW. Models of these arrays have been developed from cryoelectron microscopy, crystal structures of binary and ternary complexes, NMR spectroscopy, mutational, data and biochemical studies. A new 3.2 Å resolution crystal structure of a Thermotoga maritima MCP protein interaction region in complex with the CheA kinase-regulatory module (P4-P5) and adaptor protein CheW provides sufficient detail to define residue contacts at the interfaces formed among the three proteins. As in a previous 4.5 Å resolution structure, CheA-P5 and CheW interact through conserved hydrophobic surfaces at the ends of their β-barrels to form pseudo 6-fold symmetric rings in which the two proteins alternate around the circumference. The interface between P5 subdomain 1 and CheW subdomain 2 was anticipated from previous studies, whereas the related interface between CheW subdomain 1 and P5 subdomain 2 has only been observed in these ring assemblies. The receptor forms an unexpected structure in that the helical hairpin tip of each subunit has "unzipped" into a continuous α-helix; four such helices associate into a bundle, and the tetramers bridge adjacent P5-CheW rings in the lattice through interactions with both P5 and CheW. P5 and CheW each bind a receptor helix with a groove of conserved hydrophobic residues between subdomains 1 and 2. P5 binds the receptor helix N-terminal to the tip region (lower site), whereas CheW binds the same helix with inverted polarity near the bundle end (upper site). Sequence comparisons among different evolutionary classes of chemotaxis proteins show that the binding partners undergo correlated changes at key residue positions that involve the lower site. Such evolutionary analyses argue that both CheW and P5 bind to the receptor tip at overlapping positions

  13. Identification and analysis of key residues involved in folding and binding of protein-carbohydrate complexes.

    Science.gov (United States)

    Gromiha, Michael; Shanmugam, N R Siva; Selvin, J Fermin Angelo; Veluraja, K

    2018-02-21

    Protein-carbohydrate interactions play vital roles in several biological processes in living organisms. The comparative analysis of binding site residues along with stabilizing residues in protein-carbohydrate complexes provides ample insights to understand the structure, function and recognition mechanism. In this work, we have identified 2.45% binding site residues in a non-redundant dataset of 1130 complexes using distance-based criteria and 7.07% stabilizing residues using the concepts of hydrophobicity, long-range interactions and conservation of residues. Further, 5.9% of binding and 2.04% of stabilizing residues are common to each other, which are termed as key residues. The key residues have been analyzed based on protein classes, carbohydrate types, gene ontology functional classifications, amino acid preference and structure-based parameters. We found that all-β, α+β and α/β have more key residues than other protein classes and most of the KRs are present in β-strands, which shows their importance in stability and binding of complexes. On the ligand side, L-saccharide has the highest number of key residues and it has a high percentage of KRs in SRs and BRs than other carbohydrate types. Further, polar and charged residues have a high tendency to serve as key residues. Classifications based on gene ontology terms revealed that Lys is preferred in all the three groups: molecular functions, biological processes and cellular components. Key residues have 6 to 9 contacts within the protein and make only one contact with the carbohydrate ligand. These contacts are dominant to form polar-nonpolar contacts followed by the contacts between charged atoms. Further, the influence of sequence and structural parameters such as surrounding hydrophobicity, solvent accessibility, secondary structure, long-range order and conservation score has been discussed. This analysis helps in understanding the interplay between stability and binding in protein

  14. Sulforaphane inhibits pancreatic cancer through disrupting Hsp90-p50(Cdc37) complex and direct interactions with amino acids residues of Hsp90.

    Science.gov (United States)

    Li, Yanyan; Karagöz, G Elif; Seo, Young Ho; Zhang, Tao; Jiang, Yiqun; Yu, Yanke; Duarte, Afonso M S; Schwartz, Steven J; Boelens, Rolf; Carroll, Kate; Rüdiger, Stefan G D; Sun, Duxin

    2012-12-01

    Sulforaphane [1-isothiocyanato-4-(methyl-sulfinyl) butane)], an isothiocyanate derived from cruciferous vegetables, has been shown to possess potent chemopreventive activity. We analyzed the effect of sulforaphane on the proliferation of pancreatic cancer cells. Sulforaphane inhibited pancreatic cancer cell growth in vitro with IC(50)s of around 10-15 μM and induced apoptosis. In pancreatic cancer xenograft mouse model, administration of sulforaphane showed remarkable inhibition of tumor growth without apparent toxicity noticed. We found that sulforaphane induced the degradation of heat shock protein 90 (Hsp90) client proteins and blocked the interaction of Hsp90 with its cochaperone p50(Cdc37) in pancreatic cancer cells. Using nuclear magnetic resonance spectroscopy (NMR) with an isoleucine-specific labeling strategy, we overcame the protein size limit of conventional NMR and studied the interaction of sulforaphane with full-length Hsp90 dimer (170 kDa) in solution. NMR revealed multiple chemical shifts in sheet 2 and the adjacent loop in Hsp90 N-terminal domain after incubation of Hsp90 with sulforaphane. Liquid chromatography coupled to mass spectrometry further mapped a short peptide in this region that was tagged with sulforaphane. These data suggest a new mechanism of sulforaphane that disrupts protein-protein interaction in Hsp90 complex for its chemopreventive activity. Copyright © 2012 Elsevier Inc. All rights reserved.

  15. Sulforaphane inhibits pancreatic cancer through disrupting Hsp90-p50Cdc37 complex and direct interactions with amino acids residues of Hsp90

    Science.gov (United States)

    Li, Yanyan; Karagöz, G. Elif; Seo, Young Ho; Zhang, Tao; Jiang, Yiqun; Yu, Yanke; Duarte, Afonso M.S.; Schwartz, Steven J.; Boelens, Rolf; Carroll, Kate; Rüdiger, Stefan G. D.; Sun, Duxin

    2011-01-01

    Sulforaphane [1-isothiocyanato-4-(methyl-sulfinyl) butane)], an isothiocyanate derived from cruciferous vegetables, has been shown to possess potent chemopreventive activity. We analyzed the effect of sulforaphane on the proliferation of pancreatic cancer cells. Sulforaphane inhibited pancreatic cancer cell growth in vitro with the IC50's around 10-15 μM and induced apoptosis. In pancreatic cancer xenograft mouse model, administration of sulforaphane showed remarkable inhibition of tumor growth without apparent toxicity noticed. We found that sulforaphane induced the degradation of heat shock protein 90 (Hsp90) client proteins and blocked the interaction of Hsp90 with its cochaperone p50Cdc37 in pancreatic cancer cells. Using Nuclear Magnetic Resonance Spectroscopy (NMR) with an isoleucine-specific labeling strategy, we overcame the protein size limit of conventional NMR and studied the interaction of sulforaphane with full-length Hsp90 dimer (170 kDa) in solution. NMR revealed multiple chemical shifts in sheet 2 and the adjacent loop in Hsp90 N-terminal domain after incubation of Hsp90 with sulforaphane. Liquid Chromatography coupled to Mass Spectrometry (LC-MS) further mapped a short peptide in this region that was tagged with sulforaphane. These data suggest a new mechanism of sulforaphane that disrupts protein-protein interaction in Hsp90 complex for its chemopreventive activity. PMID:22444872

  16. Leptogenesis and residual CP symmetry

    International Nuclear Information System (INIS)

    Chen, Peng; Ding, Gui-Jun; King, Stephen F.

    2016-01-01

    We discuss flavour dependent leptogenesis in the framework of lepton flavour models based on discrete flavour and CP symmetries applied to the type-I seesaw model. Working in the flavour basis, we analyse the case of two general residual CP symmetries in the neutrino sector, which corresponds to all possible semi-direct models based on a preserved Z 2 in the neutrino sector, together with a CP symmetry, which constrains the PMNS matrix up to a single free parameter which may be fixed by the reactor angle. We systematically study and classify this case for all possible residual CP symmetries, and show that the R-matrix is tightly constrained up to a single free parameter, with only certain forms being consistent with successful leptogenesis, leading to possible connections between leptogenesis and PMNS parameters. The formalism is completely general in the sense that the two residual CP symmetries could result from any high energy discrete flavour theory which respects any CP symmetry. As a simple example, we apply the formalism to a high energy S 4 flavour symmetry with a generalized CP symmetry, broken to two residual CP symmetries in the neutrino sector, recovering familiar results for PMNS predictions, together with new results for flavour dependent leptogenesis.

  17. Influence of MSD crack pattern on the residual strength of flat stiffened sheets

    Science.gov (United States)

    Nilsson, K.-F.

    A parameter study of the residual strength for a multiple site damaged (MSD) stiffened sheet is presented. The analysis is based on an elastic-plastic fracture analysis using the yield-strip model for interaction between a lead crack and the smaller MSD cracks. Two crack growth criteria, one with a pronounced crack growth resistance and one with no crack growth resistance and five different MSD crack patterns, are analysed for different sizes of the lead crack and the smaller MSD cracks. The analysis indicates that the residual strength reduction depends on all these parameters and that MSD may totally erode the crack arrest capability of a tear strap. Another important outcome is that for certain combinations also very small MSD cracks may induce a significant residual strength reduction.

  18. High residue contents indebted by platinum and silica synergistic action during the pyrolysis of silicone formulations.

    Science.gov (United States)

    Delebecq, Etienne; Hamdani-Devarennes, Siska; Raeke, Julia; Lopez Cuesta, José-Marie; Ganachaud, François

    2011-03-01

    The synergistic role of platinum and silica as a way to increase the final residue of pyrolized silicone was investigated and explained, giving new interpretations. Conditions were first set to study the thermal degradation of silicones in the presence of platinum based on the simplest silicone/silica/platinum formulation. Numerous parameters, e.g., platinum and silica content or silica surface modifications, were varied to track their influences on the final residues. A thorough DSC study, together with SEM/EDX and Pyrolysis/GC-MS analyses, led us to propose a three-stage process. The key parameter governing thermal stability and final content of the residue is the conjugated actions of immobilizing/cross-linking PDMS chains. Silica particles tether silicone chains through physical interactions, i.e., hydrogen bonding, facilitating a platinum radically catalyzed cross-linking reaction. Practical implications and possible improvements on LSR formulations are finally given.

  19. Phactr3/scapinin, a member of protein phosphatase 1 and actin regulator (phactr family, interacts with the plasma membrane via basic and hydrophobic residues in the N-terminus.

    Directory of Open Access Journals (Sweden)

    Akihiro Itoh

    Full Text Available Proteins that belong to the protein phosphatase 1 and actin regulator (phactr family are involved in cell motility and morphogenesis. However, the mechanisms that regulate the actin cytoskeleton are poorly understood. We have previously shown that phactr3, also known as scapinin, localizes to the plasma membrane, including lamellipodia and membrane ruffles. In the present study, experiments using deletion and point mutants showed that the basic and hydrophobic residues in the N-terminus play crucial roles in the localization to the plasma membrane. A BH analysis (http://helixweb.nih.gov/bhsearch is a program developed to identify membrane-binding domains that comprise basic and hydrophobic residues in membrane proteins. We applied this program to phactr3. The results of the BH plot analysis agreed with the experimentally determined region that is responsible for the localization of phactr3 to the plasma membrane. In vitro experiments showed that the N-terminal itself binds to liposomes and acidic phospholipids. In addition, we showed that the interaction with the plasma membrane via the N-terminal membrane-binding sequence is required for phactr3-induced morphological changes in Cos7 cells. The membrane-binding sequence in the N-terminus is highly conserved in all members of the phactr family. Our findings may provide a molecular basis for understanding the mechanisms that allow phactr proteins to regulate cell morphogenesis.

  20. Abstracts and parameter index database for reports pertaining to the unsaturated zone and surface water-ground water interactions at the Idaho National Engineering Laboratory

    International Nuclear Information System (INIS)

    Bloomsburg, G.; Finnie, J.; Horn, D.; King, B.; Liou, J.

    1993-05-01

    This report is a product generated by faculty at the University of Idaho in support of research and development projects on Unsaturated Zone Contamination and Transport Processes, and on Surface Water-Groundwater Interactions and Regional Groundwater Flow at the Idaho National Engineering Laboratory. These projects are managed by the State of Idaho's INEL Oversight Program under a grant from the US Department of Energy. In particular, this report meets project objectives to produce a site-wide summary of hydrological information based on a literature search and review of field, laboratory and modeling studies at INEL, including a cross-referenced index to site-specific physical, chemical, mineralogic, geologic and hydrologic parameters determined from these studies. This report includes abstracts of 149 reports with hydrological information. For reports which focus on hydrological issues, the abstracts are taken directly from those reports; for reports dealing with a variety of issues beside hydrology, the abstracts were generated by the University of Idaho authors concentrating on hydrology-related issues. Each abstract is followed by a ''Data'' section which identifies types of technical information included in a given report, such as information on parameters or chemistry, mineralogy, stream flows, water levels. The ''Data'' section does not include actual values or data

  1. Characterization of extracellular vesicles in whole blood: Influence of pre-analytical parameters and visualization of vesicle-cell interactions using imaging flow cytometry.

    Science.gov (United States)

    Fendl, Birgit; Weiss, René; Fischer, Michael B; Spittler, Andreas; Weber, Viktoria

    2016-09-09

    Extracellular vesicles are central players in intercellular communication and are released from the plasma membrane under tightly regulated conditions, depending on the physiological and pathophysiological state of the producing cell. Their heterogeneity requires a spectrum of methods for isolation and characterization, where pre-analytical parameters have profound impact on vesicle analysis, particularly in blood, since sampling, addition of anticoagulants, as well as post-sampling vesicle generation may influence the outcome. Here, we characterized microvesicles directly in whole blood using a combination of flow cytometry and imaging flow cytometry. We assessed the influence of sample agitation, anticoagulation, and temperature on post-sampling vesicle generation, and show that vesicle counts remained stable over time in samples stored without agitation. Storage with gentle rolling mimicking agitation, in contrast, resulted in strong release of platelet-derived vesicles in blood anticoagulated with citrate or heparin, whereas vesicle counts remained stable upon anticoagulation with EDTA. Using imaging flow cytometry, we could visualize microvesicles adhering to blood cells and revealed an anticoagulant-dependent increase in vesicle-cell aggregates over time. We demonstrate that vesicles adhere preferentially to monocytes and granulocytes in whole blood, while no microvesicles could be visualized on lymphocytes. Our data underscore the relevance of pre-analytical parameters in vesicle analysis and demonstrate that imaging flow cytometry is a suitable tool to study the interaction of extracellular vesicles with their target cells. Copyright © 2016 Elsevier Inc. All rights reserved.

  2. Assessing Hazards Related to Volcano-Ice Interactions at POPOCATÉPETL Volcano (mexico): Determination of Physical Parameters of 1999-2000 Laharic Flows

    Science.gov (United States)

    Delgado Granados, H.; Oropeza Villalobos, B.; Gonzalez Huesca, A.

    2010-12-01

    During glacier-ice melting by eruptions laharic flows form in proportions that may impose a threat to the surrounding populations. So, it is important to identify the potential at ice-capped volcanoes to produce lahars. In Mexico, the largest mountains glacier-clad, active volcanoes so, the interactions between eruptive activity and ice in Mexico should be evaluated for hazards assessment and building up preventing and mitigating programs. Popocatépetl volcano has produced laharic flows due to the interaction of the eruptive activity with the ice. The nearest village to the volcano, called Santiago Xalitzintla was threatened by these flows several times between June 1997 and the year 2000. The signals recorded by an acoustic flow monitoring (AFM) network allowed to determine the main physical parameters of lahars occurring between January 1999 and October 2000. We determined magnitude, acoustic flow, velocity and discharge. We obtained velocities of seismic data and the military-personnel descriptions by the Mexican Army station posted specifically to observe laharic flows. This threat has disappeared due to the extinction of glaciers at the volcano, although ice-bodies (seracs) still remain on the higher slopes of the volcano. According to these results, at the present level of eruptive magnitude, risk associated with laharic flows consists mainly in passive inundation of zones nearby the Huiloac ravine in the NE sector of the volcano. These results however might be used for further networks at other volcanoes in the country.

  3. 1HN, 13C, and 15N Resonance Assignments of the CDTb-Interacting Domain (CDTaBID) from the Clostridium difficile Binary Toxin Catalytic Component (CDTa, residues 1–221)

    Science.gov (United States)

    Roth, Braden M.; Varney, Kristen M.; Rustandi, Richard R.; Weber, David J.

    2016-01-01

    Once considered a relatively harmless bacterium, Clostridium difficile has become a major concern for healthcare facilities, now the most commonly reported hospital-acquired pathogen. C. difficile infection (CDI) is usually contracted when the normal gut microbiome is compromised by antibiotic therapy, allowing the opportunistic pathogen to grow and produce its toxins. The severity of infection ranges from watery diarrhea and abdominal cramping to pseudomembranous colitis, sepsis, or death. The past decade has seen a marked increase in the frequency and severity of CDI among industrialized nations owing directly to the emergence of a highly virulent C. difficile strain, NAP1. Along with the large Clostridial toxins expressed by non-epidemic strains, C. difficile NAP1 produces a binary toxin, CDT (C. difficile transferase). As the name suggests, CDT is a two-component toxin comprised of an ADP-ribosyltransferase (ART) component (CDTa) and a cell-binding/translocation component (CDTb) that function to destabilize the host cytoskeleton by covalent modification of actin monomers. Central to the mechanism of binary toxin-induced pathogenicity is the formation of CDTa/CDTb complexes at the cell surface. From the perspective of CDTa, this interaction is mediated by the N-terminal domain (residues 1–215) and is spatially and functionally independent of ART activity, which is located in the C-terminal domain (residues 216–420). Here we report the 1HN, 13C, and 15N backbone resonance assignments of a 212 amino acid, ~23 kDa N-terminal CDTb-interacting domain (CDTaBID) construct by heteronuclear NMR spectroscopy. These NMR assignments represent the first component coordination domain for a family of Clostridium or Bacillus species harboring ART activity. Our assignments lay the foundation for detailed solution state characterization of structure-function relationships, toxin complex formation, and NMR-based drug discovery efforts. PMID:27351891

  4. An Analysis of Central Residues Between Ligand-Bound and Ligand-Free Protein Structures Based on Network Approach.

    Science.gov (United States)

    Amala, Arumugam; Emerson, Isacc Arnold

    2017-08-01

    Depiction of protein structures as networks of interacting residues has enabled us to understand the structure and function of the protein. Previous investigations on closeness centrality have identified protein functional sites from three- dimensional structures. It is well recognized that ligand binding to a receptor protein induces a wide range of structural changes. An interesting question is how central residues function during conformational changes triggered during ligand binding? The aim of this study is to comprehend at what extent central residues change during ligand binding to receptor proteins. To determine this, we examined 37 pairs of protein structures consisting of ligand-bound and ligand-free forms. These protein structures were modelled as an undirected network and significant central residues were obtained using residue centrality measures. In addition to these, the basic network parameters were also analysed. On analysing the residue centrality measures, we observed that 60% of central residues were common in both the ligand-bound and ligand-free states. The geometry of the central residues revealed that they were situated closer to the protein center of the mass. Finally, we demonstrated the effectiveness of central residues in amino acids substitutions and in the evolution itself. The closeness centrality was also analyzed among different protein domain sizes and the values gradually declined from single-domains to multi-domain proteins suggesting that the network has potential for hierarchical organization. Betweenness centrality measure was also used to determine the central residues and 31% of these residues were common between the holo/apo states. Findings reveal that central residues play a significant role in determining the functional properties of proteins. These results have implications in predicting binding/active site residues, specifically in the context of drug designing, if additional information concerning ligand binding is

  5. Aromatic Residues in the Fourth Transmembrane-Spanning Helix M4 Are Important for GABAρ Receptor Function.

    Science.gov (United States)

    Cory-Wright, James; Alqazzaz, Mona; Wroe, Francesca; Jeffreys, Jenny; Zhou, Lu; Lummis, Sarah C R

    2018-02-21

    GABAρ receptors are a subfamily of the GABA A receptor family of pentameric ligand-gated ion channels (pLGICs). Each of the five subunits has four transmembrane α-helices (M1-M4), with M4 most distant from the central pore. Aromatic residues in this M4 helix are important for receptor assembly in pLGICs and also may interact with adjacent lipids and/or residues in neighboring α-helices and the extracellular domain to modify or enable channel gating. This study examines the role of M4 receptor aromatic residues in the GABAρ receptor transmembrane domain using site-directed mutagenesis and subsequent expression in HEK293 cells, probing functional parameters using a fluorescent membrane-potential-sensitive dye. The data indicate that many of the aromatic residues in M4 play a role in receptor function, as substitution with other residues can ablate and/or modify functional parameters. Modeling showed that these residues likely interact with residues in the adjacent M1 and M3 α-helices and/or residues in the Cys-loop in the extracellular domain. We suggest that many of these aromatic interactions contribute to an "aromatic zipper", which allows interactions between M4 and the rest of the receptor that are essential for function. Thus, the data support other studies showing that M4 does not play a passive role in "protecting" the other transmembrane helices from the lipid bilayer but is actively involved in the function of the protein.

  6. A 3D interactive method for estimating body segmental parameters in animals: application to the turning and running performance of Tyrannosaurus rex.

    Science.gov (United States)

    Hutchinson, John R; Ng-Thow-Hing, Victor; Anderson, Frank C

    2007-06-21

    We developed a method based on interactive B-spline solids for estimating and visualizing biomechanically important parameters for animal body segments. Although the method is most useful for assessing the importance of unknowns in extinct animals, such as body contours, muscle bulk, or inertial parameters, it is also useful for non-invasive measurement of segmental dimensions in extant animals. Points measured directly from bodies or skeletons are digitized and visualized on a computer, and then a B-spline solid is fitted to enclose these points, allowing quantification of segment dimensions. The method is computationally fast enough so that software implementations can interactively deform the shape of body segments (by warping the solid) or adjust the shape quantitatively (e.g., expanding the solid boundary by some percentage or a specific distance beyond measured skeletal coordinates). As the shape changes, the resulting changes in segment mass, center of mass (CM), and moments of inertia can be recomputed immediately. Volumes of reduced or increased density can be embedded to represent lungs, bones, or other structures within the body. The method was validated by reconstructing an ostrich body from a fleshed and defleshed carcass and comparing the estimated dimensions to empirically measured values from the original carcass. We then used the method to calculate the segmental masses, centers of mass, and moments of inertia for an adult Tyrannosaurus rex, with measurements taken directly from a complete skeleton. We compare these results to other estimates, using the model to compute the sensitivities of unknown parameter values based upon 30 different combinations of trunk, lung and air sac, and hindlimb dimensions. The conclusion that T. rex was not an exceptionally fast runner remains strongly supported by our models-the main area of ambiguity for estimating running ability seems to be estimating fascicle lengths, not body dimensions. Additionally, the

  7. Investigation of the interactions of critical scale-up parameters (pH, pO2 and pCO2) on CHO batch performance and critical quality attributes.

    Science.gov (United States)

    Brunner, Matthias; Fricke, Jens; Kroll, Paul; Herwig, Christoph

    2017-02-01

    Understanding process parameter interactions and their effects on mammalian cell cultivations is an essential requirement for robust process scale-up. Furthermore, knowledge of the relationship between the process parameters and the product critical quality attributes (CQAs) is necessary to satisfy quality by design guidelines. So far, mainly the effect of single parameters on CQAs was investigated. Here, we present a comprehensive study to investigate the interactions of scale-up relevant parameters as pH, pO 2 and pCO 2 on CHO cell physiology, process performance and CQAs, which was based on design of experiments and extended product quality analytics. The study used a novel control strategy in which process parameters were decoupled from each other, and thus allowed their individual control at defined set points. Besides having identified the impact of single parameters on process performance and product quality, further significant interaction effects of process parameters on specific cell growth, specific productivity and amino acid metabolism could be derived using this method. Concerning single parameter effects, several monoclonal antibody (mAb) charge variants were affected by process pCO 2 and pH. N-glycosylation analysis showed positive correlations between mAb sialylation and high pH values as well as a relationship between high mannose variants and process pH. This study additionally revealed several interaction effects as process pH and pCO 2 interactions on mAb charge variants and N-glycosylation pattern. Hence, through our process control strategy and multivariate investigation, novel significant process parameter interactions and single effects were identified which have to be taken into account especially for process scale-up.

  8. Kinetic model framework for aerosol and cloud surface chemistry and gas-particle interactions - Part 1: General equations, parameters, and terminology

    Science.gov (United States)

    Pöschl, U.; Rudich, Y.; Ammann, M.

    2007-12-01

    Aerosols and clouds play central roles in atmospheric chemistry and physics, climate, air pollution, and public health. The mechanistic understanding and predictability of aerosol and cloud properties, interactions, transformations, and effects are, however, still very limited. This is due not only to the limited availability of measurement data, but also to the limited applicability and compatibility of model formalisms used for the analysis, interpretation, and description of heterogeneous and multiphase processes. To support the investigation and elucidation of atmospheric aerosol and cloud surface chemistry and gas-particle interactions, we present a comprehensive kinetic model framework with consistent and unambiguous terminology and universally applicable rate equations and parameters. It enables a detailed description of mass transport and chemical reactions at the gas-particle interface, and it allows linking aerosol and cloud surface processes with gas phase and particle bulk processes in systems with multiple chemical components and competing physicochemical processes. The key elements and essential aspects of the presented framework are: a simple and descriptive double-layer surface model (sorption layer and quasi-static layer); straightforward flux-based mass balance and rate equations; clear separation of mass transport and chemical reactions; well-defined and consistent rate parameters (uptake and accommodation coefficients, reaction and transport rate coefficients); clear distinction between gas phase, gas-surface, and surface-bulk transport (gas phase diffusion, surface and bulk accommodation); clear distinction between gas-surface, surface layer, and surface-bulk reactions (Langmuir-Hinshelwood and Eley-Rideal mechanisms); mechanistic description of concentration and time dependences (transient and steady-state conditions); flexible addition of unlimited numbers of chemical species and physicochemical processes; optional aggregation or resolution

  9. Effect of gamma radiation on the microbiological and physicochemical parameters and on the phenolic compounds of a fruit residue flour during storage; Efeito da radiação gama nos parâmetros microbiológicos, físico-químicos e compostos fenólicos de farinha de resíduos de frutas durante armazenamento

    Energy Technology Data Exchange (ETDEWEB)

    Aranha, Jessica Bomtorin; Negri, Talita Costa; Martin, José Guilherme Prado; Spoto, Marta Helena Fillet, E-mail: jessica.aranha@usp.br [Escola Superior de Agricultura Luiz de Queiroz (ESALQ/USP), Piracicaba, SP (Brazil). Dept. de Agroindústria, Alimentos e Nutrição

    2017-07-01

    Agroindustrial residues have high levels of nutrients, but are little exploited for consumption because they require prior treatment to ensure microbiological safety. Irradiation is an effective process for the reduction of microbial counts with maintenance of the product characteristics. The objective of this study was to evaluate the effect of irradiation on the microbiological quality, physicochemical properties and phenolic compounds of a fruit residue flour during storage. The flour was obtained from dehydrated residues of pineapple, melon, papaya and apple, which were submitted to irradiation doses of (0, 1, 2 and 3 kGy). The microbiological (coliforms, moulds, yeast and Salmonella sp. counts) and physicochemical (pH, titratable acidity, soluble solids, water activity, colour parameters L⁎, a⁎ and b⁎ and phenolic compounds) parameters were evaluated after 0, 7, 14 and 21 days of storage. All the irradiation treatments reduced the microbial count, and the presence of Salmonella sp was not detected in any of the samples. The acidity and pH showed changes during storage. The soluble solids and water activity showed no significant differences between the doses during storage. The phenolic compounds were preserved by the application of irradiation. The colour of the flour samples darkened slightly with irradiation. It was concluded that the most effective doses for the maintenance of the microbiological quality and physicochemical characteristics of the flour were 2 and 3 kGy. (author)

  10. Food and Environmental Protection Laboratory, Seibersdorf: Discrimination of honey of different floral origins by a combination of various chemical parameters; Stable Isotopes Applied to Authenticating Honey; The use of analyte protectants in pesticide residue analytical work

    International Nuclear Information System (INIS)

    Zora Jandrić, Zora; Frew, Russell; Abrahim, Aiman; Maestroni, Britt; Ochoa, Victoria

    2014-01-01

    In the previous newsletter, we reported on research into methodology for the classification of honey of various floral and geographical origins using UPLC-QToF MS and MVA.The research on honey authenticity was expanded using multivariate data analysis of data generated by a number of different analytical techniques to discriminate honeys of different floral origins. The feasibility of a multivariate approach, including various chemical parameters and multivariate data analysis, for the discrimination of various honeys originating from one region, was explored. One of the earliest applications of nuclear techniques for food authenticity was the use of carbon isotopes to detect the addition of cheap sugars in honey in the 1970s. The principle is that the cheap sugar (fructose) is derived from corn and has a higher 13 C/ 12 C that the fructose from honey. This difference is due to the different photosynthetic pathways; corn is a C4 plant and that mechanism does not discriminate against the 13 C as much as the C3 pathway used by most honey-producing plants. Consequently the two plant types have quite different carbon isotope ratios. Thus measurements of the carbon isotope ratios can distinguish between the two sources of fructose. However, within each plant population there is natural variability in isotope ratios. This makes detecting the addition of small amounts of corn syrup difficult. The test was further refined by its developers to use 13 C/ 12 C measurements on protein purified from the honey as an internal reference, based on the fact that if the sugar and protein are from the same plant then they should be closely related in isotopic ratio. This refined method was adopted by the Association of Analytical Chemists as an official method (AOAC 998.12) and is part of the Codex Alimentarius standard for testing authenticity of honey. This test is generally reliable. However, some honey, notably New Zealand manuka, has a frequent fail rate. Manuka is a premium

  11. Influence of environmental parameters and of their interactions on the release of metal(loid)s from a construction material in hydraulic engineering

    International Nuclear Information System (INIS)

    Schmukat, A.; Duester, L.; Goryunova, E.; Ecker, D.; Heininger, P.; Ternes, T.A.

    2016-01-01

    Highlights: • DoE supported multi-factorial study on the metal(loid) release from copper slag. • Interactions of four parameters were studied and weighted. • An effective separation method between slag and sediment was established. • The metal(loid) partitioning between sediment, slag and eluent is described. • The knowledge on the potential environmental impact of copper slag is increased. - Abstract: Besides the leaching behaviour of a construction material under standardised test-specific conditions with laboratory water, for some construction materials it is advisable to test their environmental behaviour also under close to end use conditions. The envisaged end use combined with the product characteristics (e.g. mineral phases) is decisive for the choice of environmental factors that may change the release of substance that potentially cause adverse environmental effects (e.g. fertilisation or ecotoxicity). At the moment an experimental link is missing between mono-factorial standardised test systems and non standardised complex incubation experiments such as mesocosms which are closer to environmental conditions. Multi-factorial batch experiments may have the potential to close the gap. To verify this, batch experiments with copper slag were performed which is used as armour stones in hydraulic engineering. Design of experiments (DoE) was applied to evaluate the impact of pH, ionic strength, temperature and sediment content on the release of As, Cu, Mo, Ni, Pb, Sb and Zn. The study shows that release and sediment-eluent partitioning of metal(loid)s are impacted by interactions between the studied factors. Under the prevalent test conditions sediment acts as a sink enhancing most strongly the release of elements from the material.

  12. Influence of environmental parameters and of their interactions on the release of metal(loid)s from a construction material in hydraulic engineering

    Energy Technology Data Exchange (ETDEWEB)

    Schmukat, A., E-mail: schmukat@harzwasserwerke.de [Harzwasserwerke GmbH, Zur Granetalsperre 8, 38685 Langelsheim (Germany); Federal Institute of Hydrology, Department of Aquatic Chemistry, Am Mainzer Tor 1, 56068 Koblenz (Germany); Duester, L. [Federal Institute of Hydrology, Department of Aquatic Chemistry, Am Mainzer Tor 1, 56068 Koblenz (Germany); Goryunova, E. [Federal Institute of Hydrology, Department of Aquatic Chemistry, Am Mainzer Tor 1, 56068 Koblenz (Germany); KAPP-Chemie GmbH & Co. KG, Industriestr. 2-4, 56357 Miehlen (Germany); Ecker, D.; Heininger, P.; Ternes, T.A. [Federal Institute of Hydrology, Department of Aquatic Chemistry, Am Mainzer Tor 1, 56068 Koblenz (Germany)

    2016-03-05

    Highlights: • DoE supported multi-factorial study on the metal(loid) release from copper slag. • Interactions of four parameters were studied and weighted. • An effective separation method between slag and sediment was established. • The metal(loid) partitioning between sediment, slag and eluent is described. • The knowledge on the potential environmental impact of copper slag is increased. - Abstract: Besides the leaching behaviour of a construction material under standardised test-specific conditions with laboratory water, for some construction materials it is advisable to test their environmental behaviour also under close to end use conditions. The envisaged end use combined with the product characteristics (e.g. mineral phases) is decisive for the choice of environmental factors that may change the release of substance that potentially cause adverse environmental effects (e.g. fertilisation or ecotoxicity). At the moment an experimental link is missing between mono-factorial standardised test systems and non standardised complex incubation experiments such as mesocosms which are closer to environmental conditions. Multi-factorial batch experiments may have the potential to close the gap. To verify this, batch experiments with copper slag were performed which is used as armour stones in hydraulic engineering. Design of experiments (DoE) was applied to evaluate the impact of pH, ionic strength, temperature and sediment content on the release of As, Cu, Mo, Ni, Pb, Sb and Zn. The study shows that release and sediment-eluent partitioning of metal(loid)s are impacted by interactions between the studied factors. Under the prevalent test conditions sediment acts as a sink enhancing most strongly the release of elements from the material.

  13. Measurement of the β-asymmetry parameter of Cu67 in search for tensor-type currents in the weak interaction

    Science.gov (United States)

    Soti, G.; Wauters, F.; Breitenfeldt, M.; Finlay, P.; Herzog, P.; Knecht, A.; Köster, U.; Kraev, I. S.; Porobic, T.; Prashanth, P. N.; Towner, I. S.; Tramm, C.; Zákoucký, D.; Severijns, N.

    2014-09-01

    Background: Precision measurements at low energy search for physics beyond the standard model in a way complementary to searches for new particles at colliders. In the weak sector the most general β-decay Hamiltonian contains, besides vector and axial-vector terms, also scalar, tensor, and pseudoscalar terms. Current limits on the scalar and tensor coupling constants from neutron and nuclear β decay are on the level of several percent. Purpose: Extracting new information on tensor coupling constants by measuring the β-asymmetry parameter in the pure Gamow-Teller decay of Cu67, thereby testing the V-A structure of the weak interaction. Method: An iron sample foil into which the radioactive nuclei were implanted was cooled down to mK temperatures in a 3He-4He dilution refrigerator. An external magnetic field of 0.1 T, in combination with the internal hyperfine magnetic field, oriented the nuclei. The anisotropic β radiation was observed with planar high-purity germanium detectors operating at a temperature of about 10 K. An on-line measurement of the β asymmetry of Cu68 was performed as well for normalization purposes. Systematic effects were investigated using geant4 simulations. Results: The experimental value, Ã=0.587(14), is in agreement with the standard model value of 0.5991(2) and is interpreted in terms of physics beyond the standard model. The limits obtained on possible tensor-type charged currents in the weak interaction Hamiltonian are -0.045<(CT+CT')/CA<0.159 (90% C.L.). Conclusions: The obtained limits are comparable to limits from other correlation measurements in nuclear β decay and contribute to further constraining tensor coupling constants.

  14. Interaction between cytokine gene polymorphisms and the effect of physical exercise on clinical and inflammatory parameters in older women: study protocol for a randomized controlled trial

    Directory of Open Access Journals (Sweden)

    Pereira Daniele S

    2012-08-01

    Full Text Available Abstract Background Aging is associated with chronic low-grade inflammatory activity with an elevation of cytokine levels. An association between regular physical activity and reduction of blood levels of anti-inflammatory cytokines is demonstrated in the literature pointing to an anti-inflammatory effect related to exercise. However, there is no consensus regarding which type of exercise and which parameters are the most appropriate to influence inflammatory markers. Evidence indicates that the single nucleotide polymorphism (SNP can influence the synthesis of those cytokines affecting their production. Methods/Design The design of this study is a randomized controlled trial. The aim of this study is to investigate the interaction between the cytokine genes SNP and the effect of physical activity on older women. The main outcomes are: serum levels of sTNFR-1, sTNFR-2, interleukin (IL-6, IL-10, measured by the ELISA method; genotyping of tumor necrosis factor- (TNF-alpha (rs1800629, IL6 (rs1800795, IL10 (rs1800896 by the TaqMan Method (Applied Biosystems, Foster City, CA, USA; and physical performance assessed by Timed Up and Go and 10-Meter Walk Tests. Secondary outcomes include: Geriatric Depression Scale, Perceived Stress Scaleand aerobic capacity, assessed by the six-minute walk; and lower limb muscle strength, using an isokinetic dinamometer (Biodex Medical Systems, Inc., Shirley, NY,USA. Both exercise protocols will be performed three times a week for 10 weeks, 30 sessions in total. Discussion Investigating the interaction between genetic factors and exercise effects of both protocols of exercise on the levels of inflammatory cytokine levels can contribute to guide clinical practice related to treatment and prevention of functional changes due to chronic inflammatory activity in older adults. This approach could develop new perspectives on preventive and treatment proposals in physical therapy and in the management of the older patient

  15. Noise and noise disturbances from wind power plants - Tests with interactive control of sound parameters for more comfortable and less perceptible sounds

    International Nuclear Information System (INIS)

    Persson-Waye, K.; Oehrstroem, E.; Bjoerkman, M.; Agge, A.

    2001-12-01

    In experimental pilot studies, a methodology has been worked out for interactively varying sound parameters in wind power plants. In the tests, 24 persons varied the center frequency of different band-widths, the frequency of a sinus-tone and the amplitude-modulation of a sinus-tone in order to create as comfortable a sound as possible. The variations build on the noise from the two wind turbines Bonus and Wind World. The variations were performed with a constant dba level. The results showed that the majority preferred a low-frequency tone (94 Hz and 115 Hz for Wind World and Bonus, respectively). The mean of the most comfortable amplitude-modulation varied between 18 and 22 Hz, depending on the ground frequency. The mean of the center-frequency for the different band-widths varied from 785 to 1104 Hz. In order to study the influence of the wind velocity on the acoustic character of the noise, a long-time measurement program has been performed. A remotely controlled system has been developed, where wind velocity, wind direction, temperature and humidity are registered simultaneously with the noise. Long-time registrations have been performed for four different wing turbines

  16. Use of specific features of electron and positron interactions with monocrystals for the control of high-energy particle beam parameters

    International Nuclear Information System (INIS)

    Bochek, G.L.; Vit'ko, V.I.; Grishaev, I.A.; Kovalenko, G.D.; Kulibaba, V.I.; Morokhovskij, V.L.; Shramenko, B.I.

    1977-01-01

    To study possibilities of using the effect of high energy positron and electron interactions with crystals in practice at the 2 GeV Kharkov lineac the effect of a light particle charge sign on the processes of bremsstrahlung, elastic scattering and revealing ''blocking effect'' in elastic scatterina has been investigated experimentally of 1 GeV electron (positron) beam is directed to a silicon crystal of 185 μkm thickness. Dependence of total bremsstrahlung flow on the angle between the beam direction and crystal axis has shown, that positron bremsstrahlung is minimum (positrons are channelling, but electron bremsstrahlung is maximum, when crystallographic axis direction coincides with particle direction. The process of positron annihilation in flight has been investigated in 300 μkm thick silicon monocrystal. Bremsstrahlung intensity for channeling positrons drops 4.4 times, and intensity of annihilation radiation - 1.6 times as compared to the case, when channeling regime is absent. Experimental data point out the possibility of using monocrystals for control of the parameters of high-energy particle control beams

  17. Thermodynamic parameters for the protonation and the interaction of arsenate with Mg2+, Ca2+ and Sr2+: Application to natural waters.

    Science.gov (United States)

    Chillè, Donatella; Foti, Claudia; Giuffrè, Ottavia

    2018-01-01

    Thermodynamic parameters for the protonation of AsO 4 3- and for the interaction with Mg 2+ , Ca 2+ and Sr 2+ were reported, comprehensive also of their dependence on ionic strength, considering the 0.1 ≤ I ≤ 1 M range and using NaCl as background salt. The same speciation models were obtained for Mg 2+ , Ca 2+ and Sr 2+ systems, with the formation of three different species: ML, MLH and MLH 2 (L = AsO 4 3- ). Mono- and di-protonated species were very weak, with formation constant values (log K) ranging from 1.45 to 3.23. In order to have a complete picture of thermodynamic properties of the systems under study and to fill the shortage of thermodynamic data on arsenate complex systems, the ligand protonation and metal complex enthalpies were also determined by calorimetric titrations, at t = 25 °C and in NaCl at I = 0.7 M (for H + -AsO 4 3- species also at I = 0.1 M). On the light of the proposed speciation models, examples of As(V) distribution in some natural waters are reported. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Supplementation with Ca salts of soybean oil interacts with concentrate level in grazing dairy cows: intake, ingestive behavior, and ruminal parameters.

    Science.gov (United States)

    Macedo, Fernanda Lopes; Batistel, Fernanda; de Souza, Jonas; Chagas, Lucas Jado; Santos, Flávio Augusto Portela

    2016-12-01

    In this study, we investigated the associative effects of concentrate levels and Ca salts of soybean oil (CSSO) supplementation on performance and ruminal parameters of mid-lactation dairy cows grazing on tropical pasture. Twenty-four Jersey × Holstein cows were used in a randomized block design and assigned to four treatments arranged in a 2 × 2 factorial design. Factors evaluated were concentrate levels (low, 3 kg/day vs. high, 7 kg/day of concentrate) and CSSO supplementation (without CSSO vs. with 250 g CSSO cow/day). All cows grazed on elephant grass (Pennisetum purpureum cv. Cameroon) and received the supplemental treatments for a 90-day period. The high concentrate level decreased forage intake and grazing time. In addition, the high concentrate level increased rumen propionate concentration and microbial synthesis and tended to decrease ammonia-N compared with low concentrate level. The addition of CSSO tended to decrease valerate, isobutyrate, isovalerate, and microbial synthesis. In conclusion, feeding CSSO for mid lactating cows grazing on tropical pasture had negative effects on rumen function. In contrast, CSSO supplementation tended to interact with concentrate level and increased energy intake when fed at low concentrate level. Feeding the high level of concentrate was an effective strategy to increase energy intake and microbial synthesis and improve N utilization.

  19. Neuroimmune interactions in Sjögren's syndrome: relationship of exocrine gland dysfunction with autoantibodies to muscarinic acetylcholine receptor-3 and mental health status parameters.

    Science.gov (United States)

    Deák, Magdolna; Szvetnik, Attila; Balog, Attila; Sohár, Nicolette; Varga, Renáta; Pokorny, Gyula; Tóth, Gábor; Kiss, Mária; Kovács, László

    2013-01-01

    Antimuscarinic acetylcholine receptor-3 (m3AChR) autoantibodies have been described in primary Sjögren's syndrome (pSS). The aim of this study was to compare various methods for their detection and to assess the contributions of anti-m3AChR and other immunological and psychosocial factors to the pathomechanism of secondary SS (sSS). Sixty-five rheumatoid arthritis (RA) patients, 103 systemic lupus erythematosus (SLE) patients, 76 pSS patients and 50 controls were compared. Three immunodominant epitopes of m3AChR were synthesized and used in ELISA. Two extracellular epitopes were also prepared in fusion with glutathione-S-transferase and one in conjugation with bovine serum albumin. Mental health status was assessed with the 36-item Short-Form Health Survey and Functional Assessment of Chronic Illness Therapy fatigue scale. Correlations were evaluated between glandular function and anti-m3AChR positivities and specificities, features of SLE and RA, and mental health parameters. Fourteen RA and 27 SLE patients had sSS. The autoantibody levels to all epitopes of m3AChR were significantly higher in pSS and SLE patients than in the controls. The fusion protein forms discriminated RA from pSS and SLE; furthermore, the YNIP fusion protein also distinguished pSS from SLE. The prevalence and the mean levels of all autoantibodies did not differ statistically between sicca and non-sicca SLE or RA patients. Glandular dysfunction correlated with higher age in SLE and RA and an impaired health-related quality of life in SLE. The second and third extracellular loops of m3AChR are antigenic in pSS. Immunoassays with antigens as fusion peptides demonstrate the best performance. Sicca SLE patients have worse mental health status. Anti-m3AChR antibodies represent a peculiar example of neuroimmune interactions. Copyright © 2012 S. Karger AG, Basel.

  20. PSAIA – Protein Structure and Interaction Analyzer

    Directory of Open Access Journals (Sweden)

    Vlahoviček Kristian

    2008-04-01

    Full Text Available Abstract Background PSAIA (Protein Structure and Interaction Analyzer was developed to compute geometric parameters for large sets of protein structures in order to predict and investigate protein-protein interaction sites. Results In addition to most relevant established algorithms, PSAIA offers a new method PIADA (Protein Interaction Atom Distance Algorithm for the determination of residue interaction pairs. We found that PIADA produced more satisfactory results than comparable algorithms implemented in PSAIA. Particular advantages of PSAIA include its capacity to combine different methods to detect the locations and types of interactions between residues and its ability, without any further automation steps, to handle large numbers of protein structures and complexes. Generally, the integration of a variety of methods enables PSAIA to offer easier automation of analysis and greater reliability of results. PSAIA can be used either via a graphical user interface or from the command-line. Results are generated in either tabular or XML format. Conclusion In a straightforward fashion and for large sets of protein structures, PSAIA enables the calculation of protein geometric parameters and the determination of location and type for protein-protein interaction sites. XML formatted output enables easy conversion of results to various formats suitable for statistic analysis. Results from smaller data sets demonstrated the influence of geometry on protein interaction sites. Comprehensive analysis of properties of large data sets lead to new information useful in the prediction of protein-protein interaction sites.

  1. Properties of residuals for spatial point processes

    DEFF Research Database (Denmark)

    Baddeley, A.; Møller, Jesper; Pakes, A. G.

    2008-01-01

    For any point process in Rd that has a Papangelou conditional intensity λ, we define a random measure of ‘innovations' which has mean zero. When the point process model parameters are estimated from data, there is an analogous random measure of ‘residuals'. We analyse properties of the innovation...... and residuals, including first and second moments, conditional independence, a martingale property, and lack of correlation. Some large sample asymptotics are studied. We derive the marginal distribution of smoothed residuals by solving a distributional equivalence....

  2. 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.)

  3. Estimation of genetic parameters and genotype-by-environment interactions related to acute ammonia stress in Pacific white shrimp (Litopenaeus vannamei) juveniles at two different salinity levels.

    Science.gov (United States)

    Lu, Xia; Luan, Sheng; Cao, Baoxiang; Meng, Xianhong; Sui, Juan; Dai, Ping; Luo, Kun; Shi, Xiaoli; Hao, Dengchun; Han, Guomin; Kong, Jie

    2017-01-01

    Regarding the practical farming of Litopenaeus vannamei, the deterioration of water quality from intensive culture systems and environmental pollution is a common but troublesome problem in the cultivation of this species. The toxicities that result from deteriorating water quality, such as that from ammonia stress, have lethal effects on juvenile shrimp and can increase their susceptibility to pathogens. The toxicity of ammonia plays an important role in the frequently high mortality during the early stage on shrimp farms. However, little information is available regarding the genetic parameters of the ammonia tolerance of juveniles in the early stage, but this information is necessary to understand the potential for the genetic improvement of this trait. Considering the euryhalinity of L. vannamei and the fact that low salinity can increase the toxicity of ammonia stress, we estimated the heritability of ammonia tolerance in juveniles in 30‰ (normal) and 5‰ (low) salinity in this study using the survival time (ST) at individual level and the survival status at the half-lethal time (SS50) at the family level. In the normal and low salinity conditions and for the merged data, the heritability estimates of the ST (0.784±0.070, 0.575±0.068, and 0.517±0.058, respectively) and SS50 (0.402±0.061, 0.216±0.050, and 0.264±0.050, respectively) were all significantly greater than zero, which indicates that the ammonia-tolerance of shrimp can be greatly improved. So it might provide an alternative method to reduce mortality, help to enhance resistance to pathogens and reduce the occurrence of infectious diseases. The significant positive genetic correlation between ST and body length suggested that ammonia is more toxic to shrimp in the early stage. The medium-strength genetic correlations of the ST and SS50 between the two environments (0.394±0.097 and 0.377±0.098, respectively) indicate a strong genotype-by-environment (G×E) interaction for ammonia tolerance

  4. Residual generator for cardiovascular anomalies detection

    KAUST Repository

    Belkhatir, Zehor

    2014-06-01

    This paper discusses the possibility of using observer-based approaches for cardiovascular anomalies detection and isolation. We consider a lumped parameter model of the cardiovascular system that can be written in a form of nonlinear state-space representation. We show that residuals that are sensitive to variations in some cardiovascular parameters and to abnormal opening and closure of the valves, can be generated. Since the whole state is not easily available for measurement, we propose to associate the residual generator to a robust extended kalman filter. Numerical results performed on synthetic data are provided.

  5. Interaction of the alpha-toxin of Staphylococcus aureus with the liposome membrane.

    Science.gov (United States)

    Ikigai, H; Nakae, T

    1987-02-15

    When the liposome membrane is exposed to the alpha-toxin of Staphylococcus aureus, fluorescence of the tryptophan residue(s) of the toxin molecule increases concomitantly with the degree of toxin-hexamer formation (Ikigai, H., and Nakae, T. (1985) Biochem. Biophys. Res. Commun. 130, 175-181). In the present study, the toxin-membrane interaction was distinguished from the hexamer formation by the fluorescence energy transfer from the tryptophan residue(s) of the toxin molecule to the dansylated phosphatidylethanolamine in phosphatidylcholine liposome. Measurement of these two parameters yielded the following results. The effect of the toxin concentration and phospholipid concentration on these two parameters showed first order kinetics. The effect of liposome size on the energy transfer and the fluorescence increment of the tryptophan residue(s) was only detectable in small liposomes. Under moderately acidic or basic conditions, the fluorescence energy transfer always preceded the fluorescence increment of the tryptophan residue(s). The fluorescence increment at 336 nm at temperatures below 20 degrees C showed a latent period, whereas the fluorescence energy transfer did not. These results were thought to indicate that when alpha-toxin damages the target membrane, the molecule interacts with the membrane first, and then undergoes oligomerization within the membrane.

  6. Agricultural pesticide residues

    International Nuclear Information System (INIS)

    Fuehr, F.

    1984-01-01

    The utilization of tracer techniques in the study of agricultural pesticide residues is reviewed under the following headings: lysimeter experiments, micro-ecosystems, translocation in soil, degradation of pesticides in soil, biological availability of soil-applied substances, bound residues in the soil, use of macro- and microautography, double and triple labelling, use of tracer labelling in animal experiments. (U.K.)

  7. Prediction of machining induced residual stresses

    Science.gov (United States)

    Pramod, Monangi; Reddy, Yarkareddy Gopi; Prakash Marimuthu, K.

    2017-07-01

    Whenever a component is machined, residual stresses are induced in it. These residual stresses induced in the component reduce its fatigue life, corrosion resistance and wear resistance. Thus it is important to predict and control the machining-induced residual stress. A lot of research is being carried out in this area in the past decade. This paper aims at prediction of residual stresses during machining of Ti-6Al-4V. A model was developed and under various combinations of cutting conditions such as, speed, feed and depth of cut, the behavior of residual stresses were simulated using Finite Element Model. The present work deals with the development of thermo-mechanical model to predict the machining induced residual stresses in Titanium alloy. The simulation results are compared with the published results. The results are in good agreement with the published results. Future work involves optimization or the cutting parameters that effect the machining induced residual stresses. The results obtained were validated with previous work.

  8. 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

  9. Parameter Estimation

    DEFF Research Database (Denmark)

    Sales-Cruz, Mauricio; Heitzig, Martina; Cameron, Ian

    2011-01-01

    In this chapter the importance of parameter estimation in model development is illustrated through various applications related to reaction systems. In particular, rate constants in a reaction system are obtained through parameter estimation methods. These approaches often require the application...... of algebraic equations as the basis for parameter estimation.These approaches are illustrated using estimations of kinetic constants from reaction system models....

  10. [Residual neuromuscular blockade].

    Science.gov (United States)

    Fuchs-Buder, T; Schmartz, D

    2017-06-01

    Even small degrees of residual neuromuscular blockade, i. e. a train-of-four (TOF) ratio >0.6, may lead to clinically relevant consequences for the patient. Especially upper airway integrity and the ability to swallow may still be markedly impaired. Moreover, increasing evidence suggests that residual neuromuscular blockade may affect postoperative outcome of patients. The incidence of these small degrees of residual blockade is relatively high and may persist for more than 90 min after a single intubating dose of an intermediately acting neuromuscular blocking agent, such as rocuronium and atracurium. Both neuromuscular monitoring and pharmacological reversal are key elements for the prevention of postoperative residual blockade.

  11. TENORM: Wastewater Treatment Residuals

    Science.gov (United States)

    Water and wastes which have been discharged into municipal sewers are treated at wastewater treatment plants. These may contain trace amounts of both man-made and naturally occurring radionuclides which can accumulate in the treatment plant and residuals.

  12. Residuation in orthomodular lattices

    Directory of Open Access Journals (Sweden)

    Chajda Ivan

    2017-04-01

    Full Text Available We show that every idempotent weakly divisible residuated lattice satisfying the double negation law can be transformed into an orthomodular lattice. The converse holds if adjointness is replaced by conditional adjointness. Moreover, we show that every positive right residuated lattice satisfying the double negation law and two further simple identities can be converted into an orthomodular lattice. In this case, also the converse statement is true and the corresponence is nearly one-to-one.

  13. First-order exchange coefficient coupling for simulating surface water-groundwater interactions: Parameter sensitivity and consistency with a physics-based approach

    Science.gov (United States)

    Ebel, B.A.; Mirus, B.B.; Heppner, C.S.; VanderKwaak, J.E.; Loague, K.

    2009-01-01

    Distributed hydrologic models capable of simulating fully-coupled surface water and groundwater flow are increasingly used to examine problems in the hydrologic sciences. Several techniques are currently available to couple the surface and subsurface; the two most frequently employed approaches are first-order exchange coefficients (a.k.a., the surface conductance method) and enforced continuity of pressure and flux at the surface-subsurface boundary condition. The effort reported here examines the parameter sensitivity of simulated hydrologic response for the first-order exchange coefficients at a well-characterized field site using the fully coupled Integrated Hydrology Model (InHM). This investigation demonstrates that the first-order exchange coefficients can be selected such that the simulated hydrologic response is insensitive to the parameter choice, while simulation time is considerably reduced. Alternatively, the ability to choose a first-order exchange coefficient that intentionally decouples the surface and subsurface facilitates concept-development simulations to examine real-world situations where the surface-subsurface exchange is impaired. While the parameters comprising the first-order exchange coefficient cannot be directly estimated or measured, the insensitivity of the simulated flow system to these parameters (when chosen appropriately) combined with the ability to mimic actual physical processes suggests that the first-order exchange coefficient approach can be consistent with a physics-based framework. Copyright ?? 2009 John Wiley & Sons, Ltd.

  14. Surface Finish and Residual Stresses Induced by Orthogonal Dry Machining of AA7075-T651.

    Science.gov (United States)

    Jomaa, Walid; Songmene, Victor; Bocher, Philippe

    2014-02-28

    The surface finish was extensively studied in usual machining processes (turning, milling, and drilling). For these processes, the surface finish is strongly influenced by the cutting feed and the tool nose radius. However, a basic understanding of tool/surface finish interaction and residual stress generation has been lacking. This paper aims to investigate the surface finish and residual stresses under the orthogonal cutting since it can provide this information by avoiding the effect of the tool nose radius. The orthogonal machining of AA7075-T651 alloy through a series of cutting experiments was performed under dry conditions. Surface finish was studied using height and amplitude distribution roughness parameters. SEM and EDS were used to analyze surface damage and built-up edge (BUE) formation. An analysis of the surface topography showed that the surface roughness was sensitive to changes in cutting parameters. It was found that the formation of BUE and the interaction between the tool edge and the iron-rich intermetallic particles play a determinant role in controlling the surface finish during dry orthogonal machining of the AA7075-T651 alloy. Hoop stress was predominantly compressive on the surface and tended to be tensile with increased cutting speed. The reverse occurred for the surface axial stress. The smaller the cutting feed, the greater is the effect of cutting speed on both axial and hoop stresses. By controlling the cutting speed and feed, it is possible to generate a benchmark residual stress state and good surface finish using dry machining.

  15. Effect of process variables on the Drucker-Prager cap model and residual stress distribution of tablets estimated by the finite element method.

    Science.gov (United States)

    Hayashi, Yoshihiro; Otoguro, Saori; Miura, Takahiro; Onuki, Yoshinori; Obata, Yasuko; Takayama, Kozo

    2014-01-01

    A multivariate statistical technique was applied to clarify the causal correlation between variables in the manufacturing process and the residual stress distribution of tablets. Theophylline tablets were prepared according to a Box-Behnken design using the wet granulation method. Water amounts (X1), kneading time (X2), lubricant-mixing time (X3), and compression force (X4) were selected as design variables. The Drucker-Prager cap (DPC) model was selected as the method for modeling the mechanical behavior of pharmaceutical powders. Simulation parameters, such as Young's modulus, Poisson rate, internal friction angle, plastic deformation parameters, and initial density of the powder, were measured. Multiple regression analysis demonstrated that the simulation parameters were significantly affected by process variables. The constructed DPC models were fed into the analysis using the finite element method (FEM), and the mechanical behavior of pharmaceutical powders during the tableting process was analyzed using the FEM. The results of this analysis revealed that the residual stress distribution of tablets increased with increasing X4. Moreover, an interaction between X2 and X3 also had an effect on shear and the x-axial residual stress of tablets. Bayesian network analysis revealed causal relationships between the process variables, simulation parameters, residual stress distribution, and pharmaceutical responses of tablets. These results demonstrated the potential of the FEM as a tool to help improve our understanding of the residual stress of tablets and to optimize process variables, which not only affect tablet characteristics, but also are risks of causing tableting problems.

  16. Spectrophotometric studies on the interaction between (-)-epigallocatechin gallate and lysozyme

    Science.gov (United States)

    Ghosh, Kalyan Sundar; Sahoo, Bijaya Ketan; Dasgupta, Swagata

    2008-02-01

    Various reported antibacterial activities of (-)-epigallocatechin-3-gallate (EGCG), the major polyphenol of green tea prompted us to study its binding with lysozyme. This has been investigated by fluorescence, circular dichroism (CD) and protein-ligand docking. The binding parameters were determined using a modified Stern-Volmer equation. The thermodynamic parameters are indicative of an initial hydrophobic association. The complex is, however, held together predominantly by van der Waals interactions and hydrogen bonding. CD studies do not indicate any significant changes in the secondary structure of lysozyme. Docking studies revealed that specific interactions are observed with residues Trp 62 and Trp 63.

  17. Eviromental Economic and Technological Residues Management Demands: An Optimization Tool.

    Directory of Open Access Journals (Sweden)

    Marisa Soares Borges

    2012-12-01

    Full Text Available Industrial residues management is a very demanding task since many different goals must be achieved. The combination of different approaches used by people from different stuff is very challenging activity that can misuse the residues potential value and applicability. An interactive WEB base tool, to integrate different sectors and overcome residues management difficulties will be presented. The system must be loaded with all data concerning the residue life cycle, and through data integration and modeling routine will give the best alternative as output. As wider and complete the system data becomes, by information loading from differen t segment, more efficient the residues management becomes. The user friendly tool will encourage the participation of industries, labs and research institutions to obtain qualified information about industrial residues inventory, raw materials recovery, characteristics, treatment and alternative uses, to achieve residues management sustainability.

  18. Efeito residual de quatro aplicações anuais de lodo de esgoto e vinhaça na qualidade tecnológica da cana-de-açúcar Sugarcane technological parameters affected by sewage sludge and vinasse added in soil for four consecutive years

    Directory of Open Access Journals (Sweden)

    Caramo Có Júnior

    2008-03-01

    Full Text Available O principal objetivo deste trabalho foi avaliar os efeitos residuais, por quatro anos seguidos, de diferentes tipos de resíduos, aplicados de formas e em doses distintas, sobre a qualidade tecnológica da cana-de-açúcar de quinto corte (cultivar SP 81-3250. Os tratamentos testados são combinações de dois tipos de resíduos (lodo de esgoto; vinhaça; lodo de esgoto + vinhaça com dois modos de aplicação (ao lado da linha de cultivo e em área total e com duas doses (100 e 200%, e um tratamento-testemunha. O delineamento experimental foi em blocos casualizados, com três repetições, totalizando 39 parcelas. As variáveis analisadas foram: percentagem de sólidos solúveis no caldo extraído (Brix % C.E., percentagem aparente de sacarose no caldo extraído (Pol % C.E., percentagem da fibra na cana (Fibra % cana, pureza (%, percentagem aparente de sacarose na cana (Pol % cana, percentagem de açúcares redutores na cana (AR % cana, percentagem de açúcares redutores totais na cana (ART % cana e açúcares totais recuperáveis (ATR. Os fatores de variação testados (tipo de resíduo, modo de aplicação e doses não promoveram alterações na qualidade e não comprometeram a valorização da cana-de-açúcar.The main objective of this research was to evaluate the residual effect of different residues applied during four years in distinct application modes and rates, on the technological quality of the 5th ratoon of sugar cane (cultivar SP 81-3250. The treatments were from combination of two residues (sewage sludge, vinasse, sewage sludge + vinasse applied according two different ways (close to the sugar cane line and spread in the whole area, in two rates (100 and 200% besides a control treatment. The experimental design was randomized blocks with thirteen treatments and three replications, resulting 39 experimental plots. The following parameters were analyzed: percentage of soluble solids in juice (Brix % JC, apparent percentage of

  19. 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

  20. Nitrogen mineralization from organic residues: research opportunities.

    Science.gov (United States)

    Cabrera, M L; Kissel, D E; Vigil, M F

    2005-01-01

    Research on nitrogen (N) mineralization from organic residues is important to understand N cycling in soils. Here we review research on factors controlling net N mineralization as well as research on laboratory and field modeling efforts, with the objective of highlighting areas with opportunities for additional research. Among the factors controlling net N mineralization are organic composition of the residue, soil temperature and water content, drying and rewetting events, and soil characteristics. Because C to N ratio of the residue cannot explain all the variability observed in N mineralization among residues, considerable effort has been dedicated to the identification of specific compounds that play critical roles in N mineralization. Spectroscopic techniques are promising tools to further identify these compounds. Many studies have evaluated the effect of temperature and soil water content on N mineralization, but most have concentrated on mineralization from soil organic matter, not from organic residues. Additional work should be conducted with different organic residues, paying particular attention to the interaction between soil temperature and water content. One- and two-pool exponential models have been used to model N mineralization under laboratory conditions, but some drawbacks make it difficult to identify definite pools of mineralizable N. Fixing rate constants has been used as a way to eliminate some of these drawbacks when modeling N mineralization from soil organic matter, and may be useful for modeling N mineralization from organic residues. Additional work with more complex simulation models is needed to simulate both gross N mineralization and immobilization to better estimate net N mineralized from organic residues.

  1. Protein structure based prediction of catalytic residues

    Science.gov (United States)

    2013-01-01

    Background Worldwide structural genomics projects continue to release new protein structures at an unprecedented pace, so far nearly 6000, but only about 60% of these proteins have any sort of functional annotation. Results We explored a range of features that can be used for the prediction of functional residues given a known three-dimensional structure. These features include various centrality measures of nodes in graphs of interacting residues: closeness, betweenness and page-rank centrality. We also analyzed the distance of functional amino acids to the general center of mass (GCM) of the structure, relative solvent accessibility (RSA), and the use of relative entropy as a measure of sequence conservation. From the selected features, neural networks were trained to identify catalytic residues. We found that using distance to the GCM together with amino acid type provide a good discriminant function, when combined independently with sequence conservation. Using an independent test set of 29 annotated protein structures, the method returned 411 of the initial 9262 residues as the most likely to be involved in function. The output 411 residues contain 70 of the annotated 111 catalytic residues. This represents an approximately 14-fold enrichment of catalytic residues on the entire input set (corresponding to a sensitivity of 63% and a precision of 17%), a performance competitive with that of other state-of-the-art methods. Conclusions We found that several of the graph based measures utilize the same underlying feature of protein structures, which can be simply and more effectively captured with the distance to GCM definition. This also has the added the advantage of simplicity and easy implementation. Meanwhile sequence conservation remains by far the most influential feature in identifying functional residues. We also found that due the rapid changes in size and composition of sequence databases, conservation calculations must be recalibrated for specific

  2. Solar degradation of diclofenac using Eosin-Y-activated TiO2: cost estimation, process optimization and parameter interaction study.

    Science.gov (United States)

    Hashim, Noshin; Thakur, Shaila; Patang, Mouska; Crapulli, Ferdinando; Ray, Ajay K

    2017-04-01

    Diclofenac (DCF), a widely used non-steroidal anti-inflammatory drug, is a commonly detected substance that readily accumulates in tissues of aquatic fish and poses a threat to wildlife and freshwater quality. Advanced Oxidation Processes have been employed as an alternative due to the inadequacy of conventional treatment methods of trace contaminants. This study utilized an innovative method of solar-activation of TiO 2 using Eosin-Y dye for the degradation of DCF. Furthermore, the study incorporated a central composite design (CCD) to optimize the dye concentration and estimated the cost for the present process. Optimized parameters for light intensity (750 mW/cm 2 ), Eosin-Y dye concentration (2 mg/L), TiO 2 loading (37.5 mg/cm 2 ) and DCF concentration (25 mg/L) were determined through a CCD. The optimized parameters convey a DCF degradation rate of 40% and 49% for 2 ppm (low range) and 4 ppm (high range) dye concentrations, respectively, for a 5-minute reaction time. Cost estimation for the materials used was for the current process was also performed. It was determined that the additional cost of using 4 ppm instead of 2 ppm to achieve only 10% more DCF degradation is not warranted and would require additional treatment to remove subsequently formed halogenated compounds.

  3. 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).

  4. The roles of selected arginine and lysine residues of TAFI (Pro-CPU) in its activation to TAFIa by the thrombin-thrombomodulin complex.

    Science.gov (United States)

    Wu, Chengliang; Kim, Paul Y; Manuel, Reg; Seto, Marian; Whitlow, Marc; Nagashima, Mariko; Morser, John; Gils, Ann; Declerck, Paul; Nesheim, Michael E

    2009-03-13

    Thrombomodulin (TM) increases the catalytic efficiency of thrombin (IIa)-mediated activation of thrombin-activable fibrinolysis inhibitor (TAFI) 1250-fold. Negatively charged residues of the C-loop of TM-EGF-like domain 3 are required for TAFI activation. Molecular models suggested several positively charged residues of TAFI with which the C-loop residues could interact. Seven TAFI mutants were constructed to determine if these residues are required for efficient TAFI activation. TAFI wild-type or mutants were activated in the presence or absence of TM and the kinetic parameters of TAFI activation were determined. When the three consecutive lysine residues in the activation peptide of TAFI were substituted with alanine (K42/43/44A), the catalytic efficiencies for TAFI activation with TM decreased 8-fold. When other positively charged surface residues of TAFI (Lys-133, Lys-211, Lys-212, Arg-220, Lys-240, or Arg-275) were mutated to alanine, the catalytic efficiencies for TAFI activation with TM decreased by 1.7-2.7-fold. All decreases were highly statistically significant. In the absence of TM, catalytic efficiencies ranged from 2.8-fold lower to 1.24-fold higher than wild-type. None of these, except the 2.8-fold lower value, was statistically significant. The average half-life of the TAFIa mutants was 8.1+/-0.6 min, and that of wild type was 8.4+/-0.3 min at 37 degrees C. Our data show that these residues are important in the activation of TAFI by IIa, especially in the presence of TM. Whether the mutated residues promote a TAFI-TM or TAFI-IIa interaction remains to be determined. In addition, these residues do not influence spontaneous inactivation of TAFIa.

  5. Usage and validation of a fluid structure interaction methodology for the study of different suction valve parameters of a hermetic reciprocating compressor

    Directory of Open Access Journals (Sweden)

    W Lang

    2016-09-01

    Full Text Available The dynamics of the flatter valves inside a hermetic reciprocating compressor used in household appliances is the most important factor concerning the gas dynamic behaviour of such a compressor. Hence for a good valve design and for a reliable simulation of the compressor the ability to predict the movement of the valves is indispensable. The present paper describes a methodology which allows the prediction of the valve dynamics. For the validation of the methodology the simulation results of the suction valve dynamics have been compared with experimental data obtained out of measurements with a Laser-Doppler-Vibrometer. Furthermore the method has been used for the variation of some suction valve parameters and their influence onto the overall compressor performance has been shown. The whole methodology has been implemented into a commercial available CFD code (FLUENT as a user defined function (UDF.

  6. Inventory parameters

    CERN Document Server

    Sharma, Sanjay

    2017-01-01

    This book provides a detailed overview of various parameters/factors involved in inventory analysis. It especially focuses on the assessment and modeling of basic inventory parameters, namely demand, procurement cost, cycle time, ordering cost, inventory carrying cost, inventory stock, stock out level, and stock out cost. In the context of economic lot size, it provides equations related to the optimum values. It also discusses why the optimum lot size and optimum total relevant cost are considered to be key decision variables, and uses numerous examples to explain each of these inventory parameters separately. Lastly, it provides detailed information on parameter estimation for different sectors/products. Written in a simple and lucid style, it offers a valuable resource for a broad readership, especially Master of Business Administration (MBA) students.

  7. Composition of carbonization residues

    Energy Technology Data Exchange (ETDEWEB)

    Hupfer; Leonhardt

    1943-11-27

    This report compared the composition of samples from Wesseling and Leuna. In each case the sample was a residue from carbonization of the residues from hydrogenation of the brown coal processed at the plant. The composition was given in terms of volatile components, fixed carbon, ash, water, carbon, hydrogen, oxygen, nitrogen, volatile sulfur, and total sulfur. The result of carbonization was given in terms of (ash and) coke, tar, water, gas and losses, and bitumen. The composition of the ash was given in terms of silicon dioxide, ferric oxide, aluminum oxide, calcium oxide, magnesium oxide, potassium and sodium oxides, sulfur trioxide, phosphorus pentoxide, chlorine, and titanium oxide. The most important difference between the properties of the two samples was that the residue from Wesseling only contained 4% oil, whereas that from Leuna had about 26% oil. Taking into account the total amount of residue processed yearly, the report noted that better carbonization at Leuna could save 20,000 metric tons/year of oil. Some other comparisons of data included about 33% volatiles at Leuna vs. about 22% at Wesseling, about 5 1/2% sulfur at Leuna vs. about 6 1/2% at Leuna, but about 57% ash for both. Composition of the ash differed quite a bit between the two. 1 table.

  8. Designing with residual materials

    NARCIS (Netherlands)

    Walhout, W.; Wever, R.; Blom, E.; Addink-Dölle, L.; Tempelman, E.

    2013-01-01

    Many entrepreneurial businesses have attempted to create value based on the residual material streams of third parties. Based on ‘waste’ materials they designed products, around which they built their company. Such activities have the potential to yield sustainable products. Many of such companies

  9. Multifaceted interplay between lipophilicity, protein interaction and luminescence parameters of non-intercalative ruthenium(II) polypyridyl complexes controlling cellular imaging and cytotoxic properties.

    Science.gov (United States)

    Mazuryk, Olga; Magiera, Katarzyna; Rys, Barbara; Suzenet, Franck; Kieda, Claudine; Brindell, Małgorzata

    2014-12-01

    Here, we examine the photophysical properties of five ruthenium(II) complexes comprising two 4,7-diphenyl-1,10-phenanthroline (dip) ligands and functionalized bipyridine (R₁bpy-R₂, where R₁= H or CH3, R₂= H, CH₃, COO⁻,4-[3-(2-nitro-1H-imidazol-1-yl)propyl] or 1,3-dicyclohexyl-1-carbonyl-urea) towards development of luminescence probes for cellular imaging. These complexes have been shown to interact with albumin and the formed adducts exhibited up to eightfold increase in the luminescence quantum yield as well as the average lifetime of emission. It was demonstrated that they cannot bind to DNA through the intercalation mode and its luminescence in the presence of DNA is quenching. Cell viability experiments indicated that all complexes possess significant dose-dependent cytotoxicity (with IC₅₀ 5-19 μM) on 4T1 breast cancer cell line and their anti-proliferative activity correlates very well with their lipophilicity. Cellular uptake was studied by measuring the ruthenium content in cells using ICP-MS technique. As expected, the better uptake is directly related to higher lipophilicity of doubly charged ruthenium complexes while uptake of monocationic one is much lower in spite of the highest lipophilicity. Additionally staining properties were assessed using flow cytometry and fluorescence microscopy. These experiments showed that complex with 1,3-dicyclohexyl-1-carbonyl-urea substituent exhibits the best staining properties in spite of the lowest luminescence quantum yield in buffered solution (pH 7.4). Our results point out that both the imaging and cytotoxic properties of the studied ruthenium complexes are strongly influence by the level of internalization and protein interaction.

  10. Fluid-Rock Characterization and Interactions in NMR Well Logging

    Energy Technology Data Exchange (ETDEWEB)

    Hirasaki, George J.; Mohanty, Kishore K.

    2003-02-10

    The objective of this project was to characterize the fluid properties and fluid-rock interactions which are needed for formation evaluation by NMR well logging. NMR well logging is finding wide use in formation evaluation. The formation parameters commonly estimated were porosity, permeability, and capillary bound water. Special cases include estimation of oil viscosity, residual oil saturation, location of oil/water contact, and interpretation on whether the hydrocarbon is oil or gas.

  11. Investigation of the effect of laser parameters on the target, plume and plasma behavior during and after laser-solid interaction

    Science.gov (United States)

    Stancalie, A.; Ciobanu, S. S.; Sporea, D.

    2017-09-01

    A detailed theoretical and experimental analysis is performed for a wide range of laser operating conditions, typical for laser induced breakdown spectroscopy (LIBS) and laser ablation (LA) experiments on copper metallic target. The plasma parameters were experimentally estimated from the line intensities ratio which reflects the relative population of neutral excited species in the plasma. In the case of LA experiments the highest temperature observed was 8210 ± 370 K. In case of LIBS measurements, a maximum temperature of 8123 K has been determined. The experimental results are in good agreement with a stationary, hydrodynamic model. We have theoretically investigated the plasma emission based on the generalized collisional-radiative model as implemented in the ADAS interconnected set of computer codes and data collections. The ionic population density distribution over the ground and excited states into the cooper plasma is graphically displayed as output from the code. The theoretical line intensity ratios are in good agreement with experimental values for the electron density and temperature range measured in our experiments.

  12. Particle size, surface hydrophobicity and interaction with serum of parenteral fat emulsions and model drug carriers as parameters related to RES uptake.

    Science.gov (United States)

    Carrstensen, H; Müller, R H; Müller, B W

    1992-10-01

    Fat emulsions for parenteral nutrition, stabilized by egg lecithin, were characterized in terms of parameters relevant to uptake by the reticuloendothelial system (RES), e.g. size distribution, surface hydrophobicity and adsorption of serum components as a measure of the degree of opsonization. Adsorption of serum components was quantified by zeta potential measurement. Fat emulsions for nutrition were compared with emulsions used for drug delivery and model drug carries for intravenous injection. The emulsions for drug delivery were stabilized by the blockcopolymers Poloxamer 188 and 407 (Pluronic F68 and F127) and Poloxamine 908. Model drug carriers were hydrophobic and hydrophilic polystyrene latex particles. Hydrophilic particles were prepared by adsorption of Poloxamine 908 (coating) onto the particle surface. The hydrophobicity and serum protein adsorption decreased from hydrophobic latex particles to egg lecithin emulsions and blockcopolymer emulsions and particles. The data correlated with that in the literature concerning liver uptake in vivo showing complete RES clearance of hydrophobic latex particles, reduced uptake of egg lecithin emulsions and avoidance of RES uptake by Poloxamine 908 coated particles.

  13. Reconciliation of essential process parameters for an enhanced predictability of Arctic stratospheric ozone loss and its climate interactions (RECONCILE: activities and results

    Directory of Open Access Journals (Sweden)

    M. von Hobe

    2013-09-01

    Full Text Available The international research project RECONCILE has addressed central questions regarding polar ozone depletion, with the objective to quantify some of the most relevant yet still uncertain physical and chemical processes and thereby improve prognostic modelling capabilities to realistically predict the response of the ozone layer to climate change. This overview paper outlines the scope and the general approach of RECONCILE, and it provides a summary of observations and modelling in 2010 and 2011 that have generated an in many respects unprecedented dataset to study processes in the Arctic winter stratosphere. Principally, it summarises important outcomes of RECONCILE including (i better constraints and enhanced consistency on the set of parameters governing catalytic ozone destruction cycles, (ii a better understanding of the role of cold binary aerosols in heterogeneous chlorine activation, (iii an improved scheme of polar stratospheric cloud (PSC processes that includes heterogeneous nucleation of nitric acid trihydrate (NAT and ice on non-volatile background aerosol leading to better model parameterisations with respect to denitrification, and (iv long transient simulations with a chemistry-climate model (CCM updated based on the results of RECONCILE that better reproduce past ozone trends in Antarctica and are deemed to produce more reliable predictions of future ozone trends. The process studies and the global simulations conducted in RECONCILE show that in the Arctic, ozone depletion uncertainties in the chemical and microphysical processes are now clearly smaller than the sensitivity to dynamic variability.

  14. Controlling residual hydrogen gas in mass spectra during pulsed laser atom probe tomography.

    Science.gov (United States)

    Kolli, R Prakash

    2017-01-01

    Residual hydrogen (H 2 ) gas in the analysis chamber of an atom probe instrument limits the ability to measure H concentration in metals and alloys. Measuring H concentration would permit quantification of important physical phenomena, such as hydrogen embrittlement, corrosion, hydrogen trapping, and grain boundary segregation. Increased insight into the behavior of residual H 2 gas on the specimen tip surface in atom probe instruments could help reduce these limitations. The influence of user-selected experimental parameters on the field adsorption and desorption of residual H 2 gas on nominally pure copper (Cu) was studied during ultraviolet pulsed laser atom probe tomography. The results indicate that the total residual hydrogen concentration, H TOT , in the mass spectra exhibits a generally decreasing trend with increasing laser pulse energy and increasing laser pulse frequency. Second-order interaction effects are also important. The pulse energy has the greatest influence on the quantity H TOT , which is consistently less than 0.1 at.% at a value of 80 pJ.

  15. Influence of environmental parameters and of their interactions on the release of metal(loid)s from a construction material in hydraulic engineering.

    Science.gov (United States)

    Schmukat, A; Duester, L; Goryunova, E; Ecker, D; Heininger, P; Ternes, T A

    2016-03-05

    Besides the leaching behaviour of a construction material under standardised test-specific conditions with laboratory water, for some construction materials it is advisable to test their environmental behaviour also under close to end use conditions. The envisaged end use combined with the product characteristics (e.g. mineral phases) is decisive for the choice of environmental factors that may change the release of substance that potentially cause adverse environmental effects (e.g. fertilisation or ecotoxicity). At the moment an experimental link is missing between mono-factorial standardised test systems and non standardised complex incubation experiments such as mesocosms which are closer to environmental conditions. Multi-factorial batch experiments may have the potential to close the gap. To verify this, batch experiments with copper slag were performed which is used as armour stones in hydraulic engineering. Design of experiments (DoE) was applied to evaluate the impact of pH, ionic strength, temperature and sediment content on the release of As, Cu, Mo, Ni, Pb, Sb and Zn. The study shows that release and sediment-eluent partitioning of metal(loid)s are impacted by interactions between the studied factors. Under the prevalent test conditions sediment acts as a sink enhancing most strongly the release of elements from the material. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. Residual stresses in material processing

    Science.gov (United States)

    Kozaczek, K. J.; Watkins, T. R.; Hubbard, C. R.; Wang, Xun-Li; Spooner, S.

    Material manufacturing processes often introduce residual stresses into the product. The residual stresses affect the properties of the material and often are detrimental. Therefore, the distribution and magnitude of residual stresses in the final product are usually an important factor in manufacturing process optimization or component life prediction. The present paper briefly discusses the causes of residual stresses. It then addresses the direct, nondestructive methods of residual stress measurement by X ray and neutron diffraction. Examples are presented to demonstrate the importance of residual stress measurement in machining and joining operations.

  17. DCE-MRI-Derived Parameters in Evaluating Abraxane-Induced Early Vascular Response and the Effectiveness of Its Synergistic Interaction with Cisplatin.

    Directory of Open Access Journals (Sweden)

    Xilin Sun

    Full Text Available Our previous studies revealed molecular alterations of tumor vessels, varying from immature to mature alterations, resulting from Abraxane, and demonstrated that the integrin-specific PET tracer 18F-FPPRGD2 can be used to noninvasively monitor such changes. However, changes in the tumor vasculature at functional levels such as perfusion and permeability are also important for monitoring Abraxane treatment outcomes in patients with cancer. The purpose of this study is to further investigate the vascular response during Abraxane therapy and the effectiveness of its synergistic interaction with cisplatin using Dynamic contrast enhanced-magnetic resonance imaging (DCE-MRI. Thirty MDA-MB-435 tumor mice were randomized into three groups: PBS control (C group, Abraxane only (A group, and sequential treatment with Abraxane followed by cisplatin (A-P group. Tumor volume was monitored based on caliper measurements. A DCE-MRI protocol was performed at baseline and day 3. The Ktrans, Kep and Ve were calculated and compared with CD31, α-SMA, and Ki67 histology data. Sequential treatment with Abraxane followed by cisplatin produced a significantly greater inhibition of tumor growth during the three weeks of the observation period. Decreases in Ktrans and Kep for the A and A-P groups were observed on day 3. Immunohistological staining suggested vascular remodeling during the Abraxane therapy. The changes in Ktrans and Kep values were correlated with alterations in the permeability of the tumor vasculature induced by the Abraxane treatment. In conclusion, Abraxane-mediated permeability variations in tumor vasculature can be quantitatively visualized by DCE-MRI, making this a useful method for studying the effects of early cancer treatment, especially the early vascular response. Vascular remodeling by Abraxane improves the efficiency of cisplatin delivery and thus results in a favorable treatment outcome.

  18. Dissecting and analyzing key residues in protein-DNA complexes.

    Science.gov (United States)

    Kulandaisamy, A; Srivastava, Ambuj; Nagarajan, R; Gromiha, M Michael

    2018-04-01

    Protein-DNA interactions are involved in various fundamental biological processes such as replication, transcription, DNA repair, and gene regulation. To understand the interaction in protein-DNA complexes, the integrative study of binding and stabilizing residues is important. In the present study, we have identified key residues that play a dual role in both binding and stability from a nonredundant dataset of 319 protein-DNA complexes. We observed that key residues are identified in very less number of complexes (29%) and only about 4% of stabilizing/binding residues are identified as key residues. Specifically, stabilizing residues have higher preference to be key residues than binding residues. These key residues include polar, nonpolar, aliphatic, aromatic, and charged amino acids. Moreover, we have analyzed and discussed the key residues in different protein-DNA complexes, which are classified based on protein structural class, function, DNA strand, and their conformations. Especially, Ser, Thr, Tyr, Arg, and Lys residues are commonly found in most of the subclasses of protein-DNA complexes. Further, we analyzed atomic contacts, which show that polar-nonpolar is more enriched than other types of contacts. In addition, the charged contacts are highly preferred in protein-DNA complexes compared with protein-protein and protein-RNA complexes. Finally, we have discussed the sequence and structural features of key residues such as conservation score, surrounding hydrophobicity, solvent accessibility, secondary structure, and long-range order. This study will be helpful to understand the recognition mechanism and structural and functional aspects of protein-DNA complexes. Copyright © 2017 John Wiley & Sons, Ltd.

  19. Properties of residuals for spatial point processes

    DEFF Research Database (Denmark)

    Baddeley, A.; Møller, Jesper; Pakes, A.G.

    For any point process in $R^d$ that has a Papangelou conditional intensity $lambda$, we define a random measure of ‘innovations’ which has mean zero. When the point process model parameters are estimated from data, there is an analogous random measure of ‘residuals’. We analyse properties of the ...... of the innovations and residuals, including first and second moments, conditional independence, a martingale property, lack of correlation, and marginal distributions....

  20. The importance of high impact parameter interactions in the collision induced dissociation of protonated water clusters by argon using a Wien velocity filter

    Science.gov (United States)

    Cowen, Kenneth A.; Plastridge, Bob; Wood, Deron A.; Coe, James V.

    1993-09-01

    High impact parameter, i.e., glancing collisions, are of particular interest in ion beam experiments because ions experiencing such collisions remain available in the ion beam for further experiments. The collisional activation and dissociation processes for glancing collisions of protonated water clusters and argon have been studied with a new and simple, single-stage technique to detect fragment ions using a Wien velocity filter. The technique is specific with regard to the mass of a fragment ion and the mass of the parent from which it originates. A relation is derived and experimentally verified which governs the operation of the device. Absolute values of the attenuation cross section with argon of 11(6), 25(8), 36(11), 47(17), and 66(10) Å have been determined for H3O+, H5O2+, H7O3+, H9O4+, and H11O5+, respectively, at beam energies in the range of 300-1000 eV. Absolute values of the glancing collision induced dissociation cross section of 0.62(4), 4.3(1), and 9.1(6) Å2 have been determined for the detectable fragment ions of H5O2+, H7O3+, and H9O4+, respectively. Branching ratios upon activation by glancing collisions of 0.91:0.09:0 and 0.78:0.18:0.04:0 have been determined for successive loss of waters by H7O3+ and H9O4+, respectively. The one water loss channel predominates. A multiple collision analysis was performed which characterizes the fraction of parent ions which suffer a glancing collision without dissociating or being knocked out of the beam. Our results suggest that the ion beam which emerges from a collision cell can harbor a surprisingly large fraction of parent ions that have obtained a large amount of internal excitation, perhaps ˜0.7 eV per ion suffering a glancing collision.

  1. SRC Residual fuel oils

    Science.gov (United States)

    Tewari, Krishna C.; Foster, Edward P.

    1985-01-01

    Coal solids (SRC) and distillate oils are combined to afford single-phase blends of residual oils which have utility as fuel oils substitutes. The components are combined on the basis of their respective polarities, that is, on the basis of their heteroatom content, to assure complete solubilization of SRC. The resulting composition is a fuel oil blend which retains its stability and homogeneity over the long term.

  2. Composition of carbonization residues

    Energy Technology Data Exchange (ETDEWEB)

    Hupfer; Leonhardt

    1943-11-30

    This report gave a record of the composition of several samples of residues from carbonization of various hydrogenation residue from processing some type of coal or tar in the Bergius process. These included Silesian bituminous coal processed at 600 atm. with iron catalyst, in one case to produce gasoline and middle oil and in another case to produce heavy oil excess, Scholven coal processed at 250 atm. with tin oxalate and chlorine catalyst, Bruex tar processed in a 10-liter oven using iron catalyst, and a pitch mixture from Welheim processed in a 10-liter over using iron catalyst. The values gathered were compared with a few corresponding values estimated for Boehlen tar and Gelsenberg coal based on several assumptions outlined in the report. The data recorded included percentage of ash in the dry residue and percentage of carbon, hydrogen, oxygen, nitrogen, chlorine, total sulfur, and volatile sulfur. The percentage of ash varied from 21.43% in the case of Bruex tar to 53.15% in the case of one of the Silesian coals. Percentage of carbon varied from 44.0% in the case of Scholven coal to 78.03% in the case of Bruex tar. Percentage of total sulfur varied from 2.28% for Bruex tar to a recorded 5.65% for one of the Silesian coals and an estimated 6% for Boehlen tar. 1 table.

  3. Testing the efficiency of extraction of incurred residues from soil with optimized multi-residue method.

    Science.gov (United States)

    Suszter, Gabriella K; Ambrus, Árpád

    2017-08-03

    The reproducibility of extraction of residues from spiked soil samples and from soils containing incurred residues was tested with 14 C-labeled test compounds of different physical-chemical properties. Nearly 100% of the compounds added to the sample before extraction could be recovered with an average reproducibility relative standard deviation (CV) of 5.4%. The additional steps of the determination process (cleanup, evaporation, etc.) contributed to the major part of the variability of the results (CV = 10-20%). The incurred residues were most efficiently extracted with acetone for 30 min followed by the mixture of acetone/ethyl acetate 1:1 for additional 30 min. However, they could only be recovered at various extent (64-90% of total residues), underlying the importance of testing the efficiency of extraction. The residues were identified and quantified by gas chromatography applying thermionic detector. The performance parameters of the method complied with the international method validation guidelines, and they proved to be robust and suitable for determination of pesticide residues in soils of widely different physical-chemical properties.

  4. Microclimatic Parameters

    DEFF Research Database (Denmark)

    Kragh, Mikkel Kristian; Svendsen, Sv Aa Højgaard

    1996-01-01

    Review paper dealing with the outspoken need for models describing the microclimate at the exterior of the building envelope. In building physics, detailed hygrothermal calculations are performed on the basis of meteorological data, not considering the complex interaction with specific features...... of the proposed building and its surroundings. KEYWORDS: Microclimate, moisture balance, driving rain, condensation, convection, recommendations for further studies....

  5. Lignin biochemistry and soil N determine crop residue decomposition and soil priming

    Science.gov (United States)

    Cropping history can affect soil properties, including available N, but little is known about the interactive effects of residue biochemistry, temperature and cropping history on residue decomposition. A laboratory incubation examined the role of residue biochemistry and temperature on the decomposi...

  6. Bomb parameters

    International Nuclear Information System (INIS)

    Kerr, George D.; Young, Rebert W.; Cullings, Harry M.; Christry, Robert F.

    2005-01-01

    The reconstruction of neutron and gamma-ray doses at Hiroshima and Nagasaki begins with a determination of the parameters describing the explosion. The calculations of the air transported radiation fields and survivor doses from the Hiroshima and Nagasaki bombs require knowledge of a variety of parameters related to the explosions. These various parameters include the heading of the bomber when the bomb was released, the epicenters of the explosions, the bomb yields, and the tilt of the bombs at time of explosion. The epicenter of a bomb is the explosion point in air that is specified in terms of a burst height and a hypocenter (or the point on the ground directly below the epicenter of the explosion). The current reassessment refines the energy yield and burst height for the Hiroshima bomb, as well as the locations of the Hiroshima and Nagasaki hypocenters on the modern city maps used in the analysis of the activation data for neutrons and TLD data for gamma rays. (J.P.N.)

  7. Quadratic residues and non-residues selected topics

    CERN Document Server

    Wright, Steve

    2016-01-01

    This book offers an account of the classical theory of quadratic residues and non-residues with the goal of using that theory as a lens through which to view the development of some of the fundamental methods employed in modern elementary, algebraic, and analytic number theory. The first three chapters present some basic facts and the history of quadratic residues and non-residues and discuss various proofs of the Law of Quadratic Reciprosity in depth, with an emphasis on the six proofs that Gauss published. The remaining seven chapters explore some interesting applications of the Law of Quadratic Reciprocity, prove some results concerning the distribution and arithmetic structure of quadratic residues and non-residues, provide a detailed proof of Dirichlet’s Class-Number Formula, and discuss the question of whether quadratic residues are randomly distributed. The text is a valuable resource for graduate and advanced undergraduate students as well as for mathematicians interested in number theory.

  8. On the residual stress modeling of shot-peened AISI 4340 steel: finite element and response surface methods

    Science.gov (United States)

    Asgari, Ali; Dehestani, Pouya; Poruraminaie, Iman

    2018-02-01

    Shot peening is a well-known process in applying the residual stress on the surface of industrial parts. The induced residual stress improves fatigue life. In this study, the effects of shot peening parameters such as shot diameter, shot speed, friction coefficient, and the number of impacts on the applied residual stress will be evaluated. To assess these parameters effect, firstly the shot peening process has been simulated by finite element method. Then, effects of the process parameters on the residual stress have been evaluated by response surface method as a statistical approach. Finally, a strong model is presented to predict the maximum residual stress induced by shot peening process in AISI 4340 steel. Also, the optimum parameters for the maximum residual stress are achieved. The results indicate that effect of shot diameter on the induced residual stress is increased by increasing the shot speed. Also, enhancing the friction coefficient magnitude always cannot lead to increase in the residual stress.

  9. Sharing Residual Liability

    DEFF Research Database (Denmark)

    Carbonara, Emanuela; Guerra, Alice; Parisi, Francesco

    2016-01-01

    Economic models of tort law evaluate the efficiency of liability rules in terms of care and activity levels. A liability regime is optimal when it creates incentives to maximize the value of risky activities net of accident and precaution costs. The allocation of primary and residual liability...... the virtues and limits of loss-sharing rules in generating optimal (second-best) incentives and allocations of risk. We find that loss sharing may be optimal in the presence of countervailing policy objectives, homogeneous risk avoiders, and subadditive risk, which potentially offers a valuable tool...

  10. Role of residues in the adenosine binding site of NAD of the Ascaris suum malic enzyme.

    Science.gov (United States)

    Aktas, Deniz F; Cook, Paul F

    2008-12-01

    Ascaris suum mitochondrial malic enzyme catalyzes the divalent metal ion dependent conversion of l-malate to pyruvate and CO(2), with concomitant reduction of NAD(P) to NAD(P)H. In this study, some of the residues that form the adenosine binding site of NAD were mutated to determine their role in binding of the cofactor and/or catalysis. D361, which is completely conserved among species, is located in the dinucleotide-binding Rossmann fold and makes a salt bridge with R370, which is also highly conserved. D361 was mutated to E, A and N. R370 was mutated to K and A. D361E and A mutant enzymes were inactive, likely a result of the increase in the volume in the case of the D361E mutant enzyme that caused clashes with the surrounding residues, and loss of the ionic interaction between D361 and R370, for D361A. Although the K(m) for the substrates and isotope effect values did not show significant changes for the D361N mutant enzyme, V/E(t) decreased by 1400-fold. Data suggested the nonproductive binding of the cofactor, giving a low fraction of active enzyme. The R370K mutant enzyme did not show any significant changes in the kinetic parameters, while the R370A mutant enzyme gave a slight change in V/E(t), contrary to expectations. Overall, results suggest that the salt bridge between D361 and R370 is important for maintaining the productive conformation of the NAD binding site. Mutation of residues involved leads to nonproductive binding of NAD. The interaction stabilizes one of the Rossmann fold loops that NAD binds. Mutation of H377 to lysine, which is conserved in NADP-specific malic enzymes and proposed to be a cofactor specificity determinant, did not cause a shift in cofactor specificity of the Ascaris malic enzyme from NAD to NADP. However, it is confirmed that this residue is an important second layer residue that affects the packing of the first layer residues that directly interact with the cofactor.

  11. An Additive-Multiplicative Restricted Mean Residual Life Model

    DEFF Research Database (Denmark)

    Mansourvar, Zahra; Martinussen, Torben; Scheike, Thomas H.

    2016-01-01

    The mean residual life measures the expected remaining life of a subject who has survived up to a particular time. When survival time distribution is highly skewed or heavy tailed, the restricted mean residual life must be considered. In this paper, we propose an additive-multiplicative restricted...... mean residual life model to study the association between the restricted mean residual life function and potential regression covariates in the presence of right censoring. This model extends the proportional mean residual life model using an additive model as its covariate dependent baseline....... For the suggested model, some covariate effects are allowed to be time-varying. To estimate the model parameters, martingale estimating equations are developed, and the large sample properties of the resulting estimators are established. In addition, to assess the adequacy of the model, we investigate a goodness...

  12. Bioenergy from sisal residues

    Energy Technology Data Exchange (ETDEWEB)

    Jungersen, G. [Dansk Teknologisk Inst. (Denmark); Kivaisi, A.; Rubindamayugi, M. [Univ. of Dar es Salaam (Tanzania, United Republic of)

    1998-05-01

    The main objectives of this report are: To analyse the bioenergy potential of the Tanzanian agro-industries, with special emphasis on the Sisal industry, the largest producer of agro-industrial residues in Tanzania; and to upgrade the human capacity and research potential of the Applied Microbiology Unit at the University of Dar es Salaam, in order to ensure a scientific and technological support for future operation and implementation of biogas facilities and anaerobic water treatment systems. The experimental work on sisal residues contains the following issues: Optimal reactor set-up and performance; Pre-treatment methods for treatment of fibre fraction in order to increase the methane yield; Evaluation of the requirement for nutrient addition; Evaluation of the potential for bioethanol production from sisal bulbs. The processing of sisal leaves into dry fibres (decortication) has traditionally been done by the wet processing method, which consumes considerable quantities of water and produces large quantities of waste water. The Tanzania Sisal Authority (TSA) is now developing a dry decortication method, which consumes less water and produces a waste product with 12-15% TS, which is feasible for treatment in CSTR systems (Continously Stirred Tank Reactors). (EG)

  13. Identification of Catalytic Residues Using a Novel Feature that Integrates the Microenvironment and Geometrical Location Properties of Residues

    Science.gov (United States)

    Han, Lei; Zhang, Yong-Jun; Song, Jiangning; Liu, Ming S.; Zhang, Ziding

    2012-01-01

    Enzymes play a fundamental role in almost all biological processes and identification of catalytic residues is a crucial step for deciphering the biological functions and understanding the underlying catalytic mechanisms. In this work, we developed a novel structural feature called MEDscore to identify catalytic residues, which integrated the microenvironment (ME) and geometrical properties of amino acid residues. Firstly, we converted a residue's ME into a series of spatially neighboring residue pairs, whose likelihood of being located in a catalytic ME was deduced from a benchmark enzyme dataset. We then calculated an ME-based score, termed as MEscore, by summing up the likelihood of all residue pairs. Secondly, we defined a parameter called Dscore to measure the relative distance of a residue to the center of the protein, provided that catalytic residues are typically located in the center of the protein structure. Finally, we defined the MEDscore feature based on an effective nonlinear integration of MEscore and Dscore. When evaluated on a well-prepared benchmark dataset using five-fold cross-validation tests, MEDscore achieved a robust performance in identifying catalytic residues with an AUC1.0 of 0.889. At a ≤10% false positive rate control, MEDscore correctly identified approximately 70% of the catalytic residues. Remarkably, MEDscore achieved a competitive performance compared with the residue conservation score (e.g. CONscore), the most informative singular feature predominantly employed to identify catalytic residues. To the best of our knowledge, MEDscore is the first singular structural feature exhibiting such an advantage. More importantly, we found that MEDscore is complementary with CONscore and a significantly improved performance can be achieved by combining CONscore with MEDscore in a linear manner. As an implementation of this work, MEDscore has been made freely accessible at http://protein.cau.edu.cn/mepi/. PMID:22829945

  14. Forest residues in cattle feed

    Directory of Open Access Journals (Sweden)

    João Elzeário Castelo Branco Iapichini

    2012-12-01

    Full Text Available The ruminants are capable of converting low-quality food, when they are complementes with high-energy source. Through the use of regional agricultural residues is possible to conduct more economical production systems, since energetic foods have high cost in animal production. There is very abundant availability of residues in agroforestry activities worldwide, so that if a small fraction of them were used with appropriate technical criteria they could largely meet the needs of existing herds in the world and thus meet the demands of consumption of protein of animal origin. The Southwest Region of São Paulo State has large area occupied by reforestation and wide availability of non-timber forest residues, which may represent more concentrated energetic food for ruminant production. This experiment aimed to evaluate the acceptability of ground pine (20, 30 and 40%, replacing part of the energetic food (corn, present in the composition of the concentrate and was performed at the Experimental Station of Itapetininga - Forest Institute / SMA, in the dry season of 2011. It were used four crossbred steers, mean 18 months old, average body weight of 250 kg, housed in a paddock provided with water ad libitum and covered troughs for supplementation with the experimental diet. The adjustment period of the animals was of 07 days and the measurement of the levels of consumption, physiological changes, acceptability and physiological parameters were observed during the following 25 days. The concentrate supplement was formulated based on corn (76.2%, Soybean Meal (20%, urea (2%, Ammonium sulfate (0.4%, calcite (1.4%, Mineral Core (1% and finely ground Pine Cone, replacing corn. In preparing food, the formulas were prepared to make them isoproteic/energetic, containing the following nutrient levels: 22% Crude Protein (CP and 79% of Total Nutrients (TDN. The animals received the supplement in three steps for each level of cone replaced, being offered in the

  15. Free flight in parameter space

    DEFF Research Database (Denmark)

    Dahlstedt, Palle; Nilsson, Per Anders

    2008-01-01

    The well-known difficulty of controlling many synthesis parameters in performance, for exploration and expression, is addressed. Inspired by interactive evolution, random vectors in parameter space are assigned to an array of pressure sensitive pads. Vectors are scaled with pressure and added...

  16. ACTIVATION PARAMETERS AND EXCESS THERMODYANAMIC ...

    African Journals Online (AJOL)

    Applying these data, viscosity-B-coefficients, activation parameters (Δμ10≠) and (Δμ20≠) and excess thermodynamic functions, viz., excess molar volume (VE), excess viscosity, ηE and excess molar free energy of activation of flow, (GE) were calculated. The value of interaction parameter, d, of Grunberg and Nissan ...

  17. Semiparametric regression for restricted mean residual life under right censoring

    DEFF Research Database (Denmark)

    Mansourvar, Zahra; Martinussen, Torben; Scheike, Thomas H.

    2015-01-01

    A mean residual life function (MRLF) is the remaining life expectancy of a subject who has survived to a certain time point. In the presence of covariates, regression models are needed to study the association between the MRLFs and covariates. If the survival time tends to be too long or the tail...... is not observed, the restricted mean residual life must be considered. In this paper, we propose the proportional restricted mean residual life model for fitting survival data under right censoring. For inference on the model parameters, martingale estimating equations are developed, and the asymptotic properties...

  18. Physical properties of the binary systems methylcyclopentane with ketones (acetone, butanone and 2-pentanone) at T = (293.15, 298.15, and 303.15) K. New UNIFAC-VISCO interaction parameters

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez, B. [Department of Chemical Engineering, University of Vigo, Lagoas-Marconende, s/n Apartado 874, 36200 Vigo (Spain); Dominguez, A. [Department of Chemical Engineering, University of Vigo, Lagoas-Marconende, s/n Apartado 874, 36200 Vigo (Spain); Tojo, J. [Department of Chemical Engineering, University of Vigo, Lagoas-Marconende, s/n Apartado 874, 36200 Vigo (Spain)]. E-mail: jtojo@uvigo.es

    2006-06-15

    In this work, the physical properties, dynamic viscosities, densities, and speed of sound have been measured over the whole composition range and atmospheric pressure for the binary mixtures (methylcyclopentane with acetone, butanone, and 2-pentanone) at several temperatures T = (293.15, 298.15, and 303.15) K along with the properties of the pure components. Excess molar volumes, isentropic compressibility, deviations in isentropic compressibility and viscosity deviation for the binary systems at the above-mentioned temperatures were calculated and fitted to the Redlich-Kister equation to determine the fitting parameters and the root-mean-square deviations. The UNIQUAC equation was used to correlate the experimental viscosity data. The UNIFAC-VISCO method and ASOG-VISCO method, based on contribution groups, were used to predict the dynamic viscosities of the binary mixtures. The interaction parameters of cycloalkanes with ketones (CH{sub cy}/CO) have been determined for their application in the predictive UNIFAC-VISCO method.

  19. Dynamic viscosities of binary mixtures of cycloalkanes with primary alcohols at T = (293.15, 298.15, and 303.15) K: New UNIFAC-VISCO interaction parameters

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez, Begona [Chemical Engineering Department, Vigo University, 36200 Vigo (Spain); Calvar, Noelia [Chemical Engineering Department, Vigo University, 36200 Vigo (Spain); Dominguez, Angeles [Chemical Engineering Department, Vigo University, 36200 Vigo (Spain)]. E-mail: admguez@uvigo.es; Tojo, Jose [Chemical Engineering Department, Vigo University, 36200 Vigo (Spain)

    2007-02-15

    In this work, dynamic viscosities, densities, and speed of sound have been measured over the whole composition range and 0.1 MPa for the binary mixtures (cyclopentane and cyclohexane with ethanol, 1-propanol, and 1-butanol) at several temperatures (293.15, 298.15, 303.15) K along with the properties of the pure components. Excess molar volumes, molar isentropic compression, excess molar isentropic compression, and excess free energy of activation for the binary systems at the above mentioned temperatures, were calculated and fitted to the Redlich-Kister equation to determine the fitting parameters and the root-mean-square deviations. The UNIQUAC equation was used to correlate the experimental viscosity data. The UNIFAC-VISCO method and ASOG-VISCO method, based on contribution groups, were used to predict the dynamic viscosities of the binary mixtures. The interaction parameters of cycloalkanes with primary alcohol (CH{sub cy}/-OH) have been determined for their application in the predictive UNIFAC-VISCO method.

  20. Supergranular Parameters

    Science.gov (United States)

    Udayashankar, Paniveni

    2016-07-01

    I study the complexity of supergranular cells using intensity patterns from Kodaikanal solar observatory. The chaotic and turbulent aspect of the solar supergranulation can be studied by examining the interrelationships amongst the parameters characterizing supergranular cells namely size, horizontal flow field, lifetime and physical dimensions of the cells and the fractal dimension deduced from the size data. The findings are supportive of Kolmogorov's theory of turbulence. The Data consists of visually identified supergranular cells, from which a fractal dimension 'D' for supergranulation is obtained according to the relation P α AD/2 where 'A' is the area and 'P' is the perimeter of the supergranular cells. I find a fractal dimension close to about 1.3 which is consistent with that for isobars and suggests a possible turbulent origin. The cell circularity shows a dependence on the perimeter with a peak around (1.1-1.2) x 105 m. The findings are supportive of Kolmogorov's theory of turbulence.

  1. Phenomenological analysis of the Δ resonance parameters

    International Nuclear Information System (INIS)

    Vasan, S.S.

    1976-01-01

    The positions of the poles in the complex energy plane corresponding to the resonances Δ ++ and Δ 0 , and the associated residues, are determined by fitting the π + p and π - p hadronic phase shift data from the CARTER 73 analysis. As an illustration of the use of the Δ pole parameters, their application to the problem of parametrizing the residue function associated with the Δ Regge trajectory is considered. The input for the parametrization is given partly by the pole position and the residue of the Δ(1950), the first recurrence of the Δ(1236). These pole parameters are deduced from fits to the F 37 partial wave data from the AYED 74 phase shift analysis. Together with the Δ(1236) pole parameters, these provide information on the behavior of the Regge residue in the resonance region u less than 0 (in the context of s-channel backward scattering being dominated by u-channel Regge exchanges). Attempts to incorporate this information in parametrizations of the residue by means of real and complex functions lead to the conclusion that both the residue and the trajectory are better represented in the resonance region by complex parametrizations

  2. Residue preference mapping of ligand fragments in the Protein Data Bank.

    Science.gov (United States)

    Wang, Lirong; Xie, Zhaojun; Wipf, Peter; Xie, Xiang-Qun

    2011-04-25

    The interaction between small molecules and proteins is one of the major concerns for structure-based drug design because the principles of protein-ligand interactions and molecular recognition are not thoroughly understood. Fortunately, the analysis of protein-ligand complexes in the Protein Data Bank (PDB) enables unprecedented possibilities for new insights. Herein, we applied molecule-fragmentation algorithms to split the ligands extracted from PDB crystal structures into small fragments. Subsequently, we have developed a ligand fragment and residue preference mapping (LigFrag-RPM) algorithm to map the profiles of the interactions between these fragments and the 20 proteinogenic amino acid residues. A total of 4032 fragments were generated from 71 798 PDB ligands by a ring cleavage (RC) algorithm. Among these ligand fragments, 315 unique fragments were characterized with the corresponding fragment-residue interaction profiles by counting residues close to these fragments. The interaction profiles revealed that these fragments have specific preferences for certain types of residues. The applications of these interaction profiles were also explored and evaluated in case studies, showing great potential for the study of protein-ligand interactions and drug design. Our studies demonstrated that the fragment-residue interaction profiles generated from the PDB ligand fragments can be used to detect whether these fragments are in their favorable or unfavorable environments. The algorithm for a ligand fragment and residue preference mapping (LigFrag-RPM) developed here also has the potential to guide lead chemistry modifications as well as binding residues predictions.

  3. Surface Finish and Residual Stresses Induced by Orthogonal Dry Machining of AA7075-T651

    Directory of Open Access Journals (Sweden)

    Walid Jomaa

    2014-02-01

    Full Text Available The surface finish was extensively studied in usual machining processes (turning, milling, and drilling. For these processes, the surface finish is strongly influenced by the cutting feed and the tool nose radius. However, a basic understanding of tool/surface finish interaction and residual stress generation has been lacking. This paper aims to investigate the surface finish and residual stresses under the orthogonal cutting since it can provide this information by avoiding the effect of the tool nose radius. The orthogonal machining of AA7075-T651 alloy through a series of cutting experiments was performed under dry conditions. Surface finish was studied using height and amplitude distribution roughness parameters. SEM and EDS were used to analyze surface damage and built-up edge (BUE formation. An analysis of the surface topography showed that the surface roughness was sensitive to changes in cutting parameters. It was found that the formation of BUE and the interaction between the tool edge and the iron-rich intermetallic particles play a determinant role in controlling the surface finish during dry orthogonal machining of the AA7075-T651 alloy. Hoop stress was predominantly compressive on the surface and tended to be tensile with increased cutting speed. The reverse occurred for the surface axial stress. The smaller the cutting feed, the greater is the effect of cutting speed on both axial and hoop stresses. By controlling the cutting speed and feed, it is possible to generate a benchmark residual stress state and good surface finish using dry machining.

  4. Marine Tar Residues: a Review

    OpenAIRE

    Warnock, April M.; Hagen, Scott C.; Passeri, Davina L.

    2015-01-01

    Marine tar residues originate from natural and anthropogenic oil releases into the ocean environment and are formed after liquid petroleum is transformed by weathering, sedimentation, and other processes. Tar balls, tar mats, and tar patties are common examples of marine tar residues and can range in size from millimeters in diameter (tar balls) to several meters in length and width (tar mats). These residues can remain in the ocean environment indefinitely, decomposing or becoming buried in ...

  5. Physiological parameters

    International Nuclear Information System (INIS)

    Natera, E.S.

    1998-01-01

    The physiological characteristics of man depend on the intake, metabolism and excretion of stable elements from food, water, and air. The physiological behavior of natural radionuclides and radionuclides from nuclear weapons testing and from the utilization of nuclear energy is believed to follow the pattern of stable elements. Hence information on the normal physiological processes occurring in the human body plays an important role in the assessment of the radiation dose received by man. Two important physiological parameters needed for internal dose determination are the pulmonary function and the water balance. In the Coordinated Research Programme on the characterization of Asian population, five participants submitted data on these physiological characteristics - China, India, Japan, Philippines and Viet Nam. During the CRP, data on other pertinent characteristics such as physical and dietary were simultaneously being collected. Hence, the information on the physiological characteristics alone, coming from the five participants were not complete and are probably not sufficient to establish standard values for the Reference Asian Man. Nonetheless, the data collected is a valuable contribution to this research programme

  6. 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.

  7. Study of some nitrogen transformation reactions as influenced by the agrochemicals in some soils of north Iraq by using labelled compounds. Part of a coordinated programme on isotopic-tracer-aided studies of agrochemical residue - soil biota interactions

    International Nuclear Information System (INIS)

    Shali, K.G.

    1982-06-01

    The effect is described of different pesticides when applied to autoclaved soils to which the mixture of nitrifier, ammonifier, and azotobacter were added and incubated for 90 days. The results are given of the respiration parameter of 14 CO 2 evolved at 30 and 60 days of incubation from soil samples obtained at depths of 15, 30, 45, and 60 cm. Graphs show the survival of mixture of nitrifier, ammonifier, and azotobacter treated with pesticides Benlate, Sevin, and Diptrex at three dose levels. Total bacterial counts as estimated by 14 C-glucose oxidation are also shown

  8. A Theoretical Study on Quantitative Prediction and Evaluation of Thermal Residual Stresses in Metal Matrix Composite (Case 1 : Two-Dimensional In-Plane Fiber Distribution)

    International Nuclear Information System (INIS)

    Lee, Joon Hyun; Son, Bong Jin

    1997-01-01

    Although discontinuously reinforced metal matrix composite(MMC) is one of the most promising materials for applications of aerospace, automotive industries, the thermal residual stresses developed in the MMC due to the mismatch in coefficients of thermal expansion between the matrix and the fiber under a temperature change has been pointed out as one of the serious problem in practical applications. There are very limited nondestructive techniques to measure the residual stress of composite materials. However, many difficulties have been reported in their applications. Therefore it is important to establish analytical model to evaluate the thermal residual stress of MMC for practical engineering application. In this study, an elastic model is developed to predict the average thermal residual stresses in the matrix and fiber of a misoriented short fiber composite. The thermal residual stresses are induced by the mismatch in the coefficient of the thermal expansion of the matrix and fiber when the composite is subjected to a uniform temperature change. The model considers two-dimensional in-plane fiber misorientation. The analytical formulation of the model is based on Eshelby's equivalent inclusion method and is unique in that it is able to account for interactions among fibers. This model is more general than past models to investigate the effect of parameters which might influence thermal residual stress in composites. The present model is to investigate the effects of fiber volume fraction, distribution type, distribution cut-off angle, and aspect ratio on thermal residual stress for in-plane fiber misorientation. Fiber volume fraction, aspect ratio, and distribution cut-off angle are shown to have more significant effects on the magnitude of the thermal residual stresses than fiber distribution type for in-plane misorientation

  9. Prediction of amino acid residues protected from hydrogen-deuterium exchange in a protein chain.

    Science.gov (United States)

    Dovidchenko, N V; Lobanov, M Yu; Garbuzynskiy, S O; Galzitskaya, O V

    2009-08-01

    We have investigated the possibility to predict protection of amino acid residues from hydrogen-deuterium exchange. A database containing experimental hydrogen-deuterium exchange data for 14 proteins for which these data are known has been compiled. Different structural parameters related to flexibility of amino acid residues and their amide groups have been analyzed to answer the question whether these parameters can be used for predicting the protection of amino acid residues from hydrogen-deuterium exchange. A method for prediction of protection of amino acid residues, which uses only the amino acid sequence of a protein, has been elaborated.

  10. Landfilling of waste incineration residues

    DEFF Research Database (Denmark)

    Christensen, Thomas Højlund; Astrup, Thomas; Cai, Zuansi

    2002-01-01

    Residues from waste incineration are bottom ashes and air-pollution-control (APC) residues including fly ashes. The leaching of heavy metals and salts from the ashes is substantial and a wide spectrum of leaching tests and corresponding criteria have been introduced to regulate the landfilling...

  11. Identification of a direct interaction between residue 19 in the helical portion of calcitonin and the amino-terminal domain of the calcitonin receptor from photoaffinity cross-linking and mutational studies

    International Nuclear Information System (INIS)

    Pham, V.; Wade, J.; McDowall, S.G.; Quiza, M.; Sexton, P.M.

    2001-01-01

    Full text: Calcitonins (CTs) are 32 amino acid hormones with both peripheral and central actions mediated via specific cell surface receptors, which belong to the superfamily of class II G-protein coupled receptors. Chimeric receptor and mutational data suggested that the helical portion (residues 8-22) of salmon CT (sCT) is important for high affinity binding to the amino-terminal extracellular domain of the human CT receptor (hCTR). In this study, we have developed photoactive sCT analogues [Arg 11, 18 , Bpa 19 ]sCT and [Arg 11 , 18 , Bpa 19 ]sCT(8-32) that incorporate a photolabile Bpa (p-benzoyl-L-phenylalanine) into position 19 of the helical domain of the ligand and used this to determine a specific receptor fragment proximate to it. These analogues saturably bound to the CTR with high affinity (IC 50 = 3 nM) which was similar to that of the natural sCT and its antagonist (IC 50 = 2 nM and 20 nM, respectively). Upon photolysis, radioiodinated 125 I-[Arg 11, 18 , Bpa 19 ]sCT and 125 I-[Arg 11,18 , Bpa 19 ]sCT(8-32) efficiently and specifically cross-linked to hCTR stably expressed in baby hamster kidney cells (Hollexl cells, ∼ 800,000 receptors per cell), generating a single radiolabeled band of ∼ 72-kDa on SDS/PAGE autoradiography. To identify the 'contact domain' within CTR involved in binding of 125 I-[Arg1 1 , 18 , Bpa 19 ]sCT and 125 I-[Arg 11, 18 , Bpa 19 ]sCT(8-32), the radiolabeled band containing the ligand-receptor conjugate was subjected to chemical and enzymatic cleavage. Cyanogen bromide cleavage of the native receptor yielded a radiolabeled fragment of apparent Mr ∼ 31-kDa that shifted to Mr ∼ 14 kDa after deglycosylation. This receptor domain corresponded to amino acids 59-134 of the hCTR, located at the amino-terminal extracellular region of the receptor. These results provide the first direct demonstration of a contact domain between calcitonin and its receptor, and will contribute towards the modelling of CT-CTR interface. Copyright

  12. 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.

  13. Automatic prediction of catalytic residues by modeling residue structural neighborhood

    Directory of Open Access Journals (Sweden)

    Passerini Andrea

    2010-03-01

    Full Text Available Abstract Background Prediction of catalytic residues is a major step in characterizing the function of enzymes. In its simpler formulation, the problem can be cast into a binary classification task at the residue level, by predicting whether the residue is directly involved in the catalytic process. The task is quite hard also when structural information is available, due to the rather wide range of roles a functional residue can play and to the large imbalance between the number of catalytic and non-catalytic residues. Results We developed an effective representation of structural information by modeling spherical regions around candidate residues, and extracting statistics on the properties of their content such as physico-chemical properties, atomic density, flexibility, presence of water molecules. We trained an SVM classifier combining our features with sequence-based information and previously developed 3D features, and compared its performance with the most recent state-of-the-art approaches on different benchmark datasets. We further analyzed the discriminant power of the information provided by the presence of heterogens in the residue neighborhood. Conclusions Our structure-based method achieves consistent improvements on all tested datasets over both sequence-based and structure-based state-of-the-art approaches. Structural neighborhood information is shown to be responsible for such results, and predicting the presence of nearby heterogens seems to be a promising direction for further improvements.

  14. Evaluation Of Residual Stresses In Inner Ring Of The Bearings

    Science.gov (United States)

    Malotová, Šárka; Hemžský, Pavel; Pitela, David; Nicielnik, Henryk; Šoková, Dagmar; Kyncl, Ladislav; Mrázik, Jozef

    2015-12-01

    Residual stresses are undesirable and it should not be underestimated. They occur in many components and it is necessary to identify and try to avoid them. For detection the Residual stresses, there are many methods, but not all are suitable, because they can completely destroy of the components. The article deals with the evaluation of Residual stresses in the inner rings of Bearings, which are made from steel 100Cr6 (ČSN 14 109.4. The surfaces were turning at different cutting parameters and subsequently are evaluated Residual stresses. The stresses have been evaluated by non - destructive method X - Ray. The experiment was realized in cooperation Faculty of Mechanical Engineering VSB - TU Ostrava and Faculty of Mechanical Engineering of ZU Zilina - machining in the laboratories of ZU Žilina, Slovak Republic.

  15. Neutron diffraction studies of laser welding residual stresses

    Science.gov (United States)

    Petrov, Peter I.; Bokuchava, Gizo D.; Papushkin, Igor V.; Genchev, Gancho; Doynov, Nikolay; Michailov, Vesselin G.; Ormanova, Maria A.

    2016-01-01

    The residual stress and microstrain distribution induced by laser beam welding of the low-alloyed C45 steel plate was investigated using high-resolution time-of-flight (TOF) neutron diffraction. The neutron diffraction experiments were performed on FSD diffractometer at the IBR-2 pulsed reactor in FLNP JINR (Dubna, Russia). The experiments have shown that the residual stress distribution across weld seam exhibit typical alternating sign character as it was observed in our previous studies. The residual stress level is varying in the range from -60 MPa to 450 MPa. At the same time, the microstrain level exhibits sharp maxima at weld seam position with maximal level of 4.8·10-3. The obtained experimental results are in good agreement with FEM calculations according to the STAAZ model. The provided numerical model validated with measured data enables to study the influence of different conditions and process parameters on the development of residual welding stresses.

  16. Noise and noise disturbances from wind power plants - Tests with interactive control of sound parameters for more comfortable and less perceptible sounds; Buller och bullerstoerningar fraan vindkraftverk - Foersoek med interaktiv styrning av ljudparametrar foer behagligare och mindre maerkbara ljud

    Energy Technology Data Exchange (ETDEWEB)

    Persson-Waye, K.; Oehrstroem, E.; Bjoerkman, M.; Agge, A. [Goeteborg Univ. (Sweden). Dept. of Environmental Medicine

    2001-12-01

    In experimental pilot studies, a methodology has been worked out for interactively varying sound parameters in wind power plants. In the tests, 24 persons varied the center frequency of different band-widths, the frequency of a sinus-tone and the amplitude-modulation of a sinus-tone in order to create as comfortable a sound as possible. The variations build on the noise from the two wind turbines Bonus and Wind World. The variations were performed with a constant dba level. The results showed that the majority preferred a low-frequency tone (94 Hz and 115 Hz for Wind World and Bonus, respectively). The mean of the most comfortable amplitude-modulation varied between 18 and 22 Hz, depending on the ground frequency. The mean of the center-frequency for the different band-widths varied from 785 to 1104 Hz. In order to study the influence of the wind velocity on the acoustic character of the noise, a long-time measurement program has been performed. A remotely controlled system has been developed, where wind velocity, wind direction, temperature and humidity are registered simultaneously with the noise. Long-time registrations have been performed for four different wing turbines.

  17. 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)

  18. Economic Modeling of Residual Generation for the Lingayen Gulf Watershed

    Directory of Open Access Journals (Sweden)

    Douglas McGlone

    2000-12-01

    Full Text Available The Philippines is one of four countries involved in the Southeast Asian core project of LOICZ (Land Ocean Interactions in the Coastal Zone which has among its general goals the determination of how changes in human activities affect the fluxes of materials between land, sea, and atmosphere through the coastal zone. The economic component of the Philippine project addresses the question: “How does a change in economic activity affect coastal waters?” Of particular concern is the introduction of anthropogenically-derived residuals (N, P, C, SS into coastal waters. A regional input-output (IO model for Region 1 of the Philippines has been developed to estimate how projected changes in economic activity may affect residual flows into Lingayen Gulf. A residual coefficient matrix, derived from information obtained with a rapid assessment model (RA of residual generation in the Lingayen Gulf watershed, has been incorporated into the IO model. Such a model allows for analysis of various economic scenarios for the region, with projections of residual generation as the output. The resulting changes in residual flows may then serve as inputs to biogeochemical models of Lingayen Gulf. From this process, the impact of various economic scenarios on the water quality of Lingayen Gulf may be ascertained.This paper discusses and compares the RA and IO models of residual generation for the Lingayen Gulf watershed and provides examples of the scenario analysis process.

  19. RESIDUAL RISK ASSESSMENT: ETHYLENE OXIDE ...

    Science.gov (United States)

    This document describes the residual risk assessment for the Ethylene Oxide Commercial Sterilization source category. For stationary sources, section 112 (f) of the Clean Air Act requires EPA to assess risks to human health and the environment following implementation of technology-based control standards. If these technology-based control standards do not provide an ample margin of safety, then EPA is required to promulgate addtional standards. This document describes the methodology and results of the residual risk assessment performed for the Ethylene Oxide Commercial Sterilization source category. The results of this analyiss will assist EPA in determining whether a residual risk rule for this source category is appropriate.

  20. 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.

  1. Residual stress analysis: a review

    International Nuclear Information System (INIS)

    Finlayson, T.R.

    1983-01-01

    The techniques which are or could be employed to measure residual stresses are outlined. They include X-ray and neutron diffraction. Comments are made on the reliability and accuracy to be expected from particular techniques

  2. OECD Maximum Residue Limit Calculator

    Science.gov (United States)

    With the goal of harmonizing the calculation of maximum residue limits (MRLs) across the Organisation for Economic Cooperation and Development, the OECD has developed an MRL Calculator. View the calculator.

  3. Microclimate effects of crop residues on biological processes

    Science.gov (United States)

    Hatfield, J. L.; Prueger, J. H.

    1996-03-01

    plant to maintain transpiration rates at optimal levels during the early vegetative growth period. The biological implications of crop residue on the soil surface can be more positive than negative and increasing our understanding of the physical environment and biological system interactions will lead to improved resource management.

  4. Vesícula residual

    Directory of Open Access Journals (Sweden)

    Júlio C. U. Coelho

    Full Text Available Our objective is to report three patients with recurrent severe upper abdominal pain secondary to residual gallbladder. All patients had been subjected to cholecystectomy from 1 to 20 years before. The diagnosis was established after several episodes of severe upper abdominal pain by imaging exams: ultrasonography, tomography, or endoscopic retrograde cholangiography. Removal of the residual gallbladder led to complete resolution of symptoms. Partial removal of the gallbladder is a very rare cause of postcholecystectomy symptoms.

  5. Experimental investigation of residual stress distribution during turning of weak stiffness revolving parts

    Science.gov (United States)

    Jiao, Sicheng; Zhang, Chengyan; Liu, Guancheng; Lu, Jiping; Tang, Shuiyuan

    2017-08-01

    A series of turning experiments have been carried out to study the effect of different cutting speed, feed rate and pre-tightening torque on residual stress distribution during turning of weak stiffness revolving parts. Surface residual stress and the peak residual compressive stress are selected from the typical residual stress distribution profile. The residual stress by turning was measured by X-ray diffraction method. In order to get the distribution of residual stress along depth direction, the specimens need to be etched layer by layer. From this investigation, it can be concluded that it is practicable to control the distribution of residual stress by changing the pre-tightening torque and cutting parameters during turning of weak stiffness revolving parts.

  6. Finding coevolving amino acid residues using row and column weighting of mutual information and multi-dimensional amino acid representation

    DEFF Research Database (Denmark)

    Oliveira, Rodrigo Gouveia; Pedersen, Anders Gorm

    2007-01-01

    ABSTRACT: BACKGROUND: Some amino acid residues functionally interact with each other. This interaction will result in an evolutionary co-variation between these residues - coevolution. Our goal is to find these coevolving residues. RESULTS: We present six new methods for detecting coevolving...... residues. Among other things, we suggest measures that are variants of Mutual Information, and measures that use a multidimensional representation of each residue in order to capture the physico-chemical similarities between amino acids. We created a benchmarking system, in silico, able to evaluate...

  7. Marine Tar Residues: a Review.

    Science.gov (United States)

    Warnock, April M; Hagen, Scott C; Passeri, Davina L

    Marine tar residues originate from natural and anthropogenic oil releases into the ocean environment and are formed after liquid petroleum is transformed by weathering, sedimentation, and other processes. Tar balls, tar mats, and tar patties are common examples of marine tar residues and can range in size from millimeters in diameter (tar balls) to several meters in length and width (tar mats). These residues can remain in the ocean environment indefinitely, decomposing or becoming buried in the sea floor. However, in many cases, they are transported ashore via currents and waves where they pose a concern to coastal recreation activities, the seafood industry and may have negative effects on wildlife. This review summarizes the current state of knowledge on marine tar residue formation, transport, degradation, and distribution. Methods of detection and removal of marine tar residues and their possible ecological effects are discussed, in addition to topics of marine tar research that warrant further investigation. Emphasis is placed on benthic tar residues, with a focus on the remnants of the Deepwater Horizon oil spill in particular, which are still affecting the northern Gulf of Mexico shores years after the leaking submarine well was capped.

  8. 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.

  9. Micro-Environmental Signature of The Interactions between Druggable Target Protein, Dipeptidyl Peptidase-IV, and Anti-Diabetic Drugs.

    Science.gov (United States)

    Chakraborty, Chiranjib; Mallick, Bidyut; Sharma, Ashish Ranjan; Sharma, Garima; Jagga, Supriya; Doss, C George Priya; Nam, Ju-Suk; Lee, Sang-Soo

    2017-01-01

    Druggability of a target protein depends on the interacting micro-environment between the target protein and drugs. Therefore, a precise knowledge of the interacting micro-environment between the target protein and drugs is requisite for drug discovery process. To understand such micro-environment, we performed in silico interaction analysis between a human target protein, Dipeptidyl Peptidase-IV (DPP-4), and three anti-diabetic drugs (saxagliptin, linagliptin and vildagliptin). During the theoretical and bioinformatics analysis of micro-environmental properties, we performed drug-likeness study, protein active site predictions, docking analysis and residual interactions with the protein-drug interface. Micro-environmental landscape properties were evaluated through various parameters such as binding energy, intermolecular energy, electrostatic energy, van der Waals'+H-bond+desolvo energy (E VHD ) and ligand efficiency (LE) using different in silico methods. For this study, we have used several servers and software, such as Molsoft prediction server, CASTp server, AutoDock software and LIGPLOT server. Through micro-environmental study, highest log P value was observed for linagliptin (1.07). Lowest binding energy was also observed for linagliptin with DPP-4 in the binding plot. We also identified the number of H-bonds and residues involved in the hydrophobic interactions between the DPP-4 and the anti-diabetic drugs. During interaction, two H-bonds and nine residues, two H-bonds and eleven residues as well as four H-bonds and nine residues were found between the saxagliptin, linagliptin as well as vildagliptin cases and DPP-4, respectively. Our in silico data obtained for drug-target interactions and micro-environmental signature demonstrates linagliptin as the most stable interacting drug among the tested anti-diabetic medicines.

  10. Evidence of the Participation of Remote Residues in the Catalytic Activity of Co-Type Nitrile Hydratase from Pseudomonas putida

    Energy Technology Data Exchange (ETDEWEB)

    Brodkin, Heather R.; Novak, Walter R.P.; Milne, Amy C.; D’Aquino, J. Alejandro; Karabacak, N.M.; Goldberg, Ilana G.; Agar, Jeffrey N.; Payne, Mark S.; Petsko, Gregory A.; Ondrechen, Mary Jo; Ringe, Dagmar (Brandeis); (E.I. DuPont); (NEU)

    2011-09-28

    Active sites may be regarded as layers of residues, whereby the residues that interact directly with substrate also interact with residues in a second shell and these in turn interact with residues in a third shell. These residues in the second and third layers may have distinct roles in maintaining the essential chemical properties of the first-shell catalytic residues, particularly their spatial arrangement relative to the substrate binding pocket, and their electrostatic and dynamic properties. The extent to which these remote residues participate in catalysis and precisely how they affect first-shell residues remains unexplored. To improve our understanding of the roles of second- and third-shell residues in catalysis, we used THEMATICS to identify residues in the second and third shells of the Co-type nitrile hydratase from Pseudomonas putida (ppNHase) that may be important for catalysis. Five of these predicted residues, and three additional, conserved residues that were not predicted, have been conservatively mutated, and their effects have been studied both kinetically and structurally. The eight residues have no direct contact with the active site metal ion or bound substrate. These results demonstrate that three of the predicted second-shell residues ({alpha}-Asp164, {beta}-Glu56, and {beta}-His147) and one predicted third-shell residue ({beta}-His71) have significant effects on the catalytic efficiency of the enzyme. One of the predicted residues ({alpha}-Glu168) and the three residues not predicted ({alpha}-Arg170, {alpha}-Tyr171, and {beta}-Tyr215) do not have any significant effects on the catalytic efficiency of the enzyme.

  11. Bayesian Analysis Diagnostics: Diagnosing Predictive and Parameter Uncertainty for Hydrological Models

    Science.gov (United States)

    Thyer, Mark; Kavetski, Dmitri; Evin, Guillaume; Kuczera, George; Renard, Ben; McInerney, David

    2015-04-01

    All scientific and statistical analysis, particularly in natural sciences, is based on approximations and assumptions. For example, the calibration of hydrological models using approaches such as Nash-Sutcliffe efficiency and/or simple least squares (SLS) objective functions may appear to be 'assumption-free'. However, this is a naïve point of view, as SLS assumes that the model residuals (residuals=observed-predictions) are independent, homoscedastic and Gaussian. If these assumptions are poor, parameter inference and model predictions will be correspondingly poor. An essential step in model development is therefore to verify the assumptions and approximations made in the modeling process. Diagnostics play a key role in verifying modeling assumptions. An important advantage of the formal Bayesian approach is that the modeler is required to make the assumptions explicit. Specialized diagnostics can then be developed and applied to test and verify their assumptions. This paper presents a suite of statistical and modeling diagnostics that can be used by environmental modelers to test their modeling calibration assumptions and diagnose model deficiencies. Three major types of diagnostics are presented: Residual Diagnostics Residual diagnostics are used to test whether the assumptions of the residual error model within the likelihood function are compatible with the data. This includes testing for statistical independence, homoscedasticity, unbiasedness, Gaussianity and any distributional assumptions. Parameter Uncertainty and MCMC Diagnostics An important part of Bayesian analysis is assess parameter uncertainty. Markov Chain Monte Carlo (MCMC) methods are a powerful numerical tool for estimating these uncertainties. Diagnostics based on posterior parameter distributions can be used to assess parameter identifiability, interactions and correlations. This provides a very useful tool for detecting and remedying model deficiencies. In addition, numerical diagnostics are

  12. Setting Parameters for Biological Models With ANIMO

    NARCIS (Netherlands)

    Schivo, Stefano; Scholma, Jetse; Karperien, Hermanus Bernardus Johannes; Post, Janine Nicole; van de Pol, Jan Cornelis; Langerak, Romanus; André, Étienne; Frehse, Goran

    2014-01-01

    ANIMO (Analysis of Networks with Interactive MOdeling) is a software for modeling biological networks, such as e.g. signaling, metabolic or gene networks. An ANIMO model is essentially the sum of a network topology and a number of interaction parameters. The topology describes the interactions

  13. Fractal structure and predictive strategy of the daily extreme temperature residuals at Fabra Observatory (NE Spain, years 1917-2005)

    Science.gov (United States)

    Lana, X.; Burgueño, A.; Serra, C.; Martínez, M. D.

    2015-07-01

    A compilation of daily extreme temperatures recorded at the Fabra Observatory (Catalonia, NE Spain) since 1917 up to 2005 has permitted an exhaustive analysis of the fractal behaviour of the daily extreme temperature residuals, DTR, defined as the difference between the observed daily extreme temperature and the daily average value. The lacunarity characterises the lag distribution on the residual series for several thresholds. Hurst, H, and Hausdorff, Ha, exponents, together with the exponent β of the decaying power law, describing the evolution of power spectral density with frequency, permit to characterise the persistence, antipersistence or randomness of the residual series. The self-affine character of DTR series is verified, and additionally, they are simulated by means of fractional Gaussian noise, fGn. The reconstruction theorem leads to the quantification of the complexity (correlation dimension, μ*, and Kolmogorov entropy, κ) and predictive instability (Lyapunov exponents, λ, and Kaplan-Yorke dimension, D KY) of the residual series. All fractal parameters are computed for consecutive and independent segments of 5-year lengths. This strategy permits to obtain a high enough number of fractal parameter samples to estimate time trends, including their statistical significance. Comparisons are made between results of predictive algorithms based on fGn models and an autoregressive autoregressive integrated moving average (ARIMA) process, with the latter leading to slightly better results than the former. Several dynamic atmospheric mechanisms and local effects, such as local topography and vicinity to the Mediterranean coast, are proposed to explain the complex and instable predictability of DTR series. The memory of the physical system (Kolmogorov entropy) would be attributed to the interaction with the Mediterranean Sea.

  14. IAHR List of Sea Parameters

    DEFF Research Database (Denmark)

    Frigaard, Peter; Helm-Petersen, J; Klopman, G.

    1997-01-01

    A Working Group on multidirectional waves formed by the International Association for Hydraulic Research has proposed an update of the IAHR List of Sea State Parameters from 1986 in the part concerning directional. Especially wave structure interaction with reflection of the waves have been treated....

  15. 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

  16. Evaluation of Crops Sensitivity to Atrazine Soil Residual

    Directory of Open Access Journals (Sweden)

    E Izadi

    2012-02-01

    Full Text Available Abstract In order to study the sensitivity of 9 crops to atrazine soil residual, two separate experiments were conducted in field and greenhouse conditions. First experiment was conducted in a field with treated soil by atrazine based on split plot and the results evaluated in greenhouse conditions. Treatments in the field experiment included two organic manure application rates (0 and 50 t/ha as main plots and 2 atrazine application rates (2 and 4 kg/ha atrazine a.i. as sob plots. After corn harvesting soil was sampled at 0-15 cm surface layer in each plots in 15 points, after mixing the samples. Wheat, barley, sugar beet, pea, lens and colza planted in pots at greenhouse. Second experiment conducted in greenhouse conditions for evaluation of atrazine soil residual in completely randomized design. Treatments included atrazine soil residual concentrations (0, 0.2, 0.5, 1, 5, 10 and 15 mg/kg soil and crops included wheat, barley, sugar beet, pea, lens, rape, bean and tomato. Results showed that atrazine residue had no effect on crops growth in field experiment treated with atrazine. It seems that atrazine residue in filed soil is lower that its damage threshold for crops or maybe for its fast removal in field than in control conditions. But in bioassay experiment (greenhouse experiment crops response to atrazine residues were different. Results showed that onion and pea were most susceptible ant tolerant crops between studied species and based of ED50 parameter the other crops tolerance to total residue ranked as: pea< bean< lentil< sugar beet< tomato< barley< wheat< rape< onion. Keywords: Atrazine residue, Pea, Bean, Lentil, Sugar beet, Barley, Wheat, Rape, Tomato

  17. Liquefaction behaviors of bamboo residues in a glycerol-based solvent using microwave energy

    Science.gov (United States)

    Jiulong Xie; Chung-Yun Hse; Todd F. Shupe; Jinqiu Qi; Hui Pan

    2014-01-01

    Liquefaction of bamboo was performed in glycerol–methanol as co-solvent using microwave energy and was evaluated by characterizing the liquefied residues. High efficiency conversion of bamboo was achieved under mild reaction conditions. Liquefaction temperature and time interacted to affect the liquefaction reaction. Fourier transform infrared analyzes of the residues...

  18. Impact of sugarcane field residue and mill bagasse on seed germination

    Science.gov (United States)

    Research indicates that sugarcane field residue and sugarcane mill bagasse may be allelopathic. Allelopathy is the chemical interaction between plants, which may result in the inhibition of plant growth and development. Previous research in Louisiana indicated that sugarcane field residue may inhibi...

  19. Allelopathic impact of HoCP 96-540 field residue on seed germination

    Science.gov (United States)

    Research indicates that sugarcane field residue and sugarcane mill bagasse may be allelopathic. Allelopathy is the chemical interaction between plants, which may result in the inhibition of plant growth and development. Previous research in Louisiana indicated that sugarcane field residue may inhibi...

  20. Actinide recovery from pyrochemical residues

    International Nuclear Information System (INIS)

    Avens, L.R.; Clifton, D.G.; Vigil, A.R.

    1984-01-01

    A new process for recovery of plutonium and americium from pyrochemical waste has been demonstrated. It is based on chloride solution anion exchange at low acidity, which eliminates corrosive HCl fumes. Developmental experiments of the process flowsheet concentrated on molten salt extraction (MSE) residues and gave >95% plutonium and >90% americium recovery. The recovered plutonium contained 6 = from high chloride-low acid solution. Americium and other metals are washed from the ion exchange column with 1N HNO 3 -4.8M NaCl. The plutonium is recovered, after elution, via hydroxide precipitation, while the americium is recovered via NaHCO 3 precipitation. All filtrates from the process are discardable as low-level contaminated waste. Production-scale experiments are now in progress for MSE residues. Flow sheets for actinide recovery from electrorefining and direct oxide reduction residues are presented and discussed

  1. Actinide recovery from pyrochemical residues

    International Nuclear Information System (INIS)

    Avens, L.R.; Clifton, D.G.; Vigil, A.R.

    1985-05-01

    We demonstrated a new process for recovering plutonium and americium from pyrochemical waste. The method is based on chloride solution anion exchange at low acidity, or acidity that eliminates corrosive HCl fumes. Developmental experiments of the process flow chart concentrated on molten salt extraction (MSE) residues and gave >95% plutonium and >90% americium recovery. The recovered plutonium contained 6 2- from high-chloride low-acid solution. Americium and other metals are washed from the ion exchange column with lN HNO 3 -4.8M NaCl. After elution, plutonium is recovered by hydroxide precipitation, and americium is recovered by NaHCO 3 precipitation. All filtrates from the process can be discardable as low-level contaminated waste. Production-scale experiments are in progress for MSE residues. Flow charts for actinide recovery from electro-refining and direct oxide reduction residues are presented and discussed

  2. Reducing agent and exogenous protease additions, individually and in combination, to wheat- and sorghum-based diets interactively influence parameters of nutrient utilisation and digestive dynamics in broiler chickens

    Directory of Open Access Journals (Sweden)

    Peter H. Selle

    2016-12-01

    Full Text Available The objective of the study was to investigate the possibility that tandem inclusions of a reducing agent and a protease may advantage chicken-meat production and to ascertain if the established benefits of including sodium metabisulphite in sorghum-based diets extend to wheat-based diets. The study comprised a 2 × 2 × 2 factorial array of treatments in which either nutritionally iso-nitrogenous and iso-energetic wheat- or sorghum-based diets, without and with sodium metabisulphite (2.75 g/kg, without and with protease (1,000 units/kg were offered to broiler chickens from 7 to 28 days post–hatch. The effects of dietary treatments on growth performance, nutrient utilisation, protein (N and starch digestibility coefficients and digestive dynamics were determined. A preliminary investigation into the effects of two treatments on concentrations of free amino acids and glucose in the portal circulation was conducted. There was significant feed grain by sodium metabisulphite interactions (P = 0.03 to 0.005 for parameters of nutrient utilisation (AME, ME:GE ratios, N retention, AMEn. For example, sodium metabisulphite inclusions in sorghum-based diets enhanced AME by 0.18 MJ (12.47 versus 12.29 MJ/kg but depressed AME by 0.43 MJ (11.88 versus 12.31 MJ/kg in wheat-based diets. There was a linear relationship between starch:protein disappearance rate ratios in the distal ileum with weight gain (r = −0.484; P = 0.0012 indicating that condensed ratios (or absorption of more protein relative to starch advantaged growth performance. Concentrations of free amino acids in the portal circulation or the post-enteral availability of certain amino acids, including the branched-chain amino acids, methionine, phenylalanine and threonine, were significantly correlated to FCR. For example, threonine concentrations were negatively correlated to FCR (r = −0.773; P = 0.005. Finally, tandem inclusions of sodium metabisulphite and protease in

  3. 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.

  4. Leaching From Biomass Gasification Residues

    DEFF Research Database (Denmark)

    Allegrini, Elisa; Boldrin, Alessio; Polletini, A.

    2011-01-01

    The aim of the present work is to attain an overall characterization of solid residues from biomass gasification. Besides the determination of chemical and physical properties, the work was focused on the study of leaching behaviour. Compliance and pH-dependence leaching tests coupled with geoche......The aim of the present work is to attain an overall characterization of solid residues from biomass gasification. Besides the determination of chemical and physical properties, the work was focused on the study of leaching behaviour. Compliance and pH-dependence leaching tests coupled...

  5. Carbaryl residues in maize products

    International Nuclear Information System (INIS)

    Zayed, S.M.A.D.; Mansour, S.A.; Mostafa, I.Y.; Hassan, A.

    1976-01-01

    The 14 C-labelled insecticide carbaryl was synthesized from [1- 14 C]-1-naphthol at a specific activity of 3.18mCig -1 . Maize plants were treated with the labelled insecticide under simulated conditions of agricultural practice. Mature plants were harvested and studied for distribution of total residues in untreated grains as popularly roasted and consumed, and in the corn oil and corn germ products. Total residues found under these conditions in the respective products were 0.2, 0.1, 0.45 and 0.16ppm. (author)

  6. Combinatorial construction of toric residues

    OpenAIRE

    Khetan, Amit; Soprounov, Ivan

    2004-01-01

    The toric residue is a map depending on n+1 semi-ample divisors on a complete toric variety of dimension n. It appears in a variety of contexts such as sparse polynomial systems, mirror symmetry, and GKZ hypergeometric functions. In this paper we investigate the problem of finding an explicit element whose toric residue is equal to one. Such an element is shown to exist if and only if the associated polytopes are essential. We reduce the problem to finding a collection of partitions of the la...

  7. Analysis of dissolution residues of irradiated fuels

    International Nuclear Information System (INIS)

    Regnaud, F.; Tcherniatine, N.

    1980-12-01

    In the industrial dissolution conditions obtaining in reprocessing plants, the acid digests the irradiated nuclear fuels and leaves an insoluble product. This phenomenon is particularly conspicuous in the case of the UO 2 , PuO 2 mixed oxides of the fast neutron system irradiated at high specific burn-up. It is observed to a lesser degree in the case of UO 2 oxides of the ordinary water system. The quantity of insoluble product appears to depend on the specific burn-up. These residues are attributed to metallic phases comprising uranium, plutonium, ruthenium, palladium, rhodium and molybdenum. Owing to the existence of these residues, the radioactivity of which is high, the reprocessing plant requires a separation process, particular care in order to avoid their build-up, and packaging and storage facilities. This is why a programme on the physical-chemical study of the compounds has been initiated to develop a chemical digestion method, elemental analysis methods and the study of certain physical parameters such as granulometry [fr

  8. Numerical Analysis of Particle Interactions with Nuclei in the Framework of Quantum Molecular Dynamic Model

    CERN Document Server

    Amirkhanov, I V; Zemlyanaya, E V; Polanski, A; Puzynina, T P; Uzhinsky, V V

    2004-01-01

    Combinations of the QMD model with various models of nuclear residual de-excitation are considered. The QMD model parameters are fitted; neutron spectra in hadron-nucleus interactions are calculated. The numerical results were compared with analogous calculations by the cascade-evaporation model and with experimental data. The comparison shows that the numerical results are in agreement between each other and with the experimental data for the energies of projectile particles lower than 200-300 MeV for fast neutrons. Cross-sections of isotope yields in the neutron interactions with radioactive iodine, americium, plutonium and others isotopes have been calculated.

  9. Weld Residual Stress in Corner Boxing Joints

    OpenAIRE

    Kazuyoshi, Matsuoka; Tokuharu, Yoshii; Ship Research Institute, Ministry of Transport; Ship Research Institute, Ministry of Transport

    1998-01-01

    Fatigue damage often occurs in corner boxing welded joints because of stress concentration and residual stress. The hot spot stress approach is applicable to stress concentration. However, the number of suitable methods for estimating residual stress in welded joints is limited. The purpose of this paper is to clarify the residual stress in corner boxing joints. The method of estimating residual stresses based on the inherent stress technique is presented. Residual stress measurements are per...

  10. On the reliability of neutron diffraction for residual stress measurement in cold-drawn steels

    International Nuclear Information System (INIS)

    Ruiz-Hervias, J; Atienza, J M; Mompean, F; Hofmann, M

    2011-01-01

    Residual strains were measured in the ferrite phase of pearlitic steel rods along the radial, axial and hoop directions. Two samples with different initial diameters were subjected to one drawing pass (using same drawing parameters) with 20% section reduction and measured in two different neutron diffraction instruments. The results show that the residual strain state is very similar in both cases, regardless of the diameter of the initial rod. This means that the final residual strain-stress state is unique and it is related to the cold-drawing process parameters. In addition, the results show the reliability of strain scanning with different neutron instruments and experimental conditions.

  11. Research on the residual stress of glass ceramic based on rotary ultrasonic drilling

    Science.gov (United States)

    Sun, Lipeng; Jin, Yuzhu; Chen, Jianhua

    2016-10-01

    In the process of machining, the glass ceramic is easy to crack and damage, etc. And the residual stress in the machined surface may cause the crack to different extent in the later stage. Some may even affect the performance of the product. The residual stress of rotary ultrasonic drilling and mechanical processing is compared in different machining parameters (spindle speed, feed rate). The effects of processing parameters and methods are researched, in order to reduce the residual stress in the mechanical processing of glass ceramic, and provide guidance for the actual processing.

  12. FPGA Implementation of Uniform Random Number based on Residue Method

    Directory of Open Access Journals (Sweden)

    Zulfikar .

    2014-04-01

    Full Text Available This paper presents the implementation and comparisons of uniform random number on Field Programable Gate Array (FPGA. Uniform random numbers are generated based on residue method. The circuit of generating uniform random number is presented in general view. The circuit is constructed from a multiplexer, a multiplier, buffers and some basic gates. FPGA implementation of the designed circuit has been done into various Xilinx chips. Simulation results are viewed clearly in the paper. Random numbers are generated based on different parameters. Comparisons upon occupied area and maximum frequency from different Xilinx chip are examined. Virtex 7 is the fastest chip and Virtex 4 is the best choice in terms of occupied area. Finally, Uniform random numbers have been generated successfully on FPGA using residue method.Keywords: FPGA implementation, random number, uniform random number, residue method, Xilinx chips

  13. Effects of twin-screw extrusion on soluble dietary fibre and physicochemical properties of soybean residue.

    Science.gov (United States)

    Jing, Yan; Chi, Yu-Jie

    2013-06-01

    Extrusion cooking technology was applied for soluble dietary fibre extraction from soybean residue. Response surface methodology (RSM) was used to optimise the effects of extrusion parameters, namely extrusion temperature (90-130°C), feed moisture (25-35%) and screw speed (160-200 rpm) on the content of soluble dietary fibre. According to the regression coefficients significance of the quadratic polynomial model, the optimum extrusion parameters were as follows: extrusion temperature, 115°C; feed moisture, 31%; and screw speed, 180 rpm. Under these conditions, the soluble dietary fibre content of soybean residue could reach to 12.65% which increased 10.60% compared with the unextruded soybean residue. In addition, the dietary fibre in extrude soybean residue had higher water retention capacity, oil retention capacity and swelling capacity than those of dietary fibre in unextruded soybean residue. Copyright © 2012 Elsevier Ltd. All rights reserved.

  14. Solidification process for sludge residue

    International Nuclear Information System (INIS)

    Pearce, K.L.

    1998-01-01

    This report investigates the solidification process used at 100-N Basin to solidify the N Basin sediment and assesses the N Basin process for application to the K Basin sludge residue material. This report also includes a discussion of a solidification process for stabilizing filters. The solidified matrix must be compatible with the Environmental Remediation Disposal Facility acceptance criteria

  15. Machine Arithmetic in Residual Classes,

    Science.gov (United States)

    1981-04-03

    rsmainder/residue, as this ascape /-nsues from thp determination of system. It can be. zaalizpd ;n the presence of th- arithmetic urit, which wor~s in thz sys...modules Nj. Page 417. Proof. Proof ascaps /ensues directly from the theorem of Gauss. Actually/really, since according to condition (py, qj)-=-. then

  16. Residual stress in polyethylene pipes

    Czech Academy of Sciences Publication Activity Database

    Poduška, Jan; Hutař, Pavel; Kučera, J.; Frank, A.; Sadílek, J.; Pinter, G.; Náhlík, Luboš

    2016-01-01

    Roč. 54, SEP (2016), s. 288-295 ISSN 0142-9418 R&D Projects: GA MŠk LM2015069; GA MŠk(CZ) LQ1601 Institutional support: RVO:68081723 Keywords : polyethylene pipe * residual stress * ring slitting method * lifetime estimation Subject RIV: JL - Materials Fatigue, Friction Mechanics Impact factor: 2.464, year: 2016

  17. Managing woodwaste: Yield from residue

    Energy Technology Data Exchange (ETDEWEB)

    Nielson, E. [LNS Services, Inc., North Vancouver, British Columbia (Canada); Rayner, S. [Pacific Waste Energy Inc., Burnaby, British Columbia (Canada)

    1993-12-31

    Historically, the majority of sawmill waste has been burned or buried for the sole purpose of disposal. In most jurisdictions, environmental legislation will prohibit, or render uneconomic, these practices. Many reports have been prepared to describe the forest industry`s residue and its environmental effect; although these help those looking for industry-wide or regional solutions, such as electricity generation, they have limited value for the mill manager, who has the on-hands responsibility for generation and disposal of the waste. If the mill manager can evaluate waste streams and break them down into their usable components, he can find niche market solutions for portions of the plant residue and redirect waste to poor/no-return, rather than disposal-cost, end uses. In the modern mill, residue is collected at the individual machine centre by waste conveyors that combine and mix sawdust, shavings, bark, etc. and send the result to the hog-fuel pile. The mill waste system should be analyzed to determine the measures that can improve the quality of residues and determine the volumes of any particular category before the mixing, mentioned above, occurs. After this analysis, the mill may find a niche market for a portion of its woodwaste.

  18. Solow Residuals Without Capital Stocks

    DEFF Research Database (Denmark)

    Burda, Michael C.; Severgnini, Battista

    2014-01-01

    We use synthetic data generated by a prototypical stochastic growth model to assess the accuracy of the Solow residual (Solow, 1957) as a measure of total factor productivity (TFP) growth when the capital stock in use is measured with error. We propose two alternative measurements based on current...

  19. Binding free energy calculations to rationalize the interactions of huprines with acetylcholinesterase.

    Science.gov (United States)

    Nascimento, Érica C M; Oliva, Mónica; Andrés, Juan

    2018-03-26

    In the present study, the binding free energy of a family of huprines with acetylcholinesterase (AChE) is calculated by means of the free energy perturbation method, based on hybrid quantum mechanics and molecular mechanics potentials. Binding free energy calculations and the analysis of the geometrical parameters highlight the importance of the stereochemistry of huprines in AChE inhibition. Binding isotope effects are calculated to unravel the interactions between ligands and the gorge of AChE. New chemical insights are provided to explain and rationalize the experimental results. A good correlation with the experimental data is found for a family of inhibitors with moderate differences in the enzyme affinity. The analysis of the geometrical parameters and interaction energy per residue reveals that Asp72, Glu199, and His440 contribute significantly to the network of interactions between active site residues, which stabilize the inhibitors in the gorge. It seems that a cooperative effect of the residues of the gorge determines the affinity of the enzyme for these inhibitors, where Asp72, Glu199, and His440 make a prominent contribution.

  20. Thermodynamics of antibody-antigen interaction revealed by mutation analysis of antibody variable regions.

    Science.gov (United States)

    Akiba, Hiroki; Tsumoto, Kouhei

    2015-07-01

    Antibodies (immunoglobulins) bind specific molecules (i.e. antigens) with high affinity and specificity. In order to understand their mechanisms of recognition, interaction analysis based on thermodynamic and kinetic parameters, as well as structure determination is crucial. In this review, we focus on mutational analysis which gives information about the role of each amino acid residue in antibody-antigen interaction. Taking anti-hen egg lysozyme antibodies and several anti-small molecule antibodies, the energetic contribution of hot-spot and non-hot-spot residues is discussed in terms of thermodynamics. Here, thermodynamics of the contribution from aromatic, charged and hydrogen bond-forming amino acids are discussed, and their different characteristics have been elucidated. The information gives fundamental understanding of the antibody-antigen interaction. Furthermore, the consequences of antibody engineering are analysed from thermodynamic viewpoints: humanization to reduce immunogenicity and rational design to improve affinity. Amino acid residues outside hot-spots in the interface play important roles in these cases, and thus thermodynamic and kinetic parameters give much information about the antigen recognition. Thermodynamic analysis of mutant antibodies thus should lead to advanced strategies to design and select antibodies with high affinity. © The Authors 2015. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

  1. Assessment of heterogeneity of residual variances using changepoint techniques

    Directory of Open Access Journals (Sweden)

    Toro Miguel A

    2000-07-01

    Full Text Available Abstract Several studies using test-day models show clear heterogeneity of residual variance along lactation. A changepoint technique to account for this heterogeneity is proposed. The data set included 100 744 test-day records of 10 869 Holstein-Friesian cows from northern Spain. A three-stage hierarchical model using the Wood lactation function was employed. Two unknown changepoints at times T1 and T2, (0 T1 T2 tmax, with continuity of residual variance at these points, were assumed. Also, a nonlinear relationship between residual variance and the number of days of milking t was postulated. The residual variance at a time t( in the lactation phase i was modeled as: for (i = 1, 2, 3, where λι is a phase-specific parameter. A Bayesian analysis using Gibbs sampling and the Metropolis-Hastings algorithm for marginalization was implemented. After a burn-in of 20 000 iterations, 40 000 samples were drawn to estimate posterior features. The posterior modes of T1, T2, λ1, λ2, λ3, , , were 53.2 and 248.2 days; 0.575, -0.406, 0.797 and 0.702, 34.63 and 0.0455 kg2, respectively. The residual variance predicted using these point estimates were 2.64, 6.88, 3.59 and 4.35 kg2 at days of milking 10, 53, 248 and 305, respectively. This technique requires less restrictive assumptions and the model has fewer parameters than other methods proposed to account for the heterogeneity of residual variance during lactation.

  2. 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

  3. Chemical modification of arginine residues in the lactose repressor

    International Nuclear Information System (INIS)

    Whitson, P.A.; Matthews, K.S.

    1987-01-01

    The lactose repressor protein was chemically modified with 2,3-butanedione and phenylglyoxal. Arginine reaction was quantitated by either amino aced analysis or incorporation of 14 C-labeled phenylglyoxal. Inducer binding activity was unaffected by the modification of arginine residues, while both operator and nonspecific DNA binding activities were diminished, although to differing degrees. The correlation of the decrease in DNA binding activities with the modification of ∼ 1-2 equiv of arginine per monomer suggests increased reactivity of a functionally essential residue(s). For both reagents, operator DNA binding activity was protected by the presence of calf thymus DNA, and the extent of reaction with phenylglyoxal was simultaneously diminished. This protection presumably results from steric restriction of reagent access to an arginine(s) that is (are) essential for DNA binding interactions. These experiments suggest that there is (are) an essential reactive arginine(s) critical for repressor binding to DNA

  4. Residual Neuromuscular Blockade in the Critical Care Setting.

    Science.gov (United States)

    Stawicki, Nicole; Gessner, Patty

    2018-01-01

    Residual neuromuscular blockade is a widespread challenge for providers in the acute care setting that, if left unrecognized or untreated, places patients at higher risk for morbidity and mortality. The condition is estimated to occur in 26% to 88% of patients undergoing general anesthesia. The role of the advanced practice nurse in the acute care setting is to facilitate a safe recovery process by identifying early signs of deterioration and supporting the patient until full muscular strength has returned. This article discusses the prevalence of residual neuromuscular blockade and associated complications and patient risk factors. A review is included of the current uses for neuromuscular blockade, pathophysiology of the neuromuscular junction, pharmacologic characteristics of neuromuscular blocking agents (including drug-drug interactions), monitoring modalities, and effectiveness of reversal agents. Treatment recommendations pertinent to residual neuromuscular blockade are outlined. ©2018 American Association of Critical-Care Nurses.

  5. 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)

  6. Direct gas-solid carbonation of serpentinite residues in the absence and presence of water vapor: a feasibility study for carbon dioxide sequestration.

    Science.gov (United States)

    Veetil, Sanoopkumar Puthiya; Pasquier, Louis-César; Blais, Jean-François; Cecchi, Emmanuelle; Kentish, Sandra; Mercier, Guy

    2015-09-01

    Mineral carbonation of serpentinite mining residue offers an environmentally secure and permanent storage of carbon dioxide. The strategy of using readily available mining residue for the direct treatment of flue gas could improve the energy demand and economics of CO2 sequestration by avoiding the mineral extraction and separate CO2 capture steps. The present is a laboratory scale study to assess the possibility of CO2 fixation in serpentinite mining residues via direct gas-solid reaction. The degree of carbonation is measured both in the absence and presence of water vapor in a batch reactor. The gas used is a simulated gas mixture reproducing an average cement flue gas CO2 composition of 18 vol.% CO2. The reaction parameters considered are temperature, total gas pressure, time, and concentration of water vapor. In the absence of water vapor, the gas-solid carbonation of serpentinite mining residues is negligible, but the residues removed CO2 from the feed gas possibly due to reversible adsorption. The presence of small amount of water vapor enhances the gas-solid carbonation, but the measured rates are too low for practical application. The maximum CO2 fixation obtained is 0.07 g CO2 when reacting 1 g of residue at 200 °C and 25 barg (pCO2 ≈ 4.7) in a gas mixture containing 18 vol.% CO2 and 10 vol.% water vapor in 1 h. The fixation is likely surface limited and restricted due to poor gas-solid interaction. It was identified that both the relative humidity and carbon dioxide-water vapor ratio have a role in CO2 fixation regardless of the percentage of water vapor.

  7. RECOVERY OF WHEAT RESIDUE NITROGEN 15 AND RESIDUAL ...

    African Journals Online (AJOL)

    Therefore 85 kg ha-1 N as labelled ammonium sulfate (9.764% atomic excess) was applied in a three-split application. Fertiliser N recovery by wheat in the first year was 33.1%. At harvest, 64.8% of fertiliser N was found in the 0 - 80 cm profile as residual fertiliser-derived N; 2.1% of the applied N could not be accounted for ...

  8. Multivariable parameter optimization for the endoglucanase production by Trichoderma reesei Rut C30 from Ocimum gratissimum seed

    Directory of Open Access Journals (Sweden)

    Mithu Das

    2008-02-01

    Full Text Available The aim of this study was to evaluate the interaction effects of the physico-chemical parameters on the endoglucanase (CMCase production by Trichoderma reesei Rut C30 on a cellulosic agro-residue by the solid-state fermentation (SSF and to determine their optimum values by the EVOP factorial design technique. The best combination of physical parameters for the maximum production of the endoglucanase (CMCase was 28ºC temperature, 79% relative humidity and 4.8 pH of the medium. The best combination of the chemical parameters was (mg/L nicotinic acid 15, naphthalene acetic acid 7, ferric chloride 5 and Tween-80 6. With the application of this technique, the yield of the CMCase increased by ~ 2.3 fold.

  9. Measuring the Michel parameter ξ''

    International Nuclear Information System (INIS)

    Knowles, P.; Deutsch, J.; Egger, J.; Fetscher, W.; Foroughi, F.; Govaerts, J.; Hadri, M.; Kirch, K.; Kistryn, S.; Lang, J.; Morelle, X.; Naviliat, O.; Ninane, A.; Prieels, R.; Severijns, N.; Simons, L.; Sromicki, J.; Vandormael, S.; Hove, P. van

    1999-01-01

    Unlike the majority of Michel parameters which are consistent with the Standard Model V-A interaction, the experimental value of ξ''(=0.65±0.36) [1] is poorly known. Our experiment will measure the longitudinal polarization, P L , of positrons emitted from the decay of polarized muons. The value of P L , equal to unity in the Standard Model, will decrease for high energy positrons emitted antiparallel to the muon spin if the combination of Michel parameters ξ''/ξξ' - 1 deviates from the Standard Model value of zero

  10. Residual life estimation of electrical insulation system for rotating equipment

    International Nuclear Information System (INIS)

    Vashishtha, Y.D.; Gupta, A.K.; Bhattacharyya, A.K.; Verma, A.K.

    1994-01-01

    Residual life assessment gains significance towards the end of designed life for granting plant life extensions and resource planning for costly equipment replacement. A critical review of all the diagnostic techniques presently used to assess either health of insulation system or to infer qualitatively the remaining life for rotating machines is presented. However more emphasis is required on developing quantitative methods. This paper also formulates the experimental plan for progressively censored ageing tests, measurement of partial discharge parameters, micro-structural study for delamination and electrical tree growth and measurement of electrical breakdown strength. Partial discharge (PD) patterns, electrical tree growth and time to failure data shall be taken as training set for the neural network learning which can be useful to predict residual life with only one candidate parameter i.e. PD patterns. (author). 9 refs

  11. Prediction of protein-protein binding site by using core interface residue and support vector machine

    Directory of Open Access Journals (Sweden)

    Sun Zhonghua

    2008-12-01

    Full Text Available Abstract Background The prediction of protein-protein binding site can provide structural annotation to the protein interaction data from proteomics studies. This is very important for the biological application of the protein interaction data that is increasing rapidly. Moreover, methods for predicting protein interaction sites can also provide crucial information for improving the speed and accuracy of protein docking methods. Results In this work, we describe a binding site prediction method by designing a new residue neighbour profile and by selecting only the core-interface residues for SVM training. The residue neighbour profile includes both the sequential and the spatial neighbour residues of an interface residue, which is a more complete description of the physical and chemical characteristics surrounding the interface residue. The concept of core interface is applied in selecting the interface residues for training the SVM models, which is shown to result in better discrimination between the core interface and other residues. The best SVM model trained was tested on a test set of 50 randomly selected proteins. The sensitivity, specificity, and MCC for the prediction of the core interface residues were 60.6%, 53.4%, and 0.243, respectively. Our prediction results on this test set were compared with other three binding site prediction methods and found to perform better. Furthermore, our method was tested on the 101 unbound proteins from the protein-protein interaction benchmark v2.0. The sensitivity, specificity, and MCC of this test were 57.5%, 32.5%, and 0.168, respectively. Conclusion By improving both the descriptions of the interface residues and their surrounding environment and the training strategy, better SVM models were obtained and shown to outperform previous methods. Our tests on the unbound protein structures suggest further improvement is possible.

  12. Optimization of electrospinning parameters for chitosan nanofibres

    CSIR Research Space (South Africa)

    Jacobs, V

    2011-06-01

    Full Text Available uniform chitosan nanofibres. The parameters studied were electric field strength, ratio of solvents - trifluoroacetic acid (TFA)/ dichloromethane (DCM), concentration of chitosan in the spinning solution, their individual and interaction effects...

  13. Review on the Influences of Bagging Treatment on Pesticide Residue in Fruits

    Directory of Open Access Journals (Sweden)

    ZHAO Xiao-yun

    2018-02-01

    Full Text Available At present, bagging technology has been widely applicated in fruit cultivation. Impact of bagging treatment on the pesticide residues have different results. On the basis of existing achievements, this paper systematically analyzed the influence of different bagging treatments on pesticide residues:such as different ways of applying pesticide, pesticide concentration, number of applying pesticide; bagging materials, bagged layer; the type of pesticide(systemic pesticide, nonendoscopic pesticide; different portions of the fruit, crop varieties and so on. The way of applying pesticide had great impact on pesticide residue, pesticide application after bagging could largely reduce the pesticide residue, and pesticide application before bagging could increase pesticide residues; The four factors including pesticide appliacation dosage, the type of pesticides and fruit portion and fruit varieties on the effects of pesticide residues, had interaction each other. The pesticide applying several times, bagging could significantly reduce pesticide residues and control within the security level. Different bagging materials could reduce pesticide residues, but the impact on pesticide residues had no significant difference. More bagging layers caused less pesticide residues.

  14. Power generation with technology innovation of residual biomass utilization; Geracao de energia com inovacao tecnologica de aproveitamento de biomassa residual

    Energy Technology Data Exchange (ETDEWEB)

    Moura, Johnson Pontes de; Selvam, P.V. Pannir [Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN (Brazil)

    2006-07-01

    In the present work, the introduction of alternative energy of biogas in agricultural communities for the sustainable development was studied through exploitation of residual biomass and also getting as by-product the biological fertilizer. A fast composting of the domestic residue with the organic was made possible where part of this residue after processing was taken together with effluent to the biodigester. The bibliographical research on the processes of generation of biogas, about composting and the equipment for processing had been carried through. The projects engineering with the use of computational tools had been developed with the software Super Pro 4,9 Design and ORC GPEC 2004 by our research group. Five case studies had been elaborated, where different scenes related with our innovation, that uses of the residue for the composting together with domestic effluent for digestion. Several economic parameters were obtained and our work proved the viability about the use of biogas for drying of the fruits banana. A economic feasibility study was carried where it was proven that the project with the innovation of the use of residues from the fruits possess more advantages than the conventional system of drying using electric energy. Considering the viability of this process and the use solar energy, it is intended to apply this technology in rural agricultural communities providing them an energy source of low cost in substitution of the conventional energy. (author)

  15. Type Ia supernova Hubble residuals and host-galaxy properties

    Energy Technology Data Exchange (ETDEWEB)

    Kim, A. G.; Aldering, G.; Aragon, C.; Bailey, S.; Fakhouri, H. K. [Physics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 (United States); Antilogus, P.; Bongard, S.; Canto, A.; Cellier-Holzem, F.; Fleury, M.; Guy, J. [Laboratoire de Physique Nucléaire et des Hautes Énergies, Université Pierre et Marie Curie Paris 6, Université Paris Diderot Paris 7, CNRS-IN2P3, 4 place Jussieu, F-75252 Paris Cedex 05 (France); Baltay, C. [Department of Physics, Yale University, New Haven, CT 06250-8121 (United States); Buton, C.; Feindt, U.; Greskovic, P.; Kowalski, M. [Physikalisches Institut, Universität Bonn, Nußallee 12, D-53115 Bonn (Germany); Childress, M. [Research School of Astronomy and Astrophysics, Australian National University, Canberra, ACT 2611 (Australia); Chotard, N.; Copin, Y.; Gangler, E. [Université de Lyon, F-69622 Lyon (France); Université de Lyon 1, Villeurbanne (France); CNRS/IN2P3, Institut de Physique Nucléaire de Lyon (France); and others

    2014-03-20

    Kim et al. introduced a new methodology for determining peak-brightness absolute magnitudes of type Ia supernovae from multi-band light curves. We examine the relation between their parameterization of light curves and Hubble residuals, based on photometry synthesized from the Nearby Supernova Factory spectrophotometric time series, with global host-galaxy properties. The K13 Hubble residual step with host mass is 0.013 ± 0.031 mag for a supernova subsample with data coverage corresponding to the K13 training; at <<1σ, the step is not significant and lower than previous measurements. Relaxing the data coverage requirement of the Hubble residual step with the host mass is 0.045 ± 0.026 mag for the larger sample; a calculation using the modes of the distributions, less sensitive to outliers, yields a step of 0.019 mag. The analysis of this article uses K13 inferred luminosities, as distinguished from previous works that use magnitude corrections as a function of SALT2 color and stretch parameters: steps at >2σ significance are found in SALT2 Hubble residuals in samples split by the values of their K13 x(1) and x(2) light-curve parameters. x(1) affects the light-curve width and color around peak (similar to the Δm {sub 15} and stretch parameters), and x(2) affects colors, the near-UV light-curve width, and the light-curve decline 20-30 days after peak brightness. The novel light-curve analysis, increased parameter set, and magnitude corrections of K13 may be capturing features of SN Ia diversity arising from progenitor stellar evolution.

  16. Residual stress evaluation and curvature behavior of aluminium 7050 peen forming processed; Avaliacao da tensao residual em aluminio 7050 conformado pelo processo peen forming

    Energy Technology Data Exchange (ETDEWEB)

    Oliveira, R.R. de; Lima, N.B., E-mail: rolivier@ipen.b, E-mail: nblima@ipen.b [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil); Braga, A.P.V.; Goncalves, M., E-mail: anapaola@ipt.b, E-mail: mgoncalves@ipt.b [Instituto de Pesquisas Tecnologicas (IPT), Sao Paulo, SP (Brazil)

    2010-07-01

    Shot peening is a superficial cold work process used to increase the fatigue life evaluated by residual stress measurements. The peen forming process is a variant of the shot peening process, where a curvature in the plate is obtained by the compression of the grains near to the surface. In this paper, the influence of the parameters such as: pressure of shot, ball shot size and thickness of aluminum 7050 samples with respect to residual stress profile and resulting arc height was studied. The evaluation of the residual stress profile was obtained by sin{sup 2} {Psi} method. (author)

  17. The Cauchy method of residues

    CERN Document Server

    Mitrinović, Dragoslav S

    1993-01-01

    Volume 1, i. e. the monograph The Cauchy Method of Residues - Theory and Applications published by D. Reidel Publishing Company in 1984 is the only book that covers all known applications of the calculus of residues. They range from the theory of equations, theory of numbers, matrix analysis, evaluation of real definite integrals, summation of finite and infinite series, expansions of functions into infinite series and products, ordinary and partial differential equations, mathematical and theoretical physics, to the calculus of finite differences and difference equations. The appearance of Volume 1 was acknowledged by the mathematical community. Favourable reviews and many private communications encouraged the authors to continue their work, the result being the present book, Volume 2, a sequel to Volume 1. We mention that Volume 1 is a revised, extended and updated translation of the book Cauchyjev raeun ostataka sa primenama published in Serbian by Nau~na knjiga, Belgrade in 1978, whereas the greater part ...

  18. Calcination/dissolution residue treatment

    International Nuclear Information System (INIS)

    Knight, R.C.; Creed, R.F.; Patello, G.K.; Hollenberg, G.W.; Buehler, M.F.; O'Rourke, S.M.; Visnapuu, A.; McLaughlin, D.F.

    1994-09-01

    Currently, high-level wastes are stored underground in steel-lined tanks at the Hanford site. Current plans call for the chemical pretreatment of these wastes before their immobilization in stable glass waste forms. One candidate pretreatment approach, calcination/dissolution, performs an alkaline fusion of the waste and creates a high-level/low-level partition based on the aqueous solubilities of the components of the product calcine. Literature and laboratory studies were conducted with the goal of finding a residue treatment technology that would decrease the quantity of high-level waste glass required following calcination/dissolution waste processing. Four elements, Fe, Ni, Bi, and U, postulated to be present in the high-level residue fraction were identified as being key to the quantity of high-level glass formed. Laboratory tests of the candidate technologies with simulant high-level residues showed reductive roasting followed by carbonyl volatilization to be successful in removing Fe, Ni, and Bi. Subsequent bench-scale tests on residues from calcination/dissolution processing of genuine Hanford Site tank waste showed Fe was separated with radioelement decontamination factors of 70 to 1,000 times with respect to total alpha activity. Thermodynamic analyses of the calcination of five typical Hanford Site tank waste compositions also were performed. The analyses showed sodium hydroxide to be the sole molten component in the waste calcine and emphasized the requirement for waste blending if fluid calcines are to be achieved. Other calcine phases identified in the thermodynamic analysis indicate the significant thermal reconstitution accomplished in calcination

  19. Atomic structure of recombinant thaumatin II reveals flexible conformations in two residues critical for sweetness and three consecutive glycine residues.

    Science.gov (United States)

    Masuda, Tetsuya; Mikami, Bunzo; Tani, Fumito

    2014-11-01

    Thaumatin, an intensely sweet-tasting protein used as a sweetener, elicits a sweet taste at 50 nM. Although two major variants designated thaumatin I and thaumatin II exist in plants, there have been few dedicated thaumatin II structural studies and, to date, data beyond atomic resolution had not been obtained. To identify the detailed structural properties explaining why thaumatin elicits a sweet taste, the structure of recombinant thaumatin II was determined at the resolution of 0.99 Å. Atomic resolution structural analysis with riding hydrogen atoms illustrated the differences in the direction of the side-chains more precisely and the electron density maps of the C-terminal regions were markedly improved. Though it had been suggested that the three consecutive glycine residues (G142-G143-G144) have highly flexible conformations, G143, the central glycine residue was successfully modelled in two conformations for the first time. Furthermore, the side chain r.m.s.d. values for two residues (R67 and R82) critical for sweetness exhibited substantially higher values, suggesting that these residues are highly disordered. These results demonstrated that the flexible conformations in two critical residues favoring their interaction with sweet taste receptors are prominent features of the intensely sweet taste of thaumatin. Copyright © 2014 Elsevier B.V. and Société française de biochimie et biologie Moléculaire (SFBBM). All rights reserved.

  20. Carbon Nanotubes Facilitate Oxidation of Cysteine Residues of Proteins.

    Science.gov (United States)

    Hirano, Atsushi; Kameda, Tomoshi; Wada, Momoyo; Tanaka, Takeshi; Kataura, Hiromichi

    2017-10-19

    The adsorption of proteins onto nanoparticles such as carbon nanotubes (CNTs) governs the early stages of nanoparticle uptake into biological systems. Previous studies regarding these adsorption processes have primarily focused on the physical interactions between proteins and nanoparticles. In this study, using reduced lysozyme and intact human serum albumin in aqueous solutions, we demonstrated that CNTs interact chemically with proteins. The CNTs induce the oxidation of cysteine residues of the proteins, which is accounted for by charge transfer from the sulfhydryl groups of the cysteine residues to the CNTs. The redox reaction simultaneously suppresses the intermolecular association of proteins via disulfide bonds. These results suggest that CNTs can affect the folding and oxidation degree of proteins in biological systems such as blood and cytosol.

  1. Safety and nutritional evaluation of biogas residue left after the production of biogas from wastewater

    Directory of Open Access Journals (Sweden)

    Baoguo Bian

    2015-07-01

    Full Text Available We investigated the safety and nutritional value of biogas residue left after the production of biogas from wastewater. In Exp. 1, ninety- six female mice were selected for acute oral toxicity testing and randomly allocated to 4 treatment groups, which received distilled water (control or the biogas residue solution at 1 g/mL, 5 g/mL, or 15 g/mL. Activity levels and serum biochemical parameters were measured after 24 hours. In Exp. 2, eighty mice were divided into 2 treatment groups for subacute and sub-chronic toxicity testing, which received either a control group diet or the biogas residue diet (20% biogas residue. In Exp. 3, to test the nutritional value of the biogas residue, four pigs were fed either a low-casein corn starch-based diet or a semi-purified diet with biogas residue as the only source of protein, and the apparent and true digestibility of crude protein and amino acids, apparent metabolic energy, and digestible energy were measured. Group differences in serum parameters and mouse weight gain were not significant 24 hours after biogas residue solution gavage, and the viscera appeared normal. At day 30 of the observation period, changes in serum biochemical parameters were not significant, but the mean spleen index of mice treated with biogas residue was greater (P<0.05 than that of the control group. In this study, biogas residue had no significant adverse effects on the body and it was safe as a feed supplement at a 20% replacement level. The current observations showed that the biogas residue might be considered as a protein feed source for pigs.

  2. 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.

  3. Polychlorinated Biphenyls (PCB) Residue Effects Database

    Data.gov (United States)

    U.S. Environmental Protection Agency — The PCB Residue Effects (PCBRes) Database was developed to assist scientists and risk assessors in correlating PCB and dioxin-like compound residues with toxic...

  4. Interpretation on Recycling Plastics from Shredder Residue

    Science.gov (United States)

    EPA is considering an interpretation of its regulations that would generally allow for recycling of plastic separated from shredder residue under the conditions described in the Voluntary Procedures for Recycling Plastics from Shredder Residue.

  5. Booster parameter list

    International Nuclear Information System (INIS)

    Parsa, Z.

    1986-10-01

    The AGS Booster is designed to be an intermediate synchrotron injector for the AGS, capable of accelerating protons from 200 MeV to 1.5 GeV. The parameters listed include beam and operational parameters and lattice parameters, as well as parameters pertaining to the accelerator's magnets, vacuum system, radio frequency acceleration system, and the tunnel. 60 refs., 41 figs

  6. Applicability of four parameter formalisms in interpreting ...

    Indian Academy of Sciences (India)

    The four parameter functions are generally considered to be adequate for representation of the thermodynamic properties for the strongly interacting binary systems. The present study involves a critical comparison in terms of applicability of the three well known four-parameter formalisms for the representation of the ...

  7. Assessing plant residue decomposition in soil using DRIFT spectroscopy

    Science.gov (United States)

    Ouellette, Lance; Van Eerd, Laura; Voroney, Paul

    2016-04-01

    Assessment of the decomposition of plant residues typically involves the use of tracer techniques combined with measurements of soil respiration. This laboratory study evaluated use of Diffuse Reflectance Fourier Transform (DRIFT) spectroscopy for its potential to assess plant residue decomposition in soil. A sandy loam soil (Orthic Humic Gleysol) obtained from a field research plot was passed through a 4.75 mm sieve moist (~70% of field capacity) to remove larger crop residues. The experimental design consisted of a randomized complete block with four replicates of ten above-ground cover crop residue-corn stover combinations, where sampling time was blocked. Two incubations were set up for 1) Drift analysis: field moist soil (250 g ODW) was placed in 500 mL glass jars, and 2) CO2 evolution: 100 g (ODW) was placed in 2 L jars. Soils were amended with the plant residues (oven-dried at 60°C and ground to <2 mm) at rates equivalent to field mean above-ground biomass yields, then moistened to 60% water holding capacity and incubated in the dark at 22±3°C. Measurements for DRIFT and CO2-C evolved were taken after 0.5, 2, 4,