Vortex matter stabilized by many-body interactions

Science.gov (United States)

Wolf, S.; Vagov, A.; Shanenko, A. A.; Axt, V. M.; Aguiar, J. Albino

2017-10-01

This work investigates interactions of vortices in superconducting materials between standard types I and II, in the domain of the so-called intertype (IT) superconductivity. Contrary to common expectations, the many-body (many-vortex) contribution is not a correction to the pair-vortex interaction here but plays a crucial role in the formation of the IT vortex matter. In particular, the many-body interactions stabilize vortex clusters that otherwise could not exist. Furthermore, clusters with large numbers of vortices become more stable when approaching the boundary between the intertype domain and type I. This indicates that IT superconductors develop a peculiar unconventional type of the vortex matter governed by the many-body interactions of vortices.

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 .

Whole body interaction with public displays

CERN Document Server

Walter, Robert

2017-01-01

This book develops valuable new approaches to digital out-of-home media and digital signage in urban environments. It offers solutions for communicating interactive features of digital signage to passers-by. Digital out-of-home media and digital signage screens are becoming increasingly interactive thanks to touch input technology and gesture recognition. To optimize their conversion rate, interactive public displays must 1) attract attention, 2) communicate to passers-by that they are interactive, 3) explain the interaction, and 4) provide a motivation for passers-by to interact. This book highlights solutions to problems 2 and 3 above. The focus is on whole-body interaction, where the positions and orientations of users and their individual body parts are captured by specialized sensors (e.g., depth cameras). The book presents revealing findings from a field study on communicating interactivity, a laboratory on analysing visual attention, a field study on mid-air gestures, and a field study on using mid-air...

The residual proton-neutron interaction and nuclear collectivity

International Nuclear Information System (INIS)

Casten, R.F.

1990-01-01

The essential role of the valence, residual p-n interaction in the development of collectivity, though long known in general terms, has recently become increasingly apparent. A brief review of the p-n interaction is given, including some very basic nuclear data that illustrate its effects and the phenomenological N p N n scheme and the P-factor. This is followed by a discussion of recent experimental extractions of p-n matrix elements throughout the periodic table and theoretical efforts to understand them, in terms of both Shell and Nilsson models. 20 refs., 13 figs

Residual correlation in two-proton interferometry from Λ-proton strong interactions

International Nuclear Information System (INIS)

Wang, Fuqiang

1999-01-01

We investigate the residual effect of Λp strong interactions in pp correlations with one proton from Λ decays. It is found that the residual correlation is about 10% of the Λp correlation strength, and has a broad distribution centered around q≅40 MeV/c. The residual correlation cannot explain the observed structure on the tail of the recently measured pp correlation function in central Pb+Pb collisions by NA49 at the Super Proton Synchrotron. (c) 1999 The American Physical Society

Molecular interactions and residues involved in force generation in the T4 viral DNA packaging motor.

Science.gov (United States)

Migliori, Amy D; Smith, Douglas E; Arya, Gaurav

2014-12-12

Many viruses utilize molecular motors to package their genomes into preformed capsids. A striking feature of these motors is their ability to generate large forces to drive DNA translocation against entropic, electrostatic, and bending forces resisting DNA confinement. A model based on recently resolved structures of the bacteriophage T4 motor protein gp17 suggests that this motor generates large forces by undergoing a conformational change from an extended to a compact state. This transition is proposed to be driven by electrostatic interactions between complementarily charged residues across the interface between the N- and C-terminal domains of gp17. Here we use atomistic molecular dynamics simulations to investigate in detail the molecular interactions and residues involved in such a compaction transition of gp17. We find that although electrostatic interactions between charged residues contribute significantly to the overall free energy change of compaction, interactions mediated by the uncharged residues are equally if not more important. We identify five charged residues and six uncharged residues at the interface that play a dominant role in the compaction transition and also reveal salt bridging, van der Waals, and solvent hydrogen-bonding interactions mediated by these residues in stabilizing the compact form of gp17. The formation of a salt bridge between Glu309 and Arg494 is found to be particularly crucial, consistent with experiments showing complete abrogation in packaging upon Glu309Lys mutation. The computed contributions of several other residues are also found to correlate well with single-molecule measurements of impairments in DNA translocation activity caused by site-directed mutations. Copyright © 2014 Elsevier Ltd. All rights reserved.

Improved Interaction Potentials for Charged Residues in Proteins

DEFF Research Database (Denmark)

Kepp, Kasper Planeta

2008-01-01

Electrostatic interactions dominate the structure and free energy of biomolecules. To obtain accurate free energies involving charged groups from molecular simulations, OPLS-AA parameters have been reoptimized using Monte Carlo free energy perturbation. New parameters fit a self-consistent, exper......Electrostatic interactions dominate the structure and free energy of biomolecules. To obtain accurate free energies involving charged groups from molecular simulations, OPLS-AA parameters have been reoptimized using Monte Carlo free energy perturbation. New parameters fit a self......, 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...

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

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

Science.gov (United States)

Serçinoglu, Onur; Ozbek, Pemra

2018-05-25

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

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.

Hubbard-Stratonovich-like Transformations for Few-Body Inter-actions

Directory of Open Access Journals (Sweden)

Körber Christopher

2018-01-01

Full Text Available Through the development of many-body methodology and algorithms, it has become possible to describe quantum systems composed of a large number of particles with great accuracy. Essential to all these methods is the application of auxiliary fields via the Hubbard-Stratonovich transformation. This transformation effectively reduces two-body interactions to interactions of one particle with the auxiliary field, thereby improving the computational scaling of the respective algorithms. The relevance of collective phenomena and interactions grows with the number of particles. For many theories, e.g. Chiral Perturbation Theory, the inclusion of three-body forces has become essential in order to further increase the accuracy on the many-body level. In this proceeding, the an-alytical framework for establishing a Hubbard-Stratonovich-like transformation, which allows for the systematic and controlled inclusion of contact three-and more-body inter-actions, is presented.

Coherent Destruction of Tunneling of Bosons with Effective Three-Body Interactions

International Nuclear Information System (INIS)

Niu Zhen-Xia; Yu Zi-Fa; Xue Ju-Kui

2015-01-01

The tunneling dynamics of dilute boson gases with three-body interactions in a periodically driven double wells are investigated both theoretically and numerically. In our findings, when the system is with only repulsive two-body interactions or only three-body interactions, the tunneling will be suppressed; while in the case of the coupling between two- and three-body interactions, the tunneling can be either suppressed or enhanced. Particularly, when attractive three-body interactions are twice large as repulsive two-body interactions, CDT occurs at isolated points of driving force, which is similar to the linear case. Considering different interaction, the system can experience different transformation from coherent tunneling to coherent destruction of tunneling (CDT). The quasi-energy of the system as the function of the periodically driving force shows a triangular structure, which provides a deep insight into the tunneling dynamics of the system. (paper)

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.

The RING 2.0 web server for high quality residue interaction networks.

Science.gov (United States)

Piovesan, Damiano; Minervini, Giovanni; Tosatto, Silvio C E

2016-07-08

Residue interaction networks (RINs) are an alternative way of representing protein structures where nodes are residues and arcs physico-chemical interactions. RINs have been extensively and successfully used for analysing mutation effects, protein folding, domain-domain communication and catalytic activity. Here we present RING 2.0, a new version of the RING software for the identification of covalent and non-covalent bonds in protein structures, including π-π stacking and π-cation interactions. RING 2.0 is extremely fast and generates both intra and inter-chain interactions including solvent and ligand atoms. The generated networks are very accurate and reliable thanks to a complex empirical re-parameterization of distance thresholds performed on the entire Protein Data Bank. By default, RING output is generated with optimal parameters but the web server provides an exhaustive interface to customize the calculation. The network can be visualized directly in the browser or in Cytoscape. Alternatively, the RING-Viz script for Pymol allows visualizing the interactions at atomic level in the structure. The web server and RING-Viz, together with an extensive help and tutorial, are available from URL: http://protein.bio.unipd.it/ring. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

The empirical residual proton-neutron interaction and the onset of collectivity in nuclei

International Nuclear Information System (INIS)

Casten, R.F.

1991-01-01

The critical role of the residual valence p-n interaction in the development and evolution of collectivity, and the onset of shape/phase transitions, is discussed from the standpoint of phenomenological approaches, and empirical extraction of individual p-n interaction strengths, and simple model calculation of them. 22 refs., 18 figs

Exact calculation of three-body contact interaction to second order

International Nuclear Information System (INIS)

Kaiser, N.

2012-01-01

For a system of fermions with a three-body contact interaction the second-order contributions to the energy per particle anti E(k f ) are calculated exactly. The three-particle scattering amplitude in the medium is derived in closed analytical form from the corresponding two-loop rescattering diagram. We compare the (genuine) second-order three-body contribution to anti E(k f )∝k f 10 with the second-order term due to the density-dependent effective two-body interaction, and find that the latter term dominates. The results of the present study are of interest for nuclear many-body calculations where chiral three-nucleon forces are treated beyond leading order via a density-dependent effective two-body interaction. (orig.)

Shock/shock interactions between bodies and wings

Directory of Open Access Journals (Sweden)

Gaoxiang XIANG

2018-02-01

Full Text Available This paper examines the Shock/Shock Interactions (SSI between the body and wing of aircraft in supersonic flows. The body is simplified to a flat wedge and the wing is assumed to be a sharp wing. The theoretical spatial dimension reduction method, which transforms the 3D problem into a 2D one, is used to analyze the SSI between the body and wing. The temperature and pressure behind the Mach stem induced by the wing and body are obtained, and the wave configurations in the corner are determined. Numerical validations are conducted by solving the inviscid Euler equations in 3D with a Non-oscillatory and Non-free-parameters Dissipative (NND finite difference scheme. Good agreements between the theoretical and numerical results are obtained. Additionally, the effects of the wedge angle and sweep angle on wave configurations and flow field are considered numerically and theoretically. The influences of wedge angle are significant, whereas the effects of sweep angle on wave configurations are negligible. This paper provides useful information for the design and thermal protection of aircraft in supersonic and hypersonic flows. Keywords: Body and wing, Flow field, Hypersonic flow, Shock/shock interaction, Wave configurations

Many-body interactions in quasi-freestanding graphene

Energy Technology Data Exchange (ETDEWEB)

Siegel, David; Park, Cheol-Hwan; Hwang, Choongyu; Deslippe, Jack; Fedorov, Alexei; Louie, Steven; Lanzara, Alessandra

2011-06-03

The Landau-Fermi liquid picture for quasiparticles assumes that charge carriers are dressed by many-body interactions, forming one of the fundamental theories of solids. Whether this picture still holds for a semimetal such as graphene at the neutrality point, i.e., when the chemical potential coincides with the Dirac point energy, is one of the long-standing puzzles in this field. Here we present such a study in quasi-freestanding graphene by using high-resolution angle-resolved photoemission spectroscopy. We see the electron-electron and electron-phonon interactions go through substantial changes when the semimetallic regime is approached, including renormalizations due to strong electron-electron interactions with similarities to marginal Fermi liquid behavior. These findings set a new benchmark in our understanding of many-body physics in graphene and a variety of novel materials with Dirac fermions.

Moving android: on social robots and body-in-interaction.

Science.gov (United States)

Alac, Morana

2009-08-01

Social robotics studies embodied technologies designed for social interaction. This paper examines the implied idea of embodiment using as data a sequence in which practitioners of social robotics are involved in designing a robot's movement. The moments of learning and work in the laboratory enact the social body as material, dynamic, and multiparty: the body-in-interaction. In describing subject-object reconfigurations, the paper explores how the well-known ideas of extending the body with instruments can be applied to a technology designed to function as our surrogate.

Association of body mass index with decline in residual kidney function after initiation of dialysis

NARCIS (Netherlands)

Drechsler, Christiane; de Mutsert, Renée; Grootendorst, Diana C.; Boeschoten, Elisabeth W.; Krediet, Raymond T.; le Cessie, Saskia; Wanner, Christoph; Dekker, Friedo W.; Apperloo, A. J.; Bijlsma, J. A.; Boekhout, M.; Boer, W. H.; Büller, H. R.; de Charro, F. T. H.; de Fijter, C. W. H.; Doorenbos, C. J.; Fagel, W. J.; Feith, G. W.; Frenken, L. A. M.; Gerlag, P. G. G.; Gorgels, J. P. M. C.; Grave, W.; Huisman, R. M.; Jager, K. J.; Jie, K.; Koning-Mulder, W. A. H.; Koolen, M. I.; Kremer Hovinga, T. K.; Lavrijssen, A. T. J.; Luik, A. J.; Parlevliet, K. J.; Raasveld, M. H. M.; Schonck, M. J. M.; Schuurmans, M. M. J.; Siegert, C. E. H.; Stegeman, C. A.; Stevens, P.; Thijssen, J. G. P.; Valentijn, R. M.; van Buren, M.; van den Dorpel, M. A.; van der Boog, P. J. M.; van der Meulen, J.; van der Sande, F. M.; van Es, A.; van Geelen, J. A. C. A.; Vastenburg, G. H.; Verburgh, C. A.; Vincent, H. H.; Vos, P. F.

2009-01-01

BACKGROUND: Obesity is a risk factor for loss of kidney function in the general population, but it is unknown whether it proceeds to affect residual kidney function when patients require dialysis. Our aim was to study the effects of body mass index (BMI) on decline in kidney function and risk to

Sampling general N-body interactions with auxiliary fields

Science.gov (United States)

Körber, C.; Berkowitz, E.; Luu, T.

2017-09-01

We present a general auxiliary field transformation which generates effective interactions containing all possible N-body contact terms. The strength of the induced terms can analytically be described in terms of general coefficients associated with the transformation and thus are controllable. This transformation provides a novel way for sampling 3- and 4-body (and higher) contact interactions non-perturbatively in lattice quantum Monte Carlo simulations. As a proof of principle, we show that our method reproduces the exact solution for a two-site quantum mechanical problem.

Screening of Coulomb interaction and many-body perturbation theory in atoms

International Nuclear Information System (INIS)

Dzyuba, V.A.; Flambaum, V.V.; Sil'vestrov, P.G.; Sushkov, O.P.

1988-01-01

Taking into account the electron Coulomb interaction screening considerably improves the convergence of perturbation theory in residual interaction. The developed technique allows to take into account screening diagrams in all orders of perturbation theory. Calculation of the correlation corrections to the thallium energy levels is carried out as an example

[A Concept Analysis for Mind-Body Interaction].

Science.gov (United States)

Chen, Hsing-Wen; Yeh, Mei-Ling; Rong, Jiin-Ru

2015-08-01

Mind-body interaction (MBI) refers the holistic association and interactive process between wisdom, thinking, belief, and physiological reaction, which critically affects health. The main goal of nursing is to maintain mind and body in a healthy state of well being. Few reports in the literatures have addressed the evaluation and application of MBI. Thus, a conceptual analysis of this subject is worth exploring in depth. This paper analyzes the MBI concept step by step based on the procedures of Walker and Avant. The result defines the characteristics of MBI as (1) being aware of psychosomatic effects, (2) interacting between psychology, neurology, immunology and others, and (3) turning out a bio-psycho-social status. Antecedents include geography, culture, race, gender, age, education, profession, values, personality, experience, and health status. Consequences of MBI include well-being, illness, and death. This paper provides new information on MBI that clarifies its meaning, provides comprehensive cognition, and suggests useful applications.

Rigid body formulation in a finite element context with contact interaction

Science.gov (United States)

Refachinho de Campos, Paulo R.; Gay Neto, Alfredo

2018-03-01

The present work proposes a formulation to employ rigid bodies together with flexible bodies in the context of a nonlinear finite element solver, with contact interactions. Inertial contributions due to distribution of mass of a rigid body are fully developed, considering a general pole position associated with a single node, representing a rigid body element. Additionally, a mechanical constraint is proposed to connect a rigid region composed by several nodes, which is useful for linking rigid/flexible bodies in a finite element environment. Rodrigues rotation parameters are used to describe finite rotations, by an updated Lagrangian description. In addition, the contact formulation entitled master-surface to master-surface is employed in conjunction with the rigid body element and flexible bodies, aiming to consider their interaction in a rigid-flexible multibody environment. New surface parameterizations are presented to establish contact pairs, permitting pointwise interaction in a frictional scenario. Numerical examples are provided to show robustness and applicability of the methods.

On the many-body foundation of the nuclear field theory

International Nuclear Information System (INIS)

Bes, D.R.; Dussel, G.G.; Liotta, R.J.; Perazzo, R.P.J.; Broglia, R.A.

1976-01-01

The equivalence between the description of the many-body finite nuclear system in terms of Feynman diagrams involving only the fermion degrees of freedom and of Feynman diagrams involving fermion and phonon degrees of freedom is proved for intermediate states in the case of a general two-body residual interaction. (Auth.)

Human body micro-environment: The benefits of controlling airflow interaction

DEFF Research Database (Denmark)

Melikov, Arsen Krikor

2015-01-01

This paper focuses on the micro-environment around a human body, and especially on its interaction with the surrounding environment. Research on the free convection flow generated by a human body (including the convective boundary layer around the body and the thermal plume above the body), its...

Integrability and chaos in body-vortex interactions

DEFF Research Database (Denmark)

Pedersen, Johan Rønby; Aref, Hassan

2009-01-01

. The equations of motion may be cast in Hamiltonian form. We analyze the equations of motion using techniques from the theory of dynamical systems. The simplest such system, a single point vortex and a circular body, is integrable. As we add vortices, or change other features of the system such as the body shape......, the motion may become chaotic. Numerical solutions are shown and analyzed with an emphasis on the transition to chaos and its physical meaning. This class of systems provides a rich family of few-degree-of-freedom systems that capture essential fluid-body interaction physics....

Four-body interaction energy for compressed solid krypton from quantum theory.

Science.gov (United States)

Tian, Chunling; Wu, Na; Liu, Fusheng; Saxena, Surendra K; Zheng, Xingrong

2012-07-28

The importance of the four-body contribution in compressed solid krypton was first evaluated using the many-body expansion method and the coupled cluster theory with full single and double excitations plus perturbative treatment of triples. All different four-atom clusters existing in the first- and second-nearest neighbor shells of face-centered cubic krypton were considered, and both self-consistent-field Hartree-Fock and correlation parts of the four-body interaction were accurately determined from the ambient conditions up to eightfold volume compression. We find that the four-body interaction energy is negative at compression ratio lower than 2, where the dispersive forces play a dominant role. With increasing the compression, the four-body contribution becomes repulsive and significantly cancels the over-softening effects of the three-body potential. The obtained equation of state (EOS) was compared with the experiments and the density-functional theory calculations. It shows that combination of the four-body effects with two- and three-body interactions leads to an excellent agreement with EOS measurements throughout the whole experimental range 0-130 GPa, and extends the prediction to 300 GPa.

Effects of three-body interactions on the dynamics of entanglement in spin chains

International Nuclear Information System (INIS)

Shi Cuihua; Wu Yinzhong; Li Zhenya

2009-01-01

With the consideration of three-body interaction, dynamics of pairwise entanglement in spin chains is studied. The dependence of pairwise entanglement dynamics on the type of coupling, and distance between the spins is analyzed in a finite chain for different initial states. It is found that, for an Ising chain, three-body interactions are not in favor of preparing entanglement between the nearest neighbor spins, while three-body interactions are favorable for creating entanglement between remote spins from a separable initial state. For an isotropic Heisenberg chain, the pairwise concurrence will decrease when three-body interactions are considered both for a separable initial state and for a maximally entangled initial state, however, three-body interactions will retard the decay of the concurrence in an Ising chain when the initial state takes the maximally entangled state.

Baseline toxicity of a chlorobenzene mixture and total body residues measured and estimated with solid-phase microextraction

NARCIS (Netherlands)

Leslie, H.A.; Hermens, J.L.; Kraak, M.H.S.

2004-01-01

Body residues of compounds with a narcotic mode of action that exceed critical levels result in baseline toxicity in organisms. Previous studies have shown that internal concentrations in organisms also can be estimated by way of passive sampling. In this experiment, solid-phase microextraction

Tidal interaction of black holes and Newtonian viscous bodies

International Nuclear Information System (INIS)

Poisson, Eric

2009-01-01

The tidal interaction of a (rotating or nonrotating) black hole with nearby bodies produces changes in its mass, angular momentum, and surface area. Similarly, tidal forces acting on a Newtonian, viscous body do work on the body, change its angular momentum, and part of the transferred gravitational energy is dissipated into heat. The equations that describe the rate of change of the black-hole mass, angular momentum, and surface area as a result of the tidal interaction are compared with the equations that describe how the tidal forces do work, torque, and produce heat in the Newtonian body. The equations are strikingly similar, and unexpectedly, the correspondence between the Newtonian-body and black-hole results is revealed to hold in near-quantitative detail. The correspondence involves the combination k 2 τ of 'Love quantities' that incorporate the details of the body's internal structure; k 2 is the tidal Love number, and τ is the viscosity-produced delay between the action of the tidal forces and the body's reaction. The combination k 2 τ is of order GM/c 3 for a black hole of mass M; it does not vanish, in spite of the fact that k 2 is known to vanish individually for a nonrotating black hole.

Mind-Body Interactions in Anxiety and Somatic Symptoms.

Science.gov (United States)

Mallorquí-Bagué, Núria; Bulbena, Antonio; Pailhez, Guillem; Garfinkel, Sarah N; Critchley, Hugo D

2016-01-01

Anxiety and somatic symptoms have a high prevalence in the general population. A mechanistic understanding of how different factors contribute to the development and maintenance of these symptoms, which are highly associated with anxiety disorders, is crucial to optimize treatments. In this article, we review recent literature on this topic and present a redefined model of mind-body interaction in anxiety and somatic symptoms, with an emphasis on both bottom-up and top-down processes. Consideration is given to the role played in this interaction by predisposing physiological and psychological traits (e.g., interoception, anxiety sensitivity, and trait anxiety) and to the levels at which mindfulness approaches may exert a therapeutic benefit. The proposed model of mind-body interaction in anxiety and somatic symptoms is appraised in the context of joint hypermobility syndrome, a constitutional variant associated with autonomic abnormalities and vulnerability to anxiety disorders.

Classical many-body theory with retarded interactions: Dynamical irreversibility and determinism without probabilities

Energy Technology Data Exchange (ETDEWEB)

Zakharov, A.Yu., E-mail: Anatoly.Zakharov@novsu.ru; Zakharov, M.A., E-mail: ma_zakharov@list.ru

2016-01-28

The exact equations of motion for microscopic density of classical many-body system with account of inter-particle retarded interactions is derived. It is shown that interactions retardation leads to irreversible behavior of many-body systems. - Highlights: • A new form of equation of motion of classical many-body system is proposed. • Interactions retardation as one of the mechanisms of many-body system irreversibility. • Irreversibility and determinism without probabilities. • The possible way to microscopic foundation of thermodynamics.

Three-body interactions and the elastic constants of hcp solid 4He

Science.gov (United States)

Barnes, Ashleigh L.; Hinde, Robert J.

2017-09-01

The effect of three-body interactions on the elastic properties of hexagonal close packed solid 4He is investigated using variational path integral (VPI) Monte Carlo simulations. The solid's nonzero elastic constants are calculated, at T = 0 K and for a range of molar volumes from 7.88 cm3/mol to 20.78 cm3/mol, from the bulk modulus and the three pure shear constants C0, C66, and C44. Three-body interactions are accounted for using our recently reported perturbative treatment based on the nonadditive three-body potential of Cencek et al. Previous studies have attempted to account for the effect of three-body interactions on the elastic properties of solid 4He; however, these calculations have treated zero point motions using either the Einstein or Debye approximations, which are insufficient in the molar volume range where solid 4He is characterized as a quantum solid. Our VPI calculations allow for a more accurate treatment of the zero point motions which include atomic correlation. From these calculations, we find that agreement with the experimental bulk modulus is significantly improved when three-body interactions are considered. In addition, three-body interactions result in non-negligible differences in the calculated pure shear constants and nonzero elastic constants, particularly at higher densities, where differences of up to 26.5% are observed when three-body interactions are included. We compare to the available experimental data and find that our results are generally in as good or better agreement with experiment as previous theoretical investigations.

A computational tool to predict the evolutionarily conserved protein-protein interaction hot-spot residues from the structure of the unbound protein.

Science.gov (United States)

Agrawal, Neeraj J; Helk, Bernhard; Trout, Bernhardt L

2014-01-21

Identifying hot-spot residues - residues that are critical to protein-protein binding - can help to elucidate a protein's function and assist in designing therapeutic molecules to target those residues. We present a novel computational tool, termed spatial-interaction-map (SIM), to predict the hot-spot residues of an evolutionarily conserved protein-protein interaction from the structure of an unbound protein alone. SIM can predict the protein hot-spot residues with an accuracy of 36-57%. Thus, the SIM tool can be used to predict the yet unknown hot-spot residues for many proteins for which the structure of the protein-protein complexes are not available, thereby providing a clue to their functions and an opportunity to design therapeutic molecules to target these proteins. Copyright © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Three-body interactions and the Landau levels using Nikiforov ...

Indian Academy of Sciences (India)

In this article, the eigenvalues for the three-body interactions on the line and the Landau levels in the presence of topological defects have been regenerated by the Nikiforov–Uvarov (NU) method. Two exhaustive lists of such exactly solvable potentials are given. Keywords. Nikiforov–Uvarov (NU) method; three-body ...

Aging/Systems Interaction Study, Component Residual Lifetime Evaluation and Feasibility of Relicensing. Progress report, FY 1985

International Nuclear Information System (INIS)

Close, J.A.; Jacobs, P.T.; Korth, G.E.; Mudlin, J.M.; Server, W.L.; Spaletta, H.W.

1985-10-01

This report documents the work performed on four research tasks in Fiscal Year 1985 (FY-1985) which were part of the Aging/Systems Interaction Study, Component Residual Lifetime Evaluation and Feasibility of Relicensing Project. The technical and management/institutional objectives for the project are described, followed by a description of the results of each task. The work on Task 1 involved identifying and prioritizing new research activities for the Nuclear Regulatory Commission (NRC) Nuclear Plant Aging Research (NPAR) Program. A proposed methodology and plan for aging-system interaction studies was developed in Task 2. The description of Task 3 work comprises a summary of nuclear plant life extension activities in the US, the technical basis associated with the residual life of metallic materials and a proposed plan for research on residual life assessment. Task 4 describes the initial evaluation of selected Standard Review Plan (NUREG-0800) sections to investigate the feasibility of relicensing. 14 refs., 13 figs., 20 tabs

Modulating Transmembrane α-Helix Interactions through pH-Sensitive Boundary Residues.

Science.gov (United States)

Ng, Derek P; Deber, Charles M

2016-08-09

Changes in pH can alter the structure and activity of proteins and may be used by the cell to control molecular function. This coupling can also be used in non-native applications through the design of pH-sensitive biomolecules. For example, the pH (low) insertion peptide (pHLIP) can spontaneously insert into a lipid bilayer when the pH decreases. We have previously shown that the α-helicity and helix-helix interactions of the TM2 α-helix of the proteolipid protein (PLP) are sensitive to the local hydrophobicity at its C-terminus. Given that there is an ionizable residue (Glu-88) at the C-terminus of this transmembrane (TM) segment, we hypothesized that changing the ionization state of this residue through pH may alter the local hydrophobicity of the peptide enough to affect both its secondary structure and helix-helix interactions. To examine this phenomenon, we synthesized peptide analogues of the PLP TM2 α-helix (wild-type sequence (66)AFQYVIYGTASFFFLYGALLLAEGF(90)). Using circular dichroism and Förster resonance energy transfer in the membrane-mimetic detergent sodium dodecyl sulfate, we found that a decrease in pH increases both peptide α-helicity and the extent of self-association. This pH-dependent effect is due specifically to the presence of Glu-88 at the C-terminus. Additional experiments in which Phe-90 was mutated to residues of varying hydrophobicities indicated that the strength of this effect is dependent on the local hydrophobicity near Glu-88. Our results have implications for the design of TM peptide switches and improve our understanding of how membrane protein structure and activity can be regulated through local molecular environmental changes.

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

Highly Enhanced Many-Body Interactions in Anisotropic 2D Semiconductors.

Science.gov (United States)

Sharma, Ankur; Yan, Han; Zhang, Linglong; Sun, Xueqian; Liu, Boqing; Lu, Yuerui

2018-05-15

Atomically thin two-dimensional (2D) semiconductors have presented a plethora of opportunities for future optoelectronic devices and photonics applications, made possible by the strong light matter interactions at the 2D quantum limit. Many body interactions between fundamental particles in 2D semiconductors are strongly enhanced compared with those in bulk semiconductors because of the reduced dimensionality and, thus, reduced dielectric screening. These enhanced many body interactions lead to the formation of robust quasi-particles, such as excitons, trions, and biexcitons, which are extremely important for the optoelectronics device applications of 2D semiconductors, such as light emitting diodes, lasers, and optical modulators, etc. Recently, the emerging anisotropic 2D semiconductors, such as black phosphorus (termed as phosphorene) and phosphorene-like 2D materials, such as ReSe 2 , 2D-perovskites, SnS, etc., show strong anisotropic optical and electrical properties, which are different from conventional isotropic 2D semiconductors, such as transition metal dichalcogenide (TMD) monolayers. This anisotropy leads to the formation of quasi-one-dimensional (quasi-1D) excitons and trions in a 2D system, which results in even stronger many body interactions in anisotropic 2D materials, arising from the further reduced dimensionality of the quasi-particles and thus reduced dielectric screening. Many body interactions have been heavily investigated in TMD monolayers in past years, but not in anisotropic 2D materials yet. The quasi-particles in anisotropic 2D materials have fractional dimensionality which makes them perfect candidates to serve as a platform to study fundamental particle interactions in fractional dimensional space. In this Account, we present our recent progress related to 2D phosphorene, a 2D system with quasi-1D excitons and trions. Phosphorene, because of its unique anisotropic properties, provides a unique 2D platform for investigating the

Two-body problem for Weber-like interactions

International Nuclear Information System (INIS)

Clemente, R.A.; Assis, A.K.T.

1991-01-01

The problem of two moving bodies interacting through a Weber-like force is presented. Trajectories are obtained analytically once relativistic and quantic considerations are neglected. The main results are that in the case of limited trajectories, in general, they are not closed and in the case of open trajectories, the deflection angles are not the same for similar particles with given energies and angular momenta but opposite potentials. This last feature suggests the possibility of a direct verification of the validity of Weber's law of force for electromagnetic interactions

Similarity of multi-fragmentation of residual nucleus created in nucleus-nucleus interactions at high energies

International Nuclear Information System (INIS)

Abdel-Hafiez, A.; Chernyavski, M.M.; Orlova, G.I.; Gulamov, K.G.; Navotny, V.SH.; Uzhinskii, V.V.

2000-01-01

Experimental data on multi-fragmentation of residual krypton nuclei created in the interactions of the krypton nuclei with photoemulsion nuclei ut energy of 0.9 GeV per nucleon are presented in a comparison with the analogous data on fragmentation of gold residual nuclei at the energy of 10.7 GeV/nucleon. It is shown for the first time that there are two regimes of nuclear multifragmentation: the former is when less than one-half of nucleons of projectile nucleus are knocked out, the later is when more than one-half of nucleons are knocked out. Residual nuclei with closed masses created at different reactions are fragmenting practically simultaneously when more than one-half of nucleons of original nuclei are knocked out. The evidence of existence of a radial flow of the spectator fragment at the decay of residual krypton nuclei is found

Simulations of collisions between N-body classical systems in interaction

International Nuclear Information System (INIS)

Morisseau, Francois

2006-05-01

The Classical N-body Dynamics (CNBD) is dedicated to the simulation of collisions between classical systems. The 2-body interaction used here has the properties of the Van der Waals potential and depends on just a few parameters. This work has two main goals. First, some theoretical approaches assume that the dynamical stage of the collisions plays an important role. Moreover, colliding nuclei are supposed to present a 1. order liquid-gas phase transition. Several signals have been introduced to show this transition. We have searched for two of them: the bimodality of the mass asymmetry and negative heat capacity. We have found them and we give an explanation of their presence in our calculations. Second, we have improved the interaction by adding a Coulomb like potential and by taking into account the stronger proton-neutron interaction in nuclei. Then we have figured out the relations that exist between the parameters of the 2-body interaction and the properties of the systems. These studies allow us to fit the properties of the classical systems to those of the nuclei. In this manuscript the first results of this fit are shown. (author)

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

Science.gov (United States)

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

2014-08-19

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

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.

Directory of Open Access Journals (Sweden)

Amanda Tse

Full Text Available 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

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

Computational Prediction of Hot Spot Residues

Science.gov (United States)

Morrow, John Kenneth; Zhang, Shuxing

2013-01-01

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

Error-transparent evolution: the ability of multi-body interactions to bypass decoherence

International Nuclear Information System (INIS)

Vy, Os; Jacobs, Kurt; Wang Xiaoting

2013-01-01

We observe that multi-body interactions, unlike two-body interactions, can implement any unitary operation on an encoded system in such a way that the evolution is uninterrupted by noise that the encoding is designed to protect against. Such ‘error-transparent’ evolution is distinct from that usually considered in quantum computing, as the latter is merely correctable. We prove that the minimum body-ness required to protect (i) a qubit from a single type of Pauli error, (ii) a target qubit from a controller with such errors and (iii) a single qubit from all errors is three-body, four-body and five-body, respectively. We also discuss applications to computing, coherent feedback control and quantum metrology. Finally, we evaluate the performance of error-transparent evolution for some examples using numerical simulations. (paper)

Investigations of the structure and electromagnetic interactions of few-body systems

International Nuclear Information System (INIS)

Lehman, D.R.; Haberzettl, H.; Maximon, L.C.; Parke, W.C.; Bennhold, C.; Ito, Hiroshi; Pratt, R.K.; Najmeddine, M.; Rakei, A.

1993-07-01

The emphasis of the nuclear theory group has been on the structure and electromagnetic interactions of few-body nuclei. Both low- and intermediate-energy electromagnetic disintegration of these nuclei is considered, including coherent photoproduction of π mesons. When the excitation energy of the target nucleus is low, the aim is to handle the continuum part of the theoretical work numerically with no approximations, that is, by means of full three- or four-body dynamics. When structure questions are the issue, numerically accurate calculations are always carried through, limited only by the underlying two-body or three-body interactions used as input. A central goal is to carry through state-of-the-art few-body calculations that will serve as a means of determining at what point standard nuclear physics requires introduction of relativity and/or quark degrees of freedom in order to understand the phenomena in question

Experimental studies on the elimination of minimal residual leukemia in vivo by alternate half body irradiation

International Nuclear Information System (INIS)

Chu Jianxin

1992-01-01

The purpose of this study is to develop a new way for leukemia patients to tolerate an ablative chemoradiotherapy without BMT. Previous studies had demonstrated that only a few leukemia cells remained in the body during remission phase following chemotherapy and did not migrate to distant organs via the circulation until they had given rise to 3 ∼ 4 x 10 5 new cells. The period required for such growth was about 20 days. However, hematopoietic stem cells migrate earlier than do leukemia cells. Therefore, alternate half body irradiation (HBI) within this period would kill the residual leukemia cells, but hematopoietic stem cells would migrate from shielded marrow to irradiated marrow and reconstruct hematopoiesis

Computational investigation of large-scale vortex interaction with flexible bodies

Science.gov (United States)

Connell, Benjamin; Yue, Dick K. P.

2003-11-01

The interaction of large-scale vortices with flexible bodies is examined with particular interest paid to the energy and momentum budgets of the system. Finite difference direct numerical simulation of the Navier-Stokes equations on a moving curvilinear grid is coupled with a finite difference structural solver of both a linear membrane under tension and linear Euler-Bernoulli beam. The hydrodynamics and structural dynamics are solved simultaneously using an iterative procedure with the external structural forcing calculated from the hydrodynamics at the surface and the flow-field velocity boundary condition given by the structural motion. We focus on an investigation into the canonical problem of a vortex-dipole impinging on a flexible membrane. It is discovered that the structural properties of the membrane direct the interaction in terms of the flow evolution and the energy budget. Pressure gradients associated with resonant membrane response are shown to sustain the oscillatory motion of the vortex pair. Understanding how the key mechanisms in vortex-body interactions are guided by the structural properties of the body is a prerequisite to exploiting these mechanisms.

Substantial conformational change mediated by charge-triad residues of the death effector domain in protein-protein interactions.

Directory of Open Access Journals (Sweden)

Edward C Twomey

Full Text Available Protein conformational changes are commonly associated with the formation of protein complexes. The non-catalytic death effector domains (DEDs mediate protein-protein interactions in a variety of cellular processes, including apoptosis, proliferation and migration, and glucose metabolism. Here, using NMR residual dipolar coupling (RDC data, we report a conformational change in the DED of the phosphoprotein enriched in astrocytes, 15 kDa (PEA-15 protein in the complex with a mitogen-activated protein (MAP kinase, extracellular regulated kinase 2 (ERK2, which is essential in regulating ERK2 cellular distribution and function in cell proliferation and migration. The most significant conformational change in PEA-15 happens at helices α2, α3, and α4, which also possess the highest flexibility among the six-helix bundle of the DED. This crucial conformational change is modulated by the D/E-RxDL charge-triad motif, one of the prominent structural features of DEDs, together with a number of other electrostatic and hydrogen bonding interactions on the protein surface. Charge-triad motif promotes the optimal orientation of key residues and expands the binding interface to accommodate protein-protein interactions. However, the charge-triad residues are not directly involved in the binding interface between PEA-15 and ERK2.

The Casimir interaction of a massive vector field between concentric spherical bodies

International Nuclear Information System (INIS)

Teo, L.P.

2011-01-01

The Casimir interaction energy due to the vacuum fluctuations of a massive vector field between two perfectly conducting concentric spherical bodies is computed. The TE contribution to the Casimir interaction energy is a direct generalization of the massless case but the TM contribution is much more complicated. Each TM mode is a linear combination of a transverse mode which is the generalization of a TM mode in the massless case and a longitudinal mode that does not appear in the massless case. In contrast to the case of two parallel perfectly conducting plates, there are no TM discrete modes that vanish identically in the perfectly conducting spherical bodies. Numerical simulations show that the Casimir interaction force between the two bodies is always attractive.

Multinucleon Ejection Model for Two Body Current Neutrino Interactions

Energy Technology Data Exchange (ETDEWEB)

Sobczyk, Jan T.; /Fermilab

2012-06-01

A model is proposed to describe nucleons ejected from a nucleus as a result of two-body-current neutrino interactions. The model can be easily implemented in Monte Carlo neutrino event generators. Various possibilities to measure the two-body-current contribution are discussed. The model can help identify genuine charge current quasielastic events and allow for a better determination of the systematic error on neutrino energy reconstruction in neutrino oscillation experiments.

Three-body interactions in sociophysics and their role in coalition forming

Science.gov (United States)

Naumis, Gerardo G.; Samaniego-Steta, F.; del Castillo-Mussot, M.; Vázquez, G. J.

2007-06-01

An study of the effects of three-body interactions in the process of coalition formation is presented. In particular, we modify a spin glass model of bimodal propensities and also a Potts model in order to include a particular three-body Hamiltonian that reproduces the main features of the required interactions. The model can be used to study conflicts, political struggles, political parties, social networks, wars and organizational structures. As an application, we analyze a simplified model of the Iraq war.

Residual stresses

International Nuclear Information System (INIS)

Macherauch, E.

1978-01-01

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

Computational prediction of protein hot spot residues.

Science.gov (United States)

Morrow, John Kenneth; Zhang, Shuxing

2012-01-01

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

Residual stresses

International Nuclear Information System (INIS)

Sahotra, I.M.

2006-01-01

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

Two-body tensor interactions in the nuclear matter response function

International Nuclear Information System (INIS)

Besprosvany, J.

1997-01-01

The inclusive scattering response of nuclear matter is studied in the regime of large momentum transfer q, and around the quasielastic peak. We review interaction corrections to free propagation as embodied in the impulse approximation. Calculations of the two-body and many-body corrections within an eikonal approach are presented. These use an approximated two-body density matrix which takes account of spin and isospin degrees of freedom. Both calculations give similar and sizable corrections at q = 550 MeV and reproduce data extrapolated from finite nuclei; this indicates the relevance of two-body tensor contributions in this regime. (Author)

Parallel Vortex Body Interaction Enabled by Active Flow Control

Science.gov (United States)

Weingaertner, Andre; Tewes, Philipp; Little, Jesse

2017-11-01

An experimental study was conducted to explore the flow physics of parallel vortex body interaction between two NACA 0012 airfoils. Experiments were carried out at chord Reynolds numbers of 740,000. Initially, the leading airfoil was characterized without the target one being installed. Results are in good agreement with thin airfoil theory and data provided in the literature. Afterward, the leading airfoil was fixed at 18° incidence and the target airfoil was installed 6 chord lengths downstream. Plasma actuation (ns-DBD), originating close to the leading edge, was used to control vortex shedding from the leading airfoil at various frequencies (0.04 governing parameters of this vortex body interaction are explored. This work was supported by the Army Research Office under ARO Grant No. W911NF-14-1-0662.

Effects of three-body interactions in the parametric and modulational instabilities of Bose–Einstein condensates

International Nuclear Information System (INIS)

Wamba, Etienne; Mohamadou, Alidou; Ekogo, Thierry B.; Atangana, Jacque; Kofane, Timoleon C.

2011-01-01

The parametric modulational instability for a discrete nonlinear Schrödinger equation with a cubic–quintic nonlinearity is analyzed. This model describes the dynamics of BECs, with both two- and three-body interatomic interactions trapped in an optical lattice. We identify and discuss the salient features of the three-body interaction in the parametric modulational instability. It is shown that the three-body interaction term can both, shift as well as narrow the window of parametric instability, and also change the behavior of a modulationally stable and parametrically unstable BEC with attractive two-body interaction. We explore this instability through the multiple-scale analysis and identify it numerically. The effect of the three body losses have also been investigated. -- Highlights: ► The parametric MI for the 1D GPE with a cubic–quintic nonlinearity is analyzed. ► The two- and three-body recombination and time-dependent scattering length is considered. ► We generate bright matter waves soliton through MI.

Dependence of the frequency spectrum of small amplitude vibrations superimposed on finite deformations of a nonlinear, cylindrical elastic body on residual stress

KAUST Repository

Gorb, Yuliya; Walton, Jay R.

2010-01-01

We model and analyze the response of nonlinear, residually stressed elastic bodies subjected to small amplitude vibrations superimposed upon large deformations. The problem derives from modeling the use of intravascular ultrasound (IVUS) imaging

The self-consistent field model for Fermi systems with account of three-body interactions

Directory of Open Access Journals (Sweden)

Yu.M. Poluektov

2015-12-01

Full Text Available On the basis of a microscopic model of self-consistent field, the thermodynamics of the many-particle Fermi system at finite temperatures with account of three-body interactions is built and the quasiparticle equations of motion are obtained. It is shown that the delta-like three-body interaction gives no contribution into the self-consistent field, and the description of three-body forces requires their nonlocality to be taken into account. The spatially uniform system is considered in detail, and on the basis of the developed microscopic approach general formulas are derived for the fermion's effective mass and the system's equation of state with account of contribution from three-body forces. The effective mass and pressure are numerically calculated for the potential of "semi-transparent sphere" type at zero temperature. Expansions of the effective mass and pressure in powers of density are obtained. It is shown that, with account of only pair forces, the interaction of repulsive character reduces the quasiparticle effective mass relative to the mass of a free particle, and the attractive interaction raises the effective mass. The question of thermodynamic stability of the Fermi system is considered and the three-body repulsive interaction is shown to extend the region of stability of the system with the interparticle pair attraction. The quasiparticle energy spectrum is calculated with account of three-body forces.

Effect of three-body interactions on the zero-temperature equation of state of HCP solid 4He

Science.gov (United States)

Barnes, Ashleigh L.; Hinde, Robert J.

2017-03-01

Previous studies have pointed to the importance of three-body interactions in high density 4He solids. However the computational cost often makes it unfeasible to incorporate these interactions into the simulation of large systems. We report the implementation and evaluation of a computationally efficient perturbative treatment of three-body interactions in hexagonal close packed solid 4He utilizing the recently developed nonadditive three-body potential of Cencek et al. This study represents the first application of the Cencek three-body potential to condensed phase 4He systems. Ground state energies from quantum Monte Carlo simulations, with either fully incorporated or perturbatively treated three-body interactions, are calculated in systems with molar volumes ranging from 21.3 cm3/mol down to 2.5 cm3/mol. These energies are used to derive the zero-temperature equation of state for comparison against existing experimental and theoretical data. The equations of state derived from both perturbative and fully incorporated three-body interactions are found to be in very good agreement with one another, and reproduce the experimental pressure-volume data with significantly better accuracy than is obtained when only two-body interactions are considered. At molar volumes below approximately 4.0 cm3/mol, neither two-body nor three-body equations of state are able to accurately reproduce the experimental pressure-volume data, suggesting that below this molar volume four-body and higher many-body interactions are becoming important.

Chaos and Integrability in Ideal Body-Fluid Interactions

DEFF Research Database (Denmark)

Pedersen, Johan Rønby

2011-01-01

by generating Poincare sections from numerically obtained solutions. By identifying the chaotic solutions and studying the body and vortex orbits, we obtain a better mechanistic understanding of the causes of chaotic behavior. As is well-known from dynamical system theory, the chaos can often be traced back...... of relative equilibria, their stability, and the qualitatively dierent kinds of motion is studied analytically and numerically. We then perform small parametric perturbations destroying the symmetry or conservation law that makes the system integrable. The emergence of chaos in the system is diagnosed...... contains both regular and chaotic regions, and may be understood from KAM theory. We also discover two separate chaotic regimes in the interaction of a body and one point vortex when the body is either noncircular or has asymmetric internal mass distribution. For one of these chaotic regimes the eect...

CCHCR1 interacts with EDC4, suggesting its localization in P-bodies

Energy Technology Data Exchange (ETDEWEB)

Ling, Y.H.; Wong, C.C. [School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong (China); Li, K.W. [Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, 1081 HV Amsterdam (Netherlands); Chan, K.M. [School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong (China); Boukamp, P. [Division of Genetics of Skin Carcinogenesis, A110 German Cancer Research Center, Im Neuenheimer Feld 280, D-69120 Heidelberg (Germany); Liu, W.K., E-mail: ken-liu@cuhk.edu.hk [School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong (China)

2014-09-10

Coiled‐coil alpha‐helical rod protein 1 (CCHCR1) is suggested as a candidate biomarker for psoriasis for more than a decade but its function remains poorly understood because of the inconsistent findings in the literature. CCHCR1 protein is suggested to be localized in the cytoplasm, nucleus, mitochondria, or centrosome and to regulate various cellular functions, including steroidogenesis, proliferation, differentiation, and cytoskeleton organization. In this study, we attempted to find a consensus between these findings by identifying the interaction partners of CCHCR1 using co-immunoprecipiation with a stable cell line expressing EGFP-tagged CCHCR1. Out of more than 100 co-immunoprecipitants identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS), the enhancer of mRNA-decapping protein 4 (EDC4), which is a processing body (P-body) component, was particularly found to be the major interacting partner of CCHCR1. Confocal imaging confirmed the localization of CCHCR1 in P-bodies and its N-terminus is required for this subcellular localization, suggesting that CCHCR1 is a novel P-body component. As P-bodies are the site for mRNA metabolism, our findings provide a molecular basis for the function of CCHCR1, any disruption of which may affect the transcriptome of the cell, and causing abnormal cell functions. - Highlights: • We identified CCHCR1 as a novel P-body component. • We identified EDC4 as the major interacting partner of CCHCR1. • N-terminus of CCHCR1 protein is required for its P-bodies localization.

Stability of the trapped nonconservative Gross-Pitaevskii equation with attractive two-body interaction

International Nuclear Information System (INIS)

Filho, Victo S.; Tomio, Lauro; Frederico, T.; Gammal, Arnaldo

2002-01-01

The dynamics of a nonconservative Gross-Pitaevskii equation for trapped atomic systems with attractive two-body interaction is numerically investigated, considering wide variations of the nonconservative parameters, related to atomic feeding and dissipation. We study the possible limitations of the mean-field description for an atomic condensate with attractive two-body interaction, by defining the parameter regions, where stable or unstable formation can be found. The present study is useful and timely considering the possibility of large variations of attractive two-body scattering lengths, which may be feasible in recent experiments

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.

On the analysis of protein-protein interactions via knowledge-based potentials for the prediction of protein-protein docking

DEFF Research Database (Denmark)

Feliu, Elisenda; Aloy, Patrick; Oliva, Baldo

2011-01-01

Development of effective methods to screen binary interactions obtained by rigid-body protein-protein docking is key for structure prediction of complexes and for elucidating physicochemical principles of protein-protein binding. We have derived empirical knowledge-based potential functions for s...... and with independence of the partner. This information is encoded at the residue level and could be easily incorporated in the initial grid scoring for Fast Fourier Transform rigid-body docking methods.......Development of effective methods to screen binary interactions obtained by rigid-body protein-protein docking is key for structure prediction of complexes and for elucidating physicochemical principles of protein-protein binding. We have derived empirical knowledge-based potential functions...... for selecting rigid-body docking poses. These potentials include the energetic component that provides the residues with a particular secondary structure and surface accessibility. These scoring functions have been tested on a state-of-art benchmark dataset and on a decoy dataset of permanent interactions. Our...

Three-body interactions and the Landau levels using Nikiforov

Indian Academy of Sciences (India)

In this article, the eigenvalues for the three-body interactions on the line and the Landau levels in the presence of topological defects have been regenerated by the Nikiforov–Uvarov (NU) method. Two exhaustive lists of such exactly solvable potentials are given.

Repulsive four-body interactions of α particles and quasistable nuclear α -particle condensates in heavy self-conjugate nuclei

Science.gov (United States)

Bai, Dong; Ren, Zhongzhou

2018-05-01

We study the effects of repulsive four-body interactions of α particles on nuclear α -particle condensates in heavy self-conjugate nuclei using a semianalytic approach, and find that the repulsive four-body interactions could decrease the critical number of α particles, beyond which quasistable α -particle condensate states can no longer exist, even if these four-body interactions make only tiny contributions to the total energy of the Hoyle-like state of 16O. Explicitly, we study eight benchmark parameter sets, and find that the critical number Ncr decreases by |Δ Ncr|˜1 -4 from Ncr˜11 with vanishing four-body interactions. We also discuss the effects of four-body interactions on energies and radii of α -particle condensates. Our study can be useful for future experiments to study α -particle condensates in heavy self-conjugate nuclei. Also, the experimental determination of Ncr will eventually help establish a better understanding on the α -particle interactions, especially the four-body interactions.

Meson spectra from two-body dirac equations with minimal interactions

International Nuclear Information System (INIS)

Crater, H.W.; Becker, R.L.; Wong, C.Y.

1991-01-01

Many authors have used two-body relativistic wave equations with spin in nonperturbative numerical quark model calculations of the meson spectrum. Usually, they adopt a truncation of the Bethe-Salpeter equation of QED and/or scalar. QED and replace the static Coulomb interactions of those field theories with a semiphenomenological Q bar Q potential whose insertion in the Breit terms give the corresponding spin corrections. However, the successes of these wave equations in QED have invariably depended on perturbative treatment of the terms in each beyond the Coulomb terms. There have been no successful nonperturbative numerical test of two-body quantum wave equations in QED, because in most equations the effective potentials beyond the Coulomb are singular and can only be treated perturbatively. This is a glaring omission that we rectify here for the case of the two-body Dirac equations of constraint dynamics. We show in this paper that a nonperturbative numerical treatment of these equations for QED yields the same spectral results as a perturbative treatment of them which in turn agrees with the standard spectral results for positronium and muonium. This establishes that the vector and scalar interaction structures of our equations accurately incorporate field theoretic interactions in a bone fide relativistic wave equation. The last portion of this work will report recent quark model calculations using these equations with the Adler-Piran static Q bar Q potential

A comprehensive treatment of electromagnetic interactions and the three-body spectator equations

Energy Technology Data Exchange (ETDEWEB)

Jiri Adam; Jay Van Orden

2004-10-01

We present a general derivation the three-body spectator (Gross) equations and the corresponding electromagnetic currents. As in previous paper on two-body systems, the wave equations and currents are derived from those for Bethe-Salpeter equation with the help of algebraic method using a concise matrix notation. The three-body interactions and currents introduced by the transition to the spectator approach are isolated and the matrix elements of the e.m. current are presented in detail for system of three indistinguishable particles, namely for elastic scattering and for two and three body break-up. The general expressions are reduced to the one-boson-exchange approximation to make contact with previous work. The method is general in that it does not rely on introduction of the electromagnetic interaction with the help of the minimal replacement. It would therefore work also for other external fields.

Dependence of the frequency spectrum of small amplitude vibrations superimposed on finite deformations of a nonlinear, cylindrical elastic body on residual stress

KAUST Repository

Gorb, Yuliya

2010-11-01

We model and analyze the response of nonlinear, residually stressed elastic bodies subjected to small amplitude vibrations superimposed upon large deformations. The problem derives from modeling the use of intravascular ultrasound (IVUS) imaging to interrogate atherosclerotic plaques in vivo in large arteries. The goal of this investigation is twofold: (i) introduce a modeling framework for residual stress that unlike traditional Fung type classical opening angle models may be used for a diseased artery, and (ii) investigate the sensitivity of the spectra of small amplitude high frequency time harmonic vibrations superimposed on a large deformation to the details of the residual stress stored in arteries through a numerical simulation using physiologic parameter values under both low and high blood pressure loadings. The modeling framework also points the way towards an inverse problem using IVUS techniques to estimate residual stress in healthy and diseased arteries. © 2010 Elsevier Ltd. All rights reserved.

Near target residues from the peripheral interaction of relativistic heavy ions with bismuth

International Nuclear Information System (INIS)

Aleklett, K.; Morrissey, D.J.; Loveland, W.; Moody, K.; Seaborg, G.T.

1979-01-01

Isotopic distributions for the near target residues Au and Tl were measured radioanalytically for the reaction of 8.0-GeV 20 Ne ions with 209 Bi. The isotopic production cross section for Au and Tl isotopes were calculated by using a macroscopic abrasion-ablation model and a microscopic intranuclear cascade-evaporation model. The importance of the neutron skin in determining the yield of these products from the peripheral interactions was also explored in the framework of the macroscopic model. 3 figures

Residual feed intake, body composition, and fertility in yearling beef heifers.

Science.gov (United States)

Shaffer, K S; Turk, P; Wagner, W R; Felton, E E D

2011-04-01

One hundred thirty-seven spring-born yearling beef heifers of British breed types were used to determine the relationships between residual feed intake (RFI) and growth rate, body composition, mature size, and fertility. Heifers were housed in a dry lot facility during the experimental period, and data were collected over a 2-yr period (yr 1, n = 67; yr 2, n = 70). Individual feed intake, BW, BCS, hip height, and ultrasonic measurements [subcutaneous rib fat (UBF), rump fat (URF), LM area (LMA), and intramuscular fat (IMF)] of body composition were recorded. Individual feed intakes (kg of TDN consumed/d) were used to calculate RFI combining both years of data. Heifers averaged 387.0 ± 19.4 d of age and 337.1 ± 29.9 kg of BW at initiation of the experiment. Mean ADG was 1.14 ± 0.21 kg/d during the trial. Based on RFI, with year of test and farm of origin included in the model as covariates, heifers were classified into groups: positive (POS; 0.74 kg of TDN/d) or negative (NEG; -0.73 kg TDN/d) for first analysis and high (HI), medium (MED), or low (LO; mean RFI = 1.06, -0.01, and -1.13 kg of TDN/d, respectively) subsequently. An initial phenotypic relationship (P r = 0.19 and 0.17, respectively) was sustained (P r = 0.27) and URF (r = 0.24) to trial conclusion. No other correlations with RFI were significant. Heifers classified as POS reached puberty earlier than those classified as NEG (414 ± 3.83 vs. 427 ± 4.67 d of age, P = 0.03), and possessed greater LMA per 100 kg of BW (LMACWT) at conclusion of the trial (P 0.10) from MED heifers at either the beginning or the end of test. Additionally, a negative linear relationship was observed between RFI and age at puberty (P 0.10). Differences in body fat and rate of metabolism associated with RFI could delay reproductive maturity.

Residual analysis for spatial point processes

DEFF Research Database (Denmark)

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

We define residuals for point process models fitted to spatial point pattern data, and propose diagnostic plots based on these residuals. The techniques apply to any Gibbs point process model, which may exhibit spatial heterogeneity, interpoint interaction and dependence on spatial covariates. Ou...... 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....

Dependence of four-body observables on the range of UPA-like effective interactions

International Nuclear Information System (INIS)

Perne, R.; Sandhas, W.

1977-07-01

A generalized unitary pole approximation (UPA) concerning the three-body amplitudes in the kernel of four-body integral equations is introduced. We furhtermore study the dependence of the 4 He binding energy and of four-body cross sections upon a position space cut-off parameter in the effective interactions. (orig.) [de

Heliosheath Space Environment Interactions with Icy Bodies in the Outermost Solar System

Science.gov (United States)

Cooper, John F.; Hill, Matthew E.; Richardson, John D.; Sturner, Steven J.

2006-01-01

The Voyager 1 and 2 spacecraft are exploring the space environment of the outermost solar system at the same time that earth-based astronomy continues to discover new icy bodies, one larger than Pluto, in the transitional region outward from the Classical Kuiper Belt to the Inner Oort Cloud. Some of the Scattered Disk Objects in this region periodically pass through the heliosheath, entered by Voyager 1 in Dec. 2004 and later expected to be reached by Voyager 2, and out even beyond the heliopause into the Very Local Interstellar Medium. The less energetic heliosheath ions, important for implantation and sputtering processes, are abundant near and beyond the termination shock inner boundary, but the source region of the more penetrating anomalous cosmic ray component has not yet been found. Advantageous for modeling of icy body interactions, the measured heliosheath flux spectra are relatively more stable within this new regime of isotropic compressional magnetic turbulence than in the upstream heliospheric environment. The deepest interactions and resultant radiation-induced chemistry arise from the inwardly diffusing component of the galactic cosmic ray ions with significant intensity modulation also arising in the heliosheath beyond Voyager 1. Surface gardening by high-velocity impacts of smaller bodies (e.g., fragments of previous KBO collisions) and dust is a further space weathering process setting the time scales for long term exposure of different regolith layers to the ion irradiation. Sputtering and ionization of impact ejecta grains may provide a substantial feedback of pickup ions for multiple cycles of heliosheath acceleration and icy body interaction. Thus the space weathering interactions are potentially of interest not only for effects on sensible surface composition of the icy bodies but also for evolution of the heliosheath plasma energetic ion, and neutral emission environment.

Hydrogen bond strengths in phosphorylated and sulfated amino acid residues.

Directory of Open Access Journals (Sweden)

Chaya Rapp

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

An Advanced N -body Model for Interacting Multiple Stellar Systems

Energy Technology Data Exchange (ETDEWEB)

Brož, Miroslav [Astronomical Institute of the Charles University, Faculty of Mathematics and Physics, V Holešovičkách 2, CZ-18000 Praha 8 (Czech Republic)

2017-06-01

We construct an advanced model for interacting multiple stellar systems in which we compute all trajectories with a numerical N -body integrator, namely the Bulirsch–Stoer from the SWIFT package. We can then derive various observables: astrometric positions, radial velocities, minima timings (TTVs), eclipse durations, interferometric visibilities, closure phases, synthetic spectra, spectral energy distribution, and even complete light curves. We use a modified version of the Wilson–Devinney code for the latter, in which the instantaneous true phase and inclination of the eclipsing binary are governed by the N -body integration. If all of these types of observations are at one’s disposal, a joint χ {sup 2} metric and an optimization algorithm (a simplex or simulated annealing) allow one to search for a global minimum and construct very robust models of stellar systems. At the same time, our N -body model is free from artifacts that may arise if mutual gravitational interactions among all components are not self-consistently accounted for. Finally, we present a number of examples showing dynamical effects that can be studied with our code and we discuss how systematic errors may affect the results (and how to prevent this from happening).

Many-Body Theory for Positronium-Atom Interactions

Science.gov (United States)

Green, D. G.; Swann, A. R.; Gribakin, G. F.

2018-05-01

A many-body-theory approach has been developed to study positronium-atom interactions. As first applications, we calculate the elastic scattering and momentum-transfer cross sections and the pickoff annihilation rate 1Zeff for Ps collisions with He and Ne. For He the cross section is in agreement with previous coupled-state calculations, while comparison with experiment for both atoms highlights discrepancies between various sets of measured data. In contrast, the calculated 1Zeff (0.13 and 0.26 for He and Ne, respectively) are in excellent agreement with the measured values.

The importance of residues 195-206 of human blood clotting factor VII in the interaction of factor VII with tissue factor

International Nuclear Information System (INIS)

Wildgoose, P.; Kisiel, W.; Kazim, A.L.

1990-01-01

Previous studies indicated that human and bovine factor VII exhibit 71% amino acid sequence identity. In the present study, competition binding experiments revealed that the interaction of human factor VII with cell-surface human tissue factor was not inhibited by 100-fold molar excess of bovine factor VII. This finding indicated that bovine and human factor VII are not structurally homologous in the region(s) where human factor VII interacts with human tissue factor. On this premise, the authors synthesized three peptides corresponding to regions of human factor VII that exhibited marked structural dissimilarity to bovine factor VII; these regions of dissimilarity included residues 195-206, 263-274, and 314-326. Peptide 195-206 inhibited the interaction of factor VII with cell-surface tissue factor and the activation of factor X by a complex of factor VIIa and tissue factor half-maximally at concentrations of 1-2 mM. A structurally rearranged form of peptide 195-206 containing an aspartimide residue inhibited these reactions half-maximally at concentrations of 250-300 μM. In contrast, neither peptide 263-274 nor peptide 314-326, at 2 mM concentration, significantly affected either factor VIIa interaction with tissue factor or factor VIIa-mediated activation of factor X. The data provide presumptive evidence that residues 195-206 of human factor VII are involved in the interaction of human factor VII with the extracellular domain of human tissue factor apoprotein

Comparison of electromagnetically induced transparency schemes in semiconductor quantum dot structures: Impact of many-body interactions

DEFF Research Database (Denmark)

Houmark-Nielsen, Jakob; Nielsen, Torben Roland; Mørk, Jesper

2009-01-01

an important impact on the slow light properties. In the case of the Lambda and V schemes, the minimum required coupling power to achieve slow light is significantly reduced by many-body interactions. V type schemes are found to be generally preferable due to a favorable redistribution of carriers in energy......We investigate the impact of many-body interactions on group-velocity slowdown achieved via electromagnetically induced transparency in quantum dots using three different coupling-probe schemes (ladder, V, and Lambda, respectively). We find that for all schemes many-body interactions have...

Identification and characterization of protein interactions in the mammalian mRNA processing body using a novel two-hybrid assay

Energy Technology Data Exchange (ETDEWEB)

Bloch, Donald B., E-mail: bloch@helix.mgh.harvard.edu; Nobre, Rita A.; Bernstein, Gillian A.; Yang, Wei-Hong

2011-09-10

Components of the mRNA processing body (P-body) regulate critical steps in mRNA storage, transport, translation and degradation. At the core of the P-body is the decapping complex, which removes the 5' cap from de-adenylated mRNAs and mediates an irreversible step in mRNA degradation. The assembly of P-bodies in Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster has been previously described. Less is known about the assembly of mammalian P-bodies. To investigate the interactions that occur between components of mammalian P-bodies, we developed a fluorescence-based, two-hybrid assay system. The assay depends on the ability of one P-body component, fused to an exogenous nuclear localization sequence (NLS), to recruit other P-body components to the nucleus. The assay was used to investigate interactions between P-body components Ge-1, DCP2, DCP1, EDC3, RAP55, and RCK. The results of this study show that the modified two-hybrid assay can be used to identify protein interactions that occur in a macromolecular complex. The assay can also be used to efficiently detect protein interaction domains. The results provide important insights into mammalian P-body assembly and demonstrate similarities, and critical differences, between P-body assembly in mammalian cells compared with that of other species. -- Research highlights: {yields} A two-hybrid assay was developed to study interactions in macromolecular complexes. {yields} The assay was applied to interactions between components of mRNA P-bodies. {yields} The assay effectively and efficiently identified protein interaction domains. {yields} P-body assembly in mammalian cells differs from that in other species.

Identification and characterization of protein interactions in the mammalian mRNA processing body using a novel two-hybrid assay

International Nuclear Information System (INIS)

Bloch, Donald B.; Nobre, Rita A.; Bernstein, Gillian A.; Yang, Wei-Hong

2011-01-01

Components of the mRNA processing body (P-body) regulate critical steps in mRNA storage, transport, translation and degradation. At the core of the P-body is the decapping complex, which removes the 5' cap from de-adenylated mRNAs and mediates an irreversible step in mRNA degradation. The assembly of P-bodies in Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster has been previously described. Less is known about the assembly of mammalian P-bodies. To investigate the interactions that occur between components of mammalian P-bodies, we developed a fluorescence-based, two-hybrid assay system. The assay depends on the ability of one P-body component, fused to an exogenous nuclear localization sequence (NLS), to recruit other P-body components to the nucleus. The assay was used to investigate interactions between P-body components Ge-1, DCP2, DCP1, EDC3, RAP55, and RCK. The results of this study show that the modified two-hybrid assay can be used to identify protein interactions that occur in a macromolecular complex. The assay can also be used to efficiently detect protein interaction domains. The results provide important insights into mammalian P-body assembly and demonstrate similarities, and critical differences, between P-body assembly in mammalian cells compared with that of other species. -- Research highlights: → A two-hybrid assay was developed to study interactions in macromolecular complexes. → The assay was applied to interactions between components of mRNA P-bodies. → The assay effectively and efficiently identified protein interaction domains. → P-body assembly in mammalian cells differs from that in other species.

Genetic interaction analysis of point mutations enables interrogation of gene function at a residue-level resolution

Science.gov (United States)

Braberg, Hannes; Moehle, Erica A.; Shales, Michael; Guthrie, Christine; Krogan, Nevan J.

2014-01-01

We have achieved a residue-level resolution of genetic interaction mapping – a technique that measures how the function of one gene is affected by the alteration of a second gene – by analyzing point mutations. Here, we describe how to interpret point mutant genetic interactions, and outline key applications for the approach, including interrogation of protein interaction interfaces and active sites, and examination of post-translational modifications. Genetic interaction analysis has proven effective for characterizing cellular processes; however, to date, systematic high-throughput genetic interaction screens have relied on gene deletions or knockdowns, which limits the resolution of gene function analysis and poses problems for multifunctional genes. Our point mutant approach addresses these issues, and further provides a tool for in vivo structure-function analysis that complements traditional biophysical methods. We also discuss the potential for genetic interaction mapping of point mutations in human cells and its application to personalized medicine. PMID:24842270

Continuous atom laser with Bose-Einstein condensates involving three-body interactions

Energy Technology Data Exchange (ETDEWEB)

Carpentier, A V; Michinel, H; Novoa, D [Area de Optica, Facultade de Ciencias de Ourense, Universidade de Vigo, As Lagoas s/n, Ourense, ES-32004 (Spain); Olivieri, D N, E-mail: avcarpentier@uvigo.e [Area de Linguaxes e sistemas informaticos, Escola Superior de EnxenerIa Informatica, Universidade de Vigo, As Lagoas s/n, Ourense, ES-32004 (Spain)

2010-05-28

We demonstrate, through numerical simulations, the emission of a coherent continuous matter wave of constant amplitude from a Bose-Einstein condensate in a shallow optical dipole trap. The process is achieved by spatial control of the variations of the scattering length along the trapping axis, including elastic three-body interactions due to dipole interactions. In our approach, the outcoupling mechanism is atomic interactions, and thus, the trap remains unaltered. We calculate analytically the parameters for the experimental implementation of this continuous wave atom laser.

Observation of the Borromean Three-Body Förster Resonances for Three Interacting Rb Rydberg Atoms.

Science.gov (United States)

Tretyakov, D B; Beterov, I I; Yakshina, E A; Entin, V M; Ryabtsev, I I; Cheinet, P; Pillet, P

2017-10-27

Three-body Förster resonances at long-range interactions of Rydberg atoms were first predicted and observed in Cs Rydberg atoms by Faoro et al. [Nat. Commun. 6, 8173 (2015)NCAOBW2041-172310.1038/ncomms9173]. In these resonances, one of the atoms carries away an energy excess preventing the two-body resonance, leading thus to a Borromean type of Förster energy transfer. But they were in fact observed as the average signal for the large number of atoms N≫1. In this Letter, we report on the first experimental observation of the three-body Förster resonances 3×nP_{3/2}(|M|)→nS_{1/2}+(n+1)S_{1/2}+nP_{3/2}(|M^{*}|) in a few Rb Rydberg atoms with n=36, 37. We have found here clear evidence that there is no signature of the three-body Förster resonance for exactly two interacting Rydberg atoms, while it is present for N=3-5 atoms. This demonstrates the assumption that three-body resonances can generalize to any Rydberg atom. As such resonance represents an effective three-body operator, it can be used to directly control the three-body interactions in quantum simulations and quantum information processing with Rydberg atoms.

Structural Characterization and Antioxidative Activity of Low-Molecular-Weights Beta-1,3-Glucan from the Residue of Extracted Ganoderma lucidum Fruiting Bodies

Directory of Open Access Journals (Sweden)

Pai-Feng Kao

2012-01-01

Full Text Available The major cell wall constituent of Ganoderma lucidum (G. lucidum is β-1,3-glucan. This study examined the polysaccharide from the residues of alkaline-extracted fruiting bodies using high-performance anion-exchange chromatography (HPAEC, and it employed nuclear magnetic resonance (NMR and mass spectrometry (MS to confirm the structures. We have successfully isolated low-molecular-weight β-1,3-glucan (LMG, in high yields, from the waste residue of extracted fruiting bodies of G. lucidum. The 3-(4,5-dimethylthiazol-2-yl-2,5-diphenyl tetrazolium bromide (MTT assay evaluated the capability of LMG to suppress H2O2-induced cell death in RAW264.7 cells, identifying that LMG protected cells from H2O2-induced damage. LMG treatment decreased H2O2-induced intracellular reactive oxygen species (ROS production. LMG also influenced sphingomyelinase (SMase activity, stimulated by cell death to induce ceramide formation, and then increase cell ROS production. Estimation of the activities of neutral and acid SMases in vitro showed that LMG suppressed the activities of both neutral and acid SMases in a concentration-dependent manner. These results suggest that LMG, a water-soluble β-1,3-glucan recycled from extracted residue of G. lucidum, possesses antioxidant capability against H2O2-induced cell death by attenuating intracellular ROS and inhibiting SMase activity.

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.

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

Algebraic diagrammatic construction formalism with three-body interactions

Science.gov (United States)

Raimondi, Francesco; Barbieri, Carlo

2018-05-01

Background: Self-consistent Green's function theory has recently been extended to the basic formalism needed to account for three-body interactions [Carbone, Cipollone, Barbieri, Rios, and Polls, Phys. Rev. C 88, 054326 (2013), 10.1103/PhysRevC.88.054326]. The contribution of three-nucleon forces has so far been included in ab initio calculations on nuclear matter and finite nuclei only as averaged two-nucleon forces. Purpose: We derive the working equations for all possible two- and three-nucleon terms that enter the expansion of the self-energy up to the third order, thus including the interaction-irreducible (i.e., not averaged) diagrams with three-nucleon forces that have been previously neglected. Methods: We employ the algebraic diagrammatic construction up to the third order as an organization scheme for generating a nonperturbative self-energy, in which ring (particle-hole) and ladder (particle-particle) diagrams are resummed to all orders. Results: We derive expressions of the static and dynamic self-energy up to the third order, by taking into account the set of diagrams required when either the skeleton or nonskeleton expansions of the single-particle propagator are assumed. A hierarchy of importance among different diagrams is revealed, and a particular emphasis is given to a third-order diagram [see Fig. 2(c)] that is expected to play a significant role among those featuring an interaction-irreducible three-nucleon force. Conclusion: A consistent formalism to resum at infinite order correlations induced by three-nucleon forces in the self-consistent Green's function theory is now available and ready to be implemented in the many-body solvers.

An Open Platform for Full Body Interactive Sonification Exergames

Directory of Open Access Journals (Sweden)

Simone Ghisio

2015-08-01

Full Text Available This paper addresses the use of a remote interactive platform to support home-based rehabilitation for children with motor and cognitive impairment. The interaction between user and platform is achieved on customizable full-body interactive serious games (exergames. These exergames perform real-time analysis of multimodal signals to quantify movement qualities and postural attitudes. Interactive sonification of movement is then applied for providing a real-time feedback based on “aesthetic resonance” and engagement of the children. The games also provide log file recordings therapists can use to assess the performance of the children and the effectiveness of the games. The platform allows the customization of the games to address the children’s needs. The platform is based on the EyesWeb XMI software, and the games are designed for home usage, based on Kinect for Xbox One and simple sensors including 3-axis accelerometers available in low-cost Android smartphones.

Contact point generation for convex polytopes in interactive rigid body dynamics

DEFF Research Database (Denmark)

Silcowitz-Hansen, Morten; Abel, Sarah Maria Niebe; Erleben, Kenny

When computing contact forces in rigid body dynamics systems, most state-of-the-art solutions use iterative methods such as the projected Gauss–Seidel (PGS) method. Methods such as the PGS method are preferred for their robustness. However, the time-critical nature of interactive applications...... combined with the linear convergence rates of such methods, will often result in visual artifacts in the final simulation. With this paper, we address an issue which is of major impact on the animation quality, when using methods such as the PGS method. The issue is robust generation of contact points...... for convex polytopes. A novel contact point generation method is presented, which is based on growth distances and Gauss maps. We demonstrate improvements when using our method in the context of interactive rigid body simulation...

Endocrine disruption: In silico interactions between phthalate plasticizers and corticosteroid binding globulin.

Science.gov (United States)

Sheikh, Ishfaq A; Beg, Mohd A

2017-12-01

Endocrine disruption is a phenomenon when a man-made or natural compound interferes with normal hormone function in human or animal body systems. Endocrine-disrupting compounds (EDCs) have assumed considerable importance as a result of industrial activity, mass production of synthetic chemicals and environmental pollution. Phthalate plasticizers are a group of chemicals used widely and diversely in industry especially in the plastic industry, and many of the phthalate compounds have endocrine-disrupting properties. Increasing evidence indicates that steroid nuclear receptors and steroid binding proteins are the main targets of endocrine disruption. Corticosteroid-binding globulin (CBG) is a steroid binding protein that binds and transports cortisol in the blood circulation and is a potential target for endocrine disruption. An imbalance of cortisol in the body leads to many health problems. Induced fit docking of nine important and environmentally relevant phthalate plasticizers (DMP, BBP, DBP, DIBP, DnHP, DEHP, DINP, DnOP, DIDP) showed interactions with 10-19 amino acid residues of CBG. Comparison of the interacting residues of CBG with phthalate ligands and cortisol showed an overlapping of the majority (53-82%) of residues for each phthalate. Five of nine phthalate compounds and cortisol shared a hydrogen bonding interaction with the Arg-252 residue of CBG. Long-chain phthalates, such as DEHP, DINP, DnOP and DIDP displayed a higher binding affinity and formed a number of interactions with CBG in comparison to short-chain phthalates. The similarity in structural binding characteristics of phthalate compounds and native ligand cortisol suggested potential competitive conflicts in CBG-cortisol binding function and possible disruption of cortisol and progesterone homeostasis. Copyright © 2017 John Wiley & Sons, Ltd.

Probing quantum and thermal noise in an interacting many-body system

DEFF Research Database (Denmark)

Hofferberth, S.; Lesanovsky, Igor; Schumm, Thorsten

2008-01-01

of the shot-to-shot variations of interference-fringe contrast for pairs of independently created one-dimensional Bose condensates. Analysing different system sizes, we observe the crossover from thermal to quantum noise, reflected in a characteristic change in the distribution functions from poissonian......The probabilistic character of the measurement process is one of the most puzzling and fascinating aspects of quantum mechanics. In many-body systems quantum-mechanical noise reveals non-local correlations of the underlying many-body states. Here, we provide a complete experimental analysis....... Furthermore, our experiments constitute the first analysis of the full distribution of quantum noise in an interacting many-body system....

Vestibular-somatosensory interactions: effects of passive whole-body rotation on somatosensory detection.

Directory of Open Access Journals (Sweden)

Elisa Raffaella Ferrè

Full Text Available Vestibular signals are strongly integrated with information from several other sensory modalities. For example, vestibular stimulation was reported to improve tactile detection. However, this improvement could reflect either a multimodal interaction or an indirect interaction driven by vestibular effects on spatial attention and orienting. Here we investigate whether natural vestibular activation induced by passive whole-body rotation influences tactile detection. In particular, we assessed the ability to detect faint tactile stimuli to the fingertips of the left and right hand during spatially congruent or incongruent rotations. We found that passive whole-body rotations significantly enhanced sensitivity to faint shocks, without affecting response bias. Critically, this enhancement of somatosensory sensitivity did not depend on the spatial congruency between the direction of rotation and the hand stimulated. Thus, our results support a multimodal interaction, likely in brain areas receiving both vestibular and somatosensory signals.

A method for solving a three-body problem with energy-dependent interactions

International Nuclear Information System (INIS)

Safronov, A.N.

1994-01-01

A method is proposed for solving a three-body problem with energy-dependent interactions. This method is based on introducing the dependence of scattering operators and state vectors on an additional external parameter. Effects caused by the energy dependence of the interaction operator are investigated by using the unitary condition for the amplitude of the 2 → 2 and 2 → 3 transitions. It is shown, in particular, that taking this dependence into account leads to a change in the relation between the asymptotic normalization factor of the wave function of the three-body bound state and the vertex constant of virtual dissociation (synthesis) of the system into two fragments. 15 refs

Does parental divorce moderate the heritability of body dissatisfaction? An extension of previous gene-environment interaction effects.

Science.gov (United States)

O'Connor, Shannon M; Klump, Kelly L; VanHuysse, Jessica L; McGue, Matt; Iacono, William

2016-02-01

Previous research suggests that parental divorce moderates genetic influences on body dissatisfaction. Specifically, the heritability of body dissatisfaction is higher in children of divorced versus intact families, suggesting possible gene-environment interaction effects. However, prior research is limited to a single, self-reported measure of body dissatisfaction. The primary aim of this study was to examine whether these findings extend to a different dimension of body dissatisfaction: body image perceptions. Participants were 1,534 female twins from the Minnesota Twin Family Study, aged 16-20 years. The Body Rating Scale (BRS) was used to assess body image perceptions. Although BRS scores were heritable in twins from divorced and intact families, the heritability estimates in the divorced group were not significantly greater than estimates in the intact group. However, there were differences in nonshared environmental effects, where the magnitude of these environmental influences was larger in the divorced as compared with the intact families. Different dimensions of body dissatisfaction (i.e., negative self-evaluation versus body image perceptions) may interact with environmental risk, such as parental divorce, in discrete ways. Future research should examine this possibility and explore differential gene-environment interactions using diverse measures. © 2015 Wiley Periodicals, Inc.

Eggshell thinning and residues in mallards on year after DDE exposure

Science.gov (United States)

Haegele, M.A.; Hudson, R.H.

1974-01-01

A group of 16 mallard hens (Anas platyrhynchos), that had been given feed containing 40 ppm ofp,p'-DDE for 96 days, laid eggs with shells averaging about 15%?20% thinner than those of ten control birds during and up to 42 days after treatment. In eight of the treated birds killed at that time, whole-body DDE residues averaged 33.1 ppm (wet weight). The other eight treated birds and ten controls were kept through the winter with no additional DDE exposure and penned separately five days for individual egg collection about three weeks after laying began in spring. At that time (nearly 11 months after DDE feeding had stopped), the treated birds laid eggs with shells averaging 7.4% thinner than control eggshells (significant at P<0.05) and their whole-body DDE residues averaged 9.6 ppm (wet weight). Variations in eggshell thickness and DDE residues were considerable among treated birds. However, regression analysis showed moderate negative correlations (r=?0.51 to ?0.62) between eggshell thickness and DDE residues in whole bodies and eggs, and strong positive correlations (r=0.73 and 0.91) between DDE residues in whole bodies and in eggs.

Genotype x diet interactions in mice predisposed to mammary cancer. I. Body weight and fat

DEFF Research Database (Denmark)

Gordon, Ryan R; Hunter, Kent W; Sørensen, Peter

2008-01-01

a very-high-fat or a matched-control-fat diet and measured growth, body composition, age at mammary tumor onset, tumor number and severity, and formation of pulmonary metastases. SNP genotyping across the genome facilitated analyses of QTL and QTL x diet interaction effects. Here we describe development...... of the F(2) population (n = 615) which resulted from a cross between the polygenic obesity model M16i and FVB/NJ-TgN (MMTV-PyMT)(634Mul), effects of diet on growth and body composition, and QTL and QTL x diet and/or gender interaction effects for growth and obesity-related phenotypes. We identified 38 QTL...... for body composition traits that were significant at the genome-wide 0.05 level, likely representing nine distinct loci after accounting for pleiotropic effects. QTL x diet and/or gender interactions were present at 15 of these QTL, indicating that such interactions play a significant role in defining...

How bodies and voices interact in early emotion perception.

Science.gov (United States)

Jessen, Sarah; Obleser, Jonas; Kotz, Sonja A

2012-01-01

Successful social communication draws strongly on the correct interpretation of others' body and vocal expressions. Both can provide emotional information and often occur simultaneously. Yet their interplay has hardly been studied. Using electroencephalography, we investigated the temporal development underlying their neural interaction in auditory and visual perception. In particular, we tested whether this interaction qualifies as true integration following multisensory integration principles such as inverse effectiveness. Emotional vocalizations were embedded in either low or high levels of noise and presented with or without video clips of matching emotional body expressions. In both, high and low noise conditions, a reduction in auditory N100 amplitude was observed for audiovisual stimuli. However, only under high noise, the N100 peaked earlier in the audiovisual than the auditory condition, suggesting facilitatory effects as predicted by the inverse effectiveness principle. Similarly, we observed earlier N100 peaks in response to emotional compared to neutral audiovisual stimuli. This was not the case in the unimodal auditory condition. Furthermore, suppression of beta-band oscillations (15-25 Hz) primarily reflecting biological motion perception was modulated 200-400 ms after the vocalization. While larger differences in suppression between audiovisual and audio stimuli in high compared to low noise levels were found for emotional stimuli, no such difference was observed for neutral stimuli. This observation is in accordance with the inverse effectiveness principle and suggests a modulation of integration by emotional content. Overall, results show that ecologically valid, complex stimuli such as joined body and vocal expressions are effectively integrated very early in processing.

Simulations of collisions between N-body classical systems in interaction; Simulations de collisions entre systemes classiques a n-corps en interaction

Energy Technology Data Exchange (ETDEWEB)

Morisseau, Francois [Laboratoire de Physique Corpusculaire de CAEN, ENSICAEN, Universite de Caen Basse-Normandie, UFR des Sciences, 6 bd Marechal Juin, 14050 Caen Cedex (France)

2006-05-15

The Classical N-body Dynamics (CNBD) is dedicated to the simulation of collisions between classical systems. The 2-body interaction used here has the properties of the Van der Waals potential and depends on just a few parameters. This work has two main goals. First, some theoretical approaches assume that the dynamical stage of the collisions plays an important role. Moreover, colliding nuclei are supposed to present a 1. order liquid-gas phase transition. Several signals have been introduced to show this transition. We have searched for two of them: the bimodality of the mass asymmetry and negative heat capacity. We have found them and we give an explanation of their presence in our calculations. Second, we have improved the interaction by adding a Coulomb like potential and by taking into account the stronger proton-neutron interaction in nuclei. Then we have figured out the relations that exist between the parameters of the 2-body interaction and the properties of the systems. These studies allow us to fit the properties of the classical systems to those of the nuclei. In this manuscript the first results of this fit are shown. (author)

Methane emissions, body composition, and rumen fermentation traits of beef heifers differing in residual feed intake.

Science.gov (United States)

Fitzsimons, C; Kenny, D A; Deighton, M H; Fahey, A G; McGee, M

2013-12-01

This study examined the relationship of residual feed intake (RFI) and performance with methane emissions, rumen fermentation, and digestion in beef heifers. Individual DMI and growth performance were measured for 22 Simmental heifers (mean initial BW 449 kg, SD = 46.2 kg) offered grass silage ad libitum for 120 d. Ultrasonically scanned muscle and fat depth, BCS, muscularity score, skeletal measurements, blood variables, rumen fermentation (via stomach tube), and total tract digestibility (indigestible marker) were measured. Methane production was estimated using the sulfur hexafluoride tracer gas technique over two 5-d periods beginning on d 20 and 75 of the RFI measurement period. Phenotypic RFI was calculated as actual DMI minus expected DMI. The residuals of the regression of DMI on ADG and midtest metabolic body weight, using all heifers, were used to compute individual RFI coefficients. Heifers were ranked by RFI and assigned to low (efficient), medium, or high (inefficient) groupings. Overall ADG and DMI were 0.58 kg (SD = 0.18) and 7.40 kg (SD = 0.72), respectively. High-RFI heifers consumed 9 and 15% more (P composition traits did not differ (P > 0.05) between low- and high-RFI groups. High-RFI heifers had higher concentrations of plasma glucose (6%) and urea (13%) and lower concentrations of plasma creatinine (9%) than low-RFI heifers (P 0.05) between RFI groups, although acetate:propionate ratio was lowest (P = 0.07) for low-RFI (3.5) and highest for high-RFI (4.6) heifers. Methane production expressed as grams per day or grams per kilogram metabolic body weight was greater (P methane emissions. Results suggest that improved RFI will reduce methane emissions without affecting productivity of growing beef cattle.

Chaos in body-vortex interactions

DEFF Research Database (Denmark)

Pedersen, Johan Rønby; Aref, Hassan

2010-01-01

of a circle is integrable. As the body is made slightly elliptic, a chaotic region grows from an unstable relative equilibrium of the circle-vortex case. The case of a cylindrical body of any shape moving in fluid otherwise at rest is also integrable. A second transition to chaos arises from the limit between...... rocking and tumbling motion of the body known in this case. In both instances, the chaos may be detected both in the body motion and in the vortex motion. The effect of increasing body mass at a fixed body shape is to damp the chaos....

Many Body Structure of Strongly Interacting Systems

CERN Document Server

Arenhövel, Hartmuth; Drechsel, Dieter; Friedrich, Jörg; Kaiser, Karl-Heinz; Walcher, Thomas; Symposium on 20 Years of Physics at the Mainz Microtron MAMI

2006-01-01

This carefully edited proceedings volume provides an extensive review and analysis of the work carried out over the past 20 years at the Mainz Microtron (MAMI). This research centered around the application of Quantum Chromodynamics in the strictly nonperturbative regime at hadronic scales of about 1 fm. Due to the many degrees of freedom in hadrons at this scale the leitmotiv of this research is "Many body structure of strongly interacting systems". Further, an outlook on the research with the forthcoming upgrade of MAMI is given. This volume is an authoritative source of reference for everyone interested in the field of the electro-weak probing of the structure of hadrons.

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...

The time-dependent Hartree-Fock equations with Coulomb two-body interaction

International Nuclear Information System (INIS)

Chadam, J.M.; Glassey, R.T.

1975-06-01

The existence and uniqueness of global solutions to the Cauchy problem is proved in the space of ''smooth'' density matrices for the time-dependent Hartree-Fock equations describing the motion of finite Fermi systems interacting via a Coulomb two-body potential [fr

Effects of the residual proton-neutron interaction in the development of collectivity in nuclei

International Nuclear Information System (INIS)

Casten, R.F.

1990-01-01

The widespread effects of the residual T=0 proton-neutron (p-n) interaction in the evolution of nuclear structure are discussed. Although these effects in inducing single nucleon configuration mixing, and hence in the development of non-spherical nuclear shapes, collectivity, and the associated shape and phase transitions have been known for four decades, it is only in recent years that their deep ramifications have become more fully appreciated. This had led to a unified phenomenological understanding of the role of the p-n interaction in nuclear collectivity and to, for example, the proposal of the N p N n scheme and the associated concept of the P factor, which is a normalized value of N p N n reflecting the average number of p-n interactions per valence nucleon. Simultaneously, experimentally-determined p-n matrix elements for many nuclei have been extracted: they disclose striking anomalies for N=Z nuclei, and intriguing microstructure. These developments and empirical results will be discussed along with microscopic calculations that can be used to interpret them. 18 refs., 13 figs

Quantum oscillation signatures of spin-orbit interactions controlling the residual nodal bilayer-splitting in underdoped high-Tc cuprates

Science.gov (United States)

Harrison, Neil; Shekhter, Arkady

2015-03-01

We investigate the origin of the small residual nodal bilayer-splitting in the underdoped high-Tc superconductor YBa2Cu3O6+x using the results of recently published angle-resolved quantum oscillation data [Sebastian et al., Nature 511, 61 (2014)]. A crucial clue to the origin of the residual bilayer-splitting is found to be provided by the anomalously small Zeeman-splitting of some of the observed cyclotron orbits. We show that such an anomalously Zeeman-splitting (or small effective g-factor) for a subset of orbits can be explained by spin-orbit interactions, which become significant in the nodal regions as a result of the vanishing bilayer coupling. The primary effect of spin-orbit interactions is to cause quasiparticles traversing the nodal region of the Brillouin zone to undergo a spin flip. We suggest that the Rashba-like spin-orbit interactions, naturally present in bilayer systems, have the right symmetry and magnitude to give rise to a network of coupled orbits consistent with experimental observations in underdoped YBa2Cu3O6+x. This work is supported by the DOEm BES proposal LANLF100, while the magnet lab is supported by the NSF and Florida State.

Coulomb-Sturmian separable expansion approach: Three-body Faddeev calculations for Coulomb-like interactions

International Nuclear Information System (INIS)

Papp, Z.; Plessas, W.

1996-01-01

We demonstrate the feasibility and efficiency of the Coulomb-Sturmian separable expansion method for generating accurate solutions of the Faddeev equations. Results obtained with this method are reported for several benchmark cases of bosonic and fermionic three-body systems. Correct bound-state results in agreement with the ones established in the literature are achieved for short-range interactions. We outline the formalism for the treatment of three-body Coulomb systems and present a bound-state calculation for a three-boson system interacting via Coulomb plus short-range forces. The corresponding result is in good agreement with the answer from a recent stochastic-variational-method calculation. copyright 1996 The American Physical Society

Interaction and activity coordination of territorial customs bodies of the State fiscal service of Ukraine with local state administrations and local self-government bodies

Directory of Open Access Journals (Sweden)

Олексій Павлович Федотов

2016-06-01

Based on the results of the study the author notes that the interaction of the Ukrainian SFS customs offices and local state administrations with local self-government bodies is an inherent quality, link and component of the Ukrainian SFS Customs offices functioning organization, which aims to improve the state customs service implementation standards by the Ukrainian SFS customs houses and to ensure the said implementation efficiency. However, in the course of interaction of the Ukrainian SFS customs with local state administrations and local self-government bodies each of the mentioned organizations specializes in solving their specific tasks in accordance with their subject expertise, and forms a clear organizational system. The complementarity of such kind helps to improve the state customs affairs conductance quality and is realized through the coordination of performance of the Ukrainian SFS customs offices, local state administrations and local self-government bodies as the interaction subjects through normative, informational and analytical provision for the interaction and concretization of the activities of each subject within the planned activities.

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

Directory of Open Access Journals (Sweden)

Robert Kalescky

2016-04-01

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

Investigations of the structure and electromagnetic interactions of few-body systems

International Nuclear Information System (INIS)

Lehman, D.R.

1991-07-01

In order to make it easy for the reader to see the specific research carried out and the progress make, the following report of progress is done by topic. Each item has a format layout of Topic, Investigators, Objective, Significance, and Description of Progress, followed at the end by the relevant references. As is clear from the topics listed, the emphasis of the GWU theory group has been on the structure and electromagnetic interactions of few-body nuclei. Both low- and intermediate-energy electromagnetic disintegration of these nuclei is considered. When the excitation energy of the target nucleus is low, the aim has been carry out the continuum part of the theoretical work exactly, this is, by means of exact three- and four-body dynamics. When structure questions are the issue, exact calculations are always carried through, limited only by the underlying two-body or three-body interactions used as input. Implicit in our work is the question of how far one can go within the traditional nuclear physics framework, i.e., nucleons and mesons in a nonrelativistic setting. Our central goal is to carry through state-of-the-art few-body calculations that will serve as an unambiguous means of determining at what point standard nuclear physics requires quark degrees of freedom in order to understand the phenomena in question. So far, in the problems considered, there has been no evidence of the necessity to go beyond the traditional approach, though we always keep in mind that possibility. As our work is involved with questions in the intermediate-energy realm, moving from a nonrelativistic framework to a relativistic one is always a consideration. Currently, for the problems that have been pursued in this domain of energy, the issues concern far more the mechanisms of the reactions and structural questions than the need to move to relativistic dynamics

Performance, body measurements, carcass and cut yields, and meat quality in lambs fed residues from processing agroindustry of fruits

Directory of Open Access Journals (Sweden)

Darcilene Maria de Figueiredo

2015-02-01

Full Text Available This research was conducted with the objective to evaluate the use of residue dry matter (DM from pineapple (Ananas comosus L., banana (Musa sp., mango (Mangifera indica and passion fruit (Passiflora spp. in feeding of the feedlot on productive performance, carcass yield and qualitative and quantitative characteristics of meat. Twenty-five crossbred lamps with Santa Inês breed and mixed breed were used. The treatments consisted of the replacement of 75% of sorghum silage by respective residue DM, whereas in the control treatment forage had only sorghum silage the diets had a houghageto- concentrate ratio of 40:60 interns of DM being isonitrogenous and isoenergetics. The animals were slaughtered at 32 kg liveweight. Before slaughter were obtained biometric measurements, after the same, was performed the hot carcasses weight and morphometric measurements. After 24 hours in a cold chamber at 4 ° C, was determined the cold carcass weight and yield calculation. The left half carcass was divided into five sections: neck, shoulder, shank, rib and loin, by performing the calculation of income cuts. Analyses meat quality such as pH, color (L, a, b, chroma and Ho, by cooking weight loss, water retention capacity and shear strength were carried out in the Longissimus dorsi sample. The completely randomized design was adapted. The data were interpreted using analysis of variance with the test a Tukey 5% probability. There was no effect of diet (P> 0.05 according to the parameters: growth performance, body measurements, and meat quality of lambs. There was also no effect of the diets (P> 0.05 on the loin eye area assuming that carcasses remained similar muscularity important fact to market acceptance standard. It is concluded that replacing up to 75% of sorghum silage by residues fruit (pineapple, banana, mango and passion fruit in lambs feeding becomes feasible not to change the productive performance, body measurements, yields carcass and cuts and meat

An interactive VR system based on full-body tracking and gesture recognition

Science.gov (United States)

Zeng, Xia; Sang, Xinzhu; Chen, Duo; Wang, Peng; Guo, Nan; Yan, Binbin; Wang, Kuiru

2016-10-01

Most current virtual reality (VR) interactions are realized with the hand-held input device which leads to a low degree of presence. There is other solutions using sensors like Leap Motion to recognize the gestures of users in order to interact in a more natural way, but the navigation in these systems is still a problem, because they fail to map the actual walking to virtual walking only with a partial body of the user represented in the synthetic environment. Therefore, we propose a system in which users can walk around in the virtual environment as a humanoid model, selecting menu items and manipulating with the virtual objects using natural hand gestures. With a Kinect depth camera, the system tracks the joints of the user, mapping them to a full virtual body which follows the move of the tracked user. The movements of the feet can be detected to determine whether the user is in walking state, so that the walking of model in the virtual world can be activated and stopped by means of animation control in Unity engine. This method frees the hands of users comparing to traditional navigation way using hand-held device. We use the point cloud data getting from Kinect depth camera to recognize the gestures of users, such as swiping, pressing and manipulating virtual objects. Combining the full body tracking and gestures recognition using Kinect, we achieve our interactive VR system in Unity engine with a high degree of presence.

Interaction of ethanol and mercury body burden in the mouse

Energy Technology Data Exchange (ETDEWEB)

Dunn, J.D.

1978-01-01

The interaction of ethanol with mercury in the body resulting in increased exhalation of the metal was studied in the mouse. A persistent elimination of the metal in the breath was demonstrated after single, sublethal (<1 mgHg/Kg body weight) exposures to mercury vapor (Hg/sup 0/) or mercury II chloride (HgCl/sub 2/). The amount of mercury exhaled per unit time was enhanced by oral or parenteral administration of ethanol solutions. These modifications were investigated in dose-response studies in which the drug was administered in doses ranging from 0.2g to 5.5g/Kg to mice pretreated with mercury. The EC/sub 50/ for blood ethanol with respect to mercury exhalation was determined to be approximately 200 mg/dl corresponding to an output rate of approximately 0.1% of the simultaneous body burden in 30 min several days after mercury. A hypothesis that mercury expired by these animals was proportional to the body burden after mercury administration was addressed in experiments whereby mice given one of several doses of mercuric chloride (0.16 to 500 ..mu..g/Kg) were monitored for pulmonary mercury elimination for a fifteen day period. The high correlation obtained between the amount of mercury exhaled in a standard time period and the body burden by group indicated that breath sampling could be applied as an indicator of the mercury body burden which may not be limited to the mouse.

Genome-Wide Interactions with Dairy Intake for Body Mass Index in Adults of European Descent

DEFF Research Database (Denmark)

Smith, Caren E; Follis, Jack L; Dashti, Hassan S

2018-01-01

SCOPE: Body weight responds variably to the intake of dairy foods. Genetic variation may contribute to inter-individual variability in associations between body weight and dairy consumption. METHODS AND RESULTS: A genome-wide interaction study to discover genetic variants that account for variati...

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

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.

Determining High-Quality Critical Body Residues for Multiple Species and Chemicals by Applying Improved Experimental Design and Data Interpretation Concepts

DEFF Research Database (Denmark)

van der Heijden, Stephan A.; Hermens, Joop L. M.; Sinnige, Theo L.

2015-01-01

Ecotoxicological effect data are generally expressed as effective concentrations in the external exposure medium and do thus not account for differences in chemical uptake, bioavailability, and metabolism, which can introduce substantial data variation. The Critical Body Residue (CBR) concept......, and by a factor of 2.6 between the three species but for individual chemicals. Accounting for the chemicals internal distribution to different partitioning domains and relating effects to estimated concentrations in the target compartment (i.e., membrane lipids) was expected to but did not decrease the overall...

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

Science.gov (United States)

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

2018-08-01

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

Human UBL5 protein interacts with coilin and meets the Cajal bodies

International Nuclear Information System (INIS)

Švéda, Martin; Častorálová, Markéta; Lipov, Jan; Ruml, Tomáš; Knejzlík, Zdeněk

2013-01-01

Highlights: •Localization of the UBL5 protein in Hela cells was determined by fluorescence microscopy and biochemical fractionation. •Colocalization of UBL5 with Cajal bodies was observed. •Interaction of UBL5 with coilin was proven by pull-down. -- Abstract: UBL5 protein, a structural homologue of ubiquitin, was shown to be involved in pre-mRNA splicing and transcription regulation in yeast and Caenorhabditis elegans, respectively. However, role of the UBL5 human orthologue is still elusive. In our study, we observed that endogenous human UBL5 that was localized in the nucleus, partially associates with Cajal bodies (CBs), nuclear domains where spliceosomal components are assembled. Simultaneous expression of exogenous UBL5 and coilin resulted in their nuclear colocalization in HeLa cells. The ability of UBL5 to interact with coilin was proved by GST pull-down assay using coilin that was either in vitro translated or extracted from HEK293T cells. Further, our results showed that the UBL5–coilin interaction was not influenced by coilin phosphorylation. These results suggest that UBL5 could be targeted to CBs via its interaction with coilin. Relation between human UBL5 protein and CBs is in the agreement with current observations about yeast orthologue Hub1 playing important role in alternative splicing

Human UBL5 protein interacts with coilin and meets the Cajal bodies

Energy Technology Data Exchange (ETDEWEB)

Švéda, Martin; Častorálová, Markéta; Lipov, Jan; Ruml, Tomáš; Knejzlík, Zdeněk, E-mail: knejzliz@vscht.cz

2013-06-28

Highlights: •Localization of the UBL5 protein in Hela cells was determined by fluorescence microscopy and biochemical fractionation. •Colocalization of UBL5 with Cajal bodies was observed. •Interaction of UBL5 with coilin was proven by pull-down. -- Abstract: UBL5 protein, a structural homologue of ubiquitin, was shown to be involved in pre-mRNA splicing and transcription regulation in yeast and Caenorhabditis elegans, respectively. However, role of the UBL5 human orthologue is still elusive. In our study, we observed that endogenous human UBL5 that was localized in the nucleus, partially associates with Cajal bodies (CBs), nuclear domains where spliceosomal components are assembled. Simultaneous expression of exogenous UBL5 and coilin resulted in their nuclear colocalization in HeLa cells. The ability of UBL5 to interact with coilin was proved by GST pull-down assay using coilin that was either in vitro translated or extracted from HEK293T cells. Further, our results showed that the UBL5–coilin interaction was not influenced by coilin phosphorylation. These results suggest that UBL5 could be targeted to CBs via its interaction with coilin. Relation between human UBL5 protein and CBs is in the agreement with current observations about yeast orthologue Hub1 playing important role in alternative splicing.

Role of the SUMO-interacting motif in HIPK2 targeting to the PML nuclear bodies and regulation of p53

International Nuclear Information System (INIS)

Sung, Ki Sa; Lee, Yun-Ah; Kim, Eui Tae; Lee, Seung-Rock; Ahn, Jin-Hyun; Choi, Cheol Yong

2011-01-01

Homeodomain-interacting protein kinase 2 (HIPK2) is a key regulator of various transcription factors including p53 and CtBP in the DNA damage signaling pathway. PML-nuclear body (NB) is required for HIPK2-mediated p53 phosphorylation at Ser46 and induction of apoptosis. Although PML-NB targeting of HIPK2 has been shown, much is not clear about the molecular mechanism of HIPK2 recruitment to PML-NBs. Here we show that HIPK2 colocalizes specifically with PML-I and PML-IV. Mutational analysis showed that HIPK2 recruitment to PML-IV-NBs is mediated by the SUMO-interaction motifs (SIMs) of both PML-IV and HIPK2. Wild-type HIPK2 associated with SUMO-conjugated PML-IV at a higher affinity than with un-conjugated PML-IV, while the association of a HIPK2 SIM mutant with SUMO-modified PML-IV was impaired. In colony formation assays, HIPK2 strongly suppressed cell proliferation, but HIPK2 SIM mutants did not. In addition, activation and phosphorylation of p53 at the Ser46 residue were impaired by HIPK2 SIM mutants. These results suggest that SIM-mediated HIPK2 targeting to PML-NBs is crucial for HIPK2-mediated p53 activation and induction of apoptosis.

Simulation of aerosol flow interaction with a solid body on molecular level

Science.gov (United States)

Amelyushkin, Ivan A.; Stasenko, Albert L.

2018-05-01

Physico-mathematical models and numerical algorithm of two-phase flow interaction with a solid body are developed. Results of droplet motion and its impingement upon a rough surface in real gas boundary layer simulation on the molecular level obtained via molecular dynamics technique are presented.

Probing many-body interactions in an optical lattice clock

Energy Technology Data Exchange (ETDEWEB)

Rey, A.M., E-mail: arey@jilau1.colorado.edu [JILA, NIST and University of Colorado, Department of Physics, Boulder, CO 80309 (United States); Gorshkov, A.V. [Joint Quantum Institute, NIST and University of Maryland, Department of Physics, College Park, MD 20742 (United States); Kraus, C.V. [Institute for Quantum Optics and Quantum Information of the Austrian Academy of Sciences, A-6020 Innsbruck (Austria); Institute for Theoretical Physics, University of Innsbruck, A-6020 Innsbruck (Austria); Martin, M.J. [JILA, NIST and University of Colorado, Department of Physics, Boulder, CO 80309 (United States); Institute for Quantum Information and Matter, California Institute of Technology, Pasadena, CA 91125 (United States); Bishof, M.; Swallows, M.D.; Zhang, X.; Benko, C.; Ye, J. [JILA, NIST and University of Colorado, Department of Physics, Boulder, CO 80309 (United States); Lemke, N.D.; Ludlow, A.D. [National Institute of Standards and Technology, Boulder, CO 80305 (United States)

2014-01-15

We present a unifying theoretical framework that describes recently observed many-body effects during the interrogation of an optical lattice clock operated with thousands of fermionic alkaline earth atoms. The framework is based on a many-body master equation that accounts for the interplay between elastic and inelastic p-wave and s-wave interactions, finite temperature effects and excitation inhomogeneity during the quantum dynamics of the interrogated atoms. Solutions of the master equation in different parameter regimes are presented and compared. It is shown that a general solution can be obtained by using the so called Truncated Wigner Approximation which is applied in our case in the context of an open quantum system. We use the developed framework to model the density shift and decay of the fringes observed during Ramsey spectroscopy in the JILA {sup 87}Sr and NIST {sup 171}Yb optical lattice clocks. The developed framework opens a suitable path for dealing with a variety of strongly-correlated and driven open-quantum spin systems. -- Highlights: •Derived a theoretical framework that describes many-body effects in a lattice clock. •Validated the analysis with recent experimental measurements. •Demonstrated the importance of beyond mean field corrections in the dynamics.

The partition function of an interacting many body system

International Nuclear Information System (INIS)

Rummel, C.; Ankerhold, J.

2002-01-01

Based on the path integral approach the partition function of a many body system with separable two body interaction is calculated in the sense of a semiclassical approximation. The commonly used Gaussian type of approximation, known as the perturbed static path approximation (PSPA), breaks down near a crossover temperature due to instabilities of the classical mean field solution. It is shown how the PSPA is systematically improved within the crossover region by taking into account large non-Gaussian fluctuation and an approximation applicable down to very low temperatures is carried out. These findings are tested against exact results for the archetypical cases of a particle moving in a one dimensional double well and the exactly solvable Lipkin-Meshkov-Glick model. The extensions should have applications in finite systems at low temperatures as in nuclear physics and mesoscopic systems, e. g. for gap fluctuations in nano-scale superconducting devices previously studied within a PSPA type of approximation. (author)

A single arginine residue is required for the interaction of the electron transferring flavoprotein (ETF) with three of its dehydrogenase partners.

Science.gov (United States)

Parker, Antony R

2003-12-01

The interaction of several dehydrogenases with the electron transferring flavoprotein (ETF) is a crucial step required for the successful transfer of electrons into the electron transport chain. The exact determinants regarding the interaction of ETF with its dehydrogenase partners are still unknown. Chemical modification of ETF with arginine-specific reagents resulted in the loss, to varying degrees, of activity with medium chain acyl-coenzyme A dehydrogenase (MCAD). The kinetic profiles showed the inactivations followed pseudo-first-order kinetics for all reagents used. For activity with MCAD, maximum inactivation of ETF was accomplished by 2,3-butanedione (4% residual activity after 120 min) and it was shown that modification of one arginine residue was responsible for the inactivation. Almost 100% restoration of this ETF activity was achieved upon incubation with free arginine. However, the same 2,3-butanedione modified ETF only possessed decreased activity with dimethylglycine-(DMGDH, 44%) and sarcosine- (SDH, 27%) dehydrogenases unlike the abolition with MCAD. Full protection of ETF from arginine modification by 2,3-butanedione was achieved using substrate-protected DMGDH, MCAD and SDH respectively. Cross-protection studies of ETF with the three dehydrogenases implied use of the same single arginine residue in the binding of all three dehydrogenases. These results lead us to conclude that this single arginine residue is essential in the binding of the ETF to MCAD, but only contributes partially to the binding of ETF to SDH and DMGDH and thus, the determinants of the dehydrogenase binding sites overlap but are not identical.

Genotype-covariate interaction effects and the heritability of adult body mass index

NARCIS (Netherlands)

Robinson, Matthew R.; English, Geoffrey; Moser, Gerhard; Lloyd-Jones, Luke R; Triplett, Marcus A; Zhu, Zhihong; Nolte, Ilja M; van Vliet-Ostaptchouk, Jana V; Snieder, Harold; Esko, Tonu; Milani, Lili; Mägi, Reedik; Metspalu, Andres; Magnusson, Patrik K. E.; Pedersen, Nancy L.; Ingelsson, Erik; Johannesson, Magnus; Yang, Jian; Cesarini, David; Visscher, Peter M.

Obesity is a worldwide epidemic, with major health and economic costs. Here we estimate heritability for body mass index (BMI) in 172,000 sibling pairs and 150,832 unrelated individuals and explore the contribution of genotype-covariate interaction effects at common SNP loci. We find evidence for

Comparison of permutationally invariant polynomials, neural networks, and Gaussian approximation potentials in representing water interactions through many-body expansions

Science.gov (United States)

Nguyen, Thuong T.; Székely, Eszter; Imbalzano, Giulio; Behler, Jörg; Csányi, Gábor; Ceriotti, Michele; Götz, Andreas W.; Paesani, Francesco

2018-06-01

The accurate representation of multidimensional potential energy surfaces is a necessary requirement for realistic computer simulations of molecular systems. The continued increase in computer power accompanied by advances in correlated electronic structure methods nowadays enables routine calculations of accurate interaction energies for small systems, which can then be used as references for the development of analytical potential energy functions (PEFs) rigorously derived from many-body (MB) expansions. Building on the accuracy of the MB-pol many-body PEF, we investigate here the performance of permutationally invariant polynomials (PIPs), neural networks, and Gaussian approximation potentials (GAPs) in representing water two-body and three-body interaction energies, denoting the resulting potentials PIP-MB-pol, Behler-Parrinello neural network-MB-pol, and GAP-MB-pol, respectively. Our analysis shows that all three analytical representations exhibit similar levels of accuracy in reproducing both two-body and three-body reference data as well as interaction energies of small water clusters obtained from calculations carried out at the coupled cluster level of theory, the current gold standard for chemical accuracy. These results demonstrate the synergy between interatomic potentials formulated in terms of a many-body expansion, such as MB-pol, that are physically sound and transferable, and machine-learning techniques that provide a flexible framework to approximate the short-range interaction energy terms.

Interactions between internal forces, body stiffness, and fluid environment in a neuromechanical model of lamprey swimming.

Science.gov (United States)

Tytell, Eric D; Hsu, Chia-Yu; Williams, Thelma L; Cohen, Avis H; Fauci, Lisa J

2010-11-16

Animal movements result from a complex balance of many different forces. Muscles produce force to move the body; the body has inertial, elastic, and damping properties that may aid or oppose the muscle force; and the environment produces reaction forces back on the body. The actual motion is an emergent property of these interactions. To examine the roles of body stiffness, muscle activation, and fluid environment for swimming animals, a computational model of a lamprey was developed. The model uses an immersed boundary framework that fully couples the Navier-Stokes equations of fluid dynamics with an actuated, elastic body model. This is the first model at a Reynolds number appropriate for a swimming fish that captures the complete fluid-structure interaction, in which the body deforms according to both internal muscular forces and external fluid forces. Results indicate that identical muscle activation patterns can produce different kinematics depending on body stiffness, and the optimal value of stiffness for maximum acceleration is different from that for maximum steady swimming speed. Additionally, negative muscle work, observed in many fishes, emerges at higher tail beat frequencies without sensory input and may contribute to energy efficiency. Swimming fishes that can tune their body stiffness by appropriately timed muscle contractions may therefore be able to optimize the passive dynamics of their bodies to maximize peak acceleration or swimming speed.

Nonlinear morphoelastic plates I: Genesis of residual stress

KAUST Repository

McMahon, J.

2011-04-28

Volumetric growth of an elastic body may give rise to residual stress. Here a rigorous analysis is given of the residual strains and stresses generated by growth in the axisymmetric Kirchhoff plate. Balance equations are derived via the Global Constraint Principle, growth is incorporated via a multiplicative decomposition of the deformation gradient, and the system is closed by a response function. The particular case of a compressible neo-Hookean material is analyzed, and the existence of residually stressed states is established. © SAGE Publications 2011.

Nonlinear morphoelastic plates I: Genesis of residual stress

KAUST Repository

McMahon, J.; Goriely, A.; Tabor, M.

2011-01-01

Volumetric growth of an elastic body may give rise to residual stress. Here a rigorous analysis is given of the residual strains and stresses generated by growth in the axisymmetric Kirchhoff plate. Balance equations are derived via the Global Constraint Principle, growth is incorporated via a multiplicative decomposition of the deformation gradient, and the system is closed by a response function. The particular case of a compressible neo-Hookean material is analyzed, and the existence of residually stressed states is established. © SAGE Publications 2011.

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

Directory of Open Access Journals (Sweden)

Genki Terashi

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

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

Science.gov (United States)

Terashi, Genki; Takeda-Shitaka, Mayuko

2015-01-01

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

Traveller: An Interactive Cultural Training System Controlled by User-Defined Body Gestures

NARCIS (Netherlands)

Kistler, F.; André, E.; Mascarenhas, S.; Silva, A.; Paiva, A.; Degens, D.M.; Hofstede, G.J.; Krumhuber, E.; Kappas, A.; Aylett, R.

2013-01-01

In this paper, we describe a cultural training system based on an interactive storytelling approach and a culturally-adaptive agent architecture, for which a user-defined gesture set was created. 251 full body gestures by 22 users were analyzed to find intuitive gestures for the in-game actions in

Baryon femtoscopy considering residual correlations as a tool to extract strong interaction potentials

Directory of Open Access Journals (Sweden)

Szymański Maciej

2015-01-01

Full Text Available In this article, the analysis of baryon-antibaryon femtoscopic correlations is presented. In particular, it is shown that taking into account residual correlations is crucial for the description of pΛ¯$\\bar \\Lambda $ and p̄Λ correlation functions measured by the STAR experiment in Au–Au collisions at the centre-of-mass energy per nucleon pair √sNN = 200 GeV. This approach enables to obtain pΛ¯$\\bar \\Lambda $ (p̄Λ source size consistent with the sizes extracted from correlations in pΛ (p̄Λ¯$\\bar \\Lambda $ and lighter pair systems as well as with model predictions. Moreover, with this analysis it is possible to derive the unknown parameters of the strong interaction potential for baryon-antibaryon pairs under several assumptions.

Identification of the gamma subunit-interacting residues on photoreceptor cGMP phosphodiesterase, PDE6alpha '.

Science.gov (United States)

Granovsky, A E; Artemyev, N O

2000-12-29

Photoreceptor cGMP phosphodiesterase (PDE6) is the effector enzyme in the G protein-mediated visual transduction cascade. In the dark, the activity of PDE6 is shut off by the inhibitory gamma subunit (Pgamma). Chimeric proteins between cone PDE6alpha' and cGMP-binding and cGMP-specific PDE (PDE5) have been constructed and expressed in Sf9 cells to study the mechanism of inhibition of PDE6 catalytic activity by Pgamma. Substitution of the segment PDE5-(773-820) by the corresponding PDE6alpha'-(737-784) sequence in the wild-type PDE5 or in a PDE5/PDE6alpha' chimera containing the catalytic domain of PDE5 results in chimeric enzymes capable of inhibitory interaction with Pgamma. The catalytic properties of the chimeric PDEs remained similar to those of PDE5. Ala-scanning mutational analysis of the Pgamma-binding region, PDE6alpha'-(750-760), revealed PDE6alpha' residues essential for the interaction. The M758A mutation markedly impaired and the Q752A mutation moderately impaired the inhibition of chimeric PDE by Pgamma. The analysis of the catalytic properties of mutant PDEs and a model of the PDE6 catalytic domain suggest that residues Met(758) and Gln(752) directly bind Pgamma. A model of the PDE6 catalytic site shows that PDE6alpha'-(750-760) forms a loop at the entrance to the cGMP-binding pocket. Binding of Pgamma to Met(758) would effectively block access of cGMP to the catalytic cavity, providing a structural basis for the mechanism of PDE6 inhibition.

Interactions of bluff-body obstacles with turbulent airflows affecting evaporative fluxes from porous surfaces

Science.gov (United States)

Haghighi, Erfan; Or, Dani

2015-11-01

Bluff-body obstacles interacting with turbulent airflows are common in many natural and engineering applications (from desert pavement and shrubs over natural surfaces to cylindrical elements in compact heat exchangers). Even with obstacles of simple geometry, their interactions within turbulent airflows result in a complex and unsteady flow field that affects surface drag partitioning and transport of scalars from adjacent evaporating surfaces. Observations of spatio-temporal thermal patterns on evaporating porous surfaces adjacent to bluff-body obstacles depict well-defined and persistent zonation of evaporation rates that were used to construct a simple mechanistic model for surface-turbulence interactions. Results from evaporative drying of sand surfaces with isolated cylindrical elements (bluff bodies) subjected to constant turbulent airflows were in good agreement with model predictions for localized exchange rates. Experimental and theoretical results show persistent enhancement of evaporative fluxes from bluff-rough surfaces relative to smooth flat surfaces under similar conditions. The enhancement is attributed to formation of vortices that induce a thinner boundary layer over part of the interacting surface footprint. For a practical range of air velocities (0.5-4.0 m/s), low-aspect ratio cylindrical bluff elements placed on evaporating sand surfaces enhanced evaporative mass losses (relative to a flat surface) by up to 300% for high density of elements and high wind velocity, similar to observations reported in the literature. Concepts from drag partitioning were used to generalize the model and upscale predictions to evaporation from surfaces with multiple obstacles for potential applications to natural bluff-rough surfaces.

Dynamic behaviour of Bose-Einstein condensates in optical lattices with two- and three-body interactions

International Nuclear Information System (INIS)

Chen Yan; Chen Yong; Zhang Kezhi

2009-01-01

We study the dynamic behaviour of Bose-Einstein condensates with two- and three-atom interactions in optical lattices with analytical and numerical methods. It is found that the steady-state relative population displays tuning-fork bifurcation when the system parameters are changed to certain critical values. In particular, the existence of the three-body interaction not only transforms the bifurcation point of the system but also greatly affects the macroscopic quantum self-trapping behaviours associated with the critically stable steady-state solution. In addition, we investigated the influence of the initial conditions, three-body interaction, and the energy bias on the macroscopic quantum self-trapping. Finally, by applying the periodic modulation on the energy bias, we observed that the relative population oscillation exhibits a process from order to chaos, via a series of period-doubling bifurcations.

Size-density scaling in protists and the links between consumer-resource interaction parameters.

Science.gov (United States)

DeLong, John P; Vasseur, David A

2012-11-01

Recent work indicates that the interaction between body-size-dependent demographic processes can generate macroecological patterns such as the scaling of population density with body size. In this study, we evaluate this possibility for grazing protists and also test whether demographic parameters in these models are correlated after controlling for body size. We compiled data on the body-size dependence of consumer-resource interactions and population density for heterotrophic protists grazing algae in laboratory studies. We then used nested dynamic models to predict both the height and slope of the scaling relationship between population density and body size for these protists. We also controlled for consumer size and assessed links between model parameters. Finally, we used the models and the parameter estimates to assess the individual- and population-level dependence of resource use on body-size and prey-size selection. The predicted size-density scaling for all models matched closely to the observed scaling, and the simplest model was sufficient to predict the pattern. Variation around the mean size-density scaling relationship may be generated by variation in prey productivity and area of capture, but residuals are relatively insensitive to variation in prey size selection. After controlling for body size, many consumer-resource interaction parameters were correlated, and a positive correlation between residual prey size selection and conversion efficiency neutralizes the apparent fitness advantage of taking large prey. Our results indicate that widespread community-level patterns can be explained with simple population models that apply consistently across a range of sizes. They also indicate that the parameter space governing the dynamics and the steady states in these systems is structured such that some parts of the parameter space are unlikely to represent real systems. Finally, predator-prey size ratios represent a kind of conundrum, because they are

Three- and five-quasiparticle isomers, rotational bands and residual interactions in 175Hf

International Nuclear Information System (INIS)

Dracoulis, G.D.; Walker, P.M.

1980-03-01

Two 3-quasiparticle isomers with spins, parities and half lives of 19/2 + , 1.1 μ and 23/2 - , 1.2 ns have been identified at 1433 and 1766 keV in 175 Hf. A third isomer possibly 35/2 - with a 1.2 μs half-life is found at 3015 keV. The first two are characterised as a 7/2 + (633) neutron coupled to the known 6 + and 8 - 2-proton isomers of the core nuclei. Rotational bands based on the 3-qp isomers are highly perturbed, due to Coriolis mixing, and their structure is reproduced in a band mixing calculation. The energy depression of the 3-quasiparticle states relative to the 2-quasiproton core states is attributed mainly to the residual proton-neutron interaction, and possibly also to blocking effects through neutron admixtures

Metastable decoherence-free subspaces and electromagnetically induced transparency in interacting many-body systems

DEFF Research Database (Denmark)

Macieszczak, Katarzyna; Zhou, Yanli; Hofferberth, Sebastian

2017-01-01

to stationarity this leads to a slow dynamics, which renders the typical assumption of fast relaxation invalid. We derive analytically the effective nonequilibrium dynamics in the decoherence-free subspace, which features coherent and dissipative two-body interactions. We discuss the use of this scenario...

Residual Stress Testing of Outer 3013 Containers

International Nuclear Information System (INIS)

Dunn, K.

2004-01-01

A Gas Tungsten Arc Welded (GTAW) outer 3013 container and a laser welded outer 3013 container have been tested for residual stresses according to the American Society for Testing Materials (ASTM) Standard G-36-94 [1]. This ASTM standard describes a procedure for conducting stress-corrosion cracking tests in boiling magnesium chloride (MgCl2) solution. Container sections in both the as-fabricated condition as well as the closure welded condition were evaluated. Significantly large residual stresses were observed in the bottom half of the as-fabricated container, a result of the base to can fabrication weld because through wall cracks were observed perpendicular to the weld. This observation indicates that regardless of the closure weld technique, sufficient residual stresses exist in the as-fabricated container to provide the stress necessary for stress corrosion cracking of the container, at the base fabrication weld. Additionally, sufficiently high residual stresses were observed in both the lid and the body of the GTAW as well as the laser closure welded containers. The stresses are oriented perpendicular to the closure weld in both the container lid and the container body. Although the boiling MgCl2 test is not a quantitative test, a comparison of the test results from the closure welds shows that there are noticeably more through wall cracks in the laser closure welded container than in the GTAW closure welded container

The d-α elastic scattering and the lithium-6 in a three-body model with separable interactions

International Nuclear Information System (INIS)

Charnomordic, Brigitte.

1976-01-01

This work consists in a three-body treatment of the six nucleon system. The model is constructed by considering two identical nucleons and a structureless alpha particle. Such a system can be described by the Faddeev-Lovelace equations. A partial antisymetrization is performed taking into account the identity of the nucleons. Pairwise interacting particles with nonlocal separable forces are introduced. Two-body potentials are chosen in each n-n and n-α partial wave. After an analysis of the existing separable interactions, new n-α and 1S0 parametrization are constructed. The sensitivity to the tensor force and the role of the N-α description are especially studied. The case of d-α elastic scattering is also discussed. The observables: differential cross-section, analyzing powers and transfer polarization coefficients are calculated and compared with experiments. The results show the ability of a three-body model with separable interactions in describing the main properties of the d-α elastic scattering and lithium-6 [fr

Terminology for the body in social interaction, as appearing in papers published in the journal 'Research on Language and Social Interaction', 1987-2013

DEFF Research Database (Denmark)

Nevile, Maurice Richard

2016-01-01

This is a list of terms referring generally to the body in descriptions and analyses of social interaction, as used by authors in papers published in ROLSI. The list includes over 200 items, grouped according to common phrasing and within alphabetical order. The list was compiled in preparation...... for the review paper: Nevile, M. (2015) The embodied turn in research on language and social interaction. Research on Language and Social Interaction,48(2): 121-151....

Study on the characteristics of interaction flowfields induced by supersonic jet on a revolution body

Directory of Open Access Journals (Sweden)

S.J. Luo

2017-11-01

Full Text Available The paper focuses on the triple jets interaction with a hypersonic external flow on a revolution body. The experimental model is a ogive-cylinder body with three supersonic nozzles, which are aligned along the flow direction. The freestream Mach numbers are 5 and 6. The spatial and surface flow characteristics are illustrated by the schlieren photographs and the typical pressure distribution. The results show that there are multi-wave system, separation, reattachment, multi-peak pressure, high-pressure and low-pressure zone boundaries obvious distinction in tri-jets interference flowfield. The present paper also analyzes how do the pressure ratio, the angle of attack, and Mach number effect on tri-jets interaction characteristics.

Application of equivalent electrodes method to analysis of interaction between ELF-LF electric fields and human body

International Nuclear Information System (INIS)

Ceselkoska, Vesna C.; Velickovic, Dragutin M.

2002-01-01

This paper presents the use of equivalent electrodes method, numerical method, based on surface-charge equation to quantify the interaction of low frequencies electric fields with various models of human body. The evaluation of the electric field intensity on the body surface is performed for a realistic model of the human body. Several examples for different postures of the model are given. (Author)

Does seeing ice really feel cold? Visual-thermal interaction under an illusory body-ownership.

Directory of Open Access Journals (Sweden)

Shoko Kanaya

Full Text Available Although visual information seems to affect thermal perception (e.g. red color is associated with heat, previous studies have failed to demonstrate the interaction between visual and thermal senses. However, it has been reported that humans feel an illusory thermal sensation in conjunction with an apparently-thermal visual stimulus placed on a prosthetic hand in the rubber hand illusion (RHI wherein an individual feels that a prosthetic (rubber hand belongs to him/her. This study tests the possibility that the ownership of the body surface on which a visual stimulus is placed enhances the likelihood of a visual-thermal interaction. We orthogonally manipulated three variables: induced hand-ownership, visually-presented thermal information, and tactically-presented physical thermal information. Results indicated that the sight of an apparently-thermal object on a rubber hand that is illusorily perceived as one's own hand affects thermal judgments about the object physically touching this hand. This effect was not observed without the RHI. The importance of ownership of a body part that is touched by the visual object on the visual-thermal interaction is discussed.

B8B8 interaction in the SU6 quark model and its applications to few-body systems

International Nuclear Information System (INIS)

Fujiwara, Y.; Miyagawa, K.; Kohno, M.; Suzuki, Y.; Nakamoto, C.

2004-01-01

The recent QCD-inspired spin-flavor SU 6 quark model for the baryon-baryon interaction, proposed by the Kyoto-Niigata group, is a unified model for the complete baryon octet (B 8 =N, Λ, Σ and Ξ), which has achieved very accurate description of the NN and YN interactions. These quark-model interactions are now applied to realistic calculations of few-body systems in a new three-cluster Faddeev formalism which uses the 2-cluster resonating-group method kernel explicitly. We review the essential features of the most recent models, fss2 and FSS, and their predictions to few-body systems in confrontation with the available experimental data. As the few-body systems, we discuss the three-nucleon bound states, 2αΛ system for Λ 9 Be, and 2Λα system for ΛΛ 6 He. (author)

Emerging bosons with three-body interactions from spin-1 atoms in optical lattices

International Nuclear Information System (INIS)

Mazza, L.; Rizzi, M.; Cirac, J. I.; Lewenstein, M.

2010-01-01

We study two many-body systems of bosons interacting via an infinite three-body contact repulsion in a lattice: a pairs quasicondensate induced by correlated hopping and the discrete version of the Pfaffian wave function. We propose to experimentally realize systems characterized by such interaction by means of a proper spin-1 lattice Hamiltonian: spin degrees of freedom are locally mapped into occupation numbers of emerging bosons, in a fashion similar to spin-1/2 and hardcore bosons. Such a system can be realized with ultracold spin-1 atoms in a Mott insulator with a filling factor of 1. The high versatility of these setups allows us to engineer spin-hopping operators breaking the SU(2) symmetry, as needed to approximate interesting bosonic Hamiltonians with three-body hardcore constraint. For this purpose we combine bichromatic spin-independent superlattices and Raman transitions to induce a different hopping rate for each spin orientation. Finally, we illustrate how our setup could be used to experimentally realize the first setup, that is, the transition to a pairs quasicondensed phase of the emerging bosons. We also report on a route toward the realization of a discrete bosonic Pfaffian wave function and list some open problems for reaching this goal.

Investigations of the structure and electromagnetic interactions of few-body systems

International Nuclear Information System (INIS)

Lehman, D.R.; Haberzettl, H.; Maximon, L.C.; Parke, W.C.

1992-07-01

In order to make it easy for the reader to see the specific research carried out and the progress made, the following report of progress is done by topic. Each item has a format layout of Topic, Investigators, Objective, Significance, and Description of Progress, followed at the end by the relevant references. As is clear from the topics listed, the emphasis of the George Washington University (GWU) theory group has been on the structure and electromagnetic interactions of few-body nuclei. Both low- and intermediate-energy electromagnetic disintegration of these nuclei is considered. When the excitation energy of the target nucleus is low, the aim has been to handle the continuum part of the theoretical work numerically with no approximations, that is, by means of full three- or four-body dynamics. When structure questions axe the issue, numerically accurate calculations axe always carried through, limited only by the underlying two-body or three-body interactions used as input. Implicit in our work is the question of how far one can go within the traditional nuclear physics framework, i.e., nucleons and mesons in a nonrelativistic setting. Our central goal is to carry through state-of-the-art fewbody calculations that wig serve as a means of determining at what point standard nuclear physics requires quark degrees of freedom in order to understand the phenomena in question. So far, in the problems considered, there has been no evidence of the necessity to go beyond the traditional approach, though we always keep in mind that possibility. As our work is involved with questions in the intermediate-energy realm, moving from a nonrelativistic framework to a relativistic one is always a consideration. Currently, for the problems that have been pursued in this domain of energy, the issues concern far more the mechanisms of the reactions and structural questions than the need to move to relativistic dynamics

Re-docking scheme for generating near-native protein complexes by assembling residue interaction fingerprints.

Directory of Open Access Journals (Sweden)

Nobuyuki Uchikoga

Full Text Available Interaction profile method is a useful method for processing rigid-body docking. After the docking process, the resulting set of docking poses could be classified by calculating similarities among them using these interaction profiles to search for near-native poses. However, there are some cases where the near-native poses are not included in this set of docking poses even when the bound-state structures are used. Therefore, we have developed a method for generating near-native docking poses by introducing a re-docking process. We devised a method for calculating the profile of interaction fingerprints by assembling protein complexes after determining certain core-protein complexes. For our analysis, we used 44 bound-state protein complexes selected from the ZDOCK benchmark dataset ver. 2.0, including some protein pairs none of which generated near-native poses in the docking process. Consequently, after the re-docking process we obtained profiles of interaction fingerprints, some of which yielded near-native poses. The re-docking process involved searching for possible docking poses in a restricted area using the profile of interaction fingerprints. If the profile includes interactions identical to those in the native complex, we obtained near-native docking poses. Accordingly, near-native poses were obtained for all bound-state protein complexes examined here. Application of interaction fingerprints to the re-docking process yielded structures with more native interactions, even when a docking pose, obtained following the initial docking process, contained only a small number of native amino acid interactions. Thus, utilization of the profile of interaction fingerprints in the re-docking process yielded more near-native poses.

Re-docking scheme for generating near-native protein complexes by assembling residue interaction fingerprints.

Science.gov (United States)

Uchikoga, Nobuyuki; Matsuzaki, Yuri; Ohue, Masahito; Hirokawa, Takatsugu; Akiyama, Yutaka

2013-01-01

Interaction profile method is a useful method for processing rigid-body docking. After the docking process, the resulting set of docking poses could be classified by calculating similarities among them using these interaction profiles to search for near-native poses. However, there are some cases where the near-native poses are not included in this set of docking poses even when the bound-state structures are used. Therefore, we have developed a method for generating near-native docking poses by introducing a re-docking process. We devised a method for calculating the profile of interaction fingerprints by assembling protein complexes after determining certain core-protein complexes. For our analysis, we used 44 bound-state protein complexes selected from the ZDOCK benchmark dataset ver. 2.0, including some protein pairs none of which generated near-native poses in the docking process. Consequently, after the re-docking process we obtained profiles of interaction fingerprints, some of which yielded near-native poses. The re-docking process involved searching for possible docking poses in a restricted area using the profile of interaction fingerprints. If the profile includes interactions identical to those in the native complex, we obtained near-native docking poses. Accordingly, near-native poses were obtained for all bound-state protein complexes examined here. Application of interaction fingerprints to the re-docking process yielded structures with more native interactions, even when a docking pose, obtained following the initial docking process, contained only a small number of native amino acid interactions. Thus, utilization of the profile of interaction fingerprints in the re-docking process yielded more near-native poses.

Subnanomolar Inhibitor of Cytochrome bc1 Complex Designed via Optimizing Interaction with Conformationally Flexible Residues

Science.gov (United States)

Zhao, Pei-Liang; Wang, Le; Zhu, Xiao-Lei; Huang, Xiaoqin; Zhan, Chang-Guo; Wu, Jia-Wei; Yang, Guang-Fu

2009-01-01

Cytochrome bc1 complex (EC 1.10.2.2, bc1), an essential component of the cellular respiratory chain and the photosynthetic apparatus in photosynthetic bacteria, has been identified as a promising target for new drugs and agricultural fungicides. X-ray diffraction structures of the free bc1 complex and its complexes with various inhibitors revealed that the phenyl group of Phe274 in the binding pocket exhibited significant conformational flexibility upon different inhibitors binding to optimize respective π-π interactions, whereas the side chains of other hydrophobic residues showed conformational stability. Therefore, in the present study, a strategy of optimizing the π-π interaction with conformationally flexible residues was proposed to design and discover new bc1 inhibitors with a higher potency. Eight new compounds were designed and synthesized, among which compound 5c with a Ki value of 570 pM was identified as the most promising drug or fungicide candidate, significantly more potent than the commercially available bc1 inhibitors including azoxystrobin (AZ), kresoxim-methyl (KM), and pyraclostrobin (PY). To our knowledge, this is the first bc1 inhibitor discovered from structure-based design with a potency of subnanomolar Ki value. For all of the compounds synthesized and assayed, the calculated binding free energies correlated reasonably well with the binding free energies derived from the experimental Ki values with a correlation coefficient of r2 = 0.89. The further inhibitory kinetics studies revealed that compound 5c is a non-competitive inhibitor with respect to substrate cytochrome c, but is a competitive inhibitor with respect to substrate ubiquinol. Due to its subnanomolar Ki potency and slow dissociation rate constant (k−0 = 0.00358 s−1), compound 5c could be used as a specific probe for further elucidation of the mechanism of bc1 function and as a new lead compound for future drug discovery. PMID:19928849

[Understanding social interaction in children with autism spectrum disorders: does whole-body motion mean anything to them?].

Science.gov (United States)

Centelles, L; Assaiante, C; Etchegoyhen, K; Bouvard, M; Schmitz, C

2012-06-01

Autism spectrum disorders (ASD) are characterized by difficulties in social interaction and verbal and non verbal reciprocal communication. Face and gaze direction, which participate in non verbal communication, are described as atypical in ASD. Also body movements carry multiple social cues. Under certain circumstances, for instance when seeing two persons from far, they constitute the only support that allows the grasping of a social content. Here, we investigated the contribution of whole-body motion processing in social understanding. The aim of the study was to evaluate whether children with ASD make use of information carried by body motion to categorize dynamic visual scenes that portrayed social interactions. In 1973, Johansson devised a technique for studying the perception of biological motion that minimizes static form information from the stimulus, but retains motion information. In these point-light displays, the movement figure, such as a body, is represented by a small number of illuminated dots positioned to highlight the motion of the body parts. We used Johansson's model to explore the ability of children with ASD to understand social interactions based on human movement analysis. Three-second silent point-light displays were created by videotaping two actors. The two actors were either interacting together or moving side by side without interacting. A large range of social interaction displays were used to cover social scenes depicting social norms (conventional gestures and courteous attitudes), emotional situations (carrying positive or negative valences) and scenes from games (sports, dance, etc.). Children were asked to carefully watch the stimuli and to classify them according to the question "Are the two persons communicating or not?". Four sessions of 3 minutes were performed by each child. Children with ASD were compared with typically developing control children matched with either non verbal mental age or chronological age. Response and

Three-body models of the 6ΛΛHe and 9ΛBe hypernuclei with non-local interactions

International Nuclear Information System (INIS)

Theeten, M.; Baye, D.; Descouvemont, P.

2005-01-01

A three-body model involving non-local interactions is developed in configuration space. It is based on a hyperspherical-harmonics expansion and the Lagrange-mesh method. The 6 ΛΛ He and 9 Λ Be hypernuclei are studied as three-body αΛΛ and ααΛ systems. Recently proposed quark-model based ΛN and ΛΛ interactions are used. A non-local Λα interaction is obtained by folding the ΛN interaction with a Gaussian α density. Various phenomenological αα interactions are employed. The results agree within 1 keV with recent Faddeev calculations in momentum space. Energies and radii of 6 ΛΛ He and 9 Λ Be are compared with a purely local model. The B(E2) between the 9 Λ Be bound states is also calculated. The role of non-locality is discussed

Accurate first principles calculation of many-body interactions

International Nuclear Information System (INIS)

Tawa, G.J.; Moskowitz, J.W.; Schmidt, K.E.

1991-01-01

This paper reports on the electronic structure Schrodinger equation that is solved for the van der Waals complexes spin-polarized H 2 and H 3 , and the closed-shell systems He 2 and He 3 by Monte Carlo methods. Two types of calculations are performed, variational Monte Carlo, which gives an upper bound to the eigenvalue of the Schrodinger equation, and Green's function Monte Carlo, which can solve the Schrodinger equation exactly within statistical sampling errors. The simulations are carried out on an ETA-10 supercomputer, and already existing computer codes were extensively modified to ensure highly efficient coding. A major component of the computations was the development of highly optimized many-electron wave functions. The results from the variational Monte Carlo simulations are reported for both the two- and three-body interaction energies

Ensemble Architecture for Prediction of Enzyme-ligand Binding Residues Using Evolutionary Information.

Science.gov (United States)

Pai, Priyadarshini P; Dattatreya, Rohit Kadam; Mondal, Sukanta

2017-11-01

Enzyme interactions with ligands are crucial for various biochemical reactions governing life. Over many years attempts to identify these residues for biotechnological manipulations have been made using experimental and computational techniques. The computational approaches have gathered impetus with the accruing availability of sequence and structure information, broadly classified into template-based and de novo methods. One of the predominant de novo methods using sequence information involves application of biological properties for supervised machine learning. Here, we propose a support vector machines-based ensemble for prediction of protein-ligand interacting residues using one of the most important discriminative contributing properties in the interacting residue neighbourhood, i. e., evolutionary information in the form of position-specific- scoring matrix (PSSM). The study has been performed on a non-redundant dataset comprising of 9269 interacting and 91773 non-interacting residues for prediction model generation and further evaluation. Of the various PSSM-based models explored, the proposed method named ROBBY (pRediction Of Biologically relevant small molecule Binding residues on enzYmes) shows an accuracy of 84.0 %, Matthews Correlation Coefficient of 0.343 and F-measure of 39.0 % on 78 test enzymes. Further, scope of adding domain knowledge such as pocket information has also been investigated; results showed significant enhancement in method precision. Findings are hoped to boost the reliability of small-molecule ligand interaction prediction for enzyme applications and drug design. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Bose-Einstein atoms in atomic traps with predominantly attractive two-body interactions

International Nuclear Information System (INIS)

Hussein, M.S.; Vorov, O.K.

2002-01-01

Using the Perron-Frobenius theorem, we prove that the results by Wilkin, Gunn, and Smith [Phys. Rev. Lett. 80, 2265 (1998)] for the ground states at angular momentum L of N harmonically trapped Bose atoms, interacting via weak attractive δ 2 (r) forces, are valid for a broad class of predominantly attractive interactions V(r), not necessarily attractive for any r. This class is described by sufficient conditions on the two-body matrix elements of the potential V(r). It includes, in particular, the Gaussian attraction of arbitrary radius, -1/r-Coulomb and log(r)-Coulomb forces, as well as all the short-range interactions satisfying inequality ∫d 2 r-vectorV(r)<0. In the precollapse regime, the angular momentum L is concentrated in the collective 'center-of-mass' mode, and there is no condensation at high L

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...

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

Science.gov (United States)

Sun, Weitao

2018-01-01

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

Avian basal metabolic rates : their association with body composition and energy expenditure in nature

NARCIS (Netherlands)

Daan, Serge; Masman, Dirkjan; Groenewold, Alex

Measurements of basal metabolic rate (BMR), body water, fat, and lean dry mass of different organs were obtained in 22 bird species, ranging from 10.8 to 1,253 g body mass. Residuals of BMR (after subtracting BMR allometrically predicted from body mass) were positively correlated with residuals of

LMKB/MARF1 localizes to mRNA processing bodies, interacts with Ge-1, and regulates IFI44L gene expression.

Directory of Open Access Journals (Sweden)

Donald B Bloch

Full Text Available The mRNA processing body (P-body is a cellular structure that regulates the stability of cytoplasmic mRNA. MARF1 is a murine oocyte RNA-binding protein that is associated with maintenance of mRNA homeostasis and genomic stability. In this study, autoantibodies were used to identify Limkain B (LMKB, the human orthologue of MARF1, as a P-body component. Indirect immunofluorescence demonstrated that Ge-1 (a central component of the mammalian core-decapping complex co-localized with LMKB in P-bodies. Two-hybrid and co-immunoprecipitation assays were used to demonstrate interaction between Ge-1 and LMKB. The C-terminal 120 amino acids of LMKB mediated interaction with Ge-1 and the N-terminal 1094 amino acids of Ge-1 were required for interaction with LMKB. LMKB is the first protein identified to date that interacts with this portion of Ge-1. LMKB was expressed in human B and T lymphocyte cell lines; depletion of LMKB increased expression of IFI44L, a gene that has been implicated in the cellular response to Type I interferons. The interaction between LMKB/MARF1, a protein that contains RNA-binding domains, and Ge-1, which interacts with core-decapping proteins, suggests that LMKB has a role in the regulation of mRNA stability. LMKB appears to have different functions in different cell types: maintenance of genomic stability in developing oocytes and possible dampening of the inflammatory response in B and T cells.

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.

General relativistic dynamics of an extreme mass-ratio binary interacting with an external body

Science.gov (United States)

Yang, Huan; Casals, Marc

2017-10-01

We study the dynamics of a hierarchical three-body system in the general relativistic regime: an extreme mass-ratio inner binary under the tidal influence of an external body. The inner binary consists of a central Schwarzschild black hole and a test body moving around it. We discuss three types of tidal effects on the orbit of the test body. First, the angular momentum of the inner binary precesses around the angular momentum of the outer binary. Second, the tidal field drives a "transient resonance" when the radial and azimuthal frequencies are commensurable. In contrast with resonances driven by the gravitational self-force, this tidal-driven resonance may boost the orbital angular momentum and eccentricity (a relativistic version of the Kozai-Lidov effect). Finally, for an orbit-dynamical effect during the nonresonant phase, we calculate the correction to the innermost stable circular (mean) orbit due to the tidal interaction. Hierarchical three-body systems are potential sources for future space-based gravitational wave missions, and the tidal effects that we find could contribute significantly to their waveform.

Metastability and coherence of repulsive polarons in a strongly interacting Fermi mixture

DEFF Research Database (Denmark)

Kohstall, Cristoph; Zaccanti, Mattheo; Jag, Matthias

2012-01-01

show that a well-defined quasiparticle exists for strongly repulsive interactions. We measure the energy and the lifetime of this ‘repulsive polaron’9, 12, 13, and probe its coherence properties by measuring the quasiparticle residue. The results are well described by a theoretical approach that takes...... into account the finite effective range of the interaction in our system. We find that when the effective range is of the order of the interparticle spacing, there is a substantial increase in the lifetime of the quasiparticles. The existence of such a long-lived, metastable many-body state offers intriguing...

Genotype by housing interaction for conformation and workability traits in Danish Holsteins

DEFF Research Database (Denmark)

Lassen, J.; Mark, Thomas

2008-01-01

A total of 30,190 first-parity Danish Holstein cows housed in free stalls or tie stalls were analyzed to quantify to what degree genotype by housing interaction existed for 21 conformation and 2 workability traits. Each trait measured in different housing systems was treated as 2 separate traits...... in a bivariate animal model. Genetic correlations between the 2 traits as well as differences in genetic and residual variance were used as measurements of whether or not genotype by housing interaction occurred. Genetic correlations were in general close to unity (>0.9), except for body width (0.87 +/- 0...

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

Science.gov (United States)

Anwar, Muhammad Ayaz; Choi, Sangdun

2017-03-01

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

Measurement of residual stresses using fracture mechanics weight functions

International Nuclear Information System (INIS)

Fan, Y.

2000-01-01

A residual stress measurement method has been developed to quantify through-the-thickness residual stresses. Accurate measurement of residual stresses is crucial for many engineering structures. Fabrication processes such as welding and machining generate residual stresses that are difficult to predict. Residual stresses affect the integrity of structures through promoting failures due to brittle fracture, fatigue, stress corrosion cracking, and wear. In this work, the weight function theory of fracture mechanics is used to measure residual stresses. The weight function theory is an important development in computational fracture mechanics. Stress intensity factors for arbitrary stress distribution on the crack faces can be accurately and efficiently computed for predicting crack growth. This paper demonstrates that the weight functions are equally useful in measuring residual stresses. In this method, an artificial crack is created by a thin cut in a structure containing residual stresses. The cut relieves the residual stresses normal to the crack-face and allows the relieved residual stresses to deform the structure. Strain gages placed adjacent to the cut measure the relieved strains corresponding to incrementally increasing depths of the cut. The weight functions of the cracked body relate the measured strains to the residual stresses normal to the cut within the structure. The procedure details, such as numerical integration of the singular functions in applying the weight function method, will be discussed

Measurement of residual stresses using fracture mechanics weight functions

International Nuclear Information System (INIS)

Fan, Y.

2001-01-01

A residual stress measurement method has been developed to quantify through-the-thickness residual stresses. Accurate measurement of residual stresses is crucial for many engineering structures. Fabrication processes such as welding and machining generate residual stresses that are difficult to predict. Residual stresses affect the integrity of structures through promoting failures due to brittle fracture, fatigue, stress corrosion cracking, and wear. In this work, the weight function theory of fracture mechanics is used to measure residual stresses. The weight function theory is an important development in computational fracture mechanics. Stress intensity factors for arbitrary stress distribution on the crack faces can be accurately and efficiently computed for predicting crack growth. This paper demonstrates that the weight functions are equally useful in measuring residual stresses. In this method, an artificial crack is created by a thin cut in a structure containing residual stresses. The cut relieves the residual stresses normal to the crack-face and allows the relieved residual stresses to deform the structure. Strain gages placed adjacent to the cut measure the relieved strains corresponding to incrementally increasing depths of the cut. The weight functions of the cracked body relate the measured strains to the residual stresses normal to the cut within the structure. The procedure details, such as numerical integration of the singular functions in applying the weight function method, will be discussed. (author)

Investigations of the structure and electromagnetic interactions of few-body systems. Progress report, September 1, 1983-August 31, 1984

International Nuclear Information System (INIS)

Harper, E.P.; Lehman, D.R.; Prats, F.

1984-01-01

The George Washington University nuclear theory group proposes to conduct investigations of the structure and electromagnetic interactions of few-body systems. The structural properties of the very light nuclei are examined by developing theoretical models that begin from the basic interactions between the constituents and that are solved exactly (numerically), i.e., full three or four-body dynamics. Such models are then used in an attempt to understand the details of the strong and electromagnetic interactions of the few-nucleon nuclei after the basic underlying reaction mechanisms are understood with simpler models. Examples of specific work proposed are the following: (1) From exact four-body dynamics, derive the equations that will permit calculation of the 4 He→ 3 He+n and 4 He→d+d asymptotic normalization constants; (2) Develop a unified picture of the p + d → 3 He = γ, p + d → 3 He = π 0 , p + d → 3 H + π + reactions at intermediate energies; (3) Calculate the elastic and inelastic (1 + →0 + ) form factors for 6 Li with three-body (αNN) wave functions; (4) Calculate static properties (RMS radius, magnetic moment, and quadrupole moment) of 6 Li with three-body wave functions; and (5) Develop the theory for the coincidence reactions 6 Li(p,2p)nα, 6 Li(e,e'p)nα, and 6 Li(e,e'd)α. It is anticipated that these efforts will expand the frontiers of our knowledge about few-body nuclei

Problems of organization of interaction of administrative bodies and the forces engaged in liquidation of after-effects of radiation accident

International Nuclear Information System (INIS)

Popov, A.P.; Perevezentsev, A.M.

1995-01-01

The paper defines the main problems arising in connection with organization of interaction of the administrative bodies and the forces involved in liquidation of after-effects of radiation accident. It is demonstrated that in order to increase the efficiency of interaction of the administrative bodies of various levels it is necessary to make it automatic. The paper revealed the meaning of the levels of relationship between various automatic systems. 4 refs

Interaction Design for and with the Lived Body: Some Implications of Merleau-Ponty’s Phenomenology

DEFF Research Database (Denmark)

Svanæs, Dag

2013-01-01

: the active and embodied nature of perception, including the body’s ability to extent its sensory apparatus through digital technology; and (2) kinaesthetic creativity: the body’s ability to relate in a direct and creative fashion with the “feel” dimension of interactive products during the design process....... for his discussion of the bodily nature of embodied interaction. This article extends Dourish’s work to introduce the human-computer interaction community to ideas related to Merleau-Ponty’s concept of the lived body. It also provides a detailed analysis of two related topics: (1) embodied perception...

Protein-protein docking with dynamic residue protonation states.

Directory of Open Access Journals (Sweden)

Krishna Praneeth Kilambi

2014-12-01

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

Bacterial inclusion bodies as potential synthetic devices for pathogen recognition and a therapeutic substance release.

Science.gov (United States)

Talafová, Klaudia; Hrabárová, Eva; Chorvát, Dušan; Nahálka, Jozef

2013-02-07

Adhesins of pathogens recognise the glycans on the host cell and mediate adherence. They are also crucial for determining the tissue preferences of pathogens. Currently, glyco-nanomaterials provide potential tool for antimicrobial therapy. We demonstrate that properly glyco-tailored inclusion bodies can specifically bind pathogen adhesins and release therapeutic substances. In this paper, we describe the preparation of tailored inclusion bodies via the conjugation of indicator protein aggregated to form inclusion bodies with soluble proteins. Whereas the indicator protein represents a remedy, the soluble proteins play a role in pathogen recognition. For conjugation, glutaraldehyde was used as linker. The treatment of conjugates with polar lysine, which was used to inactivate the residual glutaraldehyde, inhibited unwanted hydrophobic interactions between inclusion bodies. The tailored inclusion bodies specifically interacted with the SabA adhesin from Helicobacter pylori aggregated to form inclusion bodies that were bound to the sialic acids decorating the surface of human erythrocytes. We also tested the release of indicator proteins from the inclusion bodies using sortase A and Ssp DNAB intein self-cleaving modules, respectively. Sortase A released proteins in a relatively short period of time, whereas the intein cleavage took several weeks. The tailored inclusion bodies are promising "nanopills" for biomedical applications. They are able to specifically target the pathogen, while a self-cleaving module releases a soluble remedy. Various self-cleaving modules can be enabled to achieve the diverse pace of remedy release.

An Evaluation-Driven Design Approach to Develop Learning Environments Based on Full-Body Interaction

Science.gov (United States)

Malinverni, Laura; Schaper, Marie-Monique; Pares, Narcís

2016-01-01

The development of learning environments based on full-body interaction has become an increasingly important field of research in recent years. However, the design and evaluation strategies currently used present some significant limitations. Two major shortcomings are: the inadequate involvement of children in the design process and a lack of…

Reconstruction of the residual stresses in a hyperelastic body using ultrasound techniques

KAUST Repository

Joshi, Sunnie; Walton, Jay R.

2013-01-01

This paper focuses on a novel approach for characterizing the residual stress field in soft tissue using ultrasound interrogation. A nonlinear inverse spectral technique is developed that makes fundamental use of the finite strain nonlinear response

Novel essential residues of Hda for interaction with DnaA in the regulatory inactivation of DnaA: unique roles for Hda AAA Box VI and VII motifs.

Science.gov (United States)

Nakamura, Kenta; Katayama, Tsutomu

2010-04-01

Escherichia coli ATP-DnaA initiates chromosomal replication. For preventing extra-initiations, a complex of ADP-Hda and the DNA-loaded replicase clamp promotes DnaA-ATP hydrolysis, yielding inactive ADP-DnaA. However, the Hda-DnaA interaction mode remains unclear except that the Hda Box VII Arg finger (Arg-153) and DnaA sensor II Arg-334 within each AAA(+) domain are crucial for the DnaA-ATP hydrolysis. Here, we demonstrate that direct and functional interaction of ADP-Hda with DnaA requires the Hda residues Ser-152, Phe-118 and Asn-122 as well as Hda Arg-153 and DnaA Arg-334. Structural analyses suggest intermolecular interactions between Hda Ser-152 and DnaA Arg-334 and between Hda Phe-118 and the DnaA Walker B motif region, in addition to an intramolecular interaction between Hda Asn-122 and Arg-153. These interactions likely sustain a specific association of ADP-Hda and DnaA, promoting DnaA-ATP hydrolysis. Consistently, ATP-DnaA and ADP-DnaA interact with the ADP-Hda-DNA-clamp complex with similar affinities. Hda Phe-118 and Asn-122 are contained in the Box VI region, and their hydrophobic and electrostatic features are basically conserved in the corresponding residues of other AAA(+) proteins, suggesting a conserved role for Box VI. These findings indicate novel interaction mechanisms for Hda-DnaA as well as a potentially fundamental mechanism in AAA(+) protein interactions.

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

Interactive effects of body-size structure and adaptive foraging on food-web stability.

Science.gov (United States)

Heckmann, Lotta; Drossel, Barbara; Brose, Ulrich; Guill, Christian

2012-03-01

Body-size structure of food webs and adaptive foraging of consumers are two of the dominant concepts of our understanding how natural ecosystems maintain their stability and diversity. The interplay of these two processes, however, is a critically important yet unresolved issue. To fill this gap in our knowledge of ecosystem stability, we investigate dynamic random and niche model food webs to evaluate the proportion of persistent species. We show that stronger body-size structures and faster adaptation stabilise these food webs. Body-size structures yield stabilising configurations of interaction strength distributions across food webs, and adaptive foraging emphasises links to resources closer to the base. Moreover, both mechanisms combined have a cumulative effect. Most importantly, unstructured random webs evolve via adaptive foraging into stable size-structured food webs. This offers a mechanistic explanation of how size structure adaptively emerges in complex food webs, thus building a novel bridge between these two important stabilising mechanisms. © 2012 Blackwell Publishing Ltd/CNRS.

[Waste over history: perceptions about residues].

Science.gov (United States)

Velloso, Marta Pimenta

2008-01-01

This article describes how Man, over history, felt about the residues produced by human activity. The text is divided into three parts: In the first part it tells the story of the black plague pandemic during the XIV century, showing how this disease was associated with the residues produced by the human body. In the second part it explains how the first notions of waste were, and still are, related to dirt, disease and death. Finally, in the third part, it describes the first measures of hygiene in the Renaissance and refers to the first public health actions at the beginning of the XX century, starting to combat the agents of infectious diseases and their vectors.

Use of Two-Body Correlated Basis Functions with van der Waals Interaction to Study the Shape-Independent Approximation for a Large Number of Trapped Interacting Bosons

Science.gov (United States)

Lekala, M. L.; Chakrabarti, B.; Das, T. K.; Rampho, G. J.; Sofianos, S. A.; Adam, R. M.; Haldar, S. K.

2017-05-01

We study the ground-state and the low-lying excitations of a trapped Bose gas in an isotropic harmonic potential for very small (˜ 3) to very large (˜ 10^7) particle numbers. We use the two-body correlated basis functions and the shape-dependent van der Waals interaction in our many-body calculations. We present an exhaustive study of the effect of inter-atomic correlations and the accuracy of the mean-field equations considering a wide range of particle numbers. We calculate the ground-state energy and the one-body density for different values of the van der Waals parameter C6. We compare our results with those of the modified Gross-Pitaevskii results, the correlated Hartree hypernetted-chain equations (which also utilize the two-body correlated basis functions), as well as of the diffusion Monte Carlo for hard sphere interactions. We observe the effect of the attractive tail of the van der Waals potential in the calculations of the one-body density over the truly repulsive zero-range potential as used in the Gross-Pitaevskii equation and discuss the finite-size effects. We also present the low-lying collective excitations which are well described by a hydrodynamic model in the large particle limit.

Survival, growth, and body residues of hyalella azteca (Saussure) exposed to fipronil contaminated sediments from non-vegetated and vegetated microcosms.

Science.gov (United States)

Kröger, Robert; Lizotte, Richard E; Moore, Matthew T

2009-09-01

We assessed chronic effects of fipronil and metabolite contaminated sediments from non-vegetated and Thallia dealbata vegetated wetland microcosms on Hyalella azteca during wet and dry exposures. Mean sediment concentrations (ng g(-1)) ranged from 0.72-1.26, 0.01-0.69, 0.07-0.23, and 0.49-7.87 for fipronil, fipronil-sulfide, fipronil-sulfone, and fipronil-desulfinyl, respectively. No significant differences in animal survival or growth were observed between non-vegetated and vegetated microcosms during wet or dry exposures. Mean animal body residue concentrations (ng g(-1)) ranged from 28.4-77.6, 0-30.7, and 8.3-43.8 for fipronil, fipronil-sulfide, and fipronil-sulfone. Fipronil-desulfinyl was not detected in any animal samples.

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

Investigations of the structure and electromagnetic interactions of few-body systems. Progress report, 1 January 1980-1 October 1980

International Nuclear Information System (INIS)

1980-01-01

Considerable progress has been made on the long-range problems described in the original proposal document (1 February 1979 to 31 January 1980) and on the shorter-range problems described in the last renewal proposal (1 February 1980 to 31 January 1981). This progress concerns few-body structure problems (e.g., the existence of isobar components in 3 H, predictions of few-body-hypernuclei properties as a test of hyperon-nucleon interactions, investigation of the A = 6 ground states with exact three-body calculations, and the relation of triton D-state properties to the deuteron's D-state percentage) and electromagnetic properties and interactions of few-body nuclei (e.g., Coulomb effects in calculating and measuring asymptotic normalization constants, and γ + 3 He breakup reaction mechanisms at intermediate energies). Descriptions of the progress made indicate where each subject stands at present, and emphasize the significant results obtained. A publication list is attached

Scaling of human body composition to stature: new insights into body mass index.

Science.gov (United States)

Heymsfield, Steven B; Gallagher, Dympna; Mayer, Laurel; Beetsch, Joel; Pietrobelli, Angelo

2007-07-01

Although Quetelet first reported in 1835 that adult weight scales to the square of stature, limited or no information is available on how anatomical body compartments, including adipose tissue (AT), scale to height. We examined the critical underlying assumptions of adiposity-body mass index (BMI) relations and extended these analyses to major anatomical compartments: skeletal muscle (SM), bone, residual mass, weight (AT+SM+bone), AT-free mass, and organs (liver, brain). This was a cross-sectional analysis of 2 body-composition databases: one including magnetic resonance imaging and dual-energy X-ray absorptiometry (DXA) estimates of evaluated components in adults (total n=411; organs=76) and the other a larger DXA database (n=1346) that included related estimates of fat, fat-free mass, and bone mineral mass. Weight, primary lean components (SM, residual mass, AT-free mass, and fat-free mass), and liver scaled to height with powers of approximately 2 (all P2 (2.31-2.48), and the fraction of weight as bone mineral mass was significantly (Pshort and tall subjects with equivalent BMIs have similar but not identical body composition, provide new insights into earlier BMI-related observations and thus establish a foundation for height-normalized indexes, and create an analytic framework for future studies.

Estimation of human body concentrations of DDT from indoor residual spraying for malaria control

International Nuclear Information System (INIS)

Gyalpo, Tenzing; Fritsche, Lukas; Bouwman, Henk; Bornman, Riana; Scheringer, Martin; Hungerbühler, Konrad

2012-01-01

Inhabitants of dwellings treated with DDT for indoor residual spraying show high DDT levels in blood and breast milk. This is of concern since mothers transfer lipid-soluble contaminants such as DDT via breastfeeding to their children. Focusing on DDT use in South Africa, we employ a pharmacokinetic model to estimate DDT levels in human lipid tissue over the lifetime of an individual to determine the amount of DDT transferred to children during breastfeeding, and to identify the dominant DDT uptake routes. In particular, the effects of breastfeeding duration, parity, and mother's age on DDT concentrations of mother and infant are investigated. Model results show that primiparous mothers have greater DDT concentrations than multiparous mothers, which causes higher DDT exposure of first-born children. DDT in the body mainly originates from diet. Generally, our modeled DDT levels reproduce levels found in South African biomonitoring data within a factor of 3. - Highlights: ► Comparison of one-compartment pharmacokinetic model with biomonitoring data. ► Pre- and postnatal exposure of infants depends on breastfeeding duration and parity. ► Dietary exposure of DDT is the dominant uptake route in South Africa. ► Elimination half-lives of DDT and DDE are shorter in children than in adults. - Model predictions of a one-compartment pharmacokinetic model confirm the trends of DDT found in human samples of inhabitants living in DDT-treated dwellings.

Two-body interactions by tachyon exchange

International Nuclear Information System (INIS)

Maccarrone, R.; Recami, E.

1982-01-01

Due to its relevance for the possible applications to particle physics and for causality problems, is analyzed in this paper the kinematic of (classical) tachyon-exchange between two bodies A, B, for all possible relative velocities. In particular, the two cases u.-vector V-vector c 2 are carefully investigated, V are the body B and tachyon speeds relative to A, respectively

Investigations of the structure and electromagnetic interactions of few body systems. Annual progress report, 1 September 1982-31 August 1983

International Nuclear Information System (INIS)

Harper, E.P.; Lehman, D.R.; Prats, F.

1983-01-01

The George Washington University nuclear theory group proposes to conduct investigations of the structure and electromagnetic interactions of few-body systems. The structural properties of the very light nuclei are examined by developing theoretical models that begin from the basic interactions between the constituents and that are solved exactly (numerically), i.e., full three- or four-body dynamics. Such models are then used in an attempt to understand the details of the strong and electromagnetic interactions of the few-nucleon nuclei after the basic underlying reaction mechanisms are understood with simpler models. These efforts are becoming increasingly important with the advent of high duty cycle, high current electron accelerators from which valuable data will be forthcoming that should permit unraveling the structure and interactions of the very-light nuclei. Examples of specific work proposed are the following: 1) Set up the equations for the low-energy photodisintegration of 3 He and 3 H including final-state interactions and the E1 plus E2 operators; 2) Develop a unified picture of the p + d → 3 He + γ, p + d → 3 He + π 0 , p + d → 3 H + π + reactions at intermediate energies; 3) Calculate the elastic and inelastic (1 + →0 + ) form factors for 6 Li with three-body (αNN) wave functions; 4) Calculate static properties (RMS radius, magnetic moment, and quadrupole moment) of 6 Li with three-body wave functions; and 5) Develop the theory for the coincidence reactions 6 Li(p,2p)nα, 6 Li(e,e'p)nα, and 6 Li(e,e'd)α. It is anticipated that these efforts will expand the frontiers of our knowledge about few-body nuclei

Using mutagenesis to explore conserved residues in the RNA-binding groove of influenza A virus nucleoprotein for antiviral drug development

Science.gov (United States)

Liu, Chia-Lin; Hung, Hui-Chen; Lo, Shou-Chen; Chiang, Ching-Hui; Chen, I.-Jung; Hsu, John T.-A.; Hou, Ming-Hon

2016-02-01

Nucleoprotein (NP) is the most abundant type of RNA-binding viral protein in influenza A virus-infected cells and is necessary for viral RNA transcription and replication. Recent studies demonstrated that influenza NP is a valid target for antiviral drug development. The surface of the groove, covered with numerous conserved residues between the head and body domains of influenza A NP, plays a crucial role in RNA binding. To explore the mechanism by which NP binds RNA, we performed a series of site-directed mutagenesis in the RNA-binding groove, followed by surface plasmon resonance (SPR), to characterize the interactions between RNA and NP. Furthermore, a role of Y148 in NP stability and NP-RNA binding was evaluated. The aromatic residue of Y148 was found to stack with a nucleotide base. By interrupting the stacking interaction between Y148 and an RNA base, we identified an influenza virus NP inhibitor, (E, E)-1,7-bis(4-hydroxy-3-methoxyphenyl) -1,6-heptadiene-3,5-dione; this inhibitor reduced the NP’s RNA-binding affinity and hindered viral replication. Our findings will be useful for the development of new drugs that disrupt the interaction between RNA and viral NP in the influenza virus.

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...

Generic GPCR residue numbers - aligning topology maps while minding the gaps

DEFF Research Database (Denmark)

Isberg, Vignir; de Graaf, Chris; Bortolato, Andrea

2015-01-01

Generic residue numbers facilitate comparisons of, for example, mutational effects, ligand interactions, and structural motifs. The numbering scheme by Ballesteros and Weinstein for residues within the class A GPCRs (G protein-coupled receptors) has more than 1100 citations, and the recent crysta...

Investigations of the structure and electromagnetic interactions of few-body systems. Progress report, 1 January 1980-1 October 1980

Energy Technology Data Exchange (ETDEWEB)

Harper, E P; Lehman, D R; Prats, F

1980-11-07

Considerable progress has been made on the long-range problems described in the original proposal document (1 February 1979 to 31 January 1980) and on the shorter-range problems described in the last renewal proposal (1 February 1980 to 31 January 1981). This progress concerns few-body structure problems (e.g., the existence of isobar components in /sup 3/H, predictions of few-body-hypernuclei properties as a test of hyperon-nucleon interactions, investigation of the A = 6 ground states with exact three-body calculations, and the relation of triton D-state properties to the deuteron's D-state percentage) and electromagnetic properties and interactions of few-body nuclei (e.g., Coulomb effects in calculating and measuring asymptotic normalization constants, and ..gamma.. + /sup 3/He breakup reaction mechanisms at intermediate energies). Descriptions of the progress made indicate where each subject stands at present, and emphasize the significant results obtained. A publication list is attached.

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.

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.

A tool for calculating binding-site residues on proteins from PDB structures

Directory of Open Access Journals (Sweden)

Hu Jing

2009-08-01

Full Text Available Abstract Background In the research on protein functional sites, researchers often need to identify binding-site residues on a protein. A commonly used strategy is to find a complex structure from the Protein Data Bank (PDB that consists of the protein of interest and its interacting partner(s and calculate binding-site residues based on the complex structure. However, since a protein may participate in multiple interactions, the binding-site residues calculated based on one complex structure usually do not reveal all binding sites on a protein. Thus, this requires researchers to find all PDB complexes that contain the protein of interest and combine the binding-site information gleaned from them. This process is very time-consuming. Especially, combing binding-site information obtained from different PDB structures requires tedious work to align protein sequences. The process becomes overwhelmingly difficult when researchers have a large set of proteins to analyze, which is usually the case in practice. Results In this study, we have developed a tool for calculating binding-site residues on proteins, TCBRP http://yanbioinformatics.cs.usu.edu:8080/ppbindingsubmit. For an input protein, TCBRP can quickly find all binding-site residues on the protein by automatically combining the information obtained from all PDB structures that consist of the protein of interest. Additionally, TCBRP presents the binding-site residues in different categories according to the interaction type. TCBRP also allows researchers to set the definition of binding-site residues. Conclusion The developed tool is very useful for the research on protein binding site analysis and prediction.

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.

Residual symptoms and functioning in depression, does the type of residual symptom matter? A post-hoc analysis

Directory of Open Access Journals (Sweden)

Romera Irene

2013-02-01

Full Text Available Abstract Background The degrees to which residual symptoms in major depressive disorder (MDD adversely affect patient functioning is not known. This post-hoc analysis explored the association between different residual symptoms and patient functioning. Methods Patients with MDD who responded (≥50% on the 17-item Hamilton Rating Scale for Depression; HAMD-17 after 3 months of treatment (624/930 were included. Residual core mood-symptoms (HAMD-17 core symptom subscale ≥1, residual insomnia-symptoms (HAMD-17 sleep subscale ≥1, residual anxiety-symptoms (HAMD-17-anxiety subscale ≥1, residual somatic-symptoms (HAMD-17 Item 13 ≥1, pain (Visual Analogue Scale ≥30, and functioning were assessed after 3 months treatment. A stepwise logistic regression model with normal functioning (Social and Occupational Functioning Assessment Scale ≥80 as the dependent variable was used. Results After 3 months, 59.5% of patients (371/624 achieved normal functioning and 66.0% (412/624 were in remission. Residual symptom prevalence was: core mood symptoms 72%; insomnia 63%; anxiety 78%; and somatic symptoms 41%. Pain reported in 18%. Factors associated with normal functioning were absence of core mood symptoms (odds ratio [OR] 8.7; 95% confidence interval [CI], 4.6–16.7, absence of insomnia symptoms (OR 1.8; 95% CI, 1.2–2.7, episode length (4–24 weeks vs. ≥24 weeks [OR 2.0; 95% CI, 1.1–3.6] and better baseline functioning (OR 1.0; 95% CI, 1.0–1.1. A significant interaction between residual anxiety symptoms and pain was found (p = 0.0080. Conclusions Different residual symptoms are associated to different degrees with patient functioning. To achieve normal functioning, specific residual symptoms domains might be targeted for treatment.

N-Oxide-N-oxide interactions and Cl...Cl halogen bonds in pentachloropyridine N-oxide: the many-body approach to interactions in the crystal state.

Science.gov (United States)

Wzgarda-Raj, Kinga; Rybarczyk-Pirek, Agnieszka J; Wojtulewski, Sławomir; Palusiak, Marcin

2018-02-01

Pentachloropyridine N-oxide, C 5 Cl 5 NO, crystallizes in the monoclinic space group P2 1 /c. In the crystal structure, molecules are linked by C-Cl...Cl halogen bonds into infinite ribbons extending along the crystallographic [100] direction. These molecular aggregates are further stabilized by very short intermolecular N-oxide-N-oxide interactions into herringbone motifs. Computations based on quantum chemistry methods allowed for a more detailed description of the N-oxide-N-oxide interactions and Cl...Cl halogen bonds. For this purpose, Hirshfeld surface analysis and the many-body approach to interaction energy were applied.

The gravitational interaction between N-body (star clusters) and hydrodynamic (ISM) codes in disk galaxy simulations

International Nuclear Information System (INIS)

Schroeder, M.C.; Comins, N.F.

1986-01-01

During the past twenty years, three approaches to numerical simulations of the evolution of galaxies have been developed. The first approach, N-body programs, models the motion of clusters of stars as point particles which interact via their gravitational potentials to determine the system dynamics. Some N-body codes model molecular clouds as colliding, inelastic particles. The second approach, hydrodynamic models of galactic dynamics, simulates the activity of the interstellar medium as a compressible gas. These models presently do not include stars, the effect of gravitational fields, or allow for stellar evolution and exchange of mass or angular momentum between stars and the interstellar medium. The third approach, stochastic star formation simulations of disk galaxies, allows for the interaction between stars and interstellar gas, but does not allow the star particles to move under the influence of gravity

What is an attractive body? Using an interactive 3D program to create the ideal body for you and your partner.

Directory of Open Access Journals (Sweden)

Kara L Crossley

Full Text Available What is the ideal body size and shape that we want for ourselves and our partners? What are the important physical features in this ideal? And do both genders agree on what is an attractive body? To answer these questions we used a 3D interactive software system which allows our participants to produce a photorealistic, virtual male or female body. Forty female and forty male heterosexual Caucasian observers (females mean age 19.10 years, s.d. 1.01; 40 males mean age 19.84, s.d. 1.66 set their own ideal size and shape, and the size and shape of their ideal partner using the DAZ studio image manipulation programme. In this programme the shape and size of a 3D body can be altered along 94 independent dimensions, allowing each participant to create the exact size and shape of the body they want. The volume (and thus the weight assuming a standard density and the circumference of the bust, waist and hips of these 3D models can then be measured. The ideal female body set by women (BMI = 18.9, WHR = 0.70, WCR = 0.67 was very similar to the ideal partner set by men, particularly in their BMI (BMI = 18.8, WHR = 0.73, WCR = 0.69. This was a lower BMI than the actual BMI of 39 of the 40 women. The ideal male body set by the men (BMI = 25.9, WHR = 0.87, WCR = 0.74 was very similar to the ideal partner set by the women (BMI = 24.5, WHR = 0.86, WCR = 0.77. This was a lower BMI than the actual BMI of roughly half of the men and a higher BMI than the other half. The results suggest a consistent preference for an ideal male and female body size and shape across both genders. The results also suggest that both BMI and torso shape are important components for the creation of the ideal body.

Effect of mungbean residue and nitrogen levels on barley

International Nuclear Information System (INIS)

Jan, A.; Muhammad, Z.; Daur, I.; Khan, I.A.

2011-01-01

A field experiment was conducted to evaluate response of barley to mungbean residue (0, 10, 20 and 30 Mg ha/sup -1/), nitrogen levels (0, 25, 50 and 75 kg ha/sup -1/) and their interaction. Emergence m/sup -2/ (50), plant height (109 cm), leaf area tiller-1 (106 cm/sup 2/), lodging score (5.55), termites attack (3.4%), grains spike-1 (67), biological yield (12.80 Mg ha/sup -1/) and grain yield (2.32 Mg ha/sup -1/) were significantly (p=0.05) higher for 30 Mg ha/sup -1/ mungbean residue compared to other levels. Similarly plant height (110 cm), lodging score (5.29) and biological yield (13.75 Mg ha/sup -1/) were higher at 75 kg ha/sup -1/ N compared to other levels of N. Productive tillers m/sup -2/, grains spike/sup -1/, 1000 grain weight, grain yield and harvest index were optimum at 50 kg ha-1 N as compared to 75 kg ha/sup -1/ N that encouraged lodging. Interaction between residue and nitrogen indicated that 10 Mg residue and 50 kg N ha/sup -1/ is recommended to achieve maximum net return under comparable conditions. (author)

A charged residue at the subunit interface of PCNA promotes trimer formation by destabilizing alternate subunit interactions

International Nuclear Information System (INIS)

Freudenthal, Bret D.; Gakhar, Lokesh; Ramaswamy, S.; Washington, M. Todd

2009-01-01

Eukaryotic proliferating cell nuclear antigen (PCNA), an essential accessory factor in DNA replication and repair, is a ring-shaped homotrimer. A novel nontrimeric structure of E113G-mutant PCNA protein is reported, which shows that this protein forms alternate subunit interactions. It is concluded that the charged side chain of Glu113 promotes normal trimer formation by destabilizing these alternate subunit interactions. Eukaryotic proliferating cell nuclear antigen (PCNA) is an essential replication accessory factor that interacts with a variety of proteins involved in DNA replication and repair. Each monomer of PCNA has an N-terminal domain A and a C-terminal domain B. In the structure of the wild-type PCNA protein, domain A of one monomer interacts with domain B of a neighboring monomer to form a ring-shaped trimer. Glu113 is a conserved residue at the subunit interface in domain A. Two distinct X-ray crystal structures have been determined of a mutant form of PCNA with a substitution at this position (E113G) that has previously been studied because of its effect on translesion synthesis. The first structure was the expected ring-shaped trimer. The second structure was an unanticipated nontrimeric form of the protein. In this nontrimeric form, domain A of one PCNA monomer interacts with domain A of a neighboring monomer, while domain B of this monomer interacts with domain B of a different neighboring monomer. The B–B interface is stabilized by an antiparallel β-sheet and appears to be structurally similar to the A–B interface observed in the trimeric form of PCNA. The A–A interface, in contrast, is primarily stabilized by hydrophobic interactions. Because the E113G substitution is located on this hydrophobic surface, the A–A interface should be less favorable in the case of the wild-type protein. This suggests that the side chain of Glu113 promotes trimer formation by destabilizing these possible alternate subunit interactions

The translation initiation factor 3 subunit eIF3K interacts with PML and associates with PML nuclear bodies

Energy Technology Data Exchange (ETDEWEB)

Salsman, Jayme; Pinder, Jordan; Tse, Brenda [Department of Pathology, Dalhousie University, P.O. Box 15000, Halifax, Nova Scotia, Canada B3H 4R2 (Canada); Corkery, Dale [Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia (Canada); Dellaire, Graham, E-mail: dellaire@dal.ca [Department of Pathology, Dalhousie University, P.O. Box 15000, Halifax, Nova Scotia, Canada B3H 4R2 (Canada); Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia (Canada)

2013-10-15

The promyelocytic leukemia protein (PML) is a tumor suppressor protein that regulates a variety of important cellular processes, including gene expression, DNA repair and cell fate decisions. Integral to its function is the ability of PML to form nuclear bodies (NBs) that serve as hubs for the interaction and modification of over 90 cellular proteins. There are seven canonical isoforms of PML, which encode diverse C-termini generated by alternative pre-mRNA splicing. Recruitment of specific cellular proteins to PML NBs is mediated by protein–protein interactions with individual PML isoforms. Using a yeast two-hybrid screen employing peptide sequences unique to PML isoform I (PML-I), we identified an interaction with the eukaryotic initiation factor 3 subunit K (eIF3K), and in the process identified a novel eIF3K isoform, which we term eIF3K-2. We further demonstrate that eIF3K and PML interact both in vitro via pull-down assays, as well as in vivo within human cells by co-immunoprecipitation and co-immunofluorescence. In addition, eIF3K isoform 2 (eIF3K-2) colocalizes to PML bodies, particularly those enriched in PML-I, while eIF3K isoform 1 associates poorly with PML NBs. Thus, we report eIF3K as the first known subunit of the eIF3 translation pre-initiation complex to interact directly with the PML protein, and provide data implicating alternative splicing of both PML and eIF3K as a possible regulatory mechanism for eIF3K localization at PML NBs. - Highlights: • The PML-I C-terminus, encoded by exon 9, interacts with translation factor eIF3K. • We identify a novel eIF3K isoform that excludes exon 2 (eIF3K-2). • eIF3K-2 preferentially associates with PML bodies enriched in PML-I vs. PML-IV. • Alternative splicing of eIF3K regulates association with PML bodies.

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.

Dynamics of many-body localization in the presence of particle loss

Science.gov (United States)

van Nieuwenburg, EPL; Yago Malo, J.; Daley, AJ; Fischer, MH

2018-01-01

At long times, residual couplings to the environment become relevant even in the most isolated experiments, a crucial difficulty for the study of fundamental aspects of many-body dynamics. A particular example is many-body localization in a cold-atom setting, where incoherent photon scattering introduces both dephasing and particle loss. Whereas dephasing has been studied in detail and is known to destroy localization already on the level of non-interacting particles, the effect of particle loss is less well understood. A difficulty arises due to the ‘non-local’ nature of the loss process, complicating standard numerical tools using matrix product decomposition. Utilizing symmetries of the Lindbladian dynamics, we investigate the particle loss on both the dynamics of observables, as well as the structure of the density matrix and the individual states. We find that particle loss in the presence of interactions leads to dissipation and a strong suppression of the (operator space) entanglement entropy. Our approach allows for the study of the interplay of dephasing and loss for pure and mixed initial states to long times, which is important for future experiments using controlled coupling of the environment.

Two Arginine Residues of Streptococcus gordonii Sialic Acid-Binding Adhesin Hsa Are Essential for Interaction to Host Cell Receptors.

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Yumiko Urano-Tashiro

Full Text Available Hsa is a large, serine-rich protein of Streptococcus gordonii DL1 that mediates binding to α2-3-linked sialic acid termini of glycoproteins, including platelet glycoprotein Ibα, and erythrocyte membrane protein glycophorin A, and band 3. The binding of Hsa to platelet glycoprotein Ibα contributes to the pathogenesis of infective endocarditis. This interaction appears to be mediated by a second non-repetitive region (NR2 of Hsa. However, the molecular details of the interaction between the Hsa NR2 region and these glycoproteins are not well understood. In the present study, we identified the amino acid residues of the Hsa NR2 region that are involved in sialic acid recognition. To identify the sialic acid-binding site of Hsa NR2 region, we prepared various mutants of Hsa NR2 fused with glutathione transferase. Fusion proteins harboring Arg340 to Asn (R340N or Arg365 to Asn (R365N substitutions in the NR2 domain exhibited significantly reduced binding to human erythrocytes and platelets. A sugar-binding assay showed that these mutant proteins abolished binding to α2-3-linked sialic acid. Furthermore, we established S. gordonii DL1 derivatives that encoded the corresponding Hsa mutant protein. In whole-cell assays, these mutant strains showed significant reductions in hemagglutination, in platelet aggregation, and in adhesion to human leukocytes. These results indicate that the Arg340 and Arg365 residues of Hsa play an important role in the binding of Hsa to α2-3-linked sialic acid-containing glycoproteins.

Many-body Anderson localization of strongly interacting bosons in random lattices

International Nuclear Information System (INIS)

Katzer, Roman

2015-05-01

In the present work, we investigate the problem of many-body localization of strongly interacting bosons in random lattices within the disordered Bose-Hubbard model. This involves treating both the local Mott-Hubbard physics as well as the non-local quantum interference processes, which give rise to the phenomenon of Anderson localization, within the same theory. In order to determine the interaction induced transition to the Mott insulator phase, it is necessary to treat the local particle interaction exactly. Therefore, here we use a mean-field approach that approximates only the kinetic term of the Hamiltonian. This way, the full problem of interacting bosons on a random lattice is reduced to a local problem of a single site coupled to a particle bath, which has to be solved self-consistently. In accordance to previous works, we find that a finite disorder width leads to a reduced size of the Mott insulating regions. The transition from the superfluid phase to the Bose glass phase is driven by the non-local effect of Anderson localization. In order to describe this transition, one needs to work within a theory that is non-local as well. Therefore, here we introduce a new approach to the problem. Based on the results for the local excitation spectrum obtained within the mean-field theory, we reduce the full, interacting model to an effective, non-interacting model by applying a truncation scheme to the Hilbert space. Evaluating the long-ranged current density within this approximation, we identify the transition from the Bose glass to the superfluid phase with the Anderson transition of the effective model. Resolving this transition using the self-consistent theory of localization, we obtain the full phase diagram of the disordered Bose-Hubbard model in the regime of strong interaction and larger disorder. In accordance to the theorem of inclusions, we find that the Mott insulator and the superfluid phase are always separated by the compressible, but insulating

Tyrosine residues modification studied by MALDI-TOF mass spectrometry

International Nuclear Information System (INIS)

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

2004-01-01

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

Kinesthetic Interaction

DEFF Research Database (Denmark)

Fogtmann, Maiken Hillerup; Fritsch, Jonas; Kortbek, Karen Johanne

2008-01-01

Within the Human-Computer Interaction community there is a growing interest in designing for the whole body in interaction design. The attempts aimed at addressing the body have very different outcomes spanning from theoretical arguments for understanding the body in the design process, to more...... practical examples of designing for bodily potential. This paper presents Kinesthetic Interaction as a unifying concept for describing the body in motion as a foundation for designing interactive systems. Based on the theoretical foundation for Kinesthetic Interaction, a conceptual framework is introduced...... to reveal bodily potential in relation to three design themes – kinesthetic development, kinesthetic means and kinesthetic disorder; and seven design parameters – engagement, sociality, movability, explicit motivation, implicit motivation, expressive meaning and kinesthetic empathy. The framework is a tool...

HPLC identification of isoniazid residues in bovine milk

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Leite R.M.H.

2000-01-01

Full Text Available The high pressure liquid chromatography (HPLC was used for the identification of isoniazid (isonicotinic acid hydrazide in the milk of cattle treated with a dose of 25 mg/kg/day in alternated days. The effect of milk pasteurization on the isoniazid residue concentration was also studied. The drug excretion presented a cyclic variation, with higher levels in the first day after administration (aa, a mean of 1104.48µg/l, and a decrease two days aa, with a mean of 104.12µg/l. Four days after the last administration of the drug it was not possible to identify residues of isoniazid in the milk of treated animals. Body weight and milk yield influenced the amount of the excreted drug, and pasteurization decreased (mean 47.07% the concentration of isoniazid residue in milk.

The Relationship between Body Movements and Qualities of Social Interaction between a Boy with Severe Developmental Disabilities and His Caregiver

Science.gov (United States)

Dammeyer, Jesper; Koppe, Simo

2013-01-01

Research in social interaction and nonverbal communication among individuals with severe developmental disabilities also includes the study of body movements. Advances in analytical technology give new possibilities for measuring body movements more accurately and reliably. One such advance is the Qualisys Motion Capture System (QMCS), which…

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...

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...

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

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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.

Different finite element techniques to predict welding residual stresses in aluminum alloy plates

International Nuclear Information System (INIS)

Moein, Hadi; Sattari-Far, Iradj

2014-01-01

This study is a 3D thermomechanical finite element (FE) analysis of a single-pass and butt-welded work-hardened aluminum (Al) 5456 plates. It aims to validate the use of FE welding simulations to predict residual stress states in assessing the integrity of welded components. The predicted final residual stresses in the plate from the FE simulations are verified through comparison with experimental measurements. Three techniques are used to simulate the welding process. In the first two approaches, welding deposition is applied by using element birth and interaction techniques. In the third approach, the entire weld zone is simultaneously deposited. Results show a value at approximately the yield strength for longitudinal residual stresses of the welded center of the butt-welded Al alloy plates with a thickness of 2 mm. Considering the application of a comprehensive heat source, along with heat loss modeling and the temperature dependent properties of the material, the approach without deposition predicts a reasonable distribution of residual stresses. However, the element birth and interaction techniques, compared with the no-deposit technique, provide more accurate results in calculating residual stresses. Furthermore, the element interaction technique, compared with the element birth technique, exhibits higher efficiency and flexibility in modeling the deposition of welded metals as well as less modeling cost.

Ionic interaction of myosin loop 2 with residues located beyond the N-terminal part of actin probed by chemical cross-linking.

Science.gov (United States)

Pliszka, Barbara; Martin, Brian M; Karczewska, Emilia

2008-02-01

To probe ionic contacts of skeletal muscle myosin with negatively charged residues located beyond the N-terminal part of actin, myosin subfragment 1 (S1) and actin split by ECP32 protease (ECP-actin) were cross-linked with 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC). We have found that unmodified S1 can be cross-linked not only to the N-terminal part, but also to the C-terminal 36 kDa fragment of ECP-actin. Subsequent experiments performed on S1 cleaved by elastase or trypsin indicate that the cross-linking site in S1 is located within loop 2. This site is composed of Lys-636 and Lys-637 and can interact with negatively charged residues of the 36 kDa actin fragment, most probably with Glu-99 and Glu-100. Cross-links are formed both in the absence and presence of MgATP.P(i) analog, although the addition of nucleotide decreases the efficiency of the cross-linking reaction.

Transient interaction model of electromagnetic field generated by lightning current pulses and human body

International Nuclear Information System (INIS)

Iváncsy, T; Kiss, I; Tamus, Z Á; Szücs, L

2015-01-01

The lightning current generates time-varying magnetic field near the down-conductor and the down-conductors are mounted on the wall of the buildings where residential places might be situated. It is well known that the rapidly changing magnetic fields can generate dangerous eddy currents in the human body.The higher duration and gradient of the magnetic field can cause potentially life threatening cardiac stimulation. The coupling mechanism between the electromagnetic field and the human body is based on a well-known physical phenomena (e.g. Faradays law of induction). However, the calculation of the induced current is very complicated because the shape of the organs is complex and the determination of the material properties of living tissues is difficult, as well. Our previous study revealed that the cardiac stimulation is independent of the rising time of the lightning current and only the peak of the current counts.In this study, the authors introduce an improved model of the interaction of electromagnetic fields of lighting current near down-conductor and human body. Our previous models are based on the quasi stationer field calculations, the new improved model is a transient model. This is because the magnetic field around the down-conductor and in the human body can be determined more precisely, therefore the dangerous currents in the body can be estimated. (paper)

Influence of nuclear interactions in body tissues on tumor dose in carbon-ion radiotherapy

Energy Technology Data Exchange (ETDEWEB)

Inaniwa, T., E-mail: taku@nirs.go.jp; Kanematsu, N. [Medical Physics Research Program, Research Center for Charged Particle Therapy, National Institute of Radiological Sciences, Anagawa 4-9-1, Inage-ku, Chiba 263-8555 (Japan); Tsuji, H.; Kamada, T. [Hospital, Research Center for Charged Particle Therapy, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555 (Japan)

2015-12-15

Purpose: In carbon-ion radiotherapy treatment planning, the planar integrated dose (PID) measured in water is applied to the patient dose calculation with density scaling using the stopping power ratio. Since body tissues are chemically different from water, this dose calculation can be subject to errors, particularly due to differences in inelastic nuclear interactions. In recent studies, the authors proposed and validated a PID correction method for these errors. In the present study, the authors used this correction method to assess the influence of these nuclear interactions in body tissues on tumor dose in various clinical cases. Methods: Using 10–20 cases each of prostate, head and neck (HN), bone and soft tissue (BS), lung, liver, pancreas, and uterine neoplasms, the authors first used treatment plans for carbon-ion radiotherapy without nuclear interaction correction to derive uncorrected dose distributions. The authors then compared these distributions with recalculated distributions using the nuclear interaction correction (corrected dose distributions). Results: Median (25%/75% quartiles) differences between the target mean uncorrected doses and corrected doses were 0.2% (0.1%/0.2%), 0.0% (0.0%/0.0%), −0.3% (−0.4%/−0.2%), −0.1% (−0.2%/−0.1%), −0.1% (−0.2%/0.0%), −0.4% (−0.5%/−0.1%), and −0.3% (−0.4%/0.0%) for the prostate, HN, BS, lung, liver, pancreas, and uterine cases, respectively. The largest difference of −1.6% in target mean and −2.5% at maximum were observed in a uterine case. Conclusions: For most clinical cases, dose calculation errors due to the water nonequivalence of the tissues in nuclear interactions would be marginal compared to intrinsic uncertainties in treatment planning, patient setup, beam delivery, and clinical response. In some extreme cases, however, these errors can be substantial. Accordingly, this correction method should be routinely applied to treatment planning in clinical practice.

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.

Contribution of cation-π interactions to the stability of Sm/LSm oligomeric assemblies.

Science.gov (United States)

Mucić, Ivana D; Nikolić, Milan R; Stojanović, Srđan Đ

2015-07-01

In this work, we have analyzed the influence of cation-π interactions to the stability of Sm/LSm assemblies and their environmental preferences. The number of interactions formed by arginine is higher than lysine in the cationic group, while histidine is comparatively higher than phenylalanine and tyrosine in the π group. Arg-Tyr interactions are predominant among the various pairs analyzed. The furcation level of multiple cation-π interactions is much higher than that of single cation-π interactions in Sm/LSm interfaces. We have found hot spot residues forming cation-π interactions, and hot spot composition is similar for all aromatic residues. The Arg-Phe pair has the strongest interaction energy of -8.81 kcal mol(-1) among all the possible pairs of amino acids. The extent of burial of the residue side-chain correlates with the ΔΔG of binding for residues in the core and also for hot spot residues cation-π bonded across the interface. Secondary structure of the cation-π residues shows that Arg and Lys preferred to be in strand. Among the π residues, His prefers to be in helix, Phe prefers to be in turn, and Tyr prefers to be in strand. Stabilization centers for these proteins showed that all the five residues found in cation-π interactions are important in locating one or more of such centers. More than 50 % of the cation-π interacting residues are highly conserved. It is likely that the cation-π interactions contribute significantly to the overall stability of Sm/LSm proteins.

The impact of oral health on body image and social interactions among elders in long-term care.

Science.gov (United States)

Donnelly, Leeann R; Clarke, Laura Hurd; Phinney, Alison; MacEntee, Michael I

2016-12-01

The objective of this study was to explore how social interactions and body image are influenced by perceived oral health among older people who live in long-term care facilities. Social interactions among frail elders in long-term care (LTC) facilities are limited, but to what extent body image and oral health influence their social relations is poorly understood. A positive body image and the perception of adequate oral health are linked to increased social contacts, as well as improved health and well-being irrespective of age. However, as frailty increases, it is unclear whether appearance and oral health priorities remain stable. Open-ended interviews were conducted with a purposefully selected group of cognitively intact, older men and women who exhibited varying degrees of frailty, social engagement and oral health conditions and lived in one of seven long-term care facilities. The interviews were analysed using a constant comparative technique, and a second interview with participants checked the trustworthiness of the analysis. Three major categories were expressed by the participants: (1) My mouth is fine; (2) It depends; and (3) Not that important. Within each category, there were several contributing and influencing factors. Social interactions among residents in LTC may be negatively impacted by poor oral health, but only if other personal and social issues are less bothersome than conditions with the mouth. © 2015 John Wiley & Sons A/S and The Gerodontology Association. Published by John Wiley & Sons Ltd.

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

Computational modelling of string body interaction for the violin family and simulation of wolf notes

Science.gov (United States)

Inácio, O.; Antunes, J.; Wright, M. C. M.

2008-02-01

Most theoretical studies of bowed-string instruments deal with isolated strings, pinned on fixed supports. In others, the instrument body dynamics have been accounted by using extremely simplified models of the string-body interaction through the instrument bridge. Such models have, nevertheless, been instrumental to the understanding of a very common and musically undesirable phenomenon known as the wolf note—a strong beating interplay between string and body vibrations. Cellos, bad and good, are particularly prone to this problem. In previous work, a computational method that allows efficient time-domain modelling of bowed strings based on a modal approach has been introduced. This has been extended to incorporate the complex dynamics of real-life instrument bodies, and their coupling to the string motions, using experimental dynamical body data. The string is modelled using its unconstrained modes, assuming pinned-pinned boundary conditions at the tailpiece and the nut. At the intermediary bridge location, the string-body coupling is enforced using the body impulse-response or modal data, as measured at the instrument bridge. In the present paper, this computational approach is applied to a specific cello, which provided experimental wolf-behaviour data under several bowing conditions, as well as laboratory measurements of the bridge impulse responses on which the numerical simulations were based. Interesting aspects of the string-body dynamical responses are highlighted by numerical simulations and the corresponding sounds and animations produced. Finally, a qualitative (and, when possible, quantitative) comparison of the experimental and numerical results is presented.

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

Scaling of human body composition to stature: new insights into body mass index 123

Science.gov (United States)

Heymsfield, Steven B; Gallagher, Dympna; Mayer, Laurel; Beetsch, Joel; Pietrobelli, Angelo

2009-01-01

Background Although Quetelet first reported in 1835 that adult weight scales to the square of stature, limited or no information is available on how anatomical body compartments, including adipose tissue (AT), scale to height. Objective We examined the critical underlying assumptions of adiposity–body mass index (BMI) relations and extended these analyses to major anatomical compartments: skeletal muscle (SM), bone, residual mass, weight (AT+SM+bone), AT-free mass, and organs (liver, brain). Design This was a cross-sectional analysis of 2 body-composition databases: one including magnetic resonance imaging and dual-energy X-ray absorptiometry (DXA) estimates of evaluated components in adults (total n = 411; organs = 76) and the other a larger DXA database (n = 1346) that included related estimates of fat, fat-free mass, and bone mineral mass. Results Weight, primary lean components (SM, residual mass, AT-free mass, and fat-free mass), and liver scaled to height with powers of ≈2 (all P 2 (2.31–2.48), and the fraction of weight as bone mineral mass was significantly (P short and tall subjects with equivalent BMIs have similar but not identical body composition, provide new insights into earlier BMI-related observations and thus establish a foundation for height-normalized indexes, and create an analytic framework for future studies. PMID:17616766

Computer Simulations Reveal Multiple Functions for Aromatic Residues in Cellulase Enzymes (Fact Sheet)

Energy Technology Data Exchange (ETDEWEB)

2012-07-01

NREL researchers use high-performance computing to demonstrate fundamental roles of aromatic residues in cellulase enzyme tunnels. National Renewable Energy Laboratory (NREL) computer simulations of a key industrial enzyme, the Trichoderma reesei Family 6 cellulase (Cel6A), predict that aromatic residues near the enzyme's active site and at the entrance and exit tunnel perform different functions in substrate binding and catalysis, depending on their location in the enzyme. These results suggest that nature employs aromatic-carbohydrate interactions with a wide variety of binding affinities for diverse functions. Outcomes also suggest that protein engineering strategies in which mutations are made around the binding sites may require tailoring specific to the enzyme family. Cellulase enzymes ubiquitously exhibit tunnels or clefts lined with aromatic residues for processing carbohydrate polymers to monomers, but the molecular-level role of these aromatic residues remains unknown. In silico mutation of the aromatic residues near the catalytic site of Cel6A has little impact on the binding affinity, but simulation suggests that these residues play a major role in the glucopyranose ring distortion necessary for cleaving glycosidic bonds to produce fermentable sugars. Removal of aromatic residues at the entrance and exit of the cellulase tunnel, however, dramatically impacts the binding affinity. This suggests that these residues play a role in acquiring cellulose chains from the cellulose crystal and stabilizing the reaction product, respectively. These results illustrate that the role of aromatic-carbohydrate interactions varies dramatically depending on the position in the enzyme tunnel. As aromatic-carbohydrate interactions are present in all carbohydrate-active enzymes, the results have implications for understanding protein structure-function relationships in carbohydrate metabolism and recognition, carbon turnover in nature, and protein engineering

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.

Anionic Sites, Fucose Residues and Class I Human Leukocyte Antigen Fate During Interaction of Toxoplasma gondii with Endothelial Cells

Directory of Open Access Journals (Sweden)

Stumbo Ana Carolina

2002-01-01

Full Text Available Toxoplasma gondii invades and proliferates in human umbilical vein endothelial cells where it resides in a parasitophorous vacuole. In order to analyze which components of the endothelial cell plasma membrane are internalized and become part of the parasitophorous vacuole membrane, the culture of endothelial cells was labeled with cationized ferritin or UEA I lectin or anti Class I human leukocytte antigen (HLA before or after infection with T. gondii. The results showed no cationized ferritin and UEA I lectin in any parasitophorous vacuole membrane, however, the Class I HLA molecule labeling was observed in some endocytic vacuoles containing parasite until 1 h of interaction with T. gondii. After 24 h parasite-host cell interaction, the labeling was absent on the vacuolar membrane, but presents only in small vesicles near parasitophorous vacuole. These results suggest the anionic site and fucose residues are excluded at the time of parasitophorous vacuole formation while Class I HLA molecules are present only on a minority of Toxoplasma-containig vacuoles.

The proteins of intra-nuclear bodies: a data-driven analysis of sequence, interaction and expression

Directory of Open Access Journals (Sweden)

Bodén Mikael

2010-04-01

Full Text Available Abstract Background Cajal bodies, nucleoli, PML nuclear bodies, and nuclear speckles are morpohologically distinct intra-nuclear structures that dynamically respond to cellular cues. Such nuclear bodies are hypothesized to play important regulatory roles, e.g. by sequestering and releasing transcription factors in a timely manner. While the nucleolus and nuclear speckles have received more attention experimentally, the PML nuclear body and the Cajal body are still incompletely characterized in terms of their roles and protein complement. Results By collating recent experimentally verified data, we find that almost 1000 proteins in the mouse nuclear proteome are known to associate with one or more of the nuclear bodies. Their gene ontology terms highlight their regulatory roles: splicing is confirmed to be a core activity of speckles and PML nuclear bodies house a range of proteins involved in DNA repair. We train support-vector machines to show that nuclear proteins contain discriminative sequence features that can be used to identify their intra-nuclear body associations. Prediction accuracy is highest for nucleoli and nuclear speckles. The trained models are also used to estimate the full protein complement of each nuclear body. Protein interactions are found primarily to link proteins in the nuclear speckles with proteins from other compartments. Cell cycle expression data provide support for increased activity in nucleoli, nuclear speckles and PML nuclear bodies especially during S and G2 phases. Conclusions The large-scale analysis of the mouse nuclear proteome sheds light on the functional organization of physically embodied intra-nuclear compartments. We observe partial support for the hypothesis that the physical organization of the nucleus mirrors functional modularity. However, we are unable to unambiguously identify proteins' intra-nuclear destination, suggesting that critical drivers behind of intra-nuclear translocation are yet to

Residual Stress Analysis of Aircraft Part using Neutron Beam

Energy Technology Data Exchange (ETDEWEB)

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

2012-05-15

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

Crossover dynamics of dispersive shocks in Bose-Einstein condensates characterized by two- and three-body interactions

KAUST Repository

Crosta, M.; Trillo, S.; Fratalocchi, Andrea

2012-01-01

We show that the perturbative nonlinearity associated with three-atom interactions, competing with standard two-body repulsive interactions, can change dramatically the evolution of one-dimensional (1D) dispersive shock waves in a Bose-Einstein condensate. In particular, we prove the existence of a rich crossover dynamics, ranging from the formation of multiple shocks regularized by nonlinear oscillations culminating in coexisting dark and antidark matter waves to 1D-soliton collapse. For a given scattering length, all these different regimes can be accessed by varying the density of atoms in the condensate.

Crossover dynamics of dispersive shocks in Bose-Einstein condensates characterized by two- and three-body interactions

KAUST Repository

Crosta, M.

2012-04-10

We show that the perturbative nonlinearity associated with three-atom interactions, competing with standard two-body repulsive interactions, can change dramatically the evolution of one-dimensional (1D) dispersive shock waves in a Bose-Einstein condensate. In particular, we prove the existence of a rich crossover dynamics, ranging from the formation of multiple shocks regularized by nonlinear oscillations culminating in coexisting dark and antidark matter waves to 1D-soliton collapse. For a given scattering length, all these different regimes can be accessed by varying the density of atoms in the condensate.

Wetting of nonconserved residue-backbones: A feature indicative of aggregation associated regions of proteins.

Science.gov (United States)

Pradhan, Mohan R; Pal, Arumay; Hu, Zhongqiao; Kannan, Srinivasaraghavan; Chee Keong, Kwoh; Lane, David P; Verma, Chandra S

2016-02-01

Aggregation is an irreversible form of protein complexation and often toxic to cells. The process entails partial or major unfolding that is largely driven by hydration. We model the role of hydration in aggregation using "Dehydrons." "Dehydrons" are unsatisfied backbone hydrogen bonds in proteins that seek shielding from water molecules by associating with ligands or proteins. We find that the residues at aggregation interfaces have hydrated backbones, and in contrast to other forms of protein-protein interactions, are under less evolutionary pressure to be conserved. Combining evolutionary conservation of residues and extent of backbone hydration allows us to distinguish regions on proteins associated with aggregation (non-conserved dehydron-residues) from other interaction interfaces (conserved dehydron-residues). This novel feature can complement the existing strategies used to investigate protein aggregation/complexation. © 2015 Wiley Periodicals, Inc.

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.

Three-body forces in p-shell nuclei

International Nuclear Information System (INIS)

Hees, A.G.M. van; Booten, J.G.L.; Glaudemans, P.W.M.

1990-01-01

Within the (0 + 1)ℎω shell-model space for p-shell nuclei we found that a schematic three-body interaction in addition to a translationally invariant two-body interaction leads to a strongly improved description of energy levels. The present three-body interaction is related to the Δ-isobar intermediate-state model of the two-pion exchange three-nucleon interaction. (orig.)

Elastic interactions between hydrogen atoms in metals. II. Elastic interaction energies

International Nuclear Information System (INIS)

Shirley, A.I.; Hall, C.K.

1986-01-01

The fully harmonic lattice approximation derived in a previous paper is used to calculate the elastic interaction energies in the niobium-hydrogen system. The permanent-direct, permanent-indirect, induced-direct, and induced-indirect forces calculated previously each give rise to a corresponding elastic interaction between hydrogen atoms. The latter three interactions have three- and four-body terms in addition to the usual two-body terms. These quantities are calculated and compared with the corresponding two-body permanent elastic interactions obtained in the harmonic-approximation treatment of Horner and Wagner. The results show that the total induced elastic energy is approximately (1/3) the size of the total permanent elastic energy and opposite to it in sign. The total elastic energy due to three-body interactions is approximately (1/4) the size of the total two-body elastic energy, while the total four-body elastic energy is approximately 5% of the total two-body energy. These additional elastic energies are expected to have a profound effect on the thermodynamic and phase-change behavior of a metal hydride

Thermogravimetric investigation of the co-combustion between the pyrolysis oil distillation residue and lignite.

Science.gov (United States)

Li, Hao; Xia, Shuqian; Ma, Peisheng

2016-10-01

Co-combustion of lignite with distillation residue derived from rice straw pyrolysis oil was investigated by non-isothermal thermogravimetric analysis (TGA). The addition of distillation residue improved the reactivity and combustion efficiency of lignite, such as increasing the weight loss rate at peak temperature and decreasing the burnout temperature and the total burnout. With increasing distillation residue content in the blended fuels, the synergistic interactions between distillation residue and lignite firstly increased and then decreased during co-combustion stage. Results of XRF, FTIR, (13)C NMR and SEM analysis indicated that chemical structure, mineral components and morphology of samples have great influence on the synergistic interactions. The combustion mechanisms and kinetic parameters were calculated by the Coats Redfern model, suggesting that the lowest apparent activation energy (120.19kJ/mol) for the blended fuels was obtained by blending 60wt.% distillation residue during main co-combustion stage. Copyright © 2016 Elsevier Ltd. All rights reserved.

A PM7 dynamic residue-ligand interactions energy landscape of the BACE1 inhibitory pathway by hydroxyethylamine compounds. Part I: The flap closure process.

Science.gov (United States)

Gueto-Tettay, Carlos; Martinez-Consuegra, Alejandro; Zuchniarz, Joshua; Gueto-Tettay, Luis Roberto; Drosos-Ramírez, Juan Carlos

2017-09-01

BACE1 is an enzyme of scientific interest because it participates in the progression of Alzheimer's disease. Hydroxyethylamines (HEAs) are a family of compounds which exhibit inhibitory activity toward BACE1 at a nanomolar level, favorable pharmacokinetic properties and oral bioavailability. The first step in the inhibition of BACE1 by HEAs consists of their entrance into the protease active site and the resultant conformational change in the protein, from Apo to closed form. These two conformations differ in the position of an antiparallel loop (called the flap) which covers the entrance to the catalytic site. For BACE1, closure of this flap is vital to its catalytic activity and to inhibition of the enzyme due to the new interactions thereby formed with the ligand. In the present study a dynamic energy landscape of residue-ligand interaction energies (ReLIE) measured for 112 amino acids in the BACE1 active site and its immediate vicinity during the closure of the flap induced by 8 HEAs of different inhibitory power is presented. A total of 6.272 million ReLIE calculations, based on the PM7 semiempirical method, provided a deep and quantitative view of the first step in the inhibition of the aspartyl protease. The information suggests that residues Asp93, Asp289, Thr292, Thr293, Asn294 and Arg296 are anchor points for the ligand, accounting for approximately 45% of the total protein-ligand interaction. Additionally, flap closure improved the BACE1-HEA interaction by around 25%. Furthermore, the inhibitory activity of HEAs could be related to the capacity of these ligands to form said anchor point interactions and maintain them over time: the lack of some of these anchor interactions delayed flap closure or impeded it completely, or even caused the flap to reopen. The methodology employed here could be used as a tool to evaluate future structural modifications which lead to improvements in the favorability and stability of BACE1-HEA ReLIEs, aiding in the design of

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

Science.gov (United States)

Leonardi, Nicoletta; Plater, Andrew James

2017-11-01

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

The differences in hadronic cross-sections and the residues of secondary reggeons in the quark-gluon model for strong interactions

International Nuclear Information System (INIS)

Kaidalov, A.B.; Volkovitsky, P.E.

1981-01-01

In the framework of the quark-gluon picture for strong interactions based on the topological expansion and the string model, the relations between t differences of hadronic cross- section are obtained. The system of equations for the contribution of secondary reggeons (rho, ω, f, A 2 and phi and f' poles) to the elastic scattering amplitudes for arbitrary hadrons is derived. It is shown that this system has a factorized solution and the secondary reggeon residues for all hadrons are expressed in terms of the universal function g(t). The model predictions are in a good agreement with experimental data [ru

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

Simulation of Quantum Many-Body Dynamics for Generic Strongly-Interacting Systems

Science.gov (United States)

Meyer, Gregory; Machado, Francisco; Yao, Norman

2017-04-01

Recent experimental advances have enabled the bottom-up assembly of complex, strongly interacting quantum many-body systems from individual atoms, ions, molecules and photons. These advances open the door to studying dynamics in isolated quantum systems as well as the possibility of realizing novel out-of-equilibrium phases of matter. Numerical studies provide insight into these systems; however, computational time and memory usage limit common numerical methods such as exact diagonalization to relatively small Hilbert spaces of dimension 215 . Here we present progress toward a new software package for dynamical time evolution of large generic quantum systems on massively parallel computing architectures. By projecting large sparse Hamiltonians into a much smaller Krylov subspace, we are able to compute the evolution of strongly interacting systems with Hilbert space dimension nearing 230. We discuss and benchmark different design implementations, such as matrix-free methods and GPU based calculations, using both pre-thermal time crystals and the Sachdev-Ye-Kitaev model as examples. We also include a simple symbolic language to describe generic Hamiltonians, allowing simulation of diverse quantum systems without any modification of the underlying C and Fortran code.

Body-part specific interactions of action verb processing with motor behaviour.

Science.gov (United States)

Klepp, Anne; Niccolai, Valentina; Sieksmeyer, Jan; Arnzen, Stephanie; Indefrey, Peter; Schnitzler, Alfons; Biermann-Ruben, Katja

2017-06-15

The interaction of action-related language processing with actual movement is an indicator of the functional role of motor cortical involvement in language understanding. This paper describes two experiments using single action verb stimuli. Motor responses were performed with the hand or the foot. To test the double dissociation of language-motor facilitation effects within subjects, Experiments 1 and 2 used a priming procedure where both hand and foot reactions had to be performed in response to different geometrical shapes, which were preceded by action verbs. In Experiment 1, the semantics of the verbs could be ignored whereas Experiment 2 included semantic decisions. Only Experiment 2 revealed a clear double dissociation in reaction times: reactions were facilitated when preceded by verbs describing actions with the matching effector. In Experiment 1, by contrast, there was an interaction between verb-response congruence and a semantic variable related to motor features of the verbs. Thus, the double dissociation paradigm of semantic motor priming was effective, corroborating the role of the motor system in action-related language processing. Importantly, this effect was body part specific. Copyright © 2017 Elsevier B.V. All rights reserved.

Three-dimensional modeling of the Nevada Test Site and vicinity from teleseismic p-wave residuals

International Nuclear Information System (INIS)

Monfort, M.E.; Evans, J.R.

1982-01-01

A teleseismic P-wave travel-time residual study is described which reveals the regional compressional-velocity structure of southern Nevada and neighboring parts of California to a depth of 280 km. During 1980, 98 teleseismic events were recorded at 53 sites. P-wave residuals were calculated relative to a network-wide average residual for each event and are displayed on maps of the stations for each of four event-azimuth quadrants. Fluctuations in these map-patterns of residuals with approach azimuth combined with results of linear, three-dimensional inversions of some 2887 residuals indicate the following characteristics of the velocity structure of the southern Nevada region: (1) a low-velocity body exists in the upper crust 50 km northeast of Beatty, Nevada, near the Miocene Timber Mountain-Silent Canyon caldera complex. Another highly localized low-velocity anomaly occurs near the southwest corner of the Nevada Test Site (NTS). These two anomalies seem to be part of a low-velocity trough extending from Death Valley, California, to about 50 km north of NTS; (2) there is a high-velocity body in the mantle between 81 and 131 km deep centered about 10 km north of the edge of the Timber Mountain caldera; (3) a broad low-velocity body is delineated between 81 and 131 km deep centered about 30 km north of Las Vegas; (4) there is a monotonic increase in travel-time delays from west to east across the region, probably indicating an eastward decrease in velocity, and lower than average velocities in southeastern Nevada below 31 km; and (5) considerable complexity in three-dimensional velocity structure exists in this part of the southern Great Basin. Inversions of teleseismic P-wave travel-time residuals were also performed on data from 12 seismometers in the immediate vicinity of the NTS to make good use of the closer station spacing in that area

Freshwater reservoir offsets and food crusts: Isotope, AMS, and lipid analyses of experimental cooking residues

Science.gov (United States)

Taché, Karine; Lovis, William A.

2018-01-01

Freshwater reservoir offsets (FROs) occur when AMS dates on charred, encrusted food residues on pottery predate a pot’s chronological context because of the presence of ancient carbon from aquatic resources such as fish. Research over the past two decades has demonstrated that FROs vary widely within and between water bodies and between fish in those water bodies. Lipid analyses have identified aquatic biomarkers that can be extracted from cooking residues as potential evidence for FROs. However, lacking has been efforts to determine empirically how much fish with FROs needs to be cooked in a pot with other resources to result in significant FRO on encrusted cooking residue and what percentage of fish C in a residue is needed to result in the recovery of aquatic biomarkers. Here we provide preliminary assessments of both issues. Our results indicate that in historically-contingent, high alkalinity environments fish may result in a statistically significant FRO, but that biomarkers for aquatic resources may be present in the absence of a significant FRO. PMID:29694436

You are what you eat: diet shapes body composition, personality and behavioural stability.

Science.gov (United States)

Han, Chang S; Dingemanse, Niels J

2017-01-10

Behavioural phenotypes vary within and among individuals. While early-life experiences have repeatedly been proposed to underpin interactions between these two hierarchical levels, the environmental factors causing such effects remain under-studied. We tested whether an individual's diet affected both its body composition, average behaviour (thereby causing among-individual variation or 'personality') and within-individual variability in behaviour and body weight (thereby causing among-individual differences in residual within-individual variance or 'stability'), using the Southern field cricket Gryllus bimaculatus as a model. We further asked whether effects of diet on the expression of these variance components were sex-specific. Manipulating both juvenile and adult diet in a full factorial design, individuals were put, in each life-stage, on a diet that was either relatively high in carbohydrates or relatively high in protein. We subsequently measured the expression of multiple behavioural (exploration, aggression and mating activity) and morphological traits (body weight and lipid mass) during adulthood. Dietary history affected both average phenotype and level of within-individual variability: males raised as juveniles on high-protein diets were heavier, more aggressive, more active during mating, and behaviourally less stable, than conspecifics raised on high-carbohydrate diets. Females preferred more protein in their diet compared to males, and dietary history affected average phenotype and within-individual variability in a sex-specific manner: individuals raised on high-protein diets were behaviourally less stable in their aggressiveness but this effect was only present in males. Diet also influenced individual differences in male body weight, but within-individual variance in female body weight. This study thereby provides experimental evidence that dietary history explains both heterogeneous residual within-individual variance (i.e., individual variation

Identification of coevolving residues and coevolution potentials emphasizing structure, bond formation and catalytic coordination in protein evolution.

Directory of Open Access Journals (Sweden)

Daniel Y Little

Full Text Available The structure and function of a protein is dependent on coordinated interactions between its residues. The selective pressures associated with a mutation at one site should therefore depend on the amino acid identity of interacting sites. Mutual information has previously been applied to multiple sequence alignments as a means of detecting coevolutionary interactions. Here, we introduce a refinement of the mutual information method that: 1 removes a significant, non-coevolutionary bias and 2 accounts for heteroscedasticity. Using a large, non-overlapping database of protein alignments, we demonstrate that predicted coevolving residue-pairs tend to lie in close physical proximity. We introduce coevolution potentials as a novel measure of the propensity for the 20 amino acids to pair amongst predicted coevolutionary interactions. Ionic, hydrogen, and disulfide bond-forming pairs exhibited the highest potentials. Finally, we demonstrate that pairs of catalytic residues have a significantly increased likelihood to be identified as coevolving. These correlations to distinct protein features verify the accuracy of our algorithm and are consistent with a model of coevolution in which selective pressures towards preserving residue interactions act to shape the mutational landscape of a protein by restricting the set of admissible neutral mutations.

Phase separation of a Lennard-Jones fluid interacting with a long, condensed polymer chain: implications for the nuclear body formation near chromosomes.

Science.gov (United States)

Oh, Inrok; Choi, Saehyun; Jung, YounJoon; Kim, Jun Soo

2015-08-28

Phase separation in a biological cell nucleus occurs in a heterogeneous environment filled with a high density of chromatins and thus it is inevitably influenced by interactions with chromatins. As a model system of nuclear body formation in a cell nucleus filled with chromatins, we simulate the phase separation of a low-density Lennard-Jones (LJ) fluid interacting with a long, condensed polymer chain. The influence of the density variation of LJ particles above and below the phase boundary and the role of attractive interactions between LJ particles and polymer segments are investigated at a fixed value of strong self-interaction between LJ particles. For a density of LJ particles above the phase boundary, phase separation occurs and a dense domain of LJ particles forms irrespective of interactions with the condensed polymer chain whereas its localization relative to the polymer chain is determined by the LJ-polymer attraction strength. Especially, in the case of moderately weak attractions, the domain forms separately from the polymer chain and subsequently associates with the polymer chain. When the density is below the phase boundary, however, the formation of a dense domain is possible only when the LJ-polymer attraction is strong enough, for which the domain grows in direct contact with the interacting polymer chain. In this work, different growth behaviors of LJ particles result from the differences in the density of LJ particles and in the LJ-polymer interaction, and this work suggests that the distinct formation of activity-dependent and activity-independent nuclear bodies (NBs) in a cell nucleus may originate from the differences in the concentrations of body-specific NB components and in their interaction with chromatins.

Tyrosine Residues Regulate Multiple Nuclear Functions of P54nrb.

Science.gov (United States)

Lee, Ahn R; Hung, Wayne; Xie, Ning; Liu, Liangliang; He, Leye; Dong, Xuesen

2017-04-01

The non-POU-domain-containing octamer binding protein (NONO; also known as p54nrb) has various nuclear functions ranging from transcription, RNA splicing, DNA synthesis and repair. Although tyrosine phosphorylation has been proposed to account for the multi-functional properties of p54nrb, direct evidence on p54nrb as a phosphotyrosine protein remains unclear. To investigate the tyrosine phosphorylation status of p54nrb, we performed site-directed mutagenesis on the five tyrosine residues of p54nrb, replacing the tyrosine residues with phenylalanine or alanine, and immunoblotted for tyrosine phosphorylation. We then preceded with luciferase reporter assays, RNA splicing minigene assays, co-immunoprecipitation, and confocal microscopy to study the function of p54nrb tyrosine residues on transcription, RNA splicing, protein-protein interaction, and cellular localization. We found that p54nrb was not phosphorylated at tyrosine residues. Rather, it has non-specific binding affinity to anti-phosphotyrosine antibodies. However, replacement of tyrosine with phenylalanine altered p54nrb activities in transcription co-repression and RNA splicing in gene context-dependent fashions by means of differential regulation of p54nrb protein association with its interacting partners and co-regulators of transcription and splicing. These results demonstrate that tyrosine residues, regardless of phosphorylation status, are important for p54nrb function. J. Cell. Physiol. 232: 852-861, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Fluid sign in the treated bodies after percutaneous vertebroplasty

International Nuclear Information System (INIS)

Lin, Chao-Chun; Yen, Pao-Sheng; Wen, Shu-Hui

2008-01-01

The aims of this study are to describe non-healing in the treated vertebral body after percutaneous vertebroplasty and analyze the influence of vacuum cleft, location, and severity of collapse on the development of nonunion cement. Of 208 patients (266 treated vertebral bodies) who were treated with percutaneous vertebroplasty from September 2002 to May 2006, 23 patients (41 treated levels) with residual or recurrent pain underwent follow-up magnetic resonance imaging (MRI) study. Retrospective chart review with analysis of preoperative and postoperative MRIs were performed in these 23 patients. In the 41 treated vertebral bodies, 22 of 41 bodies had vacuum cleft found in the preoperative MRI study. Eight of the 22 treated vertebral bodies with preoperative vacuum clefts were found to have fluid between the interface of cement and the residual bone in the collapsed vertebral bodies on follow-up MRI. The adjacent discs of these treated vertebral bodies were upward/downward displaced. The endplate of the adjacent vertebral body exhibited fibrotic change. Treated bodies with vacuum clefts and level A location (T9, T11, T12, and L1) had higher probability of developing nonunion of the cement with statistical significance. The probability of nonunion cement in severe collapsed bodies might be higher than that of union cement in mild collapsed ones, but was not statistically significant. Fluid sign in the treated body represents unhealed bone-cement interface. The location of the treated vertebral body and existence of vacuum cleft in the treated bodies may be important factors influencing the nonunion of cement. (orig.)

Simulations of GCR interactions within planetary bodies using GEANT4

Science.gov (United States)

Mesick, K.; Feldman, W. C.; Stonehill, L. C.; Coupland, D. D. S.

2017-12-01

On planetary bodies with little to no atmosphere, Galactic Cosmic Rays (GCRs) can hit the body and produce neutrons primarily through nuclear spallation within the top few meters of the surfaces. These neutrons undergo further nuclear interactions with elements near the planetary surface and some will escape the surface and can be detected by landed or orbiting neutron radiation detector instruments. The neutron leakage signal at fast neutron energies provides a measure of average atomic mass of the near-surface material and in the epithermal and thermal energy ranges is highly sensitive to the presence of hydrogen. Gamma-rays can also escape the surface, produced at characteristic energies depending on surface composition, and can be detected by gamma-ray instruments. The intra-nuclear cascade (INC) that occurs when high-energy GCRs interact with elements within a planetary surface to produce the leakage neutron and gamma-ray signals is highly complex, and therefore Monte Carlo based radiation transport simulations are commonly used for predicting and interpreting measurements from planetary neutron and gamma-ray spectroscopy instruments. In the past, the simulation code that has been widely used for this type of analysis is MCNPX [1], which was benchmarked against data from the Lunar Neutron Probe Experiment (LPNE) on Apollo 17 [2]. In this work, we consider the validity of the radiation transport code GEANT4 [3], another widely used but open-source code, by benchmarking simulated predictions of the LPNE experiment to the Apollo 17 data. We consider the impact of different physics model options on the results, and show which models best describe the INC based on agreement with the Apollo 17 data. The success of this validation then gives us confidence in using GEANT4 to simulate GCR-induced neutron leakage signals on Mars in relevance to a re-analysis of Mars Odyssey Neutron Spectrometer data. References [1] D.B. Pelowitz, Los Alamos National Laboratory, LA-CP-05

[Extracellular hydration status and residual urinary sodium excretion in chronic hemodialysis patients: a cross-sectional multicenter study].

Science.gov (United States)

Crochette, Romain; Lobbedez, Thierry; Hanoy, Mélanie; Le Roy, Frank; Potier, Jacky; Besselièvre, Thibault; Cardineau, Éric; Landru, Isabelle; Ficheux, Maxence; Ryckelynck, Jean-Philippe; Henri, Patrick

2014-04-01

In dialysis patients, a misevaluation of dry weight may lead to an increased morbidity and mortality. The aim of this cross-sectional multicenter study was to evaluate the association between residual urinary sodium excretion and extracellular volume status in chronically treated hemodialysis patients. Dry weight was determined clinically and by whole-body bioimpedance spectroscopy (Body Composition Monitor, Fresenius Medical Care) prior to a mid-week session in 40 chronic hemodialysis patients with significant residual diuresis (more than 250 mL per day) and receiving treatment in four dialysis centers. Regarding their hydration status assessed by the Body Composition Monitor and in comparison to a healthy reference population, patients were assigned to 1 of the 3 categories: overhydrated, normohydrated and dehydrated. Urine output, urinary sodium excretion and residual renal function were measured for all patients within 30 days before dry weight assessment. The median post-HD session FO was of-0.40 L (IQR: from-1.95 to+0.90) and the median residual urinary sodium excretion was of 64 mmol/L (IQR: 46-79). Among these patients, 16 were normohydated, 16 were dehydrated and 8 were overhydrated. There was a linear relationship between the hydration status after HD session and the urinary sodium excretion (estimate: 5.6±1.5; phydration status evaluated by whole-body bioimpedance spectroscopy. Copyright © 2013 Association Société de néphrologie. Published by Elsevier SAS. All rights reserved.

Nuclear many-body problem with repulsive hard core interactions

Energy Technology Data Exchange (ETDEWEB)

Haddad, L M

1965-07-01

The nuclear many-body problem is considered using the perturbation-theoretic approach of Brueckner and collaborators. This approach is outlined with particular attention paid to the graphical representation of the terms in the perturbation expansion. The problem is transformed to centre-of-mass coordinates in configuration space and difficulties involved in ordinary methods of solution of the resulting equation are discussed. A new technique, the 'reference spectrum method', devised by Bethe, Brandow and Petschek in an attempt to simplify the numerical work in presented. The basic equations are derived in this approximation and considering the repulsive hard core part of the interaction only, the effective mass is calculated at high momentum (using the same energy spectrum for both 'particle' and 'hole' states). The result of 0.87m is in agreement with that of Bethe et al. A more complete treatment using the reference spectrum method in introduced and a self-consistent set of equations is established for the reference spectrum parameters again for the case of hard core repulsions. (author)

A Fully Immersive Set-Up for Remote Interaction and Neurorehabilitation Based on Virtual Body Ownership

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Perez-Marcos, Daniel; Solazzi, Massimiliano; Steptoe, William; Oyekoya, Oyewole; Frisoli, Antonio; Weyrich, Tim; Steed, Anthony; Tecchia, Franco; Slater, Mel; Sanchez-Vives, Maria V.

2012-01-01

Although telerehabilitation systems represent one of the most technologically appealing clinical solutions for the immediate future, they still present limitations that prevent their standardization. Here we propose an integrated approach that includes three key and novel factors: (a) fully immersive virtual environments, including virtual body representation and ownership; (b) multimodal interaction with remote people and virtual objects including haptic interaction; and (c) a physical representation of the patient at the hospital through embodiment agents (e.g., as a physical robot). The importance of secure and rapid communication between the nodes is also stressed and an example implemented solution is described. Finally, we discuss the proposed approach with reference to the existing literature and systems. PMID:22787454

Protein structure based prediction of catalytic residues.

Science.gov (United States)

Fajardo, J Eduardo; Fiser, Andras

2013-02-22

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. 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. 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 reference databases.

The Neural Correlates of the Body-Object Interaction Effect in Semantic Processing

Directory of Open Access Journals (Sweden)

Ian Scott Hargreaves

2012-02-01

Full Text Available The semantic richness dimension referred to as body-object interaction (BOI measures perceptions of the ease with which people can physically interact with words’ referents. Previous studies have shown facilitated lexical and semantic processing for words rated high in BOI (e.g., belt than for words rated low in BOI (e.g., sun (e.g., Siakaluk, Pexman, Sears, Wilson, Locheed, & Owen, 2008b. These BOI effects have been taken as evidence that embodied information is relevant to word recognition. However, to date there is no evidence linking BOI manipulations to differences in the utilization of perceptual or sensorimotor areas of the brain. The current study used event-related fMRI to examine the neural correlates of BOI in a semantic categorization task (SCT. Sixteen healthy adults participated. Results showed that high BOI words were associated with activation in the left inferior parietal lobule (supramarginal gyrus, BA 40, a sensory association area involved in kinesthetic memory. These results provide evidence that the BOI dimension captures sensorimotor information, and that this contributes to semantic processing.

Video-based quantification of body movement during social interaction indicates the severity of negative symptoms in patients with schizophrenia.

Science.gov (United States)

Kupper, Zeno; Ramseyer, Fabian; Hoffmann, Holger; Kalbermatten, Samuel; Tschacher, Wolfgang

2010-08-01

In schizophrenia, nonverbal behavior, including body movement, is of theoretical and clinical importance. Although reduced nonverbal expressiveness is a major component of the negative symptoms encountered in schizophrenia, few studies have objectively assessed body movement during social interaction. In the present study, 378 brief, videotaped role-play scenes involving 27 stabilized outpatients diagnosed with paranoid-type schizophrenia were analyzed using Motion Energy Analysis (MEA). This method enables the objective measuring of body movement in conjunction with ordinary video recordings. Correlations between movement parameters (percentage of time in movement, movement speed) and symptom ratings from independent PANSS interviews were calculated. Movement parameters proved to be highly reliable. In keeping with predictions, reduced movement and movement speed correlated with negative symptoms. Accordingly, in patients who exhibited noticeable movement for less than 20% of the observation time, prominent negative symptoms were highly probable. As a control measure, the percentage of movement exhibited by the patients during role-play scenes was compared to that of their normal interactants. Patients with negative symptoms differed from normal interactants by showing significantly reduced head and body movement. Two specific positive symptoms were possibly related to movement parameters: suspiciousness tended to correlate with reduced head movement, and the expression of unusual thought content tended to relate to increased movement. Overall, a close and theoretically meaningful association between the objective movement parameters and the symptom profiles was found. MEA appears to be an objective, reliable and valid method for quantifying nonverbal behavior, an aspect which may furnish new insights into the processes related to reduced expressiveness in schizophrenia. Copyright 2010 Elsevier B.V. All rights reserved.

Harmonically trapped cold atom systems: Few-body dynamics and application to many-body thermodynamics

Science.gov (United States)

Daily, Kevin Michael

Underlying the many-body effects of ultracold atomic gases are the few-body dynamics and interparticle interactions. Moreover, the study of few-body systems on their own has accelerated due to confining few atoms in each well of a deep optical lattice or in a single microtrap. This thesis studies the microscopic properties of few-body systems under external spherically symmetric harmonic confinement and how the few-body properties translate to the many-body system. Bosonic and fermionic few-body systems are considered and the dependence of the energetics and other quantities are investigated as functions of the s-wave scattering length, the mass ratio and the temperature. It is found that the condensate fraction of a weakly-interacting trapped Bose gas depletes quadratically with the s-wave scattering length. The next order term in the depletion depends not only, as might be expected naively, on the s-wave scattering length and the effective range but additionally on a two-body parameter that is not needed to reproduce the energy of weakly-interacting trapped Bose gases. This finding has important implications for effective field theory treatments of the system. Weakly-interacting atomic and molecular two-component Fermi gases with equal masses are described using perturbative approaches. The energy shifts are tabulated and interpreted, and a measure of the molecular condensate fraction is developed. We develop a measure of the molecular condensate fraction using the two-body density matrix and we develop a model of the spherical component of the momentum distribution that agrees well with stochastic variational calculations. We establish the existence of intersystem degeneracies for equal mass two-component Fermi gases with zero-range interactions, where the eigen energies of the spin-imbalanced system are degenerate with a subset of the eigen energies of the more spin-balanced system and the same total number of fermions. For unequal mass two-component Fermi

Interaction of Myosin Phosphatase Target Subunit (MYPT1) with Myosin Phosphatase-RhoA Interacting Protein (MRIP): A Role of Glutamic Acids in the Interaction.

Science.gov (United States)

Lee, Eunhee; Stafford, Walter F

2015-01-01

Scaffold proteins bind to and functionally link protein members of signaling pathways. Interaction of the scaffold proteins, myosin phosphatase target subunit (MYPT1) and myosin phosphatase-RhoA interacting protein (MRIP), causes co-localization of myosin phosphatase and RhoA to actomyosin. To examine biophysical properties of interaction of MYPT1 with MRIP, we employed analytical ultracentrifugation and surface plasmon resonance. In regard to MRIP, its residues 724-837 are sufficient for the MYPT1/MRIP interaction. Moreover, MRIP binds to MYPT1 as either a monomer or a dimer. With respect to MYPT1, its leucine repeat region, LR (residues 991-1030) is sufficient to account for the MYPT1/MRIP interaction. Furthermore, point mutations that replace glutamic acids 998-1000 within LR reduced the binding affinity toward MRIP. This suggests that the glutamic acids of MYPT1 play an important role in the interaction.

Effects of Mind-Body Training on Cytokines and Their Interactions with Catecholamines.

Science.gov (United States)

Jang, Joon Hwan; Park, Hye Yoon; Lee, Ui Soon; Lee, Kyung-Jun; Kang, Do-Hyung

2017-07-01

Mind-body training (MBT) may control reactions to stress and regulate the nervous and immune systems. The present study was designed to assess the effects of MBT on plasma cytokines and their interactions with catecholamines. The study group consisted of 80 subjects who practice MBT and a control group of 62 healthy subjects. Plasma catecholamine (norepinephrine, NE; epinephrine, E; and dopamine, DA) and cytokine (TNF-alpha, IL-6, IFN-gamma, and IL-10) levels were measured, and the differences between the MBT and control groups and the interactions of cytokines with catecholamines were investigated. A significant increase in IL-10+IFN-gamma was found in females of the MBT group compared with controls. Also, a significant increase of IL-10 (anti-inflammatory cytokine) in the MBT group was shown in a specific condition in which TNF-alpha and IL-6 (pro-inflammatory cytokines) are almost absent (≤1 ng/L) compared with controls. In the MBT group, significant positive correlations were found between IL-10 and the NE/E ratio and between IL-10 and the DA/E ratio, whereas the control group did not show any such correlations. MBT may increase IL-10, under specific conditions such as a decrease of pro-inflammatory cytokines or E, which may regulate the stress response and possibly contribute to effective and beneficial interactions between the nervous and immune systems.

BLAST-based structural annotation of protein residues using Protein Data Bank.

Science.gov (United States)

Singh, Harinder; Raghava, Gajendra P S

2016-01-25

In the era of next-generation sequencing where thousands of genomes have been already sequenced; size of protein databases is growing with exponential rate. Structural annotation of these proteins is one of the biggest challenges for the computational biologist. Although, it is easy to perform BLAST search against Protein Data Bank (PDB) but it is difficult for a biologist to annotate protein residues from BLAST search. A web-server StarPDB has been developed for structural annotation of a protein based on its similarity with known protein structures. It uses standard BLAST software for performing similarity search of a query protein against protein structures in PDB. This server integrates wide range modules for assigning different types of annotation that includes, Secondary-structure, Accessible surface area, Tight-turns, DNA-RNA and Ligand modules. Secondary structure module allows users to predict regular secondary structure states to each residue in a protein. Accessible surface area predict the exposed or buried residues in a protein. Tight-turns module is designed to predict tight turns like beta-turns in a protein. DNA-RNA module developed for predicting DNA and RNA interacting residues in a protein. Similarly, Ligand module of server allows one to predicted ligands, metal and nucleotides ligand interacting residues in a protein. In summary, this manuscript presents a web server for comprehensive annotation of a protein based on similarity search. It integrates number of visualization tools that facilitate users to understand structure and function of protein residues. This web server is available freely for scientific community from URL http://crdd.osdd.net/raghava/starpdb .

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

International Nuclear Information System (INIS)

Lobanov, Michail Yu; Galzitskaya, Oxana V

2011-01-01

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

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.

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...

Cooperative and uniform fish? : social interactions and variability in live body weight in the GIFT strain (Nile tilapia, Oreochromic niloticus) in Malaysia

NARCIS (Netherlands)

Khaw, H.L.

2015-01-01

Abstract

Khaw, HL. (2014). Cooperative and uniform fish? Social interactions and variability in live body weight in the GIFT strain (Nile tilapia, Oreochromic niloticus) in Malaysia. PhD thesis, Wageningen University, the Netherlands.

Social interactions

On-Skin Interaction Using Body Landmarks

DEFF Research Database (Denmark)

Steimle, Juergen; Bergstrom-Lehtovirta, Joanna; Weigel, Martin

2017-01-01

The human skin is a promising surface for input to computing devices but differs fundamentally from existing touch-sensitive devices. The authors propose the use of skin landmarks, which offer unique tactile and visual cues, to enhance body-based user interfaces....

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

Science.gov (United States)

Qi, Yifei; Im, Wonpil

2013-08-13

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

Solvable Model of a Generic Trapped Mixture of Interacting Bosons: Many-Body and Mean-Field Properties

Science.gov (United States)

Klaiman, S.; Streltsov, A. I.; Alon, O. E.

2018-04-01

A solvable model of a generic trapped bosonic mixture, N 1 bosons of mass m 1 and N 2 bosons of mass m 2 trapped in an harmonic potential of frequency ω and interacting by harmonic inter-particle interactions of strengths λ 1, λ 2, and λ 12, is discussed. It has recently been shown for the ground state [J. Phys. A 50, 295002 (2017)] that in the infinite-particle limit, when the interaction parameters λ 1(N 1 ‑ 1), λ 2(N 2 ‑ 1), λ 12 N 1, λ 12 N 2 are held fixed, each of the species is 100% condensed and its density per particle as well as the total energy per particle are given by the solution of the coupled Gross-Pitaevskii equations of the mixture. In the present work we investigate properties of the trapped generic mixture at the infinite-particle limit, and find differences between the many-body and mean-field descriptions of the mixture, despite each species being 100%. We compute analytically and analyze, both for the mixture and for each species, the center-of-mass position and momentum variances, their uncertainty product, the angular-momentum variance, as well as the overlap of the exact and Gross-Pitaevskii wavefunctions of the mixture. The results obtained in this work can be considered as a step forward in characterizing how important are many-body effects in a fully condensed trapped bosonic mixture at the infinite-particle limit.

The effect of delignification process with alkaline peroxide on lactic acid production from furfural residues

Directory of Open Access Journals (Sweden)

Yong Tang

2012-11-01

Full Text Available Furfural residues produced from the furfural industry were investigated as a substrate for lactic acid production by simultaneous saccharification and fermentation (SSF. Alkaline peroxide was used for delignification of furfural residues to improve the final lactic acid concentration. The residue was treated with 1.3% to 1.7% hydrogen peroxide at 80 °C for 1 h with a substrate concentration of 3.33%. SSF of furfural residues with different delignification degrees were carried out to evaluate the effect of delignification degree on lactic acid production. Using corn hydrolysates/ furfural residues as substrates, SSF with different media were carried out to investigate the effect of lignin on the interaction between enzymes and lactic acid bacteria. Lactic acid bacteria had a negative effect on cellulase, thus resulting in the reduction of enzyme activity. Lignin and nutrients slowed down the decreasing trend of enzyme activity. A higher delignification resulted in a slower fermentation rate and lower yield due to degradation products of lignin and the effect of lignin on the interaction between enzymes and lactic acid bacteria. For the purpose of lactic acid production, a moderate delignification (furfural residues with the lignin content of 14.8% was optimum.

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.

Investigations of the structure and electromagnetic interactions of few-body systems. Progress report, 1 July 1991--30 June 1994

International Nuclear Information System (INIS)

Lehman, D.R.; Haberzettl, H.; Maximon, L.C.; Parke, W.C.; Bennhold, C.; Ito, Hiroshi; Pratt, R.K.; Najmeddine, M.; Rakei, A.

1994-07-01

In order to make it easy for the reader to see the specific research carried out and the progress made, the following report of progress is done by topic. Each item has a format layout of Topic, Investigators, Objective, Significance, and Description of Progress, followed at the end by the relevant references. As is clear from the topics listed, the emphasis of the GW nuclear theory group has been on the structure and electromagnetic interactions of few-body nuclei. Both low- and intermediate-energy electromagnetic disintegration of these nuclei is considered, including coherent photoproduction of π mesons. When the excitation energy of the target nucleus is low, the aim has been to handle the continuum part of the theoretical work numerically with no approximations, that is, by means of full three- or four-body dynamics. When structure questions are the issue, numerically accurate calculations are always carried through, limited only by the underlying two-body or three-body interactions used as input. Implicit in our work is the question of how far one can go within the traditional nuclear physics framework i.e., nucleons and mesons in a nonrelativistic setting. Our central goal is to carry through state-of-the-art few-body calculations that will serve as a means of determining at what point standard nuclear physics requires introduction of relativity and/or quark degrees of freedom in order to understand the phenomena in question. So far, the problems considered were mostly concerned with low- to medium-energy regimes where little evidence was found that requires going beyond the traditional approach

Construction of a risk assessment system for chemical residues in agricultural products.

Science.gov (United States)

Choi, Shinai; Hong, Jiyeon; Lee, Dayeon; Paik, Minkyoung

2014-01-01

Continuous monitoring of chemical residues in agricultural and food products has been performed by various government bodies in South Korea. These bodies have made attempts to systematically manage this information by creating a monitoring database system as well as a system based on these data with which to assess the health risk of chemical residues in agricultural products. Meanwhile, a database system is being constructed consisting of information about monitoring and, following this, a demand for convenience has led to the need for an evaluation tool to be constructed with the data processing system. Also, in order to create a systematic and effective tool for the risk assessment of chemical residues in foods and agricultural products, various evaluation models are being developed, both domestically and abroad. Overseas, systems such as Dietary Exposure Evaluation Model: Food Commodity Intake Database and Cumulative and Aggregate Risk Evaluation System are being used; these use the US Environmental Protection Agency as a focus, while the EU has developed Pesticide Residue Intake Model for assessments of pesticide exposure through food intake. Following this, the National Academy of Agricultural Science (NAAS) created the Agricultural Products Risk Assessment System (APRAS) which supports the use and storage of monitoring information and risk assessments. APRAS efficiently manages the monitoring data produced by NAAS and creates an extraction feature included in the database system. Also, the database system in APRAS consists of a monitoring database system held by the NAAS and food consumption database system. Food consumption data is based on Korea National Health and Nutrition Examination Survey. This system is aimed at exposure and risk assessments for chemical residues in agricultural products with regards to different exposure scenarios.

An iterative approach to dynamic simulation of 3D rigid body motions for real-time interactive computer animation

NARCIS (Netherlands)

Overveld, van C.W.A.M.

1991-01-01

A method is presented for approximating the motions of linked 3-dimensional rigid body systems that may be applied in the context of interactive motion specification for computer animation. The method is based on decoupling the ballistic (free) component of the motion of the points that constitute

Binding properties of SUMO-interacting motifs (SIMs) in yeast.

Science.gov (United States)

Jardin, Christophe; Horn, Anselm H C; Sticht, Heinrich

2015-03-01

Small ubiquitin-like modifier (SUMO) conjugation and interaction play an essential role in many cellular processes. A large number of yeast proteins is known to interact non-covalently with SUMO via short SUMO-interacting motifs (SIMs), but the structural details of this interaction are yet poorly characterized. In the present work, sequence analysis of a large dataset of 148 yeast SIMs revealed the existence of a hydrophobic core binding motif and a preference for acidic residues either within or adjacent to the core motif. Thus the sequence properties of yeast SIMs are highly similar to those described for human. Molecular dynamics simulations were performed to investigate the binding preferences for four representative SIM peptides differing in the number and distribution of acidic residues. Furthermore, the relative stability of two previously observed alternative binding orientations (parallel, antiparallel) was assessed. For all SIMs investigated, the antiparallel binding mode remained stable in the simulations and the SIMs were tightly bound via their hydrophobic core residues supplemented by polar interactions of the acidic residues. In contrary, the stability of the parallel binding mode is more dependent on the sequence features of the SIM motif like the number and position of acidic residues or the presence of additional adjacent interaction motifs. This information should be helpful to enhance the prediction of SIMs and their binding properties in different organisms to facilitate the reconstruction of the SUMO interactome.

Three-body interactions in liquid and solid hydrogen: Evidence from vibrational spectroscopy

Science.gov (United States)

Hinde, Robert

2008-03-01

In the cryogenic low-density liquid and solid phases of H2 and D2, the H2 and D2 molecules retain good rotational and vibrational quantum numbers that characterize their internal degrees of freedom. High-resolution infrared and Raman spectroscopic experiments provide extremely sensitive probes of these degrees of freedom. We present here fully-first-principles calculations of the infrared and Raman spectra of liquid and solid H2 and D2, calculations that employ a high-quality six-dimensional coupled-cluster H2-H2 potential energy surface and quantum Monte Carlo treatments of the single-molecule translational degrees of freedom. The computed spectra agree very well with experimental results once we include three-body interactions among the molecules, interactions which we also compute using coupled-cluster quantum chemical methods. We predict the vibrational spectra of liquid and solid H2 at several temperatures and densities to provide a framework for interpreting recent experiments designed to search for superfluid behavior in small H2 droplets. We also present preliminary calculations of the spectra of mixed H2/D2 solids that show how positional disorder affects the spectral line shapes in these systems.

Proximity Interactions among Basal Body Components in Trypanosoma brucei Identify Novel Regulators of Basal Body Biogenesis and Inheritance

Directory of Open Access Journals (Sweden)

Hung Quang Dang

2017-01-01

Full Text Available The basal body shares similar architecture with centrioles in animals and is involved in nucleating flagellar axonemal microtubules in flagellated eukaryotes. The early-branching Trypanosoma brucei possesses a motile flagellum nucleated from the basal body that consists of a mature basal body and an adjacent pro-basal body. Little is known about the basal body proteome and its roles in basal body biogenesis and flagellar axoneme assembly in T. brucei. Here, we report the identification of 14 conserved centriole/basal body protein homologs and 25 trypanosome-specific basal body proteins. These proteins localize to distinct subdomains of the basal body, and several of them form a ring-like structure surrounding the basal body barrel. Functional characterization of representative basal body proteins revealed distinct roles in basal body duplication/separation and flagellar axoneme assembly. Overall, this work identified novel proteins required for basal body duplication and separation and uncovered new functions of conserved basal body proteins in basal body duplication and separation, highlighting an unusual mechanism of basal body biogenesis and inheritance in this early divergent eukaryote.

Estimating the spatial scale of herbicide and soil interactions by nested sampling, hierarchical analysis of variance and residual maximum likelihood

Energy Technology Data Exchange (ETDEWEB)

Price, Oliver R., E-mail: oliver.price@unilever.co [Warwick-HRI, University of Warwick, Wellesbourne, Warwick, CV32 6EF (United Kingdom); University of Reading, Soil Science Department, Whiteknights, Reading, RG6 6UR (United Kingdom); Oliver, Margaret A. [University of Reading, Soil Science Department, Whiteknights, Reading, RG6 6UR (United Kingdom); Walker, Allan [Warwick-HRI, University of Warwick, Wellesbourne, Warwick, CV32 6EF (United Kingdom); Wood, Martin [University of Reading, Soil Science Department, Whiteknights, Reading, RG6 6UR (United Kingdom)

2009-05-15

An unbalanced nested sampling design was used to investigate the spatial scale of soil and herbicide interactions at the field scale. A hierarchical analysis of variance based on residual maximum likelihood (REML) was used to analyse the data and provide a first estimate of the variogram. Soil samples were taken at 108 locations at a range of separating distances in a 9 ha field to explore small and medium scale spatial variation. Soil organic matter content, pH, particle size distribution, microbial biomass and the degradation and sorption of the herbicide, isoproturon, were determined for each soil sample. A large proportion of the spatial variation in isoproturon degradation and sorption occurred at sampling intervals less than 60 m, however, the sampling design did not resolve the variation present at scales greater than this. A sampling interval of 20-25 m should ensure that the main spatial structures are identified for isoproturon degradation rate and sorption without too great a loss of information in this field. - Estimating the spatial scale of herbicide and soil interactions by nested sampling.

Estimating the spatial scale of herbicide and soil interactions by nested sampling, hierarchical analysis of variance and residual maximum likelihood

International Nuclear Information System (INIS)

Price, Oliver R.; Oliver, Margaret A.; Walker, Allan; Wood, Martin

2009-01-01

An unbalanced nested sampling design was used to investigate the spatial scale of soil and herbicide interactions at the field scale. A hierarchical analysis of variance based on residual maximum likelihood (REML) was used to analyse the data and provide a first estimate of the variogram. Soil samples were taken at 108 locations at a range of separating distances in a 9 ha field to explore small and medium scale spatial variation. Soil organic matter content, pH, particle size distribution, microbial biomass and the degradation and sorption of the herbicide, isoproturon, were determined for each soil sample. A large proportion of the spatial variation in isoproturon degradation and sorption occurred at sampling intervals less than 60 m, however, the sampling design did not resolve the variation present at scales greater than this. A sampling interval of 20-25 m should ensure that the main spatial structures are identified for isoproturon degradation rate and sorption without too great a loss of information in this field. - Estimating the spatial scale of herbicide and soil interactions by nested sampling.

Investigation of scattering processes in quantum few-body systems involving long-range interaction by the complex-rotation method

International Nuclear Information System (INIS)

Volkov, M. V.; Elander, N.; Yakovlev, S. L.; Yarevsky, E. A.

2013-01-01

The complex-rotation method adapted to solving the multichannel scattering problem in the two-body system where the interaction potential contains the long-range Coulomb components is described. The scattering problem is reformulated as the problem of solving a nonhomogeneous Schrödinger equation in which the nonhomogeneous term involves a Coulomb potential cut off at large distances. The incident wave appearing in the nonhomogeneous term is a solution of the Schrödinger equation with longrange Coulomb interaction. This formulation is free from approximations associated with a direct cutoff of Coulomb interaction at large distances. The efficiency of this formalism is demonstrated by considering the example of solving scattering problems in the α-α and p-p systems.

Severe slowing-down and universality of the dynamics in disordered interacting many-body systems: ageing and ultraslow diffusion

International Nuclear Information System (INIS)

Sanders, Lloyd P; Fogelmark, Karl; Ambjörnsson, Tobias; Lomholt, Michael A; Lizana, Ludvig; Metzler, Ralf

2014-01-01

Low-dimensional, many-body systems are often characterized by ultraslow dynamics. We study a labelled particle in a generic system of identical particles with hard-core interactions in a strongly disordered environment. The disorder is manifested through intermittent motion with scale-free sticking times at the single particle level. While for a non-interacting particle we find anomalous diffusion of the power-law form 〈x 2 (t)〉≃t α of the mean squared displacement with 0<α<1, we demonstrate here that the combination of the disordered environment with the many-body interactions leads to an ultraslow, logarithmic dynamics 〈x 2 (t)〉≃log 1/2 t with a universal 1/2 exponent. Even when a characteristic sticking time exists but the fluctuations of sticking times diverge we observe the mean squared displacement 〈x 2 (t)〉≃t γ with 0<γ<1/2, that is slower than the famed Harris law 〈x 2 (t)〉≃t 1/2 without disorder. We rationalize the results in terms of a subordination to a counting process, in which each transition is dominated by the forward waiting time of an ageing continuous time process. (paper)

Anaerobia Treatments of the domestic residual waters. Limitations potentialities

International Nuclear Information System (INIS)

Giraldo Gomez, Eugenio

1993-01-01

The quick growth of the Latin American cities has prevented that an appropriate covering of public services is achieved for the whole population, One of the undesirable consequences of this situation is the indiscriminate discharge from the domestic and industrial residual waters to the nearest bodies of water with its consequent deterioration and with disastrous consequences about the ecology and the public health. The developed countries have controlled this situation using systems of purification of the residual waters previously to their discharge in the receptor source. The same as the technology of the evacuation of the served waters, they have become numerous efforts for the application of the purification systems used in the countries developed to the socioeconomic, climatic and cultural conditions of our means. One of the results obtained in these efforts is the economic inability of the municipalities to pay the high investment costs and of operation of the traditional systems for the treatment of the residual waters. Contrary to another type of public services, the treatment of the residual waters needs of appropriate technological solutions for the Climatic and socioeconomic means of the developing countries, One of the technological alternatives for the purification of the residual waters that has had a great development in the last decades has been that of the biological treatments in t anaerobia ambient. The objective of this contribution is to present, to author's trial, the limitations and potentialities of this technology type with special emphasis in the case of the domestic residual waters

Flexible recruitment of semantic richness: Context modulates body-object interaction effects in lexical-semantic processing

Directory of Open Access Journals (Sweden)

Cody eTousignant

2012-03-01

Full Text Available Body-object interaction (BOI is a semantic richness variable that measures the perceived ease with which the human body can physically interact with a word’s referent. Lexical and semantic processing is facilitated when words are associated with relatively more bodily experience (high BOI words, e.g., belt. To date, BOI effects have been examined in only one semantic decision context (is it imageable?. It has been argued that semantic processing is dynamic and can be modulated by context. We examined these influences by testing how task knowledge modulated BOI effects. We presented the same stimuli (high- and low-BOI entity words and a set of action words in each of four action/entity semantic categorization tasks (SCTs. Task framing was manipulated: participants were told about one (actions or entities or both (actions and entities categories of words in the decision task. Facilitatory BOI effects were observed when participants knew that ‘entity’ was part of the decision category, regardless of whether the high- and low-BOI entity words appeared on the affirmative or negative side of the decision. That BOI information was only useful when participants had expectations that object words would be presented suggests a strong role for the decision context in lexical-semantic processing, and supports a dynamic view of conceptual knowledge.

Combined Role of Two Tryptophane Residues of α-Factor Pheromone

Energy Technology Data Exchange (ETDEWEB)

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

2013-02-15

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

Combined Role of Two Tryptophane Residues of α-Factor Pheromone

International Nuclear Information System (INIS)

Hong, Eun Young; Hong, Nam Joo

2013-01-01

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

African genetic ancestry interacts with body mass index to modify risk for uterine fibroids.

Science.gov (United States)

Giri, Ayush; Edwards, Todd L; Hartmann, Katherine E; Torstenson, Eric S; Wellons, Melissa; Schreiner, Pamela J; Velez Edwards, Digna R

2017-07-01

Race, specifically African ancestry, and obesity are important risk factors for uterine fibroids, and likely interact to provide the right conditions for fibroid growth. However, existing studies largely focus on the main-effects rather than their interaction. Here, we firstly provide evidence for interaction between categories of body mass index (BMI) and reported-race in relation to uterine fibroids. We then investigate whether the association between inferred local European ancestry and fibroid risk is modified by BMI in African American (AA) women in the Vanderbilt University Medical Center bio-repository (BioVU) (539 cases and 794 controls) and the Coronary Artery Risk Development in Young Adults study (CARDIA, 264 cases and 173 controls). We used multiple logistic regression to evaluate interactions between local European ancestry and BMI in relation to fibroid risk, then performed fixed effects meta-analysis. Statistical significance threshold for local-ancestry and BMI interactions was empirically estimated with 10,000 permutations (p-value = 1.18x10-4). Admixture mapping detected an association between European ancestry and fibroid risk which was modified by BMI (continuous-interaction p-value = 3.75x10-5) around ADTRP (chromosome 6p24); the strongest association was found in the obese category (ancestry odds ratio (AOR) = 0.51, p-value = 2.23x10-5). Evaluation of interaction between genotyped/imputed variants and BMI in this targeted region suggested race-specific interaction, present in AAs only; strongest evidence was found for insertion/deletion variant (6:11946435), again in the obese category (OR = 1.66, p-value = 1.72x10-6). We found nominal evidence for interaction between local ancestry and BMI at a previously reported region in chromosome 2q31-32, which includes COL5A2, and TFPI, an immediate downstream target of ADTRP. Interactions between BMI and SNPs (single nucleotide polymorphisms) found in this region in AA women were also detected in an

The role of a second-shell residue in modifying substrate and inhibitor interactions in the SHV beta-lactamase: a study of ambler position Asn276.

Science.gov (United States)

Drawz, Sarah M; Bethel, Christopher R; Hujer, Kristine M; Hurless, Kelly N; Distler, Anne M; Caselli, Emilia; Prati, Fabio; Bonomo, Robert A

2009-06-02

Inhibitor-resistant class A beta-lactamases of the TEM and SHV families that arise by single amino acid substitutions are a significant threat to the efficacy of beta-lactam/beta-lactamase inhibitor combinations. To better understand the basis of the inhibitor-resistant phenotype in SHV, we performed mutagenesis to examine the role of a second-shell residue, Asn276. Of the 19 variants expressed in Escherichia coli, only the Asn276Asp enzyme demonstrated reduced susceptibility to ampicillin/clavulanate (MIC increased from 50/2 --> 50/8 microg/mL) while maintaining high-level resistance to ampicillin (MIC = 8192 microg/mL). Steady-state kinetic analyses of Asn276Asp revealed slightly diminished k(cat)/K(m) for all substrates tested. In contrast, we observed a 5-fold increase in K(i) for clavulanate (7.4 +/- 0.9 microM for Asn276Asp vs 1.4 +/- 0.2 microM for SHV-1) and a 40% reduction in k(inact)/K(I) (0.013 +/- 0.002 microM(-1 )s(-1) for Asn276Asp vs 0.021 +/- 0.004 microM(-1) s(-1) for SHV-1). Timed electrospray ionization mass spectrometry of clavulanate-inhibited SHV-1 and SHV Asn276Asp showed nearly identical mass adducts, arguing for a similar pathway of inactivation. Molecular modeling shows that novel electrostatic interactions are formed between Arg244Neta2 and both 276AspOdelta1 and Odelta2; these new forces restrict the spatial position of Arg244, a residue important in the recognition of the C(3)/C(4) carboxylate of beta-lactam substrates and inhibitors. Testing the functional consequences of this interaction, we noted considerable free energy costs (+DeltaDeltaG) for substrates and inhibitors. A rigid carbapenem (meropenem) was most affected by the Asn276Asp substitution (46-fold increase in K(i) vs SHV-1). We conclude that residue 276 is an important second-shell residue in class A beta-lactamase-mediated resistance to substrates and inhibitors, and only Asn is able to precisely modulate the conformational flexibility of Arg244 required for successful

Pesticide residues in birds and mammals

Science.gov (United States)

Stickel, L.F.; Edwards, C.A.

1973-01-01

SUMMARY: Residues of organochlorine pesticides and their breakdown products are present in the tissues of essentially all wild birds throughout the world. These chemicals accumulate in fat from a relatively small environmental exposure. DDE and dieldrin are most prevalent. Others, such as heptachlor epoxide, chlordane, endrin, and benzene hexachloride also occur, the quantities and kinds generally reflecting local or regional use. Accumulation may be sufficient to kill animals following applications for pest control. This has occurred in several large-scale programmes in the United States. Mortality has also resulted from unintentional leakage of chemical from commercial establishments. Residues may persist in the environment for many years, exposing successive generations of animals. In general, birds that eat other birds, or fish, have higher residues than those that eat seeds and vegetation. The kinetic processes of absorption, metabolism, storage, and output differ according to both kind of chemical and species of animal. When exposure is low and continuous, a balance between intake and excretion may be achieved. Residues reach a balance at an approximate animal body equilibrium or plateau; the storage is generally proportional to dose. Experiments with chickens show that dieldrin and heptachlor epoxide have the greatest propensity for storage, endrin next, then DDT, then lindane. The storage of DDT was complicated by its metabolism to DDE and DDD, but other studies show that DDE has a much greater propensity for storage than either DDD or DDT. Methoxychlor has little cumulative capacity in birds. Residues in eggs reflect and parallel those in the parent bird during accumulation, equilibrium, and decline when dosage is discontinued. Residues with the greatest propensity for storage are also lost most slowly. Rate of loss of residues can be modified by dietary components and is speeded by weight loss of the animal. Under sublethal conditions of continuous

Rootletin interacts with C-Nap1 and may function as a physical linker between the pair of centrioles/basal bodies in cells.

Science.gov (United States)

Yang, Jun; Adamian, Michael; Li, Tiansen

2006-02-01

Rootletin, a major structural component of the ciliary rootlet, is located at the basal bodies and centrosomes in ciliated and nonciliated cells, respectively. Here we investigated its potential role in the linkage of basal bodies/centrioles and the mechanism involved in such linkages. We show that rootletin interacts with C-Nap1, a protein restricted at the ends of centrioles and functioning in centrosome cohesion in interphase cells. Their interaction in vivo is supported by their colocalization at the basal bodies/centrioles and coordinated association with the centrioles during the cell cycle. Ultrastructural examinations demonstrate that rootletin fibers connect the basal bodies in ciliated cells and are present both at the ends of and in between the pair of centrioles in nonciliated cells. The latter finding stands in contrast with C-Nap1, which is present only at the ends of the centrioles. Transient expression of C-Nap1 fragments dissociated rootletin fibers from the centrioles, resulting in centrosome separation in interphase. Overexpression of rootletin in cells caused multinucleation, micronucleation, and irregularity of nuclear shape and size, indicative of defects in chromosome separation. These data suggest that rootletin may function as a physical linker between the pair of basal bodies/centrioles by binding to C-Nap1.

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.

Coil occlusion of residual shunts after surgical closure of patent ductus arteriosus.

Science.gov (United States)

Fujii, Yoko; Keene, Bruce W; Mathews, Kyle G; Atkins, Clarke E; Defrancesco, Teresa C; Hardie, Elizabeth M; Wakao, Yoshito

2006-12-01

OBJECTIVE; To describe use of coil embolization to occlude residual flow through a patent ductus arteriosus (PDA) after incomplete surgical ligation. Clinical study. Dogs (n=4) with continuous murmur after surgical ligation of PDA. After PDA ligation, residual ductal flow through the PDA was visible on color-flow Doppler examination and left ventricular end-diastolic diameter remained increased. Coil embolization by an arterial approach was performed to achieve complete occlusion of the PDA. Embolization coils were delivered without complications and hemodynamically successful occlusion was achieved. Doppler-visible flow resolved in 2 dogs within 3 months after embolization. Left ventricular end-diastolic diameter indexed to body weight decreased in all dogs. Transcatheter coil embolization appears to be a safe and minimally invasive procedure for complete occlusion of residual PDA flow after incomplete surgical ligation. Transcatheter coil embolization should be considered for correction of hemodynamically significant residual shunts in dogs that have incomplete PDA occlusion after open surgical ligation.

Role of long- and short-range hydrophobic, hydrophilic and charged residues contact network in protein’s structural organization

Directory of Open Access Journals (Sweden)

Sengupta Dhriti

2012-06-01

Full Text Available Abstract Background The three-dimensional structure of a protein can be described as a graph where nodes represent residues and the strength of non-covalent interactions between them are edges. These protein contact networks can be separated into long and short-range interactions networks depending on the positions of amino acids in primary structure. Long-range interactions play a distinct role in determining the tertiary structure of a protein while short-range interactions could largely contribute to the secondary structure formations. In addition, physico chemical properties and the linear arrangement of amino acids of the primary structure of a protein determines its three dimensional structure. Here, we present an extensive analysis of protein contact subnetworks based on the London van der Waals interactions of amino acids at different length scales. We further subdivided those networks in hydrophobic, hydrophilic and charged residues networks and have tried to correlate their influence in the overall topology and organization of a protein. Results The largest connected component (LCC of long (LRN-, short (SRN- and all-range (ARN networks within proteins exhibit a transition behaviour when plotted against different interaction strengths of edges among amino acid nodes. While short-range networks having chain like structures exhibit highly cooperative transition; long- and all-range networks, which are more similar to each other, have non-chain like structures and show less cooperativity. Further, the hydrophobic residues subnetworks in long- and all-range networks have similar transition behaviours with all residues all-range networks, but the hydrophilic and charged residues networks don’t. While the nature of transitions of LCC’s sizes is same in SRNs for thermophiles and mesophiles, there exists a clear difference in LRNs. The presence of larger size of interconnected long-range interactions in thermophiles than mesophiles, even at

Body fat assessed from body density and estimated from skinfold thickness in normal children and children with cystic fibrosis.

Science.gov (United States)

Johnston, J L; Leong, M S; Checkland, E G; Zuberbuhler, P C; Conger, P R; Quinney, H A

1988-12-01

Body density and skinfold thickness at four sites were measured in 140 normal boys, 168 normal girls, and 6 boys and 7 girls with cystic fibrosis, all aged 8-14 y. Prediction equations for the normal boys and girls for the estimation of body-fat content from skinfold measurements were derived from linear regression of body density vs the log of the sum of the skinfold thickness. The relationship between body density and the log of the sum of the skinfold measurements differed from normal for the boys and girls with cystic fibrosis because of their high body density even though their large residual volume was corrected for. However the sum of skinfold measurements in the children with cystic fibrosis did not differ from normal. Thus body fat percent of these children with cystic fibrosis was underestimated when calculated from body density and invalid when calculated from skinfold thickness.

Combined adverse effects of maternal smoking and high body mass index on heart development in offspring : evidence for interaction?

NARCIS (Netherlands)

Baardman, M.E.; Kerstjens-Frederikse, W.S.; Corpeleijn, E.; de Walle, H.E.K.; Hofstra, R.M.W.; Berger, R.M.F.; Bakker, M.K.

Objective To study the influence of a possible interaction between maternal smoking and high body mass index (BMI) on the occurrence of specific congenital heart anomalies (CHA) in offspring. Design Case-control study. Setting Data from a population-based birth defects registry in the Netherlands.

Relationship between hot spot residues and ligand binding hot spots in protein-protein interfaces.

Science.gov (United States)

Zerbe, Brandon S; Hall, David R; Vajda, Sandor; Whitty, Adrian; Kozakov, Dima

2012-08-27

In the context of protein-protein interactions, the term "hot spot" refers to a residue or cluster of residues that makes a major contribution to the binding free energy, as determined by alanine scanning mutagenesis. In contrast, in pharmaceutical research, a hot spot is a site on a target protein that has high propensity for ligand binding and hence is potentially important for drug discovery. Here we examine the relationship between these two hot spot concepts by comparing alanine scanning data for a set of 15 proteins with results from mapping the protein surfaces for sites that can bind fragment-sized small molecules. We find the two types of hot spots are largely complementary; the residues protruding into hot spot regions identified by computational mapping or experimental fragment screening are almost always themselves hot spot residues as defined by alanine scanning experiments. Conversely, a residue that is found by alanine scanning to contribute little to binding rarely interacts with hot spot regions on the partner protein identified by fragment mapping. In spite of the strong correlation between the two hot spot concepts, they fundamentally differ, however. In particular, while identification of a hot spot by alanine scanning establishes the potential to generate substantial interaction energy with a binding partner, there are additional topological requirements to be a hot spot for small molecule binding. Hence, only a minority of hot spots identified by alanine scanning represent sites that are potentially useful for small inhibitor binding, and it is this subset that is identified by experimental or computational fragment screening.

Eliciting user-sourced interaction mappings for body-based interfaces

OpenAIRE

May, Aaron

2015-01-01

Thanks to technological advancements, whole-body natural user interfaces are becoming increasingly common in modern homes and public spaces. However, because whole-body natural user interfaces lack obvious affordances, users can be unsure how to control the interface. In this thesis, I report the findings of a study of novice and expert users mock controlling a balance-based whole-body natural user interface during a Think Aloud task. I compare the strategies demonstrated by participants whi...

Void analysis of target residues at SPS energy -evidence of correlation with fractal behaviour

International Nuclear Information System (INIS)

Ghosh, Dipak; Deb, Argha; Das, Rupa . E-mail : dipakghosh_in@yahoo.com

2007-01-01

This paper presents an analysis of the target residues in 32 S -AgBr and 16 0 -AgBr interactions at 200 AGeV and 60AGeV respectively in terms of fractal moment by Takagi method and void probability scaling. The study reveals an interesting feature of the production process. In 16 O- AgBr interactions multifractal behaviour is present in both hemispheres and void probability does not show a scaling behaviour, but at high energy the situation changes. In 32 S -AgBr interactions for both hemisphere monofractal behaviour is indicated by that data and void probability also shows good scaling behaviour. This suggests that a possible correlation of void probability with fractal behaviour of target residues. (author)

Short versus long range interactions and the size of two-body weakly bound objects

International Nuclear Information System (INIS)

Lombard, R.J.; Volpe, C.

2003-01-01

Very weakly bound systems may manifest intriguing ''universal'' properties, independent of the specific interaction which keeps the system bound. An interesting example is given by relations between the size of the system and the separation energy, or scaling laws. So far, scaling laws have been investigated for short-range and long-range (repulsive) potentials. We report here on scaling laws for weakly bound two-body systems valid for a larger class of potentials, i.e. short-range potentials having a repulsive core and long-range attractive potentials. We emphasize analogies and differences between the short- and the long-range case. In particular, we show that the emergence of halos is a threshold phenomenon which can arise when the system is bound not only by short-range interactions but also by long-range ones, and this for any value of the orbital angular momentum l. These results enlarge the image of halo systems we are accustomed to. (orig.)

Risk evaluation of the Arctic environmental POP exposure based on critical body residue and critical daily dose using captive Greenland sledge dogs (Canis familiaris) as surrogate species

DEFF Research Database (Denmark)

Sonne, Christian; Gustavson, Kim; Eulaers, Igor

2016-01-01

The risk from POP (persistent organic pollutant) exposure and subsequent reproductive, immunotoxic and liver histopathological effects was evaluated in a classical parallel trial on Greenland sledge dogs (Canis familiaris) fed contaminated minke whale (Balaenoptera acutorostrata) blubber. First...... quotients (RQDD: DD/CDD; RQBR: BR/CBR; ≥1 indicates risk). The results showed that risk quotients for reproductive, immunotoxic and liver histopathological effects were significantly lowest in the control group (p... on body residues (RQBR) (all preproductive and immunotoxic effects while those for liver histopathological effects ranged from 0.7-3.0. PCBs (polychlorinated biphenyls) and chlordanes were the dominant driver behind high immune and reproductive RQs...

A statistical analysis of the body condition of cows from two veterinary stations in Zimbabwe

International Nuclear Information System (INIS)

Saporu, F.W.O.

2003-12-01

The improvement of livestock production is important for Zimbabwe's agriculturally base economy. This paper examines the relationship between the body condition and metabolic parameters of female cows, for the better understanding of traditional livestock farming in Zimbabwe. The data analysed are part of the baseline data on the improvement of livestock production, collected from two sites Chinamora and Bulawayo. Body condition is indexed by body score. Thirty-five variables are examined. The variable selection method employed is stepwise regression. Regression model assumptions of normality and independent observations are checked using normal probability plot and Durbin-Watson statistics for autocorrelation of residuals. Collinearity and outlier problems are examined using eigenanalysis and influence statistics. The effect of some factors, such as, site, which relates to livestock management, parity and season, categorized by the quality of forage available for grazing, are also studied. The data are analysed using SAS statistical package on a Personal Computer. The results show that only about four variables substantially influence the relationship in each of the two sites considered. For the better managed site, Bulawayo, these are PCV, Calcium and WBC. Strongyles, Progesterone Level, Phosphate and HB are obtained in Chinamora. Negative correlation coefficient corresponds to strongyles only. That is, the effect of stronglyes is to reduce the value of bodyscore. For other variables, an improvement in their respective values will bring about improved body condition. Site difference is identified as a factor affecting the relationship. This emphasizes the role of good management in livestock production. Parity and season are also identified. Only two interactions are significant; site-season and a progesterone level-season interaction. The latter is obtained only in Chinamora site and it can be deduced that the cyclic cows are exposed to the risk of loosing their

Intermolecular Modes between LH2 Bacteriochlorophylls and Protein Residues: The Effect on the Excitation Energies.

Science.gov (United States)

Anda, André; De Vico, Luca; Hansen, Thorsten

2017-06-08

Light-harvesting system 2 (LH2) executes the primary processes of photosynthesis in purple bacteria; photon absorption, and energy transportation to the reaction center. A detailed mechanistic insight into these operations is obscured by the complexity of the light-harvesting systems, particularly by the chromophore-environment interaction. In this work, we focus on the effects of the protein residues that are ligated to the bacteriochlorophylls (BChls) and construct potential energy surfaces of the ground and first optically excited state for the various BChl-residue systems where we in each case consider two degrees of freedom in the intermolecular region. We find that the excitation energies are only slightly affected by the considered modes. In addition, we see that axial ligands and hydrogen-bonded residues have opposite effects on both excitation energies and oscillator strengths by comparing to the isolated BChls. Our results indicate that only a small part of the chromophore-environment interaction can be associated with the intermolecular region between a BChl and an adjacent residue, but that it may be possible to selectively raise or lower the excitation energy at the axial and planar residue positions, respectively.

Stability of tetrachlorvinphos residues in faba beans and soya bean oil towards different processing procedures

International Nuclear Information System (INIS)

Zayed, S.M.A.D.; Farghaly, M.

1987-01-01

Cooking of contaminated faba beans did not degrade the originally present potentially toxic residues, namely, tetrachlorvinphos and its desmethyl derivative to any appreciable extent. Processing of contaminated soya bean oil, on the other hand, led to degradation of tetrachlorvinphos and its metabolites to give mono and dimethyl phosphates. Feeding of mice with bound residues of tetrachlorvinphos in beans for 90 days led to an apparent decrease in the rate of body weight gain. (author)

Skeletal maturation, fundamental motor skills and motor coordination in children 7-10 years.

Science.gov (United States)

Freitas, Duarte L; Lausen, Berthold; Maia, José António; Lefevre, Johan; Gouveia, Élvio Rúbio; Thomis, Martine; Antunes, António Manuel; Claessens, Albrecht L; Beunen, Gaston; Malina, Robert M

2015-01-01

Relationships between skeletal maturation and fundamental motor skills and gross motor coordination were evaluated in 429 children (213 boys and 216 girls) 7-10 years. Skeletal age was assessed (Tanner-Whitehouse 2 method), and stature, body mass, motor coordination (Körperkoordinations Test für Kinder, KTK) and fundamental motor skills (Test of Gross Motor Development, TGMD-2) were measured. Relationships among chronological age, skeletal age (expressed as the standardised residual of skeletal age on chronological age) and body size and fundamental motor skills and motor coordination were analysed with hierarchical multiple regression. Standardised residual of skeletal age on chronological age interacting with stature and body mass explained a maximum of 7.0% of the variance in fundamental motor skills and motor coordination over that attributed to body size per se. Standardised residual of skeletal age on chronological age alone accounted for a maximum of 9.0% of variance in fundamental motor skills, and motor coordination over that attributed to body size per se and interactions between standardised residual of skeletal age on chronological age and body size. In conclusion, skeletal age alone or interacting with body size has a negligible influence on fundamental motor skills and motor coordination in children 7-10 years.

Accumulation of {sup 14}C-trinitrotoluene and related nonextractable (bound) residues in Eisenia fetida

Energy Technology Data Exchange (ETDEWEB)

Belden, Jason B., E-mail: jbelden@okstate.edu [Department of Zoology, Oklahoma State University, Stillwater, OK 74078 (United States); Lotufo, Guillerme R. [US Army Engineer Research and Development Center, Vicksburg, MS 39180 (United States); Chambliss, C. Kevin [Department of Chemistry, Baylor University, Waco, TX 76798 (United States); Fisher, Jonathan C. [Department of Zoology, Oklahoma State University, Stillwater, OK 74078 (United States); Johnson, Dave R.; Boyd, Robert E.; Sims, Jerre G. [US Army Engineer Research and Development Center, Vicksburg, MS 39180 (United States)

2011-05-15

To determine if trinitrotoluene (TNT) forms nonextractable residues in earthworms and to measure the relative degree of accumulation as compared to TNT and its deaminated metabolites, Eisenia fetida was exposed to {sup 14}C-TNT using dermal contact to filter paper or exposure to soil. Nonextractable residues made up 32-68% of total body burden depending on exposure media and depuration time. Parent TNT accounted for less than 3% of radioactivity, while ADNTs accounted for 7-38%. Elimination half-lives were 61-120 h for TNT, ADNTs, and DANTs, which was significantly lower than the half-lives found for nonextractable residues, 201-240 h. However, over 80% of the nonextractable residue was solubilized using weak acid (pH 2). Based on our findings that TNT accumulation occurs primarily as nonextractable residues, which have a longer half-life, and that nonextractable residues can be solubilized, we propose that nonextractable residues could be used as a selective biomarker for assessing TNT contamination. - Highlights: > Trinitrotoluene accumulation in earthworms primarily occurs as nonextractable residues. > Nonextractable residues have a significantly longer half life in the worm as compared to TNT and its solvent-extractable deaminated metabolites. > Nonextractable residue may be useful as a biomarker for exposure to TNT. - The majority of trinitrotoluene accumulation in earthworms occurs as nonextractable residues that have a significantly longer half life in the worm as compared to TNT and its solvent-extractable deaminated metabolites.

CHARACTERIZATION OF THE INTERACTION BETWEEN GLAZES AND CERAMIC BODIES

Directory of Open Access Journals (Sweden)

Maria Kavanova

2017-07-01

Full Text Available The paper presents the study of stress relations of ceramic body - glaze systems of model and real, both historical and contemporary ceramics. The systems were characterized in terms of chemical composition, linear thermal coefficients and degradation effects. The results show that calculation of stress relations between ceramic body and glaze is affected predominantly by the difference in values of thermal expansion coefficients. Calculated results provide relevant information about the accordance of the glaze - ceramic body and for the characterization of surface defects.

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

Directory of Open Access Journals (Sweden)

Aysima Hacisuleyman

2017-01-01

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

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

Science.gov (United States)

Hacisuleyman, Aysima; Erman, Burak

2017-01-01

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

Tales from the Body Public

DEFF Research Database (Denmark)

Thelle, Mikkel

2016-01-01

English abstract: How can we approach the interaction between body and city as political? This article moves through a sequence of cases in which bodies - groups, crowds, or swarms of people - have affected the public space of Copenhagen around 1900. First, election day is investigated for its co...... in the discussion of public space in cultural history that has for some time been focusing on materiality.......English abstract: How can we approach the interaction between body and city as political? This article moves through a sequence of cases in which bodies - groups, crowds, or swarms of people - have affected the public space of Copenhagen around 1900. First, election day is investigated for its...

Maize Residue as a Viable Substrate for Farm Scale Cultivation of Oyster Mushroom (Pleurotus ostreatus

Directory of Open Access Journals (Sweden)

Abena O. Adjapong

2015-01-01

Full Text Available In the search for alternatives to sawdust as growing media in commercial mushroom cultivation, three organic substrates obtainable as crop residue, maize husk, maize cob, and maize stalk, with each being supplemented with rice bran, were evaluated as growth media for the oyster mushroom, Pleurotus ostreatus (Kummer. For the tested alternatives to sawdust, the harvested weight of fruiting bodies that sprouted on a kilogram maize husk media per crop (32.99 g was the highest. Sawdust media supported significantly (P<0.001 heavier fruiting bodies (42.18 than the maize residues. The peak mushroom harvests for the various substrates were obtained between the first and seventh fruiting body flushes. The biological efficiency of the substrates, which measured usable nutrients indicated that maize stalk supplemented with rice bran, was 39% compared to that of the sawdust media (60%. The maize husk media and the maize cob media had biological efficiencies of 32% and 9.5%, respectively. These results indicate that two of the tested growing media (maize stalk or husk produced mushrooms with yield characteristics that were comparable to the well-used sawdust in the cultivation of oyster mushrooms. The environmental and economic parameters involved in the use and carting of sawdust make these on-farm crop residues a viable alternative for mushroom cultivation in especially nonforest zones of Ghana.

Penis size interacts with body shape and height to influence male attractiveness.

Science.gov (United States)

Mautz, Brian S; Wong, Bob B M; Peters, Richard A; Jennions, Michael D

2013-04-23

Compelling evidence from many animal taxa indicates that male genitalia are often under postcopulatory sexual selection for characteristics that increase a male's relative fertilization success. There could, however, also be direct precopulatory female mate choice based on male genital traits. Before clothing, the nonretractable human penis would have been conspicuous to potential mates. This observation has generated suggestions that human penis size partly evolved because of female choice. Here we show, based upon female assessment of digitally projected life-size, computer-generated images, that penis size interacts with body shape and height to determine male sexual attractiveness. Positive linear selection was detected for penis size, but the marginal increase in attractiveness eventually declined with greater penis size (i.e., quadratic selection). Penis size had a stronger effect on attractiveness in taller men than in shorter men. There was a similar increase in the positive effect of penis size on attractiveness with a more masculine body shape (i.e., greater shoulder-to-hip ratio). Surprisingly, larger penis size and greater height had almost equivalent positive effects on male attractiveness. Our results support the hypothesis that female mate choice could have driven the evolution of larger penises in humans. More broadly, our results show that precopulatory sexual selection can play a role in the evolution of genital traits.

Interaction of convective flow generated by human body with room ventilation flow: impact on transport of pollution to the breathing zone

DEFF Research Database (Denmark)

Licina, Dusan; Melikov, Arsen Krikor; Sekhar, Chandra

2014-01-01

interaction with opposing flow from above and assisting flow from below; and secondly, implication of such a flow interaction on the particle transport from the feet to the breathing zone is examined. The results reveal that the human body heat transports the pollution to the breathing zone and increases......This study aims to investigate the interaction between the human convective boundary layer (CBL) and uniform airflow from two directions and with different velocities. The study has two objectives: first, to characterize the velocity field in the breathing zone of a thermal manikin under its...

Study of the interactions between a proline-rich protein and a flavan-3-ol by NMR: residual structures in the natively unfolded protein provides anchorage points for the ligands.

Science.gov (United States)

Pascal, Christine; Paté, Franck; Cheynier, Véronique; Delsuc, Marc-André

2009-09-01

Astringency is one of the major organoleptic properties of food and beverages that are made from plants, such as tea, chocolate, beer, or red wine. This sensation is thought to be due to interactions between tannins and salivary proline-rich proteins, which are natively unfolded proteins. A human salivary proline-rich protein, namely IB-5, was produced by the recombinant method. Its interactions with a model tannin, epigallocatechin gallate (EGCG), the major flavan-3-ol in green tea, were studied here. Circular dichroism experiments showed that IB-5 presents residual structures (PPII helices) when the ionic strength is close to that in saliva. In the presence of these residual structures, IB-5 undergoes an increase in structural content upon binding to EGCG. NMR data corroborated the presence of preformed structural elements within the protein prior to binding and a partial assignment was proposed, showing partial structuration. TOCSY experiments showed that amino acids that are involved in PPII helices are more likely to interact with EGCG than those in random coil regions, as if they were anchorage points for the ligand. The signal from IB-5 in the DOSY NMR spectrum revealed an increase in polydispersity upon addition of EGCG while the mean hydrodynamic radius remained unchanged. This strongly suggests the formation of IB-5/EGCG aggregates.

Leveraging the Pre-DFG Residue Thr-406 To Obtain High Kinase Selectivity in an Aminopyrazole-Type PAK1 Inhibitor Series.

Science.gov (United States)

Rudolph, Joachim; Aliagas, Ignacio; Crawford, James J; Mathieu, Simon; Lee, Wendy; Chao, Qi; Dong, Ping; Rouge, Lionel; Wang, Weiru; Heise, Christopher; Murray, Lesley J; La, Hank; Liu, Yanzhou; Manning, Gerard; Diederich, François; Hoeflich, Klaus P

2015-06-11

To increase kinase selectivity in an aminopyrazole-based PAK1 inhibitor series, analogues were designed to interact with the PAK1 deep-front pocket pre-DFG residue Thr-406, a residue that is hydrophobic in most kinases. This goal was achieved by installing lactam head groups to the aminopyrazole hinge binding moiety. The corresponding analogues represent the most kinase selective ATP-competitive Group I PAK inhibitors described to date. Hydrogen bonding with the Thr-406 side chain was demonstrated by X-ray crystallography, and inhibitory activities, particularly against kinases with hydrophobic pre-DFG residues, were mitigated. Leveraging hydrogen bonding side chain interactions with polar pre-DFG residues is unprecedented, and similar strategies should be applicable to other appropriate kinases.

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

Science.gov (United States)

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

2017-12-01

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

New approach to the interaction of cosmic rays with nuclei in spacecraft shielding and the human body

International Nuclear Information System (INIS)

Bush, B.W.; Nix, J.R.

1993-01-01

The interaction of high-energy cosmic rays with nuclei in spacecraft shielding and the human body is important for manned interplanetary missions and is not well understood either experimentally or theoretically. We present a new theoretical approach to this problem based on classical hadrodynamics for extended nucleons, which treats nucleons of finite size interacting with massive meson fields. This theory represents the classical analogue of the quantum hadrodynamics of Serot and Walecka without the assumptions of the mean-field approximation and point nucleons. It provides a natural covariant microscopic approach to collisions between cosmic rays and nuclei that automatically includes space-time non-locality and retardation, nonequilibrium phenomena, interactions among all nucleons, and particle production. Unlike previous models, this approach is manifestly Lorentz covariant and satisfies a priori the basic conditions that are present when cosmic rays collide with nuclei, namely an interaction time that is extremely short and a nucleon mean-free path, force range, and internucleon separation that are all comparable in size. We review the history of classical meson-field theory and derive the classical relativistic equations of motion for nucleons of finite size interacting with massive scalar and vector meson fields

Impact of Corn Residue Removal on Crop and Soil Productivity

Science.gov (United States)

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

2003-12-01

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

Post-Amputation Pain Is Associated with the Recall of an Impaired Body Representation in Dreams—Results from a Nation-Wide Survey on Limb Amputees

Science.gov (United States)

Bekrater-Bodmann, Robin; Schredl, Michael; Diers, Martin; Reinhard, Iris; Foell, Jens; Trojan, Jörg; Fuchs, Xaver; Flor, Herta

2015-01-01

The experience of post-amputation pain such as phantom limb pain (PLP) and residual limb pain (RLP), is a common consequence of limb amputation, and its presence has negative effects on a person’s well-being. The continuity hypothesis of dreams suggests that the presence of such aversive experiences in the waking state should be reflected in dream content, with the recalled body representation reflecting a cognitive proxy of negative impact. In the present study, we epidemiologically assessed the presence of post-amputation pain and other amputation-related information as well as recalled body representation in dreams in a sample of 3,234 unilateral limb amputees. Data on the site and time of amputation, residual limb length, prosthesis use, lifetime prevalence of mental disorders, presence of post-amputation pain, and presence of non-painful phantom phenomena were included in logistic regression analyses using recalled body representation in dreams (impaired, intact, no memory) as dependent variable. The effects of age, sex, and frequency of dream recall were controlled for. About 22% of the subjects indicated that they were not able to remember their body representation in dreams, another 24% of the amputees recalled themselves as always intact, and only a minority of less than 3% recalled themselves as always impaired. Almost 35% of the amputees dreamed of themselves in a mixed fashion. We found that lower-limb amputation as well as the presence of PLP and RLP was positively associated with the recall of an impaired body representation in dreams. The presence of non-painful phantom phenomena, however, had no influence. These results complement previous findings and indicate complex interactions of physical body appearance and mental body representation, probably modulated by distress in the waking state. The findings are discussed against the background of alterations in cognitive processes after amputation and hypotheses suggesting an innate body model. PMID

Post-amputation pain is associated with the recall of an impaired body representation in dreams-results from a nation-wide survey on limb amputees.

Science.gov (United States)

Bekrater-Bodmann, Robin; Schredl, Michael; Diers, Martin; Reinhard, Iris; Foell, Jens; Trojan, Jörg; Fuchs, Xaver; Flor, Herta

2015-01-01

The experience of post-amputation pain such as phantom limb pain (PLP) and residual limb pain (RLP), is a common consequence of limb amputation, and its presence has negative effects on a person's well-being. The continuity hypothesis of dreams suggests that the presence of such aversive experiences in the waking state should be reflected in dream content, with the recalled body representation reflecting a cognitive proxy of negative impact. In the present study, we epidemiologically assessed the presence of post-amputation pain and other amputation-related information as well as recalled body representation in dreams in a sample of 3,234 unilateral limb amputees. Data on the site and time of amputation, residual limb length, prosthesis use, lifetime prevalence of mental disorders, presence of post-amputation pain, and presence of non-painful phantom phenomena were included in logistic regression analyses using recalled body representation in dreams (impaired, intact, no memory) as dependent variable. The effects of age, sex, and frequency of dream recall were controlled for. About 22% of the subjects indicated that they were not able to remember their body representation in dreams, another 24% of the amputees recalled themselves as always intact, and only a minority of less than 3% recalled themselves as always impaired. Almost 35% of the amputees dreamed of themselves in a mixed fashion. We found that lower-limb amputation as well as the presence of PLP and RLP was positively associated with the recall of an impaired body representation in dreams. The presence of non-painful phantom phenomena, however, had no influence. These results complement previous findings and indicate complex interactions of physical body appearance and mental body representation, probably modulated by distress in the waking state. The findings are discussed against the background of alterations in cognitive processes after amputation and hypotheses suggesting an innate body model.

Post-amputation pain is associated with the recall of an impaired body representation in dreams-results from a nation-wide survey on limb amputees.

Directory of Open Access Journals (Sweden)

Robin Bekrater-Bodmann

Full Text Available The experience of post-amputation pain such as phantom limb pain (PLP and residual limb pain (RLP, is a common consequence of limb amputation, and its presence has negative effects on a person's well-being. The continuity hypothesis of dreams suggests that the presence of such aversive experiences in the waking state should be reflected in dream content, with the recalled body representation reflecting a cognitive proxy of negative impact. In the present study, we epidemiologically assessed the presence of post-amputation pain and other amputation-related information as well as recalled body representation in dreams in a sample of 3,234 unilateral limb amputees. Data on the site and time of amputation, residual limb length, prosthesis use, lifetime prevalence of mental disorders, presence of post-amputation pain, and presence of non-painful phantom phenomena were included in logistic regression analyses using recalled body representation in dreams (impaired, intact, no memory as dependent variable. The effects of age, sex, and frequency of dream recall were controlled for. About 22% of the subjects indicated that they were not able to remember their body representation in dreams, another 24% of the amputees recalled themselves as always intact, and only a minority of less than 3% recalled themselves as always impaired. Almost 35% of the amputees dreamed of themselves in a mixed fashion. We found that lower-limb amputation as well as the presence of PLP and RLP was positively associated with the recall of an impaired body representation in dreams. The presence of non-painful phantom phenomena, however, had no influence. These results complement previous findings and indicate complex interactions of physical body appearance and mental body representation, probably modulated by distress in the waking state. The findings are discussed against the background of alterations in cognitive processes after amputation and hypotheses suggesting an innate

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

Density-functional approach to the three-body dispersion interaction based on the exchange dipole moment

Energy Technology Data Exchange (ETDEWEB)

Proynov, Emil; Wang, Matthew; Kong, Jing, E-mail: jing.kong@mtsu.edu [Department of Chemistry and Center for Computational Sciences, Middle Tennessee State University, Murfreesboro, Tennessee 37132 (United States); Liu, Fenglai [Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, New York 14260 (United States); Gan, Zhengting [Q-Chem Inc., 5001 Baum Boulevard, Pittsburgh, Pennsylvania 15213 (United States)

2015-08-28

We implement and compute the density functional nonadditive three-body dispersion interaction using a combination of Tang-Karplus formalism and the exchange-dipole moment model of Becke and Johnson. The computation of the C{sub 9} dispersion coefficients is done in a non-empirical fashion. The obtained C{sub 9} values of a series of noble atom triplets agree well with highly accurate values in the literature. We also calculate the C{sub 9} values for a series of benzene trimers and find a good agreement with high-level ab initio values reported recently in the literature. For the question of damping of the three-body dispersion at short distances, we propose two damping schemes and optimize them based on the benzene trimers data, and the fitted analytic potentials of He{sub 3} and Ar{sub 3} trimers fitted to the results of high-level wavefunction theories available from the literature. Both damping schemes respond well to the optimization of two parameters.

Coilin, the signature protein of Cajal bodies, differentially modulates the interactions of plants with viruses in widely different taxa.

Science.gov (United States)

Shaw, Jane; Love, Andrew J; Makarova, Svetlana S; Kalinina, Natalia O; Harrison, Bryan D; Taliansky, Michael E

2014-01-01

Cajal bodies (CBs) are distinct nuclear bodies physically and functionally associated with the nucleolus. In addition to their traditional function in coordinating maturation of certain nuclear RNAs, CBs participate in cell cycle regulation, development, and regulation of stress responses. A key "signature" component of CBs is coilin, the scaffolding protein essential for CB formation and function. Using an RNA silencing (loss-of-function) approach, we describe here new phenomena whereby coilin also affects, directly or indirectly, a variety of interactions between host plants and viruses that have RNA or DNA genomes. Moreover, the effects of coilin on these interactions are manifested differently: coilin contributes to plant defense against tobacco rattle virus (tobravirus), tomato black ring virus (nepovirus), barley stripe mosaic virus (hordeivirus), and tomato golden mosaic virus (begomovirus). In contrast, with potato virus Y (potyvirus) and turnip vein clearing virus (tobamovirus), coilin serves to increase virus pathogenicity. These findings show that interactions with coilin (or CBs) may involve diverse mechanisms with different viruses and that these mechanisms act at different phases of virus infection. Thus, coilin (CBs) has novel, unexpected natural functions that may be recruited or subverted by plant viruses for their own needs or, in contrast, are involved in plant defense mechanisms that suppress host susceptibility to the viruses.

On modelling the interaction between two rotating bodies with statistically distributed features: an application to dressing of grinding wheels

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Spampinato, A.; Axinte, D. A.

2017-12-01

The mechanisms of interaction between bodies with statistically arranged features present characteristics common to different abrasive processes, such as dressing of abrasive tools. In contrast with the current empirical approach used to estimate the results of operations based on attritive interactions, the method we present in this paper allows us to predict the output forces and the topography of a simulated grinding wheel for a set of specific operational parameters (speed ratio and radial feed-rate), providing a thorough understanding of the complex mechanisms regulating these processes. In modelling the dressing mechanisms, the abrasive characteristics of both bodies (grain size, geometry, inter-space and protrusion) are first simulated; thus, their interaction is simulated in terms of grain collisions. Exploiting a specifically designed contact/impact evaluation algorithm, the model simulates the collisional effects of the dresser abrasives on the grinding wheel topography (grain fracture/break-out). The method has been tested for the case of a diamond rotary dresser, predicting output forces within less than 10% error and obtaining experimentally validated grinding wheel topographies. The study provides a fundamental understanding of the dressing operation, enabling the improvement of its performance in an industrial scenario, while being of general interest in modelling collision-based processes involving statistically distributed elements.

Model of the complex of Parathyroid hormone-2 receptor and Tuberoinfundibular peptide of 39 residues

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Persson Bengt

2010-10-01

Full Text Available Abstract Background We aim to propose interactions between the parathyroid hormone-2 receptor (PTH2R and its ligand the tuberoinfundibular peptide of 39 residues (TIP39 by constructing a homology model of their complex. The two related peptides parathyroid hormone (PTH and parathyroid hormone related protein (PTHrP are compared with the complex to examine their interactions. Findings In the model, the hydrophobic N-terminus of TIP39 is buried in a hydrophobic part of the central cavity between helices 3 and 7. Comparison of the peptide sequences indicates that the main discriminator between the agonistic peptides TIP39 and PTH and the inactive PTHrP is a tryptophan-phenylalanine replacement. The model indicates that the smaller phenylalanine in PTHrP does not completely occupy the binding site of the larger tryptophan residue in the other peptides. As only TIP39 causes internalisation of the receptor and the primary difference being an aspartic acid in position 7 of TIP39 that interacts with histidine 396 in the receptor, versus isoleucine/histidine residues in the related hormones, this might be a trigger interaction for the events that cause internalisation. Conclusions A model is constructed for the complex and a trigger interaction for full agonistic activation between aspartic acid 7 of TIP39 and histidine 396 in the receptor is proposed.

Measurement properties and usability of non-contact scanners for measuring transtibial residual limb volume.

Science.gov (United States)

Kofman, Rianne; Beekman, Anna M; Emmelot, Cornelis H; Geertzen, Jan H B; Dijkstra, Pieter U

2018-06-01

Non-contact scanners may have potential for measurement of residual limb volume. Different non-contact scanners have been introduced during the last decades. Reliability and usability (practicality and user friendliness) should be assessed before introducing these systems in clinical practice. The aim of this study was to analyze the measurement properties and usability of four non-contact scanners (TT Design, Omega Scanner, BioSculptor Bioscanner, and Rodin4D Scanner). Quasi experimental. Nine (geometric and residual limb) models were measured on two occasions, each consisting of two sessions, thus in total 4 sessions. In each session, four observers used the four systems for volume measurement. Mean for each model, repeatability coefficients for each system, variance components, and their two-way interactions of measurement conditions were calculated. User satisfaction was evaluated with the Post-Study System Usability Questionnaire. Systematic differences between the systems were found in volume measurements. Most of the variances were explained by the model (97%), while error variance was 3%. Measurement system and the interaction between system and model explained 44% of the error variance. Repeatability coefficient of the systems ranged from 0.101 (Omega Scanner) to 0.131 L (Rodin4D). Differences in Post-Study System Usability Questionnaire scores between the systems were small and not significant. The systems were reliable in determining residual limb volume. Measurement systems and the interaction between system and residual limb model explained most of the error variances. The differences in repeatability coefficient and usability between the four CAD/CAM systems were small. Clinical relevance If accurate measurements of residual limb volume are required (in case of research), modern non-contact scanners should be taken in consideration nowadays.

Crystal Structure of the Extended-Spectrum β-Lactamase PER-2 and Insights into the Role of Specific Residues in the Interaction with β-Lactams and β-Lactamase Inhibitors

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Ruggiero, Melina; Kerff, Frédéric; Herman, Raphaël; Sapunaric, Frédéric; Galleni, Moreno; Gutkind, Gabriel; Charlier, Paulette; Sauvage, Eric

2014-01-01

PER-2 belongs to a small (7 members to date) group of extended-spectrum β-lactamases. It has 88% amino acid identity with PER-1 and both display high catalytic efficiencies toward most β-lactams. In this study, we determined the X-ray structure of PER-2 at 2.20 Å and evaluated the possible role of several residues in the structure and activity toward β-lactams and mechanism-based inhibitors. PER-2 is defined by the presence of a singular trans bond between residues 166 to 167, which generates an inverted Ω loop, an expanded fold of this domain that results in a wide active site cavity that allows for efficient hydrolysis of antibiotics like the oxyimino-cephalosporins, and a series of exclusive interactions between residues not frequently involved in the stabilization of the active site in other class A β-lactamases. PER β-lactamases might be included within a cluster of evolutionarily related enzymes harboring the conserved residues Asp136 and Asn179. Other signature residues that define these enzymes seem to be Gln69, Arg220, Thr237, and probably Arg/Lys240A (“A” indicates an insertion according to Ambler's scheme for residue numbering in PER β-lactamases), with structurally important roles in the stabilization of the active site and proper orientation of catalytic water molecules, among others. We propose, supported by simulated models of PER-2 in combination with different β-lactams, the presence of a hydrogen-bond network connecting Ser70-Gln69-water-Thr237-Arg220 that might be important for the proper activity and inhibition of the enzyme. Therefore, we expect that mutations occurring in these positions will have impacts on the overall hydrolytic behavior. PMID:25070104

Development of a body motion interactive system with a weight voting mechanism and computer vision technology

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Lin, Chern-Sheng; Chen, Chia-Tse; Shei, Hung-Jung; Lay, Yun-Long; Chiu, Chuang-Chien

2012-09-01

This study develops a body motion interactive system with computer vision technology. This application combines interactive games, art performing, and exercise training system. Multiple image processing and computer vision technologies are used in this study. The system can calculate the characteristics of an object color, and then perform color segmentation. When there is a wrong action judgment, the system will avoid the error with a weight voting mechanism, which can set the condition score and weight value for the action judgment, and choose the best action judgment from the weight voting mechanism. Finally, this study estimated the reliability of the system in order to make improvements. The results showed that, this method has good effect on accuracy and stability during operations of the human-machine interface of the sports training system.

Comparative modeling and docking studies of p16ink4/Cyclin D1/Rb pathway genes in lung cancer revealed functionally interactive residue of RB1 and its functional partner E2F1

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e Zahra Syeda Naqsh

2013-01-01

Full Text Available Abstract Background Lung cancer is the major cause of mortality worldwide. Major signalling pathways that could play significant role in lung cancer therapy include (1 Growth promoting pathways (Epidermal Growth Factor Receptor/Ras/ PhosphatidylInositol 3-Kinase (2 Growth inhibitory pathways (p53/Rb/P14ARF, STK11 (3 Apoptotic pathways (Bcl-2/Bax/Fas/FasL. Insilico strategy was implemented to solve the mystery behind selected lung cancer pathway by applying comparative modeling and molecular docking studies. Results YASARA [v 12.4.1] was utilized to predict structural models of P16-INK4 and RB1 genes using template 4ELJ-A and 1MX6-B respectively. WHAT CHECK evaluation tool demonstrated overall quality of predicted P16-INK4 and RB1 with Z-score of −0.132 and −0.007 respectively which showed a strong indication of reliable structure prediction. Protein-protein interactions were explored by utilizing STRING server, illustrated that CDK4 and E2F1 showed strong interaction with P16-INK4 and RB1 based on confidence score of 0.999 and 0.999 respectively. In order to facilitate a comprehensive understanding of the complex interactions between candidate genes with their functional interactors, GRAMM-X server was used. Protein-protein docking investigation of P16-INK4 revealed four ionic bonds illustrating Arg47, Arg80,Cys72 and Met1 residues as actively participating in interactions with CDK4 while docking results of RB1 showed four hydrogen bonds involving Glu864, Ser567, Asp36 and Arg861 residues which interact strongly with its respective functional interactor E2F1. Conclusion This research may provide a basis for understanding biological insights of P16-INK4 and RB1 proteins which will be helpful in future to design a suitable drug to inhibit the disease pathogenesis as we have determined the interacting amino acids which can be targeted in order to design a ligand in-vitro to propose a drug for clinical trials. Protein -protein docking of

Interactions of a didomain fragment of the Drosophila Sex-lethal protein with single-stranded uridine-rich oligoribonucleotides derived from the transformer and Sex-lethal messenger RNA precursors: NMR with residue-selective [5-2H]uridine substitutions

International Nuclear Information System (INIS)

Kim, Insil; Muto, Yutaka; Watanabe, Satoru; Kitamura, Aya; Futamura, Yasuhiro; Yokoyama, Shigeyuki; Hosono, Kazumi; Kawai, Gota; Takaku, Hiroshi; Dohmae, Naoshi; Takio, Koji; Sakamoto, Hiroshi; Shimura, Yoshiro

2000-01-01

Proteins that contain two or more copies of the RNA-binding domain [ribonucleoprotein (RNP) domain or RNA recognition motif (RRM)] are considered to be involved in the recognition of single-stranded RNA, but the mechanisms of this recognition are poorly understood at the molecular level. For an NMR analysis of a single-stranded RNA complexed with a multi-RBD protein, residue-selective stable-isotope labeling techniques are necessary, rather than common assignment methods based on the secondary structure of RNA. In the present study, we analyzed the interaction of a Drosophila Sex-lethal (Sxl) protein fragment, consisting of two RBDs (RBD1-RBD2), with two distinct target RNAs derived from the tra and Sxl mRNA precursors with guanosine and adenosine, respectively, in a position near the 5'-terminus of a uridine stretch. First, we prepared a [5- 2 H]uridine phosphoramidite, and synthesized a series of 2 H-labeled RNAs, in which all of the uridine residues except one were replaced by [5- 2 H]uridine in the target sequence, GU 8 C. By observing the H5-H6 TOCSY cross peaks of the series of 2 H-labeled RNAs complexed with the Sxl RBD1-RBD2, all of the base H5-H6 proton resonances of the target RNA were unambiguously assigned. Then, the H5-H6 cross peaks of other target RNAs, GU 2 GU 8 , AU 8 , and UAU 8 , were assigned by comparison with those of GU 8 C. We found that the uridine residue prior to the G or A residue is essential for proper interaction with the protein, and that the interaction is tighter for A than for G. Moreover, the H1' resonance assignments were achieved from the H5-H6 assignments. The results revealed that all of the protein-bound nucleotide residues, except for only two, are in the unusual C2'-endo ribose conformation in the complex

Interactions of a didomain fragment of the Drosophila Sex-lethal protein with single-stranded uridine-rich oligoribonucleotides derived from the transformer and Sex-lethal messenger RNA precursors: NMR with residue-selective [5-2H]uridine substitutions

Energy Technology Data Exchange (ETDEWEB)

Kim, Insil; Muto, Yutaka; Watanabe, Satoru; Kitamura, Aya; Futamura, Yasuhiro; Yokoyama, Shigeyuki [University of Tokyo, Department of Biophysics and Biochemistry, Graduate School of Science (Japan); Hosono, Kazumi; Kawai, Gota; Takaku, Hiroshi [Chiba Institute of Technology, Department of Industrial Chemistry (Japan); Dohmae, Naoshi; Takio, Koji [Institute of Physical and Chemical Research (RIKEN) (Japan); Sakamoto, Hiroshi [Kobe University, Department of Biology, Faculty of Science (Japan); Shimura, Yoshiro [Biomolecular Engineering Research Institute (Japan)

2000-06-15

Proteins that contain two or more copies of the RNA-binding domain [ribonucleoprotein (RNP) domain or RNA recognition motif (RRM)] are considered to be involved in the recognition of single-stranded RNA, but the mechanisms of this recognition are poorly understood at the molecular level. For an NMR analysis of a single-stranded RNA complexed with a multi-RBD protein, residue-selective stable-isotope labeling techniques are necessary, rather than common assignment methods based on the secondary structure of RNA. In the present study, we analyzed the interaction of a Drosophila Sex-lethal (Sxl) protein fragment, consisting of two RBDs (RBD1-RBD2), with two distinct target RNAs derived from the tra and Sxl mRNA precursors with guanosine and adenosine, respectively, in a position near the 5'-terminus of a uridine stretch. First, we prepared a [5-{sup 2}H]uridine phosphoramidite, and synthesized a series of {sup 2}H-labeled RNAs, in which all of the uridine residues except one were replaced by [5-{sup 2}H]uridine in the target sequence, GU{sub 8}C. By observing the H5-H6 TOCSY cross peaks of the series of {sup 2}H-labeled RNAs complexed with the Sxl RBD1-RBD2, all of the base H5-H6 proton resonances of the target RNA were unambiguously assigned. Then, the H5-H6 cross peaks of other target RNAs, GU{sub 2}GU{sub 8}, AU{sub 8}, and UAU{sub 8}, were assigned by comparison with those of GU{sub 8}C. We found that the uridine residue prior to the G or A residue is essential for proper interaction with the protein, and that the interaction is tighter for A than for G. Moreover, the H1' resonance assignments were achieved from the H5-H6 assignments. The results revealed that all of the protein-bound nucleotide residues, except for only two, are in the unusual C2'-endo ribose conformation in the complex.

Characterization of conserved arginine residues on Cdt1 that affect licensing activity and interaction with Geminin or Mcm complex.

Science.gov (United States)

You, Zhiying; Ode, Koji L; Shindo, Mayumi; Takisawa, Haruhiko; Masai, Hisao

2016-05-02

All organisms ensure once and only once replication during S phase through a process called replication licensing. Cdt1 is a key component and crucial loading factor of Mcm complex, which is a central component for the eukaryotic replicative helicase. In higher eukaryotes, timely inhibition of Cdt1 by Geminin is essential to prevent rereplication. Here, we address the mechanism of DNA licensing using purified Cdt1, Mcm and Geminin proteins in combination with replication in Xenopus egg extracts. We mutagenized the 223th arginine of mouse Cdt1 (mCdt1) to cysteine or serine (R-S or R-C, respectively) and 342nd and 346th arginines constituting an arginine finger-like structure to alanine (RR-AA). The RR-AA mutant of Cdt1 could not only rescue the DNA replication activity in Cdt1-depleted extracts but also its specific activity for DNA replication and licensing was significantly increased compared to the wild-type protein. In contrast, the R223 mutants were partially defective in rescue of DNA replication and licensing. Biochemical analyses of these mutant Cdt1 proteins indicated that the RR-AA mutation disabled its functional interaction with Geminin, while R223 mutations resulted in ablation in interaction with the Mcm2∼7 complex. Intriguingly, the R223 mutants are more susceptible to the phosphorylation-induced inactivation or chromatin dissociation. Our results show that conserved arginine residues play critical roles in interaction with Geminin and Mcm that are crucial for proper conformation of the complexes and its licensing activity.

Spectroscopy of collective excitations in interacting low-dimensional many-body systems using quench dynamics.

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Gritsev, Vladimir; Demler, Eugene; Lukin, Mikhail; Polkovnikov, Anatoli

2007-11-16

We study the problem of rapid change of the interaction parameter (quench) in a many-body low-dimensional system. It is shown that, measuring the correlation functions after the quench, the information about a spectrum of collective excitations in a system can be obtained. This observation is supported by analysis of several integrable models and we argue that it is valid for nonintegrable models as well. Our conclusions are supplemented by performing exact numerical simulations on finite systems. We propose that measuring the power spectrum in a dynamically split 1D Bose-Einsten condensate into two coupled condensates can be used as an experimental test of our predictions.

Calculation of the hyperfine interaction using an effective-operator form of many-body theory

International Nuclear Information System (INIS)

Garpman, S.; Lindgren, I.; Lindgren, J.; Morrison, J.

1975-01-01

The effective-operator form of many-body theory is reviewed and applied to the calculation of the hyperfine structure. Numerical results are given for the 2p, 3p, and 4p excited states of Li and the 3p state of Na. This is the first complete calculation of the hyperfine structure using an effective-operator form of perturbation theory. As in the Brueckner-Goldstone form of many-body theory, the various terms in the perturbation expansion are represented by Feynman diagrams which correspond to basic physical processes. The angular part of the perturbation diagrams are evaluated by taking advantage of the formal analogy between the Feynman diagrams and the angular-momentum diagrams, introduced by Jucys et al. The radial part of the diagrams is calculated by solving one- and two-particle equations for the particular linear combination of excited states that contribute to the Feynman diagrams. In this way all second- and third-order effects are accurately evaluated without explicitly constructing the excited orbitals. For the 2p state of Li our results are in agreement with the calculations of Nesbet and of Hameed and Foley. However, our quadrupole calculation disagrees with the work of Das and co-workers. The many-body results for Li and Na are compared with semiempirical methods for evaluating the quadrupole moment from the hyperfine interaction, and a new quadrupole moment of 23 Na is given

Beliefs about emotional residue: the idea that emotions leave a trace in the physical environment.

Science.gov (United States)

Savani, Krishna; Kumar, Satishchandra; Naidu, N V R; Dweck, Carol S

2011-10-01

Drawing upon the literatures on beliefs about magical contagion and property transmission, we examined people's belief in a novel mechanism of human-to-human contagion, emotional residue. This is the lay belief that people's emotions leave traces in the physical environment, which can later influence others or be sensed by others. Studies 1-4 demonstrated that Indians are more likely than Americans to endorse a lay theory of emotions as substances that move in and out of the body, and to claim that they can sense emotional residue. However, when the belief in emotional residue is measured implicitly, both Indians and American believe to a similar extent that emotional residue influences the moods and behaviors of those who come into contact with it (Studies 5-7). Both Indians and Americans also believe that closer relationships and a larger number of people yield more detectable residue (Study 8). Finally, Study 9 demonstrated that beliefs about emotional residue can influence people's behaviors. Together, these finding suggest that emotional residue is likely to be an intuitive concept, one that people in different cultures acquire even without explicit instruction. 2011 APA, all rights reserved

A non-catalytic histidine residue influences the function of the metalloprotease of Listeria monocytogenes.

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Forster, Brian M; Bitar, Alan Pavinski; Marquis, Hélène

2014-01-01

Mpl, a thermolysin-like metalloprotease, and PC-PLC, a phospholipase C, are synthesized as proenzymes by the intracellular bacterial pathogen Listeria monocytogenes. During intracellular growth, L. monocytogenes is temporarily confined in a membrane-bound vacuole whose acidification leads to Mpl autolysis and Mpl-mediated cleavage of the PC-PLC N-terminal propeptide. Mpl maturation also leads to the secretion of both Mpl and PC-PLC across the bacterial cell wall. Previously, we identified negatively charged and uncharged amino acid residues within the N terminus of the PC-PLC propeptide that influence the ability of Mpl to mediate the maturation of PC-PLC, suggesting that these residues promote the interaction of the PC-PLC propeptide with Mpl. In the present study, we identified a non-catalytic histidine residue (H226) that influences Mpl secretion across the cell wall and its ability to process PC-PLC. Our results suggest that a positive charge at position 226 is required for Mpl functions other than autolysis. Based on the charge requirement at this position, we hypothesize that this residue contributes to the interaction of Mpl with the PC-PLC propeptide.

Exploring Interacting Quantum Many-Body Systems by Experimentally Creating Continuous Matrix Product States in Superconducting Circuits

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C. Eichler

2015-12-01

Full Text Available Improving the understanding of strongly correlated quantum many-body systems such as gases of interacting atoms or electrons is one of the most important challenges in modern condensed matter physics, materials research, and chemistry. Enormous progress has been made in the past decades in developing both classical and quantum approaches to calculate, simulate, and experimentally probe the properties of such systems. In this work, we use a combination of classical and quantum methods to experimentally explore the properties of an interacting quantum gas by creating experimental realizations of continuous matrix product states—a class of states that has proven extremely powerful as a variational ansatz for numerical simulations. By systematically preparing and probing these states using a circuit quantum electrodynamics system, we experimentally determine a good approximation to the ground-state wave function of the Lieb-Liniger Hamiltonian, which describes an interacting Bose gas in one dimension. Since the simulated Hamiltonian is encoded in the measurement observable rather than the controlled quantum system, this approach has the potential to apply to a variety of models including those involving multicomponent interacting fields. Our findings also hint at the possibility of experimentally exploring general properties of matrix product states and entanglement theory. The scheme presented here is applicable to a broad range of systems exploiting strong and tunable light-matter interactions.

Stimulation of Egg Production in Japanese Quails by Enriching Feed with Residual Yeast

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Letitia Oprean

2010-05-01

Full Text Available Quail eggs are more and more approved for consumers because they bring many benefits to the human body. Therefore, quails breeding for eggs production have become a very profitable business. Residual yeast may be a nutritional supplement, especially rich in vitamins and proteins. This article studies the influence of residual beer yeast on egg laying in Japanese quails. In order to be integrated into the diet of quails the yeast has undergone a process of autolysis; its influence has been examined on separate groups. The results were reported as a percentage compared with the control group, where the feed does not contain this supplement. Due to its content rich in vitamins and proteins, the residual beer yeast used in feeding the quails bred for eggs stimulates egg laying.

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.

Lethal critical body residues as measures of Cd, Pb, and Zn bioavailability and toxicity in the earthworm Eisenia fetida

Energy Technology Data Exchange (ETDEWEB)

Conder, J.M.; Lanno, R.P. [Oklahoma State Univ., Dept. of Zoology, Stillwater, OK (United States)

2003-07-01

Background. Earthworm heavy metal concentrations (critical body residues, CBRs) may be the most relevant measures of heavy metal bioavailability in soils and may be linkable to toxic effects in order to better assess soil ecotoxicity. However, as earthworms possess physiological mechanisms to secrete and/or sequester absorbed metals as toxicologically inactive forms, total earthworm metal concentrations may not relate well with toxicity. Objective. The objectives of this research were to: i) develop LD{sub 50}s (total earthworm metal concentration associated with 50% mortality) for Cd, Pb, and Zn; ii) evaluate the LD{sub 50} for Zn in a lethal Zn-smelter soil; iii) evaluate the lethal mixture toxicity of Cd, Pb, and Zn using earthworm metal concentrations and the toxic unit (TU) approach; and iv) evaluate total and fractionated earthworm concentrations as indicators of sublethal exposure. Methods. Earthworms (Eisenia fetida (Savigny)) were exposed to artificial soils spiked with Cd, Pb, Zn, and a Cd-Pb-Zn equitoxic mixture to estimate lethal CBRs and mixture toxicity. To evaluate the CBR developed for Zn, earthworms were also exposed to Zn-contaminated field soils receiving three different remediation treatments. Earthworm metal concentrations were measured using a procedure devised to isolate toxicologically active metal burdens via separation into cytosolic and pellet fractions. (orig.)

Interaction between an ADCY3 Genetic Variant and Two Weight-Lowering Diets Affecting Body Fatness and Body Composition Outcomes Depending on Macronutrient Distribution: A Randomized Trial

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Leticia Goni

2018-06-01

Full Text Available The adenylate cyclase 3 (ADCY3 gene is involved in the regulation of several metabolic processes including the development and function of adipose tissue. The effects of the ADCY3 rs10182181 genetic variant on changes in body composition depending on the macronutrient distribution intake after 16 weeks of the dietary intervention were tested. The ADCY3 genetic variant was genotyped in 147 overweight or obese subjects, who were randomly assigned to one of the two diets varying in macronutrient content: a moderately-high-protein diet and a low-fat diet. Anthropometric and body composition measurements (DEXA scan were recorded. Significant interactions between the ADCY3 genotype and dietary intervention on changes in weight, waist circumference, and body composition were found after adjustment for covariates. Thus, in the moderately-high-protein diet group, the G allele was associated with a lower decrease of fat mass, trunk and android fat, and a greater decrease in lean mass. Conversely, in the low-fat diet group carrying the G allele was associated with a greater decrease in trunk, android, gynoid, and visceral fat. Subjects carrying the G allele of the rs10182181 polymorphism may benefit more in terms of weight loss and improvement of body composition measurements when undertaking a hypocaloric low-fat diet as compared to a moderately-high-protein diet.

Determination of Activated Carbon Residual Life using a Microwave Cavity Resonator

International Nuclear Information System (INIS)

Mason, A; Wylie, S; Shaw, A; Al-Shamma'a, A I; Thomas, A; Keele, H

2011-01-01

This paper presents the continuation of work conducted jointly between Dstl and LJMU. This unique body of work has been, largely, concerned with detecting the residual life of high performance filter materials using electromagnetic (EM) waves within a resonant cavity. Past work has considered both HEPA [1] and ASZM-TEDA[2] activated carbon filter materials. This paper continues the later work, considering the response of ASZM-TEDA activated carbon through the co-ageing of two distinct batches of the material. The paper briefly introduces activated carbon, discusses theory relevant to the work and the methodology used for investigation. A comprehensive set of results is included which seek to validate this technique for determining the residual lifespan of activated carbon.

Initial contents of residue quality parameters predict effects of larger soil fauna on decomposition of contrasting quality residues

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Ratikorn Sanghaw

2017-10-01

Full Text Available A 52-week decomposition study employing the soil larger fauna exclusion technique through litter bags of two mesh sizes (20 and 0.135 mm was conducted in a long-term (18 yr field experiment. Organic residues of contrasting quality of N, lignin (L, polyphenols (PP and cellulose (CL all in grams per kilogram: rice straw (RS: 4.5N, 22.2L, 3.9PP, 449CL, groundnut stover (GN: 21.2N, 71.4L, 8.1PP, 361CL, dipterocarp leaf litter (DP: 5.1N, 303L, 68.9PP, 271CL and tamarind leaf litter (TM: 11.6N, 190L, 27.7PP, 212CL were applied to soil annually to assess and predict soil larger fauna effects (LFE on decomposition based on the initial contents of the residue chemical constituents. Mass losses in all residues were not different under soil fauna inclusion and exclusion treatments during the early stage (up to week 4 after residue incorporation but became significantly higher under the inclusion than the exclusion treatments during the later stage (week 8 onwards. LFE were highest (2–51% under the resistant DP at most decomposition stages. During the early stage (weeks 1–4, both the initial contents of labile (N and CL and recalcitrant C, and recalcitrant C interaction with labile constituents of residues showed significant correlations (r = 0.64–0.90 with LFE. In the middle stage (week 16, LFE under resistant DP and TM had significant positive correlations with L, L + PP and L/CL. They were also affected by these quality parameters as shown by the multiple regression analysis. In the later stages (weeks 26–52, the L/CL ratio was the most prominent quality parameter affecting LFE. Keywords: Mesofauna and macrofauna, Microorganisms, Recalcitrant and labile compounds, Residue chemical composition, Tropical sandy soil

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

Identification of residues on human receptor DPP4 critical for MERS-CoV binding and entry

Energy Technology Data Exchange (ETDEWEB)

Song, Wenfei [Ministry of Education Key Laboratory of Protein Science, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084 (China); Wang, Ying [Comprehensive AIDS Research Center, Research Center for Public Health, School of Medicine, Tsinghua University, Beijing 100084 (China); Wang, Nianshuang; Wang, Dongli [Ministry of Education Key Laboratory of Protein Science, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084 (China); Guo, Jianying; Fu, Lili [Comprehensive AIDS Research Center, Research Center for Public Health, School of Medicine, Tsinghua University, Beijing 100084 (China); Shi, Xuanling, E-mail: shixuanlingsk@tsinghua.edu.cn [Comprehensive AIDS Research Center, Research Center for Public Health, School of Medicine, Tsinghua University, Beijing 100084 (China)

2014-12-15

Middle East respiratory syndrome coronavirus (MERS-CoV) infects host cells through binding the receptor binding domain (RBD) on its spike glycoprotein to human receptor dipeptidyl peptidase 4 (hDPP4). Here, we report identification of critical residues on hDPP4 for RBD binding and virus entry through analysis of a panel of hDPP4 mutants. Based on the RBD–hDPP4 crystal structure we reported, the mutated residues were located at the interface between RBD and hDPP4, which potentially changed the polarity, hydrophobic or hydrophilic properties of hDPP4, thereby interfering or disrupting their interaction with RBD. Using surface plasmon resonance (SPR) binding analysis and pseudovirus infection assay, we showed that several residues in hDPP4–RBD binding interface were important on hDPP4–RBD binding and viral entry. These results provide atomic insights into the features of interactions between hDPP4 and MERS-CoV RBD, and also provide potential explanation for cellular and species tropism of MERS-CoV infection. - Highlights: • It has been demonstrated that MERS-CoV infects host cells through binding its envelope spike (S) glycoprotein to the host cellular receptor dipeptidyl peptidase 4 (DPP4). • To identify the critical residues on hDPP4 for RBD binding and virus entry, we constructed a panel of hDPP4 mutants based on structure-guided mutagenesis. • Using surface plasmon resonance (SPR) binding analysis and pseudovirus infection assay, we showed that several residues on hDPP4 had significant impacts on virus/receptor interactions and viral entry. • Our study has provided new insights into the features of interactions between hDPP4 and MERS-CoV RBD, and provides potential explanation for cellular and species tropism of MERS-CoV infection.

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

DEFF Research Database (Denmark)

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

2005-01-01

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

the foundation of anthropometry and body composition

African Journals Online (AJOL)

method, and, in the case of infants and children, growth monitoring is ... should be remembered that that BMI as such is not the determinant of health and disease. ... regressed on BMI, the standard deviation of residuals is considerable: about 3.2kg. ... to be considered here, including short-term (within-day) body weight.

Residual stresses measurement by using ring-core method and 3D digital image correlation technique

International Nuclear Information System (INIS)

Hu, Zhenxing; Xie, Huimin; Zhu, Jianguo; Wang, Huaixi; Lu, Jian

2013-01-01

Ring-core method/three-dimensional digital image correlation (3D DIC) residual stresses measurement is proposed. Ring-core cutting is a mechanical stress relief method, and combining with 3D DIC system the deformation of the specimen surface can be measured. An optimization iteration method is proposed to obtain the residual stress and rigid-body motion. The method has the ability to cut an annular trench at a different location out of the field of view. A compression test is carried out to demonstrate how residual stress is determined by using 3D DIC system and outfield measurement. The results determined by the approach are in good agreement with the theoretical value. Ring-core/3D DIC has shown its robustness to determine residual stress and can be extended to application in the engineering field. (paper)

Experimental evaluation of pumpjet propulsor for an axisymmetric body in wind tunnel

Directory of Open Access Journals (Sweden)

Ch. Suryanarayana

2010-03-01

Full Text Available Design of a Pump Jet Propulsor (PJP was undertaken for an underwater body with axisymmetric configuration using axial flow compressor design techniques supported by Computational Fluid Dynamics (CFD analysis for performance prediction. Experimental evaluation of the PJP was carried out through experiments in a Wind Tunnel Facility (WTF using momentum defect principle for propulsive performance prior to proceeding with extensive experimental evaluation in towing tank and cavitation tunnel. Experiments were particularly conducted with respect to Self Propulsion Point (SPP, residual torque and thrust characteristics over a range of vehicle advance ratio in order to ascertain whether sufficient thrust is developed at the design condition with least possible imbalance torque left out due to residual swirl in the slip stream. Pumpjet and body models were developed for the propulsion tests using Aluminum alloy forged material. Tests were conducted from 0 m/s to 30 m/s at four rotational speeds of the PJP. SPP was determined confirming the thrust development capability of PJP. Estimation of residual torque was carried out at SPP corresponding to speeds of 15, 20 and 25 m/s to examine the effectiveness of the stator. Estimation of thrust and residual torque was also carried out at wind speeds 0 and 6 m/s for PJP RPMs corresponding to self propulsion tests to study the propulsion characteristics during the launch of the vehicle in water where advance ratios are close to Zero. These results are essential to assess the thrust performance at very low advance ratios to accelerate the body and to control the body during initial stages. This technique has turned out to be very useful and economical method for quick assessment of overall performance of the propulsor and generation of exhaustive fluid dynamic data to validate CFD techniques employed.

Chaperone-like activity of β-casein and its effect on residual in vitro activity of horseradish peroxidase

DEFF Research Database (Denmark)

Sulewska, Anna Maria; Olsen, Karsten; Sørensen, Jens Christian

2014-01-01

, as similar experiment with bovine serum albumin resulted in residual activity of horseradish peroxidase that was significantly lower than without any addition. The effect of β-casein on HRP disappears when pH is below the isoelectric point of β-casein. It was also proven by light scattering studies that β...... proteins. Incubating HRP (0.1 mg mL-1) for 10 min at 72 °C resulted in residual activity of 59 ± 5%, while addition of 1 mg mL-1 β-casein resulted in increase in residual activity up to 85 ± 1%. Increased residual activity is not merely attributed to an effect of higher total protein concentration......-casein interacts with horseradish peroxidase when the temperature was increased from 25 to 70 °C whereas interactions seem to cease when temperature was lowered back to 25 °C. This study highlights how specific proteins can influence enzyme activity, which is of potential importance for various industries...

The interaction of fatigue cracks with a residual stress field using thermoelastic stress analysis and synchrotron X-ray diffraction experiments

Science.gov (United States)

Amjad, Khurram; Asquith, David; Sebastian, Christopher M.; Wang, Wei-Chung

2017-01-01

This article presents an experimental study on the fatigue behaviour of cracks emanating from cold-expanded holes utilizing thermoelastic stress analysis (TSA) and synchrotron X-ray diffraction (SXRD) techniques with the aim of resolving the long-standing ambiguity in the literature regarding potential relaxation, or modification, of beneficial compressive residual stresses as a result of fatigue crack propagation. The crack growth rates are found to be substantially lower as the crack tip moved through the residual stress zone induced by cold expansion. The TSA results demonstrated that the crack tip plastic zones were reduced in size by the presence of the residual compressive stresses induced by cold expansion. The crack tip plastic zones were found to be insignificant in size in comparison to the residual stress zone resulting from cold expansion, which implied that they were unlikely to have had a notable impact on the surrounding residual stresses induced by cold expansion. The residual stress distributions measured along the direction of crack growth, using SXRD, showed no signs of any significant stress relaxation or redistribution, which validates the conclusions drawn from the TSA data. Fractographic analysis qualitatively confirmed the influence on crack initiation of the residual stresses induced by the cold expansion. It was found that the application of single compressive overload caused a relaxation, or reduction in the residual stresses, which has wider implications for improving the fatigue life. PMID:29291095

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

International Nuclear Information System (INIS)

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

2003-01-01

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

Classifying a Person's Degree of Accessibility From Natural Body Language During Social Human-Robot Interactions.

Science.gov (United States)

McColl, Derek; Jiang, Chuan; Nejat, Goldie

2017-02-01

For social robots to be successfully integrated and accepted within society, they need to be able to interpret human social cues that are displayed through natural modes of communication. In particular, a key challenge in the design of social robots is developing the robot's ability to recognize a person's affective states (emotions, moods, and attitudes) in order to respond appropriately during social human-robot interactions (HRIs). In this paper, we present and discuss social HRI experiments we have conducted to investigate the development of an accessibility-aware social robot able to autonomously determine a person's degree of accessibility (rapport, openness) toward the robot based on the person's natural static body language. In particular, we present two one-on-one HRI experiments to: 1) determine the performance of our automated system in being able to recognize and classify a person's accessibility levels and 2) investigate how people interact with an accessibility-aware robot which determines its own behaviors based on a person's speech and accessibility levels.

FIB-based measurement of local residual stresses on microsystems

Science.gov (United States)

Vogel, Dietmar; Sabate, Neus; Gollhardt, Astrid; Keller, Juergen; Auersperg, Juergen; Michel, Bernd

2006-03-01

The paper comprises research results obtained for stress determination on micro and nanotechnology components. It meets the concern of controlling stresses introduced to sensors, MEMS and electronics devices during different micromachining processes. The method bases on deformation measurement options made available inside focused ion beam equipment. Removing locally material by ion beam milling existing stresses / residual stresses lead to deformation fields around the milled feature. Digital image correlation techniques are used to extract deformation values from micrographs captured before and after milling. In the paper, two main milling features have been analyzed - through hole and through slit milling. Analytical solutions for stress release fields of in-plane stresses have been derived and compared to respective experimental findings. Their good agreement allows to settle a method for determination of residual stress values, which is demonstrated for thin membranes manufactured by silicon micro technology. Some emphasis is made on the elimination of main error sources for stress determination, like rigid body object displacements and rotations due to drifts of experimental conditions under FIB imaging. In order to illustrate potential application areas of the method residual stress suppression by ion implantation is evaluated by the method and reported here.

Assessment of elimination profile of albendazole residues in fish.

Science.gov (United States)

Busatto, Zenaís; de França, Welliton Gonçalves; Cyrino, José Eurico Possebon; Paschoal, Jonas Augusto Rizzato

2018-01-01

Few drugs are specifically regulated for aquaculture. Thus this study considered albendazole (ABZ) as a potential drug for use in fish, which, however, is not yet regulated for this application. ABZ is a broad-spectrum anthelmintic approved for farmed ruminants and recently considered for treatment of fish parasites. It is the subject of careful monitoring because of potential residues in animal products. This study evaluated the depletion of ABZ and its main known metabolites: albendazole sulfoxide - ABZSO, albendazole sulfone - ABZSO 2 and albendazole amino sulfone - ABZ-2-NH 2 SO 2 , in the fillets of the Neotropical Characin pacu, Piaractus mesopotamicus, which were fed diets containing 10 mg ABZ kg -1 body weight in a single dose. Fish were euthanised at 8, 12, 24, 48, 72, 96 and 120 hours after medication and the depletion profiles of ABZ, each metabolite and the sum of all marker residues were assessed and evaluated taking into account methodological variations regarding determination of the maximum residue limits adopted by different international regulating agencies for estimation of the withdrawal period (WP). The estimated WPs ranged from 2 to 7 days.

InterProSurf: a web server for predicting interacting sites on protein surfaces

Science.gov (United States)

Negi, Surendra S.; Schein, Catherine H.; Oezguen, Numan; Power, Trevor D.; Braun, Werner

2009-01-01

Summary A new web server, InterProSurf, predicts interacting amino acid residues in proteins that are most likely to interact with other proteins, given the 3D structures of subunits of a protein complex. The prediction method is based on solvent accessible surface area of residues in the isolated subunits, a propensity scale for interface residues and a clustering algorithm to identify surface regions with residues of high interface propensities. Here we illustrate the application of InterProSurf to determine which areas of Bacillus anthracis toxins and measles virus hemagglutinin protein interact with their respective cell surface receptors. The computationally predicted regions overlap with those regions previously identified as interface regions by sequence analysis and mutagenesis experiments. PMID:17933856

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

Science.gov (United States)

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

2016-05-01

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

Electrically and mechanically induced macroscopic body couple, a newly recognized phenomenon of electromechanical interaction

International Nuclear Information System (INIS)

Chen, P.J.

1986-01-01

Microscopically, when the molecules of certain materials are under the influence of external stimuli such as mechanical and electrical forces, several processes can happen. In particular, the centers of charge of the positive and negative ions of a molecule may displace with respect to each other. This notion leads to the macroscopic concept of polarization which has been exploited in the classical studies of piezoelectric and ferroelectric materials. In addition, the ions of the molecule may also rotate angularly relative to one another. Here an entirely new macroscopic concept of body couple which differs from the classical concept is introduced. It is shown that the simplest representations of the proposed constitutive relations lead to an equation within the context of the classical bending theory of thin plates whose solution is in remarkable agreement with recent experimental results concerning the bending of thin virgin ferroelectric ceramic discs under the action of small d.c. voltages. These experimental results cannot be explained by the classical notion of polarization. Therefore, the concept of macroscopic body couple introduced here is a fundamental feature which must be taken into account in the considerations of electromechanical interactions

Short-tailed shrews: Toxicity and residue relationships of DDT, dieldrin, and endrin

Science.gov (United States)

Blus, L.J.

1978-01-01

Experiments involving dietary toxicity and residue relationships of DDT, dieldrin, and endrin were conducted with short-tailed shrews. Dietary concentrations of DDT dissolved in vegetable oils were usually more toxic than diets containing comparable amounts of powdered DDT. Younger shrews, particularly females, were more tolerant of powdered DDT than older animals; yet, there were no conspicuous age differences in toxicity of DDT dissolved in oils. In comparison to other mammals, short-tailed shrews are not unusually sensitive to DDT, dieldrin, or endrin on the basis of two-week feeding tests. The influence of age and sex on toxicity of DDT, endrin, and dieldrin was sometimes more important than body weight. Of those shrews of the same age and sex that were fed the same dietary dosage, heavier shrews were more tolerant than lighter individuals; and, heavier shrews tended to lose a greater percentage of body weight before death. There was a range of 15 to 105 DDT equivalents in brains of shrews dying on dietary dosages of DDT. Six shrews fed a high level of DDT seemed to have unusual metabolite capabilities and died with apparent lethal levels of DDD in their brains. Levels of dieldrin in brains of shrews that died on a dietary dosage of dieldrin ranged from 3.7 to 12.6 ppm. In the rates of gain and loss experiments where shrews were given diets containing 400 ppm DDT or 50 ppm dieldrin up to 17 days, high residues were noted in tissues of shrews after two weeks on a contaminated diet and a few died at that time. After shrews were placed on clean food, it was determined that >50% of the dieldrin residues in carcass and brain were lost in 50% of residues of DDT and metabolites in brains after 2 weeks on clean food; males lost nearly 50% of residues in carcasses after two weeks on clean food compared with a loss of only 11% in females.

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

Science.gov (United States)

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

1995-01-01

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

A bacteriophages journey through the human body.

Science.gov (United States)

Barr, Jeremy J

2017-09-01

The human body is colonized by a diverse collective of microorganisms, including bacteria, fungi, protozoa and viruses. The smallest entity of this microbial conglomerate are the bacterial viruses. Bacteriophages, or phages for short, exert significant selective pressure on their bacterial hosts, undoubtedly influencing the human microbiome and its impact on our health and well-being. Phages colonize all niches of the body, including the skin, oral cavity, lungs, gut, and urinary tract. As such our bodies are frequently and continuously exposed to diverse collections of phages. Despite the prevalence of phages throughout our bodies, the extent of their interactions with human cells, organs, and immune system is still largely unknown. Phages physically interact with our mucosal surfaces, are capable of bypassing epithelial cell layers, disseminate throughout the body and may manipulate our immune system. Here, I establish the novel concept of an "intra-body phageome," which encompasses the collection of phages residing within the classically "sterile" regions of the body. This review will take a phage-centric view of the microbiota, human body, and immune system with the ultimate goal of inspiring a greater appreciation for both the indirect and direct interactions between bacteriophages and their mammalian hosts. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Functional validation of Ca2+-binding residues from the crystal structure of the BK ion channel.

Science.gov (United States)

Kshatri, Aravind S; Gonzalez-Hernandez, Alberto J; Giraldez, Teresa

2018-04-01

BK channels are dually regulated by voltage and Ca 2+ , providing a cellular mechanism to couple electrical and chemical signalling. Intracellular Ca 2+ concentration is sensed by a large cytoplasmic region in the channel known as "gating ring", which is formed by four tandems of regulator of conductance for K + (RCK1 and RCK2) domains. The recent crystal structure of the full-length BK channel from Aplysia californica has provided new information about the residues involved in Ca 2+ coordination at the high-affinity binding sites located in the RCK1 and RCK2 domains, as well as their cooperativity. Some of these residues have not been previously studied in the human BK channel. In this work we have investigated, through site directed mutagenesis and electrophysiology, the effects of these residues on channel activation by voltage and Ca 2+ . Our results demonstrate that the side chains of two non-conserved residues proposed to coordinate Ca 2+ in the A. californica structure (G523 and E591) have no apparent functional role in the human BK Ca 2+ sensing mechanism. Consistent with the crystal structure, our data indicate that in the human channel the conserved residue R514 participates in Ca 2+ coordination in the RCK1 binding site. Additionally, this study provides functional evidence indicating that R514 also interacts with residues E902 and Y904 connected to the Ca 2+ binding site in RCK2. Interestingly, it has been proposed that this interaction may constitute a structural correlate underlying the cooperative interactions between the two high-affinity Ca 2+ binding sites regulating the Ca 2+ dependent gating of the BK channel. This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain. Copyright © 2017 Elsevier B.V. All rights reserved.

The effects of beta-adrenergic blockade on body composition in free-fed and diet-restricted rats.

Science.gov (United States)

Ji, L L; Doan, T D; Lennon, D L; Nagle, F J; Lardy, H A

1987-04-01

The effects of the non-selective beta-adrenergic blocking agent propranolol (known for its anti-lipolytic activity) on body composition were investigated in growing male rats on normal unrestricted diet (N = 7) and on diet restriction (N = 7, 95% of controls). Three animals in each group were injected i.p. with 30 mg propranolol per kg body weight (bw) dissolved in saline, 5 days/week. This dose attenuates exercising heart rate by 25% and exercise training-induced enzyme activity. The remaining animals received saline. Fat, glycogen, moisture and non-ether extractable residue were determined in the homogenized residue of the whole animal. After 9 weeks on the experimental regimen, bw gain was significantly lower in the diet restricted rats, whereas propranolol had no effect on the bw gain. The percentage of fat, moisture and non-ether extractable residue were unchanged by either propranolol or diet restriction. However, glycogen content was significantly lower in the beta-blocked rats either with or without diet restriction. These data indicated that neither beta-adrenergic blockade nor minimal diet restriction influences the percentage body fat, whereas body glycogen content is decreased under both conditions.

Final Report - Few-Body Studies Using Electromagnetic Interactions

Energy Technology Data Exchange (ETDEWEB)

Norum, Blaine [Univ. of Virginia, Charlottesville, VA (United States). Dept. of Physics

2018-01-25

The work discussed here is an extension of work previously funded by U.S. Department of Energy Grant DE-FG02-97ER41025. Measurements of charged pion photoproduction from deuterium using the Laser Electron Gamma Source (LEGS) at the Brookhaven National Laboratory previously made by us, as members of the LEGS Collaboration, resulted in the most interesting result of two decades of work. By measuring the production of a charged pion (π⁺) in coincidence with an emitted photon we observed structures in the residual two-nucleon system. These indicated the existence of rare, long-lived states not explicable by standard nuclear theory; they suggested a set of configurations not explicable in terms of a nucleon-nucleon pair. The existence of such “exotic” structures has formed the foundation for most of the work that has ensued. Several measurements at various laboratories have supported, but not proved, the existence of these exotic states. The rarity of these states made their existence undetectable in most previous measurements. Only by observing characteristic signatures of such states (i.e., decay photons), by using very specific kinematics which isolate certain reaction products, or by measuring polarization-dependent observables. During the period of this grant we pursued and made progress on the development of experiments to be performed at the High Intensity Gamma Source (HIGS) of the Tri Universities Nuclear Laboratory (TUNL). Our understanding of photon- and electron-induced nuclear reactions depends on understanding of the basic electron and photon interaction. Recently, the issue of two-photon contributions has arisen in the context of deeply inelastic electron scattering. One way to address this is to measure asymmetries in the Bethe-Heitler ee process. We also made progress in developing the detectors required to measure these asymmetries at HIGS. During the last several years the apparent discrepancy between the size of the proton as measured

Interactions between charged residues in the transmembrane segments of the voltage-sensing domain in the hERG channel.

Science.gov (United States)

Zhang, M; Liu, J; Jiang, M; Wu, D-M; Sonawane, K; Guy, H R; Tseng, G-N

2005-10-01

Studies on voltage-gated K channels such as Shaker have shown that positive charges in the voltage-sensor (S4) can form salt bridges with negative charges in the surrounding transmembrane segments in a state-dependent manner, and different charge pairings can stabilize the channels in closed or open states. The goal of this study is to identify such charge interactions in the hERG channel. This knowledge can provide constraints on the spatial relationship among transmembrane segments in the channel's voltage-sensing domain, which are necessary for modeling its structure. We first study the effects of reversing S4's positive charges on channel activation. Reversing positive charges at the outer (K525D) and inner (K538D) ends of S4 markedly accelerates hERG activation, whereas reversing the 4 positive charges in between either has no effect or slows activation. We then use the 'mutant cycle analysis' to test whether D456 (outer end of S2) and D411 (inner end of S1) can pair with K525 and K538, respectively. Other positive charges predicted to be able, or unable, to interact with D456 or D411 are also included in the analysis. The results are consistent with predictions based on the distribution of these charged residues, and confirm that there is functional coupling between D456 and K525 and between D411 and K538.

Extending the Body for Interaction with Reality

DEFF Research Database (Denmark)

Feuchtner, Tiare; Müller, Jörg

2017-01-01

In this paper, we explore how users can control remote devices with a virtual long arm, while preserving the perception that the artificial arm is actually part of their own body. Instead of using pointing, speech, or a remote control, the users’ arm is extended in augmented reality, allowing...

Positive and negative ion mode comparison for the determination of DNA/peptide noncovalent binding sites through the formation of "three-body" noncovalent fragment ions.

Science.gov (United States)

Brahim, Bessem; Tabet, Jean-Claude; Alves, Sandra

2018-02-01

Gas-phase fragmentation of single strand DNA-peptide noncovalent complexes is investigated in positive and negative electrospray ionization modes.Collision-induced dissociation experiments, performed on the positively charged noncovalent complex precursor ions, have confirmed the trend previously observed in negative ion mode, i.e. a high stability of noncovalent complexes containing very basic peptidic residues (i.e. R > K) and acidic nucleotide units (i.e. Thy units), certainly incoming from the existence of salt bridge interactions. Independent of the ion polarity, stable noncovalent complex precursor ions were found to dissociate preferentially through covalent bond cleavages of the partners without disrupting noncovalent interactions. The resulting DNA fragment ions were found to be still noncovalently linked to the peptides. Additionally, the losses of an internal nucleic fragment producing "three-body" noncovalent fragment ions were also observed in both ion polarities, demonstrating the spectacular salt bridge interaction stability. The identical fragmentation patterns (regardless of the relative fragment ion abundances) observed in both polarities have shown a common location of salt bridge interaction certainly preserved from solution. Nonetheless, most abundant noncovalent fragment ions (and particularly three-body ones) are observed from positively charged noncovalent complexes. Therefore, we assume that, independent of the preexisting salt bridge interaction and zwitterion structures, multiple covalent bond cleavages from single-stranded DNA/peptide complexes rely on an excess of positive charges in both electrospray ionization ion polarities.

Advancing environmental toxicology through chemical dosimetry: External exposures versus tissue residues

Science.gov (United States)

McCarty, L.S.; Landrum, P.F.; Luoma, S.N.; Meador, J.P.; Merten, A.A.; Shephard, B.K.; van Wezelzz, A.P.

2011-01-01

The tissue residue dose concept has been used, although in a limited manner, in environmental toxicology for more than 100 y. This review outlines the history of this approach and the technical background for organic chemicals and metals. Although the toxicity of both can be explained in tissue residue terms, the relationship between external exposure concentration, body and/or tissues dose surrogates, and the effective internal dose at the sites of toxic action tends to be more complex for metals. Various issues and current limitations related to research and regulatory applications are also examined. It is clear that the tissue residue approach (TRA) should be an integral component in future efforts to enhance the generation, understanding, and utility of toxicity testing data, both in the laboratory and in the field. To accomplish these goals, several key areas need to be addressed: 1) development of a risk-based interpretive framework linking toxicology and ecology at multiple levels of biological organization and incorporating organism-based dose metrics; 2) a broadly applicable, generally accepted classification scheme for modes/mechanisms of toxic action with explicit consideration of residue information to improve both single chemical and mixture toxicity data interpretation and regulatory risk assessment; 3) toxicity testing protocols updated to ensure collection of adequate residue information, along with toxicokinetics and toxicodynamics information, based on explicitly defined toxicological models accompanied by toxicological model validation; 4) continued development of residueeffect databases is needed ensure their ongoing utility; and 5) regulatory guidance incorporating residue-based testing and interpretation approaches, essential in various jurisdictions. ??:2010 SETAC.

The role and effect of residual stress on pore generation during anodization of aluminium thin films

International Nuclear Information System (INIS)

Liao, M.W.; Chung, C.K.

2013-01-01

Highlights: •Al films of varying residual stress were prepared by sputtering. •Variation of the residual stress in the Al films influences pore growth during anodization. •The change in average pore size with residual stress is fairly small. •Interaction of residual stress with oxide growth stress leads to change in structure. •Residual tensile stress increases the pore density of porous alumina. -- Abstract: The role and effect of residual stress on pore generation of anodized aluminium oxide (AAO) have been investigated into anodizing the various-residual-stresses aluminium films. The plane stresses were characterised by X-ray diffraction with sin 2 ψ method. The pore density roughly linearly increased with residual stress from 64.6 (−132.5 MPa) to 90.5 pores/μm 2 (135.9 MPa). However, the average pore size around 40 nm was not changed significantly except for the rougher film. The tensile residual stress lessened the compressive oxide growth stress to reduce AAO plastic deformation for higher pore density. The findings provide new foundations for realizing AAO films on silicon

KFC Server: interactive forecasting of protein interaction hot spots.

Science.gov (United States)

Darnell, Steven J; LeGault, Laura; Mitchell, Julie C

2008-07-01

The KFC Server is a web-based implementation of the KFC (Knowledge-based FADE and Contacts) model-a machine learning approach for the prediction of binding hot spots, or the subset of residues that account for most of a protein interface's; binding free energy. The server facilitates the automated analysis of a user submitted protein-protein or protein-DNA interface and the visualization of its hot spot predictions. For each residue in the interface, the KFC Server characterizes its local structural environment, compares that environment to the environments of experimentally determined hot spots and predicts if the interface residue is a hot spot. After the computational analysis, the user can visualize the results using an interactive job viewer able to quickly highlight predicted hot spots and surrounding structural features within the protein structure. The KFC Server is accessible at http://kfc.mitchell-lab.org.

Effects of muscle dysmorphia, social comparisons and body schema priming on desire for social interaction: an experimental approach.

Science.gov (United States)

Schneider, Catharina; Agthe, Maria; Yanagida, Takuya; Voracek, Martin; Hennig-Fast, Kristina

2017-06-15

Muscle dysmorphia (MD) is a relatively young diagnosis referring to the desire for a high degree in lean muscle mass, while simultaneously believing that one is insufficiently muscular, mostly found in men. It goes along with a risk for social withdrawal to maintain rigid exercise and dietary regimen. The aim of the current study was thus, to explore differences in men with and without a risk for muscle dysmorphia regarding their desire for social interaction. Furthermore, we investigated potential effects of individual social comparison tendencies (the tendency to compare oneself with persons who are perceived to be superior or inferior to oneself on a certain dimension) and of one's own body schema on the desire for social interaction. One hundred physically active, college aged Austrian men were recruited via social media and flyers at fitness centers and the sports department of the University of Vienna. Participants were randomly assigned to a priming condition evoking their own body schema or a control condition and had to state their desire for social interaction with male or female stimulus persons of high or average attractiveness. We conducted a 2 (group of participant; men with vs. without a risk for MD) × 2 (priming condition; priming vs. non-priming) × 2 (attractiveness of stimulus person; highly attractive vs. less attractive) experimental design with different social comparison tendencies as covariates. Men with a risk for muscle dysmorphia showed lesser desire for social interaction than men without this risk, which can be seen as a risk factor for psychopathological outcomes. Generally, men with and without a risk for muscle dysmorphia did not differ with regard to their preferences for attractive stimulus persons as subjects for social interaction. We confirmed the notion that a tendency for downward social comparisons goes along with a diminished desire for social interaction. This study showed that men with a risk for muscle dysmorphia

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

Antipyretic Therapy in Critically Ill Patients with Sepsis: An Interaction with Body Temperature

Science.gov (United States)

Zhang, Zhongheng; Chen, Lin; Ni, Hongying

2015-01-01

Background and Objective The effect of antipyretic therapy on mortality in patients with sepsis remains undetermined. The present study aimed to investigate the role of antipyretic therapy in ICU patients with sepsis by using a large clinical database. Methods The multiparameter intelligent monitoring in intensive care II (MIMIC- II) database was employed for the study. Adult patients with sepsis were included for analysis. Antipyretic therapy included antipyretic medication and external cooling. Multivariable model with interaction terms were employed to explore the association of antipyretic therapy and mortality risk. Main Results A total of 15,268 patients fulfilled inclusion criteria and were included in the study. In multivariable model by treating temperature as a continuous variable, there was significant interaction between antipyretic therapy and the maximum temperature (Tmax). While antipyretic therapy had no significant effect on mortality in low temperature quintiles, antipyretic therapy was associated with increased risk of death in the quintile with body temperature >39°C (OR: 1.29, 95% CI: 1.04–1.61). Conclusion Our study shows that there is no beneficial effect on reducing mortality risk with the use of antipyretic therapy in ICU patients with sepsis. External cooling may even be harmful in patients with sepsis. PMID:25822614

Interaction study of rice stripe virus proteins reveals a region of the nucleocapsid protein (NP) required for NP self-interaction and nuclear localization.

Science.gov (United States)

Lian, Sen; Cho, Won Kyong; Jo, Yeonhwa; Kim, Sang-Min; Kim, Kook-Hyung

2014-04-01

Rice stripe virus (RSV), which belongs to the genus Tenuivirus, is an emergent virus problem. The RSV genome is composed of four single-strand RNAs (RNA1-RNA4) and encodes seven proteins. We investigated interactions between six of the RSV proteins by yeast-two hybrid (Y2H) assay in vitro and by bimolecular fluorescence complementation (BiFC) in planta. Y2H identified self-interaction of the nucleocapsid protein (NP) and NS3, while BiFC revealed self-interaction of NP, NS3, and NCP. To identify regions(s) and/or crucial amino acid (aa) residues required for NP self-interaction, we generated various truncated and aa substitution mutants. Y2H assay showed that the N-terminal region of NP (aa 1-56) is necessary for NP self-interaction. Further analysis with substitution mutants demonstrated that additional aa residues located at 42-47 affected their interaction with full-length NP. These results indicate that the N-terminal region (aa 1-36 and 42-47) is required for NP self-interaction. BiFC and co-localization studies showed that the region required for NP self-interaction is also required for NP localization at the nucleus. Overall, our results indicate that the N-terminal region (aa 1-47) of the NP is important for NP self-interaction and that six aa residues (42-47) are essential for both NP self-interaction and nuclear localization. Copyright © 2014 Elsevier B.V. All rights reserved.

Numerically exact dynamics of the interacting many-body Schroedinger equation for Bose-Einstein condensates. Comparison to Bose-Hubbard and Gross-Pitaevskii theory

Energy Technology Data Exchange (ETDEWEB)

Sakmann, Kaspar

2010-07-21

In this thesis, the physics of trapped, interacting Bose-Einstein condensates is analyzed by solving the many-body Schroedinger equation. Particular emphasis is put on coherence, fragmentation and reduced density matrices. First, the ground state of a trapped Bose-Einstein condensate and its correlation functions are obtained. Then the dynamics of a bosonic Josephson junction is investigated by solving the time-dependent many-body Schroedinger equation numerically exactly. These are the first exact results in literature in this context. It is shown that the standard approximations of the field, Gross-Pitaevskii theory and the Bose-Hubbard model fail at weak interaction strength and within their range of expected validity. For stronger interactions the dynamics becomes strongly correlated and a new equilibration phenomenon is discovered. By comparison with exact results it is shown that a symmetry of the Bose- Hubbard model between attractive and repulsive interactions must be considered an artefact of the model. A conceptual innovation of this thesis are time-dependent Wannier functions. Equations of motion for time-dependent Wannier functions are derived from the variational principle. By comparison with exact results it is shown that lattice models can be greatly improved at little computational cost by letting the Wannier functions of a lattice model become time-dependent. (orig.)

A unified momentum equation approach for computing thermal residual stresses during melting and solidification

Science.gov (United States)

Yeo, Haram; Ki, Hyungson

2018-03-01

In this article, we present a novel numerical method for computing thermal residual stresses from a viewpoint of fluid-structure interaction (FSI). In a thermal processing of a material, residual stresses are developed as the material undergoes melting and solidification, and liquid, solid, and a mixture of liquid and solid (or mushy state) coexist and interact with each other during the process. In order to accurately account for the stress development during phase changes, we derived a unified momentum equation from the momentum equations of incompressible fluids and elastoplastic solids. In this approach, the whole fluid-structure system is treated as a single continuum, and the interaction between fluid and solid phases across the mushy zone is naturally taken into account in a monolithic way. For thermal analysis, an enthalpy-based method was employed. As a numerical example, a two-dimensional laser heating problem was considered, where a carbon steel sheet was heated by a Gaussian laser beam. Momentum and energy equations were discretized on a uniform Cartesian grid in a finite volume framework, and temperature-dependent material properties were used. The austenite-martensite phase transformation of carbon steel was also considered. In this study, the effects of solid strains, fluid flow, mushy zone size, and laser heating time on residual stress formation were investigated.

Effect of inorganic chelate of zinc and restaurant residual oil added ...

African Journals Online (AJOL)

Effect of inorganic chelate of zinc and restaurant residual oil added to feed mixture ... The interaction effects of RRO and ZnO did not result to a significant change in ... Therefore, the effects of RRO deteriorated the quality of meat by raising the ...

Identification and quantification of pesticide residues in water samples of Dhamrai Upazila, Bangladesh

Science.gov (United States)

Hasanuzzaman, M.; Rahman, M. A.; Salam, M. A.

2017-10-01

Being agricultural country, different types of pesticides are widely used in Bangladesh to prevent the crop losses due to pest attack which are ultimately drain to the water bodies. The present study was conducted to identify and quantify the organochlorine (DDT, DDE and DDD), organophosphorus (malathion, diazinon and chloropyrifos) and carbamate (carbaryl) residues in water samples of different sources from Dhamrai upazila of Bangladesh using high performance liquid chromatography (HPLC) equipped with ultra violate (UV) detector. Thirty water samples from fish pond, cultivated land and tube-well were collected in winter season to analyze the pesticide residues. Among the organophosphorus pesticides, malathion was present in seven water samples ranging from 42.58 to 922.8 μg/L, whereas diazinon was detected in water sample-8 (WS-8) and the concentration was 31.5 μg/L. None of the tested water samples was found to be contaminated with chlorpyrifos, carbaryl or DDT and its metabolites (DDE and DDD). Except for a tube-well water sample, concentrations of the detected residues are above the acceptable limit for human body as assigned by different organizations. To avoid the possible health hazards, the indiscriminate application of pesticides should be restricted and various substitute products like bio-pesticide should be introduced in a broad scale as soon as possible.

Automated monitoring of fissile and fertile materials in incinerator residue

International Nuclear Information System (INIS)

Schoenig, F.C. Jr.; Glendinning, S.G.; Tunnell, G.W.; Zucker, M.S.

1986-01-01

This patent describes an apparatus for determining the fissile and fertile material content of incinerator residue contained in a manipulatable container. The apparatus comprises a main body member formed of neutron moderating material and formed with a well for receiving the container; a first plug formed of neutron reflecting material for closing the top of the well; and a second plug containing a first neutron source for alternatively closing the top of the well and for directing neutrons into the well. It also includes a second neutron source selectively positionable in the bottom of the well for directing neutrons into the well; manipulating means for placing the container in the well and removing the container therefrom and for selectively placing one of the first and second plugs in the top of the well. Neutron detectors are positioned within the neutron moderating material of the main body member around the sides of the well. At least one gamma ray detector is positioned adjacent the bottom of the well. A means receives and processes the signals from the neutron and gamma ray detectors when the container is in the well for determining the fissile and fertile material content of the incinerator residue in the container

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

Science.gov (United States)

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

2016-05-01

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

Few body problems in nuclear and particle physics

International Nuclear Information System (INIS)

Slobodrian, R.J.; Cujec, B.; Ramavataram, K.

1975-01-01

Nucleon-nucleon interactions at all energies, meson-nucleon and meson-deuteron interactions, nuclear bremsstrahlung, on-shell and off-shell interactions, final-state interactions, bound and scattering states, few-body forces, polarization phenomena, short range correlations, quasi-free scattering, composite hadron models, subnucleon structure, multiparticle and coherent production processes, break-up reactions, electrodisintegration, relativistic effects and future resources in nuclear and particle physics are discussed in relation to the state of few-body physics in 1974. (B.F.G.)

Three-body unitary transformations, three-body forces, and trinucleon bound state properties

International Nuclear Information System (INIS)

Haftel, M.I.

1976-01-01

A three-body unitary transformation method for the study of three-body forces is presented. Starting with a three-body Hamiltonian with two-body forces, unitary transformations are introduced to generate Hamiltonians that have both two- and three-body forces. For cases of physical interest, the two-body forces of the altered Hamiltonians are phase equivalent (for two-body scattering) to the original and the three-body force vanishes when any interparticle distance is large. Specific examples are presented. Applications for studying the possible role of three-body forces in accounting for trinucleon bound state properties are examined. Calculations of the 3 He and 3 H charge form factors and Coulomb energy difference with hyperspherical radial transformations and with conventional N-N potentials are performed. The form factor calculations demonstrate how the proposed method can help obtain improved agreement with experiment by the introduction of appropriate three-body forces. Calculations of the Coulomb energy difference confirm previous estimates concerning charge symmetry breaking in the N-N interaction

Structural characteristics of an antigen required for its interaction with Ia and recognition by T cells

DEFF Research Database (Denmark)

Sette, A; Buus, S; Colon, S

1987-01-01

A detailed analysis of the residues within an immunogenic peptide that endow it with the capacity to interact with Ia and to be recognized by T cells is presented. Ia interacts with only a few of the peptide residues and overall exhibits a very broad specificity. Some residues appear to interact...... both with Ia and with T cells, leading to a model in which a peptide antigen is 'sandwiched' between Ia and the T-cell receptor....

Dosimetric Implications of Residual Tracking Errors During Robotic SBRT of Liver Metastases

Energy Technology Data Exchange (ETDEWEB)

Chan, Mark [Department for Radiation Oncology, University Medical Center Schleswig-Holstein, Kiel (Germany); Tuen Mun Hospital, Hong Kong (China); Grehn, Melanie [Department for Radiation Oncology, University Medical Center Schleswig-Holstein, Lübeck (Germany); Institute for Robotics and Cognitive Systems, University of Lübeck, Lübeck (Germany); Cremers, Florian [Department for Radiation Oncology, University Medical Center Schleswig-Holstein, Lübeck (Germany); Siebert, Frank-Andre [Department for Radiation Oncology, University Medical Center Schleswig-Holstein, Kiel (Germany); Wurster, Stefan [Saphir Radiosurgery Center Northern Germany, Güstrow (Germany); Department for Radiation Oncology, University Medicine Greifswald, Greifswald (Germany); Huttenlocher, Stefan [Saphir Radiosurgery Center Northern Germany, Güstrow (Germany); Dunst, Jürgen [Department for Radiation Oncology, University Medical Center Schleswig-Holstein, Kiel (Germany); Department for Radiation Oncology, University Clinic Copenhagen, Copenhagen (Denmark); Hildebrandt, Guido [Department for Radiation Oncology, University Medicine Rostock, Rostock (Germany); Schweikard, Achim [Institute for Robotics and Cognitive Systems, University of Lübeck, Lübeck (Germany); Rades, Dirk [Department for Radiation Oncology, University Medical Center Schleswig-Holstein, Lübeck (Germany); Ernst, Floris [Institute for Robotics and Cognitive Systems, University of Lübeck, Lübeck (Germany); and others

2017-03-15

Purpose: Although the metric precision of robotic stereotactic body radiation therapy in the presence of breathing motion is widely known, we investigated the dosimetric implications of breathing phase–related residual tracking errors. Methods and Materials: In 24 patients (28 liver metastases) treated with the CyberKnife, we recorded the residual correlation, prediction, and rotational tracking errors from 90 fractions and binned them into 10 breathing phases. The average breathing phase errors were used to shift and rotate the clinical tumor volume (CTV) and planning target volume (PTV) for each phase to calculate a pseudo 4-dimensional error dose distribution for comparison with the original planned dose distribution. Results: The median systematic directional correlation, prediction, and absolute aggregate rotation errors were 0.3 mm (range, 0.1-1.3 mm), 0.01 mm (range, 0.00-0.05 mm), and 1.5° (range, 0.4°-2.7°), respectively. Dosimetrically, 44%, 81%, and 92% of all voxels differed by less than 1%, 3%, and 5% of the planned local dose, respectively. The median coverage reduction for the PTV was 1.1% (range in coverage difference, −7.8% to +0.8%), significantly depending on correlation (P=.026) and rotational (P=.005) error. With a 3-mm PTV margin, the median coverage change for the CTV was 0.0% (range, −1.0% to +5.4%), not significantly depending on any investigated parameter. In 42% of patients, the 3-mm margin did not fully compensate for the residual tracking errors, resulting in a CTV coverage reduction of 0.1% to 1.0%. Conclusions: For liver tumors treated with robotic stereotactic body radiation therapy, a safety margin of 3 mm is not always sufficient to cover all residual tracking errors. Dosimetrically, this translates into only small CTV coverage reductions.

Dosimetric Implications of Residual Tracking Errors During Robotic SBRT of Liver Metastases

International Nuclear Information System (INIS)

Chan, Mark; Grehn, Melanie; Cremers, Florian; Siebert, Frank-Andre; Wurster, Stefan; Huttenlocher, Stefan; Dunst, Jürgen; Hildebrandt, Guido; Schweikard, Achim; Rades, Dirk; Ernst, Floris

2017-01-01

Purpose: Although the metric precision of robotic stereotactic body radiation therapy in the presence of breathing motion is widely known, we investigated the dosimetric implications of breathing phase–related residual tracking errors. Methods and Materials: In 24 patients (28 liver metastases) treated with the CyberKnife, we recorded the residual correlation, prediction, and rotational tracking errors from 90 fractions and binned them into 10 breathing phases. The average breathing phase errors were used to shift and rotate the clinical tumor volume (CTV) and planning target volume (PTV) for each phase to calculate a pseudo 4-dimensional error dose distribution for comparison with the original planned dose distribution. Results: The median systematic directional correlation, prediction, and absolute aggregate rotation errors were 0.3 mm (range, 0.1-1.3 mm), 0.01 mm (range, 0.00-0.05 mm), and 1.5° (range, 0.4°-2.7°), respectively. Dosimetrically, 44%, 81%, and 92% of all voxels differed by less than 1%, 3%, and 5% of the planned local dose, respectively. The median coverage reduction for the PTV was 1.1% (range in coverage difference, −7.8% to +0.8%), significantly depending on correlation (P=.026) and rotational (P=.005) error. With a 3-mm PTV margin, the median coverage change for the CTV was 0.0% (range, −1.0% to +5.4%), not significantly depending on any investigated parameter. In 42% of patients, the 3-mm margin did not fully compensate for the residual tracking errors, resulting in a CTV coverage reduction of 0.1% to 1.0%. Conclusions: For liver tumors treated with robotic stereotactic body radiation therapy, a safety margin of 3 mm is not always sufficient to cover all residual tracking errors. Dosimetrically, this translates into only small CTV coverage reductions.

Isotopic Hg in an Allende carbon-rich residue

Science.gov (United States)

Reed, G. W., Jr.; Jovanovic, S.

1990-01-01

A carbon-rich residue from Allende subjected to stepwise heating yielded two isotopically resolvable types of Hg: one with an (Hg-196)/(Hg-202) concentration ratio the same as terrestrial (monitor) Hg; the other enriched in Hg-196 relative to Hg-202 by about 60 percent. Hg with the 202 isotope enriched relative to 196, as is found in bulk Allende, was not observed. Whether the result of mass fractionation or nucleosynthesis, the distinct types of Hg entered different carrier phases and were not thermally mobilized since the accretion of the Allende parent body.

Universal few-body physics in a harmonic trap

International Nuclear Information System (INIS)

Tolle, S.; Hammer, H.W.; Metsch, B.Ch.

2011-01-01

Few-body systems with resonant short-range interactions display universal properties that do not depend on the details of their structure or their interactions at short distances. In the three-body system, these properties include the existence of a geometric spectrum of three-body Efimov states and a discrete scaling symmetry. Similar universal properties appear in 4-body and possibly higher-body systems as well. We set up an effective theory for few-body systems in a harmonic trap and study the modification of universal physics for 3- and 4-particle systems in external confinement. In particular, we focus on systems where the Efimov effect can occur and investigate the dependence of the 4-body spectrum on the experimental tuning parameters. (authors)

Evaluation of residue-residue contact predictions in CASP9

KAUST Repository

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

2011-01-01

This work presents the results of the assessment of the intramolecular residue-residue contact predictions submitted to CASP9. The methodology for the assessment does not differ from that used in previous CASPs, with two basic evaluation measures

Meditope-Fab interaction: threading the hole.

Science.gov (United States)

Bzymek, Krzysztof P; Ma, Yuelong; Avery, Kendra N; Horne, David A; Williams, John C

2017-12-01

Meditope, a cyclic 12-residue peptide, binds to a unique binding side between the light and heavy chains of the cetuximab Fab. In an effort to improve the affinity of the interaction, it was sought to extend the side chain of Arg8 in the meditope, a residue that is accessible from the other side of the meditope binding site, in order to increase the number of interactions. These modifications included an n-butyl and n-octyl extension as well as hydroxyl, amine and carboxyl substitutions. The atomic structures of the complexes and the binding kinetics for each modified meditope indicated that each extension threaded through the Fab `hole' and that the carboxyethylarginine substitution makes a favorable interaction with the Fab, increasing the half-life of the complex by threefold compared with the unmodified meditope. Taken together, these studies provide a basis for the design of additional modifications to enhance the overall affinity of this unique interaction.

Towards revealing the structure of bacterial inclusion bodies.

Science.gov (United States)

Wang, Lei

2009-01-01

Protein aggregation is a widely observed phenomenon in human diseases, biopharmaceutical production, and biological research. Protein aggregates are generally classified as highly ordered, such as amyloid fibrils, or amorphous, such as bacterial inclusion bodies. Amyloid fibrils are elongated filaments with diameters of 6-12 nm, they are comprised of residue-specific cross-beta structure, and display characteristic properties, such as binding with amyloid-specific dyes. Amyloid fibrils are associated with dozens of human pathological conditions, including Alzheimer disease and prion diseases. Distinguished from amyloid fibrils, bacterial inclusion bodies display apparent amorphous morphology. Inclusion bodies are formed during high-level recombinant protein production, and formation of inclusion bodies is a major concern in biotechnology. Despite of the distinctive morphological difference, bacterial inclusion bodies have been found to have some amyloid-like properties, suggesting that they might contain structures similar to amyloid-like fibrils. Recent structural data further support this hypothesis, and this review summarizes the latest progress towards revealing the structural details of bacterial inclusion bodies.

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

Indian Academy of Sciences (India)

Madhsudhan

interaction of proteins and peptides with membranes (Segrest ... favour surface activity have been described by Eisenberg et ... amphipathicity and propensity for α-helical conformation ..... Membrane destabilisation occurs due to electrostatic.

Pyrolysis of olive residue/low density polyethylene mixture:Part I Thermogravimetric kinetics

Institute of Scientific and Technical Information of China (English)

无

2008-01-01

This paper demonstrates the thermal pyrolysis of olive residue, low density polyethylene (LDPE) and olive residue/LDPE mixture in an inert atmosphere of N2 using thermogravimetric analysis (TGA). Measurements were carried out in the temperature range 300K~973K at heating rates of 2K/min, 10K/min, 20K/min and 50K/min. Based on the results obtained, three temperature regimes were selected for studying the non-isothermal kinetics of olive residue/LDPE mixture. The first two were dominated by the olive residue pyrolysis, while the third was linked to the LDPE pyrolysis, which occurred at much higher temperatures. Discrepancies between the experimental and calculated TG/DTG profiles were considered as a measurement of the extent of interactions occurring on co-pyrolysis. The maximum degradation temperatures of each component in the mixture were higher than those the individual components;thus an increase in thermal stability was expected. The kinetic parameters associated with thermal degradation were determined using Friedman isoconversional method.

Collective multipole excitations based on correlated realistic nucleon-nucleon interactions

International Nuclear Information System (INIS)

Paar, N.; Papakonstantinou, P.; Hergert, H.; Roth, R.

2006-01-01

We investigate collective multipole excitations for closed shell nuclei from 16 O to 208 Pb using correlated realistic nucleon-nucleon interactions in the framework of the random phase approximation (RPA). The dominant short-range central and tensor correlations a re treated explicitly within the Unitary Correlation Operator Method (UCOM), which provides a phase-shift equivalent correlated interaction VUCOM adapted to simple uncorrelated Hilbert spaces. The same unitary transformation that defines the correlated interaction is used to derive correlated transition operators. Using VUCOM we solve the Hartree-Fock problem and employ the single-particle states as starting point for the RPA. By construction, the UCOM-RPA is fully self-consistent, i.e. the same correlated nucleon-nucleon interact ion is used in calculations of the HF ground state and in the residual RPA interaction. Consequently, the spurious state associated with the center-of-mass motion is properly removed and the sum-rules are exhausted within ±3%. The UCOM-RPA scheme results in a collective character of giant monopole, dipole, and quadrupole resonances in closed-shell nuclei across the nuclear chart. For the isoscalar giant monopole resonance, the resonance energies are in agreement with experiment hinting at a reasonable compressibility. However, in the 1 - and 2 + channels the resonance energies are overestimated due to missing long-range correlations and three-body contributions. (orig.)

The heparin/heparan sulfate sequence that interacts with cyclophilin B contains a 3-O-sulfated N-unsubstituted glucosamine residue.

Science.gov (United States)

Vanpouille, Christophe; Deligny, Audrey; Delehedde, Maryse; Denys, Agnès; Melchior, Aurélie; Liénard, Xavier; Lyon, Malcolm; Mazurier, Joël; Fernig, David G; Allain, Fabrice

2007-08-17

Many of the biological functions of heparan sulfate (HS) proteoglycans can be attributed to specialized structures within HS moieties, which are thought to modulate binding and function of various effector proteins. Cyclophilin B (CyPB), which was initially identified as a cyclosporin A-binding protein, triggers migration and integrin-mediated adhesion of peripheral blood T lymphocytes by a mechanism dependent on interaction with cell surface HS. Here we determined the structural features of HS that are responsible for the specific binding of CyPB. In addition to the involvement of 2-O,6-O, and N-sulfate groups, we also demonstrated that binding of CyPB was dependent on the presence of N-unsubstituted glucosamine residues (GlcNH2), which have been reported to be precursors for sulfation by 3-O-sulfotransferases-3 (3-OST-3). Interestingly, 3-OST-3B isoform was found to be the main 3-OST isoenzyme expressed in peripheral blood T lymphocytes and Jurkat T cells. Moreover, down-regulation of the expression of 3-OST-3 by RNA interference potently reduced CyPB binding and consequent activation of p44/42 mitogen-activated protein kinases. Altogether, our results strongly support the hypothesis that 3-O-sulfation of GlcNH2 residues could be a key modification that provides specialized HS structures for CyPB binding to responsive cells. Given that 3-O-sulfation of GlcNH2-containing HS by 3-OST-3 also provides binding sites for glycoprotein gD of herpes simplex virus type I, these findings suggest an intriguing structural linkage between the HS sequences involved in CyPB binding and viral infection.

Chain and ladder models with two-body interactions and analytical ground states

Science.gov (United States)

Manna, Sourav; Nielsen, Anne E. B.

2018-05-01

We consider a family of spin-1 /2 models with few-body, SU(2)-invariant Hamiltonians and analytical ground states related to the one-dimensional (1D) Haldane-Shastry wave function. The spins are placed on the surface of a cylinder, and the standard 1D Haldane-Shastry model is obtained by placing the spins with equal spacing in a circle around the cylinder. Here, we show that another interesting family of models with two-body exchange interactions is obtained if we instead place the spins along one or two lines parallel to the cylinder axis, giving rise to chain and ladder models, respectively. We can change the scale along the cylinder axis without changing the radius of the cylinder. This gives us a parameter that controls the ratio between the circumference of the cylinder and all other length scales in the system. We use Monte Carlo simulations and analytical investigations to study how this ratio affects the properties of the models. If the ratio is large, we find that the two legs of the ladder decouple into two chains that are in a critical phase with Haldane-Shastry-like properties. If the ratio is small, the wave function reduces to a product of singlets. In between, we find that the behavior of the correlations and the Renyi entropy depends on the distance considered. For small distances the behavior is critical, and for long distances the correlations decay exponentially and the entropy shows an area law behavior. The distance up to which there is critical behavior gets larger as the ratio increases.

Toward transferable interatomic van der Waals interactions without electrons: The role of multipole electrostatics and many-body dispersion

International Nuclear Information System (INIS)

Bereau, Tristan; Lilienfeld, O. Anatole von

2014-01-01

We estimate polarizabilities of atoms in molecules without electron density, using a Voronoi tesselation approach instead of conventional density partitioning schemes. The resulting atomic dispersion coefficients are calculated, as well as many-body dispersion effects on intermolecular potential energies. We also estimate contributions from multipole electrostatics and compare them to dispersion. We assess the performance of the resulting intermolecular interaction model from dispersion and electrostatics for more than 1300 neutral and charged, small organic molecular dimers. Applications to water clusters, the benzene crystal, the anti-cancer drug ellipticine—intercalated between two Watson-Crick DNA base pairs, as well as six macro-molecular host-guest complexes highlight the potential of this method and help to identify points of future improvement. The mean absolute error made by the combination of static electrostatics with many-body dispersion reduces at larger distances, while it plateaus for two-body dispersion, in conflict with the common assumption that the simple 1/R 6 correction will yield proper dissociative tails. Overall, the method achieves an accuracy well within conventional molecular force fields while exhibiting a simple parametrization protocol