WorldWideScience

Sample records for anomalous structural features

  1. Anomalous features of EMT during keratinocyte transformation.

    Directory of Open Access Journals (Sweden)

    Tamar Geiger

    Full Text Available During the evolution of epithelial cancers, cells often lose their characteristic features and acquire a mesenchymal phenotype, in a process known as epithelial-mesenchymal transition (EMT. In the present study we followed early stages of keratinocyte transformation by HPV16, and observed diverse cellular changes, associated with EMT. We compared primary keratinocytes with early and late passages of HF1 cells, a cell line of HPV16-transformed keratinocytes. We have previously shown that during the progression from the normal cells to early HF1 cells, immortalization is acquired, while in the progression to late HF1, cells become anchorage independent. We show here that during the transition from the normal state to late HF1 cells, there is a progressive reduction in cytokeratin expression, desmosome formation, adherens junctions and focal adhesions, ultimately leading to poorly adhesive phenotype, which is associated with anchorage-independence. Surprisingly, unlike "conventional EMT", these changes are associated with reduced Rac1-dependent cell migration. We monitored reduced Rac1-dependent migration also in the cervical cancer cell line SiHa. Therefore we can conclude that up to the stage of tumor formation migratory activity is eliminated.

  2. Anomalous two-photon spectral features in warm rubidium vapor

    Science.gov (United States)

    Perrella, C.; Light, P. S.; Milburn, T. J.; Kielpinski, D.; Stace, T. M.; Luiten, A. N.

    2016-09-01

    We report observation of anomalous fluorescence spectral features in the environs of a two-photon transition in a rubidium vapor when excited with two different wavelength lasers that are both counterpropagating through the vapor. These features are characterized by an unusual trade-off between the detunings of the driving fields. Three different hypothetical processes are presented to explain the observed spectra: a simultaneous three-atom and four-photon collision, a four-photon excitation involving a light field produced via amplified spontaneous emission, and population pumping perturbing the expected steady-state spectra. Numerical modeling of each hypothetical process is presented, supporting the population pumping process as the most plausible mechanism.

  3. Diffraction Anomalous Near-Edge Structure

    Science.gov (United States)

    Moltaji, Habib O., Jr.

    1995-11-01

    To determine the atomic structure about atom of an element in a sample of a condensed multicomponent single crystal, contrast radiation is proposed with the use of Diffraction Anomalous Near-Edge Structure (DANES), which combines the long-range order sensitivity of the x-ray diffraction and short-range order of the x-ray absorption near-edge techniques. This is achieved by modulating the photon energy of the x-ray beam incident on the sample over a range of energies near an absorption edge of the selected element. Due to anomalous dispersion, x-ray diffraction, and x-ray absorption, the DANES intensity with respect to the selected element is obtained in a single experiment. I demonstrate that synchrotron DANES measurements for the single crystal of thin film and the powder samples and provide the same local atomic structural information as the x-ray absorption near-edge with diffraction condition and can be used to provide enhanced site selectivity. I demonstrate calculations of DAFS intensity and measurements of polarized DANES and XANES intensity.

  4. Fingerprints of Anomalous Primordial Universe on the Abundance of Large Scale Structures

    CERN Document Server

    Baghram, Shant; Firouzjahi, Hassan; Namjoo, Mohammad Hossein

    2014-01-01

    We study the predictions of anomalous inflationary models on the abundance of structures in large scale structure observations. The anomalous features encoded in primordial curvature perturbation power spectrum are (a): localized feature in momentum space, (b): hemispherical asymmetry and (c): statistical anisotropies. We present a model-independent expression relating the number density of structures to the changes in the matter density variance. Models with localized feature can alleviate the tension between observations and numerical simulations of cold dark matter structures on galactic scales as a possible solution to the missing satellite problem. In models with hemispherical asymmetry we show that the abundance of structures becomes asymmetric depending on the direction of observation to sky. In addition, we study the effects of scale-dependent dipole amplitude on the abundance of structures and, using the quasars data, we find the upper bound $n_A M_c)$ the enhancement in variance induced from anomalo...

  5. Structural controls on anomalous transport in fractured porous rock

    Science.gov (United States)

    Edery, Yaniv; Geiger, Sebastian; Berkowitz, Brian

    2016-07-01

    Anomalous transport is ubiquitous in a wide range of disordered systems, notably in fractured porous formations. We quantitatively identify the structural controls on anomalous tracer transport in a model of a real fractured geological formation that was mapped in an outcrop. The transport, determined by a continuum scale mathematical model, is characterized by breakthrough curves (BTCs) that document anomalous (or "non-Fickian") transport, which is accounted for by a power law distribution of local transition times ψ>(t>) within the framework of a continuous time random walk (CTRW). We show that the determination of ψ>(t>) is related to fractures aligned approximately with the macroscopic direction of flow. We establish the dominant role of fracture alignment and assess the statistics of these fractures by determining a concentration-visitation weighted residence time histogram. We then convert the histogram to a probability density function (pdf) that coincides with the CTRW ψ>(t>) and hence anomalous transport. We show that the permeability of the geological formation hosting the fracture network has a limited effect on the anomalous nature of the transport; rather, it is the fractures transverse to the flow direction that play the major role in forming the long BTC tail associated with anomalous transport. This is a remarkable result, given the complexity of the flow field statistics as captured by concentration transitions.

  6. Liquid Water Structure from Anomalous Density under Ambient Condition

    Institute of Scientific and Technical Information of China (English)

    SUN Qiang; ZHENG Hai-Fei

    2006-01-01

    @@ From discussion of the structure of liquid water, we deduce that water under ambient condition is mainly composed of ice Ih-like molecular clusters and clathrate-like molecular clusters. The water molecular clusters remain in a state of chemical equilibrium (reversible clustering reactions). This structural model can be demonstrated by quantitative study on anomalous density with increasing temperature at ambient pressure.

  7. Thermally anomalous features in the subsurface of Enceladus's south polar terrain

    Science.gov (United States)

    Le Gall, A.; Leyrat, C.; Janssen, M. A.; Choblet, G.; Tobie, G.; Bourgeois, O.; Lucas, A.; Sotin, C.; Howett, C.; Kirk, R.; Lorenz, R. D.; West, R. D.; Stolzenbach, A.; Massé, M.; Hayes, A. H.; Bonnefoy, L.; Veyssière, G.; Paganelli, F.

    2017-03-01

    Saturn's moon Enceladus is an active world. In 2005, the Cassini spacecraft witnessed for the first time water-rich jets venting from four anomalously warm fractures (called sulci) near its south pole1,2. Since then, several observations have provided evidence that the source of the material ejected from Enceladus is a large underground ocean, the depth of which is still debated3-6. Here, we report on the first and only opportunity that Cassini's RADAR instrument7,8 had to observe Enceladus's south polar terrain closely, targeting an area a few tens of kilometres north of the active sulci. Detailed analysis of the microwave radiometry observations highlights the ongoing activity of the moon. The instrument recorded the microwave thermal emission, revealing a warm subsurface region with prominent thermal anomalies that had not been identified before. These anomalies coincide with large fractures, similar or structurally related to the sulci. The observations imply the presence of a broadly distributed heat production and transport system below the south polar terrain with 'plate-like' features and suggest that a liquid reservoir could exist at a depth of only a few kilometres under the ice shell at the south pole. The detection of a possible dormant sulcus further suggests episodic geological activity.

  8. Anomalous Structure of Palladium-Capped Magnesium Thin Films

    Directory of Open Access Journals (Sweden)

    Kazuki Yoshimura

    2012-07-01

    Full Text Available Pd capped pure Mg thin film (50 nm thick was prepared by magnetron sputtering and its hydrogenation at room temperature has been investigated. After exposure to 4% hydrogen gas diluted by argon, the Pd/Mg thin films show drastic optical changes from the metallic state to the transparent state within five seconds by hydrogenation. Transmission electron microscope observation reveals that this sample has an anomalous structure; Mg grain is surrounded by Pd. This structure may be the reason why Pd/Mg films can be hydrogenated so quickly at room temperature.

  9. Coherent structures and anomalous transport in reversed field pinch plasmas

    Science.gov (United States)

    Antoni, V.; Drake, J. R.; Spada, E.; Spolaore, M.; Vianello, N.; Bergsåker, H.; Cavazzana, R.; Cecconello, M.; Martines, E.; Serianni, G.

    2006-02-01

    The results leading to the identification of coherent structures emerging from the background turbulence in the edge region of the reversed field pinch experiments EXTRAP-T2R and RFX are reviewed. These structures have traits of vortices in velocity field and blobs in density, and the reconstruction of their spatial structure and of their time evolution is discussed focusing on the analysis tools applied. The role of these structures in the particle anomalous transport is addressed, showing that their collisions can contribute up to 50% the total particle losses.This process is shown to be responsible for bursts in particle flux and it is found to set a characteristic collision time, which is in agreement with the statistical properties of laminar times for particle flux bursts.

  10. On the Anomalous Silicate Absorption Feature of the Prototypical Seyfert 2 Galaxy NGC 1068

    CERN Document Server

    Koehler, Melanie

    2012-01-01

    The first detection of the silicate absorption feature in AGNs was made at 9.7 micrometer for the prototypical Seyfert 2 galaxy NGC 1068 over 30 years ago, indicating the presence of a large column of silicate dust in the line-of-sight to the nucleus. It is now well recognized that type 2 AGNs exhibit prominent silicate absorption bands, while the silicate bands of type 1 AGNs appear in emission. More recently, using the Mid-Infrared Interferometric Instrument on the Very Large Telescope Interferometer, Jaffe et al. (2004) by the first time spatially resolved the parsec-sized dust torus around NGC 1068 and found that the 10 micrometer silicate absorption feature of the innermost hot component exhibits an anomalous profile differing from that of the interstellar medium and that of common olivine-type silicate dust. While they ascribed the anomalous absorption profile to gehlenite (Ca_2Al_2SiO_7, a calcium aluminum silicate species), we propose a physical dust model and argue that, although the presence of gehl...

  11. Features and Recursive Structure

    Directory of Open Access Journals (Sweden)

    Kuniya Nasukawa

    2015-01-01

    Full Text Available Based on the cross-linguistic tendency that weak vowels are realized with a central quality such as ə, ɨ, or ɯ, this paper attempts to account for this choice by proposing that the nucleus itself is one of the three monovalent vowel elements |A|, |I| and |U| which function as the building blocks of melodic structure. I claim that individual languages make a parametric choice to determine which of the three elements functions as the head of a nuclear expression. In addition, I show that elements can be freely concatenated to create melodic compounds. The resulting phonetic value of an element compound is determined by the specific elements it contains and by the head-dependency relations between those elements. This concatenation-based recursive mechanism of melodic structure can also be extended to levels above the segment, thus ultimately eliminating the need for syllabic constituents. This approach reinterprets the notion of minimalism in phonology by opposing the string-based flat structure.

  12. Emissivity corrected infrared method for imaging anomalous structural heat flows

    Science.gov (United States)

    Del Grande, Nancy K.; Durbin, Philip F.; Dolan, Kenneth W.; Perkins, Dwight E.

    1995-01-01

    A method for detecting flaws in structures using dual band infrared radiation. Heat is applied to the structure being evaluated. The structure is scanned for two different wavelengths and data obtained in the form of images. Images are used to remove clutter to form a corrected image. The existence and nature of a flaw is determined by investigating a variety of features.

  13. Anomalous Features on Anomalous Rocks — Deciphering the Physical Weathering History of Iron Meteorites found on Mars using Terrestrial Analogues

    Science.gov (United States)

    Ashley, J.

    2015-12-01

    Non-indigenous rocks (meteorites) found on Mars by rover science teams offer insights into probable recent (mid- to late-Amazonian) weathering processes within 15° of the martian equator. While source materials are often in question for indigenous martian alteration scenarios, the starting materials for most meteorites are known as unweathered, curated falls in Earth-based collections. Both chemical and mechanical weathering processes have modified at least 21 confirmed and candidate exogenic rocks found at three rover landing sites. Such processes have been shown to include acidic corrosion, oxide production, and aeolian scouring. The unknown martian surface exposure duration of the meteorites makes separating physical from chemical weathering effects challenging: Saltating sand grains may accomplish alone what oxidation and rust removal by aeolian scouring may accomplish in a shorter time interval, for example. However, aeolian abrasion appears to dominate for at least some of the surface features in martian irons. Iron meteorites are resistant to wind-blown sand relative to silicate rocks, but are malleable and able to preserve aeolian abrasion effects. These include 1) regmaglypts enlarged into hollows with overhanging cornices; 2) surfaces scalloped or deeply fluted by straight-line groves, and/or 3) deep 'boreholes' present across many surfaces. The flutings, boreholes, and scallops have oriented symmetry and are therefore potentially useful as paleo-wind direction indicators. Boreholes tend to be clean-edged, elliptical to round, of varying diameter, and often occur independently of local topography. Ventifacted igneous rocks found at Garnet Hill, San Gorgonio Pass, California, present features that resemble many aspects of those found in the metal masses on Mars. Though of different petrologies and mineralogies, both rock types are massive, homogeneous and unfractured, which may conceivably account for some apparent similarities in mechanical weathering

  14. Multiwavelength anomalous diffraction analyses of protein structures based on xenon and selenium resonances

    Science.gov (United States)

    Slama, Betty Nicole

    The 'phase problem' is central to X-ray crystallography, and multiwavelength anomalous diffraction (MAD) provides an elegant and broadly accessible solution. In the first part, the use of MAD at the xenon L3 edge is explored, as an alternative to the well established selenium K-edge phasing. In the second part, the structure of the bacterial protein Vibrio cholerae LuxQ, part of a two component signaling system involved in quorum sensing, is solved and analyzed. Keywords: anomalous scattering, x-ray diffraction, phasing, protein structure.

  15. An extended anomalous fine structure of X-ray quasi-Bragg diffuse scattering from multilayers

    CERN Document Server

    Chernov, V A; Mytnichenko, S V

    2001-01-01

    An X-ray quasi-Bragg diffuse scattering anomalous fine structure technique was probed near the absorption Ni K-edge to study the interfacial structure of the Ni/C multilayer deposited by the laser ablation. Like other combinations of the EXAFS and diffraction techniques, this method has a spatial selectivity and was shown qualitatively to provide atomic structural information from the mixed interfacial layers. The possibilities and advantages of this technique are discussed.

  16. Anomalous electronic transport features in a lateral quantum dot array sample

    Science.gov (United States)

    Pan, Wei; Dunn, R. G.; Reno, J. L.; Simmons, J. A.; Li, D.; Brueck, S. R. J.

    2006-03-01

    We will present in this talk experimental results obtained in a lateral quantum dot array sample, with a pitch size of ˜ 350 nm and a designed dot size of ˜ 150nm. The starting material is a high quality quantum well with the two-dimensional electron gas buried 200 nm below the surface. The quantum dot array is defined by a Ti/Au metal grid, which was fabricated using the interferometric lithograph and lift-off techniques. Around zero magnetic field, a pronounced positive magnetoresistance is observed, which can be explained by the semi-classical model of magnetic breakdown. The so-called commensurability oscillations together with the usual Shubnikov- de Hass oscillations are also observed. Surprisingly, in a pure DC measurement of longitudinal resistance, an anomalous resistance spike is clearly seen. The magnetic field position of this resistance spike depends on the amplitude of applied DC bias (Vds) between source and drain, and shows roughly a 1/Vds dependence.Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  17. On the structure of anomalous composite Higgs models

    Science.gov (United States)

    Gripaios, Ben; Nardecchia, Marco; You, Tevong

    2017-01-01

    We describe the anomaly structure of a composite Higgs model in which the SO(5) / SO(4) coset structure of the minimal model is extended by an additional, non-linearly realised U(1)_{η }. In addition, we show that the effective Lagrangian admits a term that, like the Wess-Zumino-Witten term in the chiral Lagrangian for QCD, is not invariant under the non-linearly realised symmetries, but rather changes by a total derivative. This term is unlike the Wess-Zumino-Witten term in that it does not arise from anomalies. If present, it may give rise to the rare decay η → h W^+ W^-Z. The phenomenology of the singlet in this model differs from that in a model based on SO(6) / SO(5), in that couplings to both gluons and photons, arising via anomalies, are present. We show that while some tuning is needed to accommodate flavour and electroweak precision constraints, the model is no worse than the minimal model in this regard.

  18. Crystal structure of thermostable catechol 2,3-dioxygenase determined by multiwavelength anomalous dispersion method

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The selenomethionyl derivative of the thermostable catechol 2,3-dioxygenase (SeMet-TC23O) is expressed,purified and crystallized. By using multiwave length anomalous dispersion (MAD) phasing techniques, the crystal structure of TC23O at 0.3 nm resolutions is determined.TC23O is a homotetramer. Each monomer is composed of N-terminal and C-terminal domains (residues 1~153 and 153~319, respectively). The two domains are proximately symmetric by a non-crystallographic axis. Each domain contains two characteristic motifs which are found in almost all of extradial dioxygenases.Kevwords: multiwavelength anomalous dispersion (MAD), X-ray diffraction, thermostable catechol 2,3-dioxygenase, crystal structure,synchrotron light source.

  19. On the Anomalous Silicate Emission Features of AGNs: A Possible Interpretation Based on Porous Dust

    CERN Document Server

    Li, M P; Li, Aigen

    2008-01-01

    The recent Spitzer detections of the 9.7 micron Si--O silicate emission in type 1 AGNs provide support for the AGN unification scheme. The properties of the silicate dust are of key importance to understanding the physical, chemical and evolutionary properties of the obscuring dusty torus around AGNs. Compared to that of the Galactic interstellar medium (ISM), the 10 micron silicate emission profile of type 1 AGNs is broadened and has a clear shift of peak position to longer wavelengths. In literature this is generally interpreted as an indication of the deviations of the silicate composition, size, and degree of crystallization of AGNs from that of the Galactic ISM. In this Letter we show that the observed peak shift and profile broadening of the 9.7 micron silicate emission feature can be explained in terms of porous composite dust consisting of ordinary interstellar amorphous silicate, amorphous carbon and vacuum. Porous dust is naturally expected in the dense circumnuclear region around AGNs, as a consequ...

  20. FEATURES OF FORMATION OF REGIONAL CLUSTER STRUCTURES

    Directory of Open Access Journals (Sweden)

    Ekaterina V. Andreyeva

    2016-01-01

    Full Text Available In article is considered features of formation of cluster structures for increase of efficiency of economic entities and growth of investment and innovative appeal of the region. Cluster structures are described as a specialized product oriented commands, which were created for common decision making about production, nancial and organizational questions.

  1. Structure determination of thin CoFe films by anomalous x-ray diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Gloskovskii, Andrei; Stryganyuk, Gregory; Ouardi, Siham [Institut fuer Anorganische und Analytische Chemie, Johannes Gutenberg-Universitaet, 55099 Mainz (Germany); Fecher, Gerhard H.; Felser, Claudia [Institut fuer Anorganische und Analytische Chemie, Johannes Gutenberg-Universitaet, 55099 Mainz (Germany); Max Planck Institute for Chemical Physics of Solids, D-01187 Dresden (Germany); Hamrle, Jaroslav; Pistora, Jaromir [Department of Physics and Nanotechnology Centre, VSB-Technical University of Ostrava, 70833 Ostrava (Czech Republic); Bosu, Subrojati; Saito, Kesami; Sakuraba, Yuya; Takanashi, Koki [Institute for Materials Research (IMR), Tohoku University, Sendai 980-8577 (Japan)

    2012-10-01

    This work reports on the investigation of structure-property relationships in thin CoFe films grown on MgO. Because of the very similar scattering factors of Fe and Co, it is not possible to distinguish the random A2 (W-type) structure from the ordered B2 (CsCl-type) structure with commonly used x-ray sources. Synchrotron radiation based anomalous x-ray diffraction overcomes this problem. It is shown that as grown thin films and 300 K post annealed films exhibit the A2 structure with a random distribution of Co and Fe. In contrast, films annealed at 400 K adopt the ordered B2 structure.

  2. Relation between the structure and catalytic activity for automotive emissions. Use of x-ray anomalous dispersion effect

    CERN Document Server

    Mizuki, J; Tanaka, H

    2003-01-01

    The employment of the X-ray anomalous dispersion effect allows us to detect the change in structure of catalytic converters with the environment exposed. Here we show that palladium atoms in a perovskite crystal move into and out of the crystal by anomalous X-ray diffraction and absorption techniques. This movement of the precious metal plays an important role to keep the catalytic activity long-lived. (author)

  3. X-ray reflection anomalous fine structure analysis of the stability of permalloy/copper multilayers

    Energy Technology Data Exchange (ETDEWEB)

    Luo, G.M.; Mai, Z.H.; Hase, T.P.A. E-mail: t.p.a.hase@dur.ac.uk; Fulthorpe, B.D.; Tanner, B.K.; Marrows, C.H.; Hickey, B.J

    2001-05-01

    We report the application of reflection anomalous fine structure analysis to the study of the changes in the layer density and local environment in sputtered permalloy/copper multilayers. By fitting the smoothly varying component of the plot of multilayer Bragg peak intensity versus incident X-ray energy, we find a strained permalloy layer at the permalloy/copper but not the copper/permalloy interface. The density difference between copper and strained permalloy layers increases on annealing at 275 deg. C and from the oscillatory component of the spectrum, we show that it is the nearest-neighbour distance around the Ni atoms which decreases.

  4. Diffraction anomalous near-edge structure in ordered GaInP

    Science.gov (United States)

    Alagna, L.; Prosperi, T.; Turchini, S.; Ferrari, C.; Francesio, L.; Franzosi, P.

    1998-04-01

    We report the diffraction anomalous near-edge structure (DANES) of a nominally lattice matched GaxIn1-xP/GaAs (x=0.51) heteroepitaxial layer, grown by metal organic chemical vapor deposition, which shows long range ordering in the cationic sublattice along the direction. DANES spectra, originating from the 004 reflections of the substrate and of the epi-layer and that from the "forbidden" -5/2 5/2 -5/2 reflection of the superstructure, have been recorded at the Ga K edge. A full theoretical simulation, based on the kinematic formalism, largely agrees with the experimental data.

  5. Feature extraction for structural dynamics model validation

    Energy Technology Data Exchange (ETDEWEB)

    Hemez, Francois [Los Alamos National Laboratory; Farrar, Charles [Los Alamos National Laboratory; Park, Gyuhae [Los Alamos National Laboratory; Nishio, Mayuko [UNIV OF TOKYO; Worden, Keith [UNIV OF SHEFFIELD; Takeda, Nobuo [UNIV OF TOKYO

    2010-11-08

    This study focuses on defining and comparing response features that can be used for structural dynamics model validation studies. Features extracted from dynamic responses obtained analytically or experimentally, such as basic signal statistics, frequency spectra, and estimated time-series models, can be used to compare characteristics of structural system dynamics. By comparing those response features extracted from experimental data and numerical outputs, validation and uncertainty quantification of numerical model containing uncertain parameters can be realized. In this study, the applicability of some response features to model validation is first discussed using measured data from a simple test-bed structure and the associated numerical simulations of these experiments. issues that must be considered were sensitivity, dimensionality, type of response, and presence or absence of measurement noise in the response. Furthermore, we illustrate a comparison method of multivariate feature vectors for statistical model validation. Results show that the outlier detection technique using the Mahalanobis distance metric can be used as an effective and quantifiable technique for selecting appropriate model parameters. However, in this process, one must not only consider the sensitivity of the features being used, but also correlation of the parameters being compared.

  6. Anomalous wave structure in magnetized materials described by non-convex equations of state

    Energy Technology Data Exchange (ETDEWEB)

    Serna, Susana, E-mail: serna@mat.uab.es [Departament de Matematiques, Universitat Autonoma de Barcelona, 08193 Bellaterra, Barcelona (Spain); Marquina, Antonio, E-mail: marquina@uv.es [Departamento de Matematicas, Universidad de Valencia, 46100 Burjassot, Valencia (Spain)

    2014-01-15

    We analyze the anomalous wave structure appearing in flow dynamics under the influence of magnetic field in materials described by non-ideal equations of state. We consider the system of magnetohydrodynamics equations closed by a general equation of state (EOS) and propose a complete spectral decomposition of the fluxes that allows us to derive an expression of the nonlinearity factor as the mathematical tool to determine the nature of the wave phenomena. We prove that the possible formation of non-classical wave structure is determined by both the thermodynamic properties of the material and the magnetic field as well as its possible rotation. We demonstrate that phase transitions induced by material properties do not necessarily imply the loss of genuine nonlinearity of the wavefields as is the case in classical hydrodynamics. The analytical expression of the nonlinearity factor allows us to determine the specific amount of magnetic field necessary to prevent formation of complex structure induced by phase transition in the material. We illustrate our analytical approach by considering two non-convex EOS that exhibit phase transitions and anomalous behavior in the evolution. We present numerical experiments validating the analysis performed through a set of one-dimensional Riemann problems. In the examples we show how to determine the appropriate amount of magnetic field in the initial conditions of the Riemann problem to transform a thermodynamic composite wave into a simple nonlinear wave.

  7. Extracting Conceptual Feature Structures from Text

    DEFF Research Database (Denmark)

    Andreasen, Troels; Bulskov, Henrik; Lassen, Tine;

    2011-01-01

    This paper describes an approach to indexing texts by their conceptual content using ontologies along with lexico-syntactic information and semantic role assignment provided by lexical resources. The conceptual content of meaningful chunks of text is transformed into conceptual feature structures...

  8. A statistical feature of anomalous seismic activities prior to large shallow earthquakes in Japan revealed by the Pattern Informatics method

    Directory of Open Access Journals (Sweden)

    M. Kawamura

    2013-03-01

    Full Text Available For revealing the preparatory processes of large inland earthquakes, we systematically applied the Pattern Informatics method (PI method to the earthquake data of Japan. We focused on 12 large earthquakes with magnitudes larger than M = 6.4 (an official magnitude of the Japan Meteorological Agency that occurred at depths shallower than 30 km between 2000 and 2010. We examined the relation between the spatiotemporal locations of such large shallow earthquakes and those of PI hotspots, which correspond to the grid cells of anomalous seismic activities in a designated time span. Based on a statistical test using Molchan's error diagram, we inquired into the existence of precursory anomalous seismic activities of the large earthquakes and, if any, their characteristic time span. The test indicated that the Japanese M ≧ 6.4 inland earthquakes tend to be preceded by anomalous seismic activities of 8-to-10-yr time scales.

  9. Feature Extraction for Structural Dynamics Model Validation

    Energy Technology Data Exchange (ETDEWEB)

    Farrar, Charles [Los Alamos National Laboratory; Nishio, Mayuko [Yokohama University; Hemez, Francois [Los Alamos National Laboratory; Stull, Chris [Los Alamos National Laboratory; Park, Gyuhae [Chonnam Univesity; Cornwell, Phil [Rose-Hulman Institute of Technology; Figueiredo, Eloi [Universidade Lusófona; Luscher, D. J. [Los Alamos National Laboratory; Worden, Keith [University of Sheffield

    2016-01-13

    As structural dynamics becomes increasingly non-modal, stochastic and nonlinear, finite element model-updating technology must adopt the broader notions of model validation and uncertainty quantification. For example, particular re-sampling procedures must be implemented to propagate uncertainty through a forward calculation, and non-modal features must be defined to analyze nonlinear data sets. The latter topic is the focus of this report, but first, some more general comments regarding the concept of model validation will be discussed.

  10. Structural features of protein folding nuclei.

    Science.gov (United States)

    Garbuzynskiy, S O; Kondratova, M S

    2008-03-05

    A crucial event of protein folding is the formation of a folding nucleus. We demonstrate the presence of a considerable coincidence between the location of folding nuclei and the location of so-called "root structural motifs", which have unique overall folds and handedness. In the case of proteins with a single root structural motif, the involvement in the formation of a folding nucleus is in average significantly higher for amino acids residues that are in root structural motifs, compared to residues in other parts of the protein. The tests carried out revealed that the observed difference is statistically reliable. Thus, a structural feature that corresponds to the protein folding nucleus is now found.

  11. Cold Thermal Anomalous Structure within Lower Mantle and Its Geodynamic Implications

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The lateral temperature anomalous structure of the lower mantle is reconstructed from the seismic tomographical model and high temperature and high pressure laboratory results. A significant correlation between the distribution of the cold anomaly and the location of past subduction belts shows that the shallower anomaly corresponds to the younger subduction sites, while the deeper anomaly to the older ones. This correlation also suggests that the cold anomaly may have come from the subduction slabs and the scale of mantle convection may have been completed. The coldest and largest anomaly is concentrated near the core-mantle boundary (CMB). Few cold anomalies float in the shallower and middle parts of the lower mantle, suggesting that the downward migration of the subduction slabs, discontinuous and step-like, may be divided into the following three stages: subduction, stagnation at the 670 km discontinuity due to the phase transition, and disintegration when the size exceeds the critical point.

  12. Structure investigation of metal ions clustering in dehydrated gel using x-ray anomalous dispersion effect

    CERN Document Server

    Soejima, Y; Sugiyama, M; Annaka, M; Nakamura, A; Hiramatsu, N; Hara, K

    2003-01-01

    The structure of copper ion clusters in dehydrated N-isopropylacrylamide/sodium acrylate (NIPA/SA) gel has been studied by means of small angle X-ray scattering (SAXS) method. In order to distinguish the intensity scattered by Cu ions, the X-ray anomalous dispersion effect around the Cu K absorption edge has been coupled with SAXS. It is found that the dispersion effect dependent on the incident X-ray energy is remarkable only at the momentum transfer q = 0.031 A sup - sup 1 , where a SAXS peak is observed. The results indicate that copper ions form clusters in the dehydrated gel, and that the mean size of clusters is the same as that of SA clusters produced by microphase separation. It is therefore naturally presumed that copper ions are adsorbed into the SA molecules. On the basis of the presumption, a mechanism is proposed for microphase-separation and clustering of Cu ions.

  13. Is there evidence for anomalous dipole anisotropy in the large-scale structure?

    CERN Document Server

    Bengaly,, C A P; Alcaniz, J S; Xavier, H S; Novaes, C P

    2016-01-01

    We probe the anisotropy of the large-scale structure (LSS) with the WISE-2MASS catalogue. This analysis is performed by a directional comparison of the galaxy number counts through the entire celestial sphere once systematic effects, such as star-galaxy separation and foregrounds contamination, are properly taken into account. We find a maximal hemispherical asymmetry whose dipolar component is $A = 0.0507 \\pm 0.0014$ toward the $(l,b) = (323^{\\circ},-5^{\\circ})$ direction. This result is consistent with previous estimations of our proper motion in low and intermediate redshifts, as those carried out with Type Ia Supernovae and similar LSS catalogues.Furthermore, this dipole amplitude obtained is statistically consistent with mock catalogues simulated according to the $\\Lambda$CDM matter density expected fluctuations, in addition to observational biases such as the incomplete celestial coverage, anisotropic sky exposure. Our results suggest, therefore, that there is no strong evidence for anomalous anisotropy...

  14. Anomalous High-Energy Waterfall-Like Electronic Structure in 5 d Transition Metal Oxide Sr2IrO4 with a Strong Spin-Orbit Coupling.

    Science.gov (United States)

    Liu, Yan; Yu, Li; Jia, Xiaowen; Zhao, Jianzhou; Weng, Hongming; Peng, Yingying; Chen, Chaoyu; Xie, Zhuojin; Mou, Daixiang; He, Junfeng; Liu, Xu; Feng, Ya; Yi, Hemian; Zhao, Lin; Liu, Guodong; He, Shaolong; Dong, Xiaoli; Zhang, Jun; Xu, Zuyan; Chen, Chuangtian; Cao, Gang; Dai, Xi; Fang, Zhong; Zhou, X J

    2015-08-12

    The low energy electronic structure of Sr2IrO4 has been well studied and understood in terms of an effective Jeff = 1/2 Mott insulator model. However, little work has been done in studying its high energy electronic behaviors. Here we report a new observation of the anomalous high energy electronic structure in Sr2IrO4. By taking high-resolution angle-resolved photoemission measurements on Sr2IrO4 over a wide energy range, we have revealed for the first time that the high energy electronic structures show unusual nearly-vertical bands that extend over a large energy range. Such anomalous high energy behaviors resemble the high energy waterfall features observed in the cuprate superconductors. While strong electron correlation plays an important role in producing high energy waterfall features in the cuprate superconductors, the revelation of the high energy anomalies in Sr2IrO4, which exhibits strong spin-orbit coupling and a moderate electron correlation, points to an unknown and novel route in generating exotic electronic excitations.

  15. Anomalous current structure in the eastern equatorial Indian Indian Ocean during the south-west monsoon of 1994

    Digital Repository Service at National Institute of Oceanography (India)

    Unnikrishnan, A.S.; Murty, V.S.N.; Babu, M.T.; Gopinathan, C.K.; Charyulu, R.J.K.

    and anomalous current structure in the upper ocean. A warm (28.4-28.8 degrees C) and less-saline (33 to 34.8) deep (60-75 m) homogeneous layer characterizes the surface mixed layer. The south-west monsoon current, advecting the Arabian Sea High Salinity Water...

  16. Anomalous origin of the left coronary artery from the pulmonary trunk. Clinical features and midterm results after surgical treatment

    Directory of Open Access Journals (Sweden)

    Amaral Fernando

    1999-01-01

    Full Text Available OBJECTIVE: To report the authors' experience with the anomalous origin of the left coronary artery (AOLCA from the pulmonary trunk, emphasizing preoperative data, surgical aspects and midterm results of the follow-up. METHODS: Retrospective analysis of 11 patients operated upon at the Royal Brompton Hospital from October, 84 to April, 97. RESULTS: Nine infants had heart failure (HF and two other children presented with dyspnea and chest pain. All had ECG changes. The echocardiogram identified the anomalous origin of the coronary artery in 7 (64% patients and hemodynamic studies were performed in 7 patients. All infants were operated upon between the 2nd and 10th month of life. Six patients were treated with aortic reimplantation of the left coronary artery, whereas five were operated upon according to the Takeuchi technique. All patients are alive, with clear improvement of the ECG changes and ventricular function, as evaluated by echocardiography. Two patients operated upon according to the Takeuchi technique required additional surgery due to severe supravalvular pulmonary stenosis. CONCLUSION: AOLCA is a rare disease. Most patients show early signs of severe HF associated with ECG findings. Surgical therapy must be instituted early in the disease, preferentially through aortic implantation of the anomalous coronary artery, with a high possibility of success. Shortly after surgery, clinical and ECG improvement, as well as normalization of left ventricular function, should be expected.

  17. Effect of extended confinement on the structure of edge channels in the quantum anomalous Hall effect

    Science.gov (United States)

    Yue, Z.; Raikh, M. E.

    2016-09-01

    The Quantum anomalous Hall (QAH) effect in the films with nontrivial band structure accompanies the ferromagnetic transition in the system of magnetic dopants. Experimentally, the QAH transition manifests itself as a jump in the dependence of longitudinal resistivity on a weak external magnetic field. Microscopically, this jump originates from the emergence of a chiral edge mode on one side of the ferromagnetic transition. We study analytically the effect of an extended confinement on the structure of the edge modes. We employ the simplest model of the extended confinement in the form of a potential step next to the hard wall. It is shown that, unlike the conventional quantum Hall effect, where all edge channels are chiral, in the QAH effect, a complex structure of the boundary leads to nonchiral edge modes which are present on both sides of the ferromagnetic transition. Wave functions of nonchiral modes are different above and below the transition: on the "topological" side, where the chiral edge mode is supported, nonchiral modes are "repelled" from the boundary; i.e., they are much less localized than on the "trivial" side. Thus, the disorder-induced scattering into these modes will boost the extension of the chiral edge mode. The prime experimental manifestation of nonchiral modes is that, by contributing to longitudinal resistance, they smear the QAH transition.

  18. Structural Features of Caspase-Activating Complexes

    Directory of Open Access Journals (Sweden)

    Hyun Ho Park

    2012-04-01

    Full Text Available Apoptosis, also called programmed cell death, is an orderly cellular suicide program that is critical for the development, immune regulation and homeostasis of a multi-cellular organism. Failure to control this process can lead to serious human diseases, including many types of cancer, neurodegenerative diseases, and autoimmununity. The process of apoptosis is mediated by the sequential activation of caspases, which are cysteine proteases. Initiator caspases, such as caspase-2, -8, -9, and -10, are activated by formation of caspase-activating complexes, which function as a platform to recruit caspases, providing proximity for self-activation. Well-known initiator caspase-activating complexes include (1 DISC (Death Inducing Signaling Complex, which activates caspases-8 and 10; (2 Apoptosome, which activates caspase-9; and (3 PIDDosome, which activates caspase-2. Because of the fundamental biological importance of capases, many structural and biochemical studies to understand the molecular basis of assembly mechanism of caspase-activating complexes have been performed. In this review, we summarize previous studies that have examined the structural and biochemical features of caspase-activating complexes. By analyzing the structural basis for the assembly mechanism of the caspase-activating complex, we hope to provide a comprehensive understanding of caspase activation by these important oligomeric complexes.

  19. The Structure of Anomalous Oceanic Circulation In The Indian Ocean Dipole

    Science.gov (United States)

    Zhao, Qigeng

    Using an Indian-Pacific Ocean Circulation Model with high resolution a simulation study on the Indian Ocean dipole (IOD) has been done. Forcing the mdel with monthly observational wind stress in 1990-1999 the main characteristics of sea temperature variations in the two IODs (in 1997 and 1994) have been reproduced well. The pat- terns and center positions of sea temperature anomalies in the tropical Indian Ocean surface and in the section of equator-depth during the IOD from the simulation are basically consistent with that from observation. The physical image of anomalous circulation during IOD is revealed from the simulation. We find that an anomalous easterly current along the equator in the upper layer of the eastern Indian Ocean dur- ing IOD period. It is very strong, narrow band and is divergent from equator to both sides. It represents a Rossby wave propagated westwards. During IOD phase there a significant anomalous current cell in the section of equator-depth: the easterly current in the upper layer; westerly compensated current below it; a strong upwelling to the east of 80 E; a weak downwelling to the west of 55 E. Meanwhile two anomalous meridian cells are in the both sides of equator in the eastern Indian Ocean. The com- mon upwelling of them is near equator. The patterns of anomalous current in the out of IOD phase are basically opposite to that in the IOD phase, besides the absolute value of the anomalous current is weaker. Therefore the anomalous sea temperature in the tropical Indian Ocean during IOD could be interpreted with anomalous horizontal and vertical current, especially large-scale upwelling and downwelling.

  20. Prion protein: structural features and related toxicity

    Institute of Scientific and Technical Information of China (English)

    Ping Ping Hu; Cheng Zhi Huang

    2013-01-01

    Transmissible spongiform encephalopathies,or prion diseases,is a group of infectious neurodegenerative disorders.The conformational conversion from cellular form (PrPC) to disease-causing isoform (PrPSc) is considered to be the most important and remarkable event in these diseases,while accumulation of PrPSc is thought to be the main reason for cell death,inflammation and spongiform degeneration observed in infected individuals.Although these rare but unique neurodegenerative disorders have attracted much attention,there are still many questions that remain to be answered.Knowledge of the scrapie agent structures and the toxic species may have significance for understanding the causes of the diseases,and could be helpful for rational design of novel therapeutic and diagnostic methods.In this review,we summarized the available experimental evidence concerning the relationship among the structural features,aggregation status of misfolded PrP and related neurotoxicity in the course of prion diseases development.In particular,most data supports the idea that the smaller oligomeric PrPSc aggregates,rather than the mature amyloid fibers,exhibit the highest toxicity to the host.

  1. Is there evidence for anomalous dipole anisotropy in the large-scale structure?

    Science.gov (United States)

    Bengaly, C. A. P., Jr.; Bernui, A.; Alcaniz, J. S.; Xavier, H. S.; Novaes, C. P.

    2017-01-01

    We probe the anisotropy of the large-scale structure (LSS) with the WISE-2MASS catalogue. This analysis is performed by a directional comparison of the galaxy number counts through the entire celestial sphere once systematic effects, such as star-galaxy separation and foregrounds contamination, are properly taken into account. We find a maximal hemispherical asymmetry whose dipolar component is A = 0.0507 ± 0.0014 towards the (l, b) = (323°, -5°) direction, whose result is consistent with previous estimations of our proper motion in low and intermediate redshifts, as those carried out with Type Ia Supernovae and similar LSS catalogues. Furthermore, this dipole amplitude is statistically consistent (p-value = 0.061) with mock catalogues simulated according to the expected Λ cold dark matter density fluctuations, in addition to observational biases such as the incomplete celestial coverage and anisotropic sky exposure. Our results suggest, therefore, that there is no strong evidence for anomalous anisotropy in the LSS, given the limitations and systematics of current data, in the concordance model scenario.

  2. Is there evidence for anomalous dipole anisotropy in the large-scale structure?

    Science.gov (United States)

    Bengaly, C. A. P.; Bernui, A.; Alcaniz, J. S.; Xavier, H. S.; Novaes, C. P.

    2016-09-01

    We probe the anisotropy of the large-scale structure (LSS) with the WISE-2MASS catalogue. This analysis is performed by a directional comparison of the galaxy number counts through the entire celestial sphere once systematic effects, such as star-galaxy separation and foregrounds contamination, are properly taken into account. We find a maximal hemispherical asymmetry whose dipolar component is A = 0.0507 ± 0.0014 toward the (l, b) = (323°, -5°) direction, whose result is consistent with previous estimations of our proper motion in low and intermediate redshifts, as those carried out with Type Ia Supernovae and similar LSS catalogues. Furthermore, this dipole amplitude is statistically consistent (p-value = 0.061) with mock catalogues simulated according to the expected ΛCDM matter density fluctuations, in addition to observational biases such as the incomplete celestial coverage and anisotropic sky exposure. Our results suggest, therefore, that there is no strong evidence for anomalous anisotropy in the LSS, given the limitations and systematics of current data, in the concordance model scenario.

  3. Correlation of structural order, anomalous density, and hydrogen bonding network of liquid water.

    Science.gov (United States)

    Bandyopadhyay, Dibyendu; Mohan, S; Ghosh, S K; Choudhury, Niharendu

    2013-07-25

    We use extensive molecular dynamics simulations employing different state-of-the-art force fields to find a common framework for comparing structural orders and density anomalies as obtained from different water models. It is found that the average number of hydrogen bonds correlates well with various order parameters as well as the temperature of maximum densities across the different models, unifying apparently disparate results from different models and emphasizing the importance of hydrogen bonding in determining anomalous properties and the structure of water. A deeper insight into the hydrogen bond network of water reveals that the solvation shell of a water molecule can be defined by considering only those neighbors that are hydrogen-bonded to it. On the basis of this view, the origin of the appearance of a non-tetrahedral peak at a higher temperature in the distribution of tetrahedral order parameters has been explained. It is found that a neighbor that is hydrogen-bonded to the central molecule is tetrahedrally coordinated even at higher temperatures. The non-tetrahedral peak at a higher temperature arises due to the strained orientation of the neighbors that are non-hydrogen-bonded to the central molecule. With the new definition of the solvation shell, liquid water can be viewed as an instantaneously changing random hydrogen-bonded network consisting of differently coordinated hydrogen-bonded molecules with their distinct solvation shells. The variation of the composition of these hydrogen-bonded molecules against temperature accounts for the density anomaly without introducing the concept of large-scale structural polyamorphism in water.

  4. Quantization and anomalous structures in the conductance of Si/SiGe quantum point contacts

    Science.gov (United States)

    von Pock, J. F.; Salloch, D.; Qiao, G.; Wieser, U.; Hackbarth, T.; Kunze, U.

    2016-04-01

    Quantum point contacts (QPCs) are fabricated on modulation-doped Si/SiGe heterostructures and ballistic transport is studied at low temperatures. We observe quantized conductance with subband separations up to 4 meV and anomalies in the first conductance plateau at 4e2/h. At a temperature of T = 22 mK in the linear transport regime, a weak anomalous kink structure arises close to 0.5(4e2/h), which develops into a distinct plateau-like structure as temperature is raised up to T = 4 K. Under magnetic field parallel to the wire up to B = 14 T, the anomaly evolves into the Zeeman spin-split level at 0.5(4e2/h), resembling the "0.7 anomaly" in GaAs/AlGaAs QPCs. Additionally, a zero-bias anomaly (ZBA) is observed in nonlinear transport spectroscopy. At T = 22 mK, a parallel magnetic field splits the ZBA peak up into two peaks. At B = 0, elevated temperatures lead to similar splitting, which differs from the behavior of ZBAs in GaAs/AlGaAs QPCs. Under finite dc bias, the differential resistance exhibits additional plateaus approximately at 0.8(4e2/h) and 0.2(4e2/h) known as "0.85 anomaly" and "0.25 anomaly" in GaAs/AlGaAs QPCs. Unlike the first regular plateau at 4e2/h, the 0.2(4e2/h) plateau is insensitive to dc bias voltage up to at least VDS = 80 mV, in-plane magnetic fields up to B = 15 T, and to elevated temperatures up to T = 25 K. We interpret this effect as due to pinching off one of the reservoirs close to the QPC. We do not see any indication of lifting of the valley degeneracy in our samples.

  5. Correlating anomalous diffusion with lipid bilayer membrane structure using single molecule tracking and atomic force microscopy

    Science.gov (United States)

    Skaug, Michael J.; Faller, Roland; Longo, Marjorie L.

    2011-06-01

    Anomalous diffusion has been observed abundantly in the plasma membrane of biological cells, but the underlying mechanisms are still unclear. In general, it has not been possible to directly image the obstacles to diffusion in membranes, which are thought to be skeleton bound proteins, protein aggregates, and lipid domains, so the dynamics of diffusing particles is used to deduce the obstacle characteristics. We present a supported lipid bilayer system in which we characterized the anomalous diffusion of lipid molecules using single molecule tracking, while at the same time imaging the obstacles to diffusion with atomic force microscopy. To explain our experimental results, we performed lattice Monte Carlo simulations of tracer diffusion in the presence of the experimentally determined obstacle configurations. We correlate the observed anomalous diffusion with obstacle area fraction, fractal dimension, and correlation length. To accurately measure an anomalous diffusion exponent, we derived an expression to account for the time-averaging inherent to all single molecule tracking experiments. We show that the length of the single molecule trajectories is critical to the determination of the anomalous diffusion exponent. We further discuss our results in the context of confinement models and the generating stochastic process.

  6. The Edgerton Structure: A Possible Meteorite Impact Feature in Eastern Kansas

    Directory of Open Access Journals (Sweden)

    Daniel F. Merriam

    2009-01-01

    Full Text Available Recognized meteorite impact features are relatively rare in the U.S. Midcontinent region, but recently with increased interest and research, the number has increased dramatically. We add another possibility to the growing list, the Edgerton structure in northwestern Miami County, Kansas. The feature is elliptical (∼5.5 × 6.5 km, slightly elongated east-west with radial surface drainage. The feature was first observed on hillshade maps of digitized topography of 7.5 minute quadrangles. Subsequent magnetic profiles show a higher magnetic value in the center of the ellipse with higher values around the edges; this shape is characteristic of an impact feature. Depth to the anomalous body is estimated to be about 1 km, which puts it in the Precambrian crystalline basement under a cover of Paleozoic sediments. There are no deep boreholes in the vicinity and no seismic profiles are available. If it is an impact structure, it will be the second such feature documented in Kansas, the first being the Brenham meteorite crater at Haviland in Kiowa County in southwestern Kansas. It would be older than the other impact structures identified in the Midcontinent—Manson in Iowa, Ames in Oklahoma, Haswell Hole in Colorado, and possibly Belton in Missouri and Merna in Nebraska. There are at least two other prospective impact features in Kansas: the Goddard ring west of Wichita and Garden City ellipse north-west of Garden City.

  7. Temperature-induced anomalous structural changes of Al-12wt.%Sn-4wt.%Si melt and its influence on as-cast structure

    Directory of Open Access Journals (Sweden)

    Wang Zhiming

    2010-05-01

    Full Text Available The temperature dependence of the viscosity of liquid Al-12wt.%Sn-4wt.%Si was studied with a high-temperature viscosity apparatus. Anomalous changes of viscosity of the melt were found at 1,103 K and 968 K in the cooling process, which indicates anomalous structural changes of the melt. It is calculated that the anomalous structural change is associated with an abrupt decrease of atomic clusters’ size and activation energy in the melt. According to the temperature of the anomalous structural changes, melt heat treatment process (quenching from superheat to pouring temperature was performed on Al-12wt.%Sn-4wt.%Si melt prior to pouring, aimed to keep the small atomic clusters from higher temperature to lower pouring temperature. The results suggest that relatively small atomic clusters at the pouring temperature in the melt could generate a deep under-cooling of nucleation in the subsequent solidification process, and refine the as-cast structure. After being quenched from superheating to pouring temperature, the relatively small atomic clusters, especially the Si-Si clusters in the melt will grow to equilibrium state (relatively big atomic clusters with holding time, resulting in the prominent coarsening of the Si morphology in the as-cast structure.

  8. Correlating Anomalous Diffusion with Membrane Obstacle Structure Using Single Molecule Tracking and AFM

    Science.gov (United States)

    Skaug, Michael; Longo, Marjorie; Faller, Roland

    2011-03-01

    Anomalous diffusion has been observed abundantly in the plasma membrane, but the underlying mechanisms are still unclear. In general, it has not been possible to directly image the obstacles to diffusion in membranes, so the dynamics of diffusing particles are used to deduce the obstacle characteristics. We present a supported lipid bilayer system in which we characterized the anomalous diffusion of lipid molecules using single molecule tracking, while at the same time imaging the obstacles to diffusion with atomic force microscopy. To explain our experimental results, we performed lattice Monte Carlo simulations of tracer diffusion in the presence of the experimentally determined obstacle configurations. We correlate the observed anomalous diffusion with obstacle area fraction, fractal dimension and correlation length. We further discuss our results in the context of confinement models and the generating stochastic process. Supported by NSF grant CBET 0506602.

  9. Count rates and structure factors in anomalous soft x-ray scattering from cuprate superconductors

    NARCIS (Netherlands)

    Abbamonte, P; Rusydi, A; Logvenov, G; Bozovic, [No Value; Sawatzky, GA; Venema, L.C.; Bozovic,; Pavuna, D

    2002-01-01

    It has recently been shown that x-ray diffraction from the doped holes in cuprates can be enhanced by 3-4 orders of magnitude by exploiting resonance effects in the oxygen K shell. This new type of anomalous scattering is direct way of probing ground state inhomogeneity in the mobile carrier liquid

  10. A semi-structured, phenomenologically oriented psychiatric interview: Descriptive congruens in assessing anomalous subjective experience and mental status

    DEFF Research Database (Denmark)

    Frederiksen, Julie Elisabeth Nordgaard; Parnas, Josef Stefan Stanislaw

    2012-01-01

    the interrater congruens between experienced clinicians with a semi structured, phenomenologically oriented psychopathological interview assessing anomalous self-experience and mental status. Method: Seventeen inpatients were interviewed by one of the raters, with both raters were present. The interview......, phenomenological-oriented semi-structured interview. Limitations: The major limitation of the study is a relatively small sample size, conditioned by the time-consuming nature of the individual interviews. Second, we should have included a measurement of reliability in a less experiencedrecently EASE......-introduced rater, since it is that kind of researchers that are typically enrolled for the empirical data collections....

  11. Structure damage detection based on random forest recursive feature elimination

    Science.gov (United States)

    Zhou, Qifeng; Zhou, Hao; Zhou, Qingqing; Yang, Fan; Luo, Linkai

    2014-05-01

    Feature extraction is a key former step in structural damage detection. In this paper, a structural damage detection method based on wavelet packet decomposition (WPD) and random forest recursive feature elimination (RF-RFE) is proposed. In order to gain the most effective feature subset and to improve the identification accuracy a two-stage feature selection method is adopted after WPD. First, the damage features are sorted according to original random forest variable importance analysis. Second, using RF-RFE to eliminate the least important feature and reorder the feature list each time, then get the new feature importance sequence. Finally, k-nearest neighbor (KNN) algorithm, as a benchmark classifier, is used to evaluate the extracted feature subset. A four-storey steel shear building model is chosen as an example in method verification. The experimental results show that using the fewer features got from proposed method can achieve higher identification accuracy and reduce the detection time cost.

  12. Origins of Anomalous Transport in Disordered Media: Structural and Dynamic Controls

    CERN Document Server

    Edery, Yaniv; Guadagnini, Alberto; Berkowitz, Brian

    2013-01-01

    We quantitatively identify the origin of anomalous transport in a representative model of a heterogeneous system---tracer migration in the complex flow patterns of a lognormally distributed hydraulic conductivity ($K$) field. The transport, determined by a particle tracking technique, is characterized by breakthrough curves; the ensemble averaged curves document anomalous transport in this system, which is entirely accounted for by a truncated power-law distribution of local transition times $\\psi(t)$ within the framework of a continuous time random walk. Unique to this study is the linking of $\\psi(t)$ directly to the system heterogeneity. We assess the statistics of the dominant preferred pathways by forming a particle-visitation weighted histogram $\\{wK\\}$. Converting the ln($K$) dependence of $\\{wK\\}$ into time yields the equivalence of $\\{wK\\}$ and $\\psi(t)$, and shows the part of $\\{wK\\}$ that forms the power-law of $\\psi(t)$, which is the origin of anomalous transport. We also derive an expression defi...

  13. Anomalous diffusion of isoelectronic antimony implant induced defects in GaAs-AlGaAs multiquantum well structures

    Science.gov (United States)

    Rao, E. V. K.; Krauz, Ph.; Thibierge, H.; Azoulay, R.; Vieu, C.

    1994-03-01

    We present here evidence on the deep diffusion of isoelectronic Sb implant induced defects in thick GaAs-AlGaAs multiquantum well structures (MQW) to depths as far as ˜30 times the implant projected range (Rp). This observation has been confirmed by performing low temperature photoluminescence depth scanning measurements and cross-sectional transmission electron microscopy (XTEM) analysis on room temperature Sb implanted thick MQW samples. An explanation based on the isoelectronic nature of Sb and its substitution on As site (SbAs) has been proposed to understand the anomalous diffusion of defects during implant and their contribution to Al/Ga disordering during post-implant annealing.

  14. Structural features of reconstituted wheat wax films.

    Science.gov (United States)

    Pambou, Elias; Li, Zongyi; Campana, Mario; Hughes, Arwel; Clifton, Luke; Gutfreund, Philipp; Foundling, Jill; Bell, Gordon; Lu, Jian R

    2016-07-01

    Cuticular waxes are essential for the well-being of all plants, from controlling the transport of water and nutrients across the plant surface to protecting them against external environmental attacks. Despite their significance, our current understanding regarding the structure and function of the wax film is limited. In this work, we have formed representative reconstituted wax film models of controlled thicknesses that facilitated an ex vivo study of plant cuticular wax film properties by neutron reflection (NR). Triticum aestivum L. (wheat) waxes were extracted from two different wheat straw samples, using two distinct extraction methods. Waxes extracted from harvested field-grown wheat straw using supercritical CO2 are compared with waxes extracted from laboratory-grown wheat straw via wax dissolution by chloroform rinsing. Wax films were produced by spin-coating the two extracts onto silicon substrates. Atomic force microscopy and cryo-scanning electron microscopy imaging revealed that the two reconstituted wax film models are ultrathin and porous with characteristic nanoscale extrusions on the outer surface, mimicking the structure of epicuticular waxes found upon adaxial wheat leaf surfaces. On the basis of solid-liquid and solid-air NR and ellipsometric measurements, these wax films could be modelled into two representative layers, with the diffuse underlying layer fitted with thicknesses ranging from approximately 65 to 70 Å, whereas the surface extrusion region reached heights exceeding 200 Å. Moisture-controlled NR measurements indicated that water penetrated extensively into the wax films measured under saturated humidity and under water, causing them to hydrate and swell significantly. These studies have thus provided a useful structural basis that underlies the function of the epicuticular waxes in controlling the water transport of crops.

  15. Structural features of sequential weak measurements

    Science.gov (United States)

    Diósi, Lajos

    2016-07-01

    We discuss the abstract structure of sequential weak measurement (WM) of general observables. In all orders, the sequential WM correlations without postselection yield the corresponding correlations of the Wigner function, offering direct quantum tomography through the moments of the canonical variables. Correlations in spin-1/2 sequential weak measurements coincide with those in strong measurements, they are constrained kinematically, and they are equivalent with single measurements. In sequential WMs with postselection, an anomaly occurs, different from the weak value anomaly of single WMs. In particular, the spread of polarization σ ̂ as measured in double WMs of σ ̂ will diverge for certain orthogonal pre- and postselected states.

  16. Detecting Lo cal Manifold Structure for Unsup ervised Feature Selection

    Institute of Scientific and Technical Information of China (English)

    FENG Ding-Cheng; CHEN Feng; XU Wen-Li

    2014-01-01

    Unsupervised feature selection is fundamental in statistical pattern recognition, and has drawn persistent attention in the past several decades. Recently, much work has shown that feature selection can be formulated as nonlinear dimensionality reduction with discrete constraints. This line of research emphasizes utilizing the manifold learning techniques, where feature selection and learning can be studied based on the manifold assumption in data distribution. Many existing feature selection methods such as Laplacian score, SPEC (spectrum decomposition of graph Laplacian), TR (trace ratio) criterion, MSFS (multi-cluster feature selection) and EVSC (eigenvalue sensitive criterion) apply the basic properties of graph Laplacian, and select the optimal feature subsets which best preserve the manifold structure defined on the graph Laplacian. In this paper, we propose a new feature selection perspective from locally linear embedding (LLE), which is another popular manifold learning method. The main difficulty of using LLE for feature selection is that its optimization involves quadratic programming and eigenvalue decomposition, both of which are continuous procedures and different from discrete feature selection. We prove that the LLE objective can be decomposed with respect to data dimensionalities in the subset selection problem, which also facilitates constructing better coordinates from data using the principal component analysis (PCA) technique. Based on these results, we propose a novel unsupervised feature selection algorithm, called locally linear selection (LLS), to select a feature subset representing the underlying data manifold. The local relationship among samples is computed from the LLE formulation, which is then used to estimate the contribution of each individual feature to the underlying manifold structure. These contributions, represented as LLS scores, are ranked and selected as the candidate solution to feature selection. We further develop a

  17. Structural health monitoring feature design by genetic programming

    Science.gov (United States)

    Harvey, Dustin Y.; Todd, Michael D.

    2014-09-01

    Structural health monitoring (SHM) systems provide real-time damage and performance information for civil, aerospace, and other high-capital or life-safety critical structures. Conventional data processing involves pre-processing and extraction of low-dimensional features from in situ time series measurements. The features are then input to a statistical pattern recognition algorithm to perform the relevant classification or regression task necessary to facilitate decisions by the SHM system. Traditional design of signal processing and feature extraction algorithms can be an expensive and time-consuming process requiring extensive system knowledge and domain expertise. Genetic programming, a heuristic program search method from evolutionary computation, was recently adapted by the authors to perform automated, data-driven design of signal processing and feature extraction algorithms for statistical pattern recognition applications. The proposed method, called Autofead, is particularly suitable to handle the challenges inherent in algorithm design for SHM problems where the manifestation of damage in structural response measurements is often unclear or unknown. Autofead mines a training database of response measurements to discover information-rich features specific to the problem at hand. This study provides experimental validation on three SHM applications including ultrasonic damage detection, bearing damage classification for rotating machinery, and vibration-based structural health monitoring. Performance comparisons with common feature choices for each problem area are provided demonstrating the versatility of Autofead to produce significant algorithm improvements on a wide range of problems.

  18. Anomalous structural disorder and distortion in metal-to-insulator-transition Ti{sub 2}O{sub 3}

    Energy Technology Data Exchange (ETDEWEB)

    Hwang, In-Hui; Jin, Zhenlan; Park, Chang-In; Han, Sang-Wook, E-mail: shan@jbnu.ac.kr [Department of Physics Education and Institute of Fusion Science, Jeonbuk(Chonbuk) National University, Jeonju 561-756 (Korea, Republic of); Jiang, Bingzhi [Department of Physics, Yanbian University, Yanji 133002 (China)

    2016-01-07

    Mott proposed that impurity bands in corundum-symmetry Ti{sub 2}O{sub 3} at high temperatures caused a collapse in the bandgap. However, the origin of the impurity bands has not yet been clarified. We examine the local structural properties of metal-to-insulator-transition Ti{sub 2}O{sub 3} using in-situ x-ray absorption fine structure (XAFS) measurements at the Ti K edge in the temperature range from 288 to 739 K. The Ti{sub 2}O{sub 3} powder is synthesized by using a chemical reaction method. X-ray diffraction (XRD) measurements from Ti{sub 2}O{sub 3} with a Rietveld refinement demonstrate a single-phased R-3c symmetry without additional distortion. Extended-XAFS combined with XRD reveals a zigzag patterned Ti position and an anomalous structural disorder in Ti-Ti pairs, accompanied by a bond length expansion of the Ti-Ti pairs along the c-axis for T > 450 K. The local structural distortion and disorder of the Ti atoms would induce impurity levels in the band gap between the Ti 3d a{sub 1g} and e{sub g}{sup π} bands, resulting in a collapse of the band gap for T > 450 K.

  19. Nonlinear feature identification of impedance-based structural health monitoring

    Energy Technology Data Exchange (ETDEWEB)

    Rutherford, A. C. (Amanda C.); Park, G. H. (Gyu Hae); Sohn, H. (Hoon); Farrar, C. R. (Charles R.)

    2004-01-01

    The impedance-based structural health monitoring technique, which utilizes electromechanical coupling properties of piezoelectric materials, has shown feasibility for use in a variety of structural health monitoring applications. Relying on high frequency local excitations (typically > 30 kHz), this technique is very sensitive to minor changes in structural integrity in the near field of piezoelectric sensors. Several damage sensitive features have been identified and used coupled with the impedance methods. Most of these methods are, however, limited to linearity assumptions of a structure. This paper presents the use of experimentally identified nonlinear features, combined with impedance methods, for structural health monitoring. Their applicability to damage detection in various frequency ranges is demonstrated using actual impedance signals measured from a portal frame structure. The performance of the nonlinear feature is compared with those of conventional impedance methods. This paper reinforces the utility of nonlinear features in structural health monitoring and suggests that their varying sensitivity in different frequency ranges may be leveraged for certain applications.

  20. Embarras de richesses – It is not good to be too anomalous: Accurate structure of selenourea, a chiral crystal of planar molecules

    Science.gov (United States)

    Luo, Zhipu

    2017-01-01

    Selenourea, SeC(NH2)2, recently found an application as a derivatization reagent providing a significant anomalous diffraction signal used for phasing macromolecular crystal structures. The crystal structure of selenourea itself was solved about 50 years ago, from data recorded on films and evaluated by eye and refined to R = 0.15 with errors of bond lengths and angles about 0.1 Å and 6°. In the current work this structure is re-evaluated on the basis of synchrotron data and refined to R1 = 0.021 with bond and angle errors about 0.007 Å and 0.5°. The nine planar molecules of selenourea pack either in the P31 or in the P32 unit cell. All unique molecules are connected by a complex network of Se•••H-N hydrogen bonds and Se•••Se contacts. The packing of selenourea molecules is highly pseudosymmetric, approximating either of the P31(2)12, R3, and R32 space groups. Because the overwhelming majority of diffracted X-ray intensity originates form the anomalously scattering selenium atoms, the measurable anomalous Bijvoet differences are diminished and it was not possible to solve this crystal structure based on the anomalous signal alone. PMID:28207770

  1. FeatureMap3D - a tool to map protein features and sequence conservation onto homologous structures in the PDB

    DEFF Research Database (Denmark)

    Wernersson, Rasmus; Rapacki, Krzysztof; Stærfeldt, Hans Henrik;

    2006-01-01

    FeatureMap3D is a web-based tool that maps protein features onto 3D structures. The user provides sequences annotated with any feature of interest, such as post-translational modifications, protease cleavage sites or exonic structure and FeatureMap3D will then search the Protein Data Bank (PDB) f...

  2. The Structure and Rainfall Features of Tropical Cyclone Rammasun (2002)

    Institute of Scientific and Technical Information of China (English)

    马雷鸣; 端义宏; 朱永褆

    2004-01-01

    Tropical Rainfall Measuring Mission (TRMM) data [TRMM Microwave Imager/Precipitation Radar/Visible and Infrared Scanner (TMI/PR/VIRS)] and a numerical model are used to investigate the structure and rainfall features of Tropical Cyclone (TC) Rammasun (2002). Based on the analysis of TRMM data, which are diagnosed together with NCEP/AVN [Aviation (global model)] analysis data,some typical features of TC structure and rainfall are preliminary discovered. Since the limitations of TRMM data are considered for their time resolution and coverage, the world observed by TRMM at several moments cannot be taken as the representation of the whole period of the TC lifecycle, therefore the picture should be reproduced by a numerical model of high quality. To better understand the structure and rainfall features of TC Rammasun, a numerical simulation is carried out with mesoscale model MM5in which the validations have been made with the data of TRMM and NCEP/AVN analysis.

  3. Structure determination of a 16.8 kDa copper protein at 2.1 A resolution using anomalous scattering data with direct methods.

    Science.gov (United States)

    Harvey, I; Hao, Q; Duke, E M; Ingledew, W J; Hasnain, S S

    1998-07-01

    The structure of rusticyanin, an acid-stable copper protein, has been determined at 2.1 A resolution by direct methods combined with the single-wavelength anomalous scattering (SAS) of copper (f" = 3.9 e-) and then conventionally refined (Rcryst = 18.7%, Rfree = 21.9%). This is the largest unknown protein structure (Mr approximately /= 16.8 kDa) to be determined using the SAS and direct-methods approach and demonstrates that by exploiting the anomalous signal at a single wavelength, direct methods can be used to determine phases at typical (approximately 2 A) macromolecular crystallographic resolutions. Extrapolating from the size of the anomalous signal for copper (f" approximately 4 e-), this result suggests that the approach could be used for proteins with molecular weights of up to 33 kDa per Se (f"max++ = 8 e- at the 'white line') and 80 kDa for a Pt derivative (f"max = 19 e- at the 'white line', L3 edge). The method provides a powerful alternative in solving a de novo protein structure without either preparing multiple crystals (i.e. isomorphous heavy-atom derivative plus native crystals) or collecting multi-wavelength anomalous diffraction (MAD) data.

  4. Feature Comparison in Structural Health Monitoring of a Vehicle Crane

    Directory of Open Access Journals (Sweden)

    J. Kullaa

    2008-01-01

    Full Text Available Vibration-based structural health monitoring of a vehicle crane was studied. The performance of different features to detect damage was investigated after eliminating the normal operational variations using factor analysis. Using eight accelerometers, ten AR parameters from each record were identified for damage detection. Also transmissibilities between sensors were estimated. Damage was introduced with additional masses at different locations of the structure. All damage cases could be detected from either features using control charts, but transmissibilities proved to be more sensitive to damage than the AR coefficients.

  5. Systematic Limitations in Concentration Analysis via Anomalous Small-Angle X-ray Scattering in the Small Structure Limit

    Directory of Open Access Journals (Sweden)

    Guenter Goerigk

    2016-03-01

    Full Text Available Anomalous small angle scattering measurements have been applied to diluted solutions of anionic polyacrylates decorated by specifically-interacting Pb2+ cations, revealing partial collapse of the polyacrylate into pearl-like subdomains with a size on the order of a few nanometers. From the pure-resonant scattering contribution of the Pb2+ cations, and from subsequent analysis of the resonant-invariant, the amount of Pb2+ cations condensed onto the polyanions with respect to the total amount of Pb2+ cations in the solvent was estimated. In order to scrutinize systematic limitations in the determination of the chemical concentrations of resonant scattering counterions in the collapsed phase, Monte Carlo simulations have been performed. The simulations are based on structural confinements at variable size in the range of few nanometers, which represent the collapsed subdomains in the polyanions. These confinements were gradually filled to a high degree of the volume fraction with resonant scattering counterions giving access to a resonant-invariant at a variable degree of filling. The simulations revealed in the limit of small structures a significant underestimation of the true degree of filling of the collapsed subdomains when determining chemical concentrations of Pb2+ cations from the resonant invariant.

  6. Nonparametric statistical structuring of knowledge systems using binary feature matches

    DEFF Research Database (Denmark)

    Mørup, Morten; Glückstad, Fumiko Kano; Herlau, Tue

    2014-01-01

    Structuring knowledge systems with binary features is often based on imposing a similarity measure and clustering objects according to this similarity. Unfortunately, such analyses can be heavily influenced by the choice of similarity measure. Furthermore, it is unclear at which level clusters ha...

  7. Electrophysical properties and structural features of shungite (natural nanostructured carbon)

    Science.gov (United States)

    Golubev, E. A.

    2013-05-01

    This paper presents the results of investigations of the electrical conductive properties with a nanoscale locality at nanoampere currents and the results of an analysis of the correlation between the electrical conductivity and structural features of natural glassy carbon, i.e., shungite. The investigations have been performed using atomic force microscopy, electric force spectroscopy, scanning spreading resistance microscopy, X-ray spectroscopic analysis, and Raman spectroscopy. It has been found that there are differences in electrical conductive properties of the structurally similar shungite samples formed under different PT conditions. Based on the analysis of the structural parameters and specific features of the shungite compositions, it has been shown that the effect of intercalation of impurities into boundary layers of graphene sheets has the most significant influence on the electrical and physical properties of the shungites. The differences in types and values of conductivity of the shungite samples are determined by the different degrees of intercalation.

  8. Anomalous magnetic structure and spin dynamics in magnetoelectric LiFePO4

    DEFF Research Database (Denmark)

    Toft-Petersen, Rasmus; Reehuis, Manfred; Jensen, Thomas Bagger Stibius

    2015-01-01

    We report significant details of the magnetic structure and spin dynamics of LiFePO4 obtained by single-crystal neutron scattering. Our results confirm a previously reported collinear rotation of the spins away from the principal b axis, and they determine that the rotation is toward the a axis...

  9. Anomalous Development of Brain Structure and Function in Spina Bifida Myelomeningocele

    Science.gov (United States)

    Juranek, Jenifer; Salman, Michael S.

    2010-01-01

    Spina bifida myelomeningocele (SBM) is a specific type of neural tube defect whereby the open neural tube at the level of the spinal cord alters brain development during early stages of gestation. Some structural anomalies are virtually unique to individuals with SBM, including a complex pattern of cerebellar dysplasia known as the Chiari II…

  10. Anomalously high lifetimes measured by quasi-steady-state photoconductance in advanced solar cell structures

    Science.gov (United States)

    Juhl, Mattias; Chan, Catherine; Abbott, Malcolm D.; Trupke, Thorsten

    2013-12-01

    Quasi-Steady-State Photoconductance is widely used in photovoltaics industry to measure the effective minority carrier lifetime of silicon wafers, a key material parameter affecting final solar cell efficiency. When interpreting photoconductance based lifetime measurements, it is important to account for various artefacts that can cause an over-estimation of the carrier lifetime, such as minority carrier trapping. This paper provides experimental evidence for another artefact in photoconductance lifetime measurements, affecting samples that have a conductive layer that is interrupted by lines of the opposite polarity doping, forming laterally alternating regions of p/n doping. This structure often appears in the emitter region of samples used to monitor the lifetime of interdigitated back contact cells. The cause of this artefact is linked to a reduction in the measured dark conductance. Experimental data are presented that suggest this is due to the formation of a phototransistor type structure on the samples surface, resulting in variations in conductivity under different illumination levels.

  11. Investigation on the anomalous structure of the nanocrystal Ti and Zr films

    Science.gov (United States)

    Shi, W.; Kong, J.; Shen, H.; Du, Guo-Ping; Yao, W.; Qi, Zhen Z.

    1991-11-01

    The nanocrystal Ti and Zr films were prepared by dc magnetron sputtering method on a liquid N2 cooled copper substrate using Ti and Zr metal targets, respectively. The grain size of the Ti and Zr films is in the range of 5 - 12 nm, determined by both TEM observation and x- ray diffraction patterns using Warren-Averbach analysis. The structure anomaly for Ti and Zr films are found by means of electron diffraction as well as x-ray diffraction. The results of x- ray diffraction show that they are typical bcc structure for Ti films, which appears only at high temperature (more than 885 degree(s)C). The tattice parameter is 0.33178 nm close to that of the diffraction data extended from Ta-Ti alloys (JCPDS-5-628). For Zr nanocrystal films, the x-ray diffraction patterns show that it is (omega) -phase which appears only at high pressure above 39 kbar.

  12. Anomalous plasma transport and induced electric field in a stochastic magnetic field structure

    Energy Technology Data Exchange (ETDEWEB)

    Kubota, Tetsuyuki; Itoh, Sanae-I.; Toda, Shinichiro; Yamaguchi, Hiroki [Kyushu Univ., Fukuoka (Japan); Fukuyama, Atsushi [Okayama Univ. (Japan)

    1995-04-01

    The plasma transport matrix is formulated using the kinetic equation for the particles in the stochastic magnetic field. The radial electric field generation is analyzed using this transport matrix. This thermoelectric field is dictated by the difference between the electron heat flux and the ion heat flux. We calculate the spatial structures of the radial electric field and the temperature in the stochastic field region. 7 refs., 3 figs.

  13. Mathematical Structure of Anomalous Dimensions and QCD Wilson Coefficients in Higher Order

    Science.gov (United States)

    Blümlein, J.

    2004-10-01

    The alternating and non-alternating harmonic sums and other algebraic objects of the same equivalence class are connected by algebraic relations which are induced by the product of these quantities and which depend on their index class rather than on their value. We show how to find a basis of the associated algebra. The length of the basis l is found to be ⩽1/d, where d is the depth of the sums considered and is given by the 2nd WITT formula. It can be also determined counting the LYNDON words of the respective index set. There are two further classes of relations: structural relations between NIELSEN-type integrals and relations due to the specific structure of Feynman diagrams which lead to a considerable reduction of the set of basic functions. The relations derived can be used to simplify results of higher order calculations in QED and QCD. We also report on results calculating the 16th non-singlet moment of unpolarized structure functions at 3-loop order in the MS¯ scheme.

  14. Mathematical structure of anomalous dimensions and QCD Wilson coefficients in higher order

    Energy Technology Data Exchange (ETDEWEB)

    Bluemlein, J. [Deutsches Elektronen Synchrotron, DESY, Platanenallee 6, D-15738 Zeuthen (Germany)

    2004-10-01

    The alternating and non-alternating harmonic sums and other algebraic objects of the same equivalence class are connected by algebraic relations which are induced by the product of these quantities and which depend on their index class rather than on their value. We show how to find a basis of the associated algebra. The length of the basis l is found to be =<1/d, where d is the depth of the sums considered and is given by the 2nd Witt formula. It can be also determined counting the Lyndon words of the respective index set. There are two further classes of relations: structural relations between Nielsen-type integrals and relations due to the specific structure of Feynman diagrams which lead to a considerable reduction of the set of basic functions. The relations derived can be used to simplify results of higher order calculations in QED and QCD. We also report on results calculating the 16th non-singlet moment of unpolarized structure functions at 3-loop order in the MS-bar scheme.

  15. Clinical features and long-term prognosis of patients with anomalous origin of the left coronary artery from the pulmonary artery

    Institute of Scientific and Technical Information of China (English)

    ZHENG Jian-yong; ZHAO Qu-ming; HAN Ling; DING Wen-hong; JIN Mei; ZHANG Gui-zhen; XIAO Yan-yan; LUO Yi; CHENG Pei; MENG Xu

    2010-01-01

    Background Anomalous origin of the left coronary artery from the pulmonary artery (ALCAPA) is a rare congenital heart anomaly. We aimed to illustrate the clinical features and long-term prognosis of patients with ALCAPA.Methods Twenty three patients (13 males and 10 females, ages ranging from 2.5 months to 65 years) identified as ALCAPA in Beijing Anzhen Hospital from April 1984 to June 2009 were divided into two groups, based on the age of onset: group 1 (≤12 months, n=16) and group 2 (>12 months, n=7).Results Fifty six point three percent of patients in group 1 had been misdiagnosed as endocardial fibroelastosis (9/16),18.8% as dilated cardiomyopathy (3/16) and 6.3% as myocardial infarction (1/16). Patients in group 2 were usually diagnosed as coronary heart disease, myocarditis, or patent ductus arteriosus. Electrocardiography in group 1 revealed abnormal Q waves with T wave inversion in leads I, avL, V4-V6, especially in lead avL (deep and wide Q wave); but no specific manifestations in group 2. A higher percentage of patients in group 1 had cardiomegaly on chest radiograph (86.7% vs. 33.3%, P=0.031), while pulmonary artery protrusion was more common in group 2 (26.7% vs. 83.3%,P=0.046). Lower left ventricular ejection fraction (LVEF) was present in group 1 than in group 2 ((48.5±11.5)% vs.(65.0±6.1)%, P <0.001). Apical ventricular aneurysm (62.5% vs. 0%, P=0.007), enhanced echogenicity of papillary muscles (87.5% vs. 28.6%, P=0.011) and endocardial thickening (93.8% vs. 14.3%, P <0.001) were more frequent in group 1 than in group 2. The ratio of the proximal right coronary artery (RCA) diameter to the aortic root diameter exceeded 0.14 in all cases, more prominent in group 2 (0.26±0.05 vs. 0.33±0.03, P=0.009). Increased coronary artery collaterals within the interventricular septum were detected in 18 patients (78.3%) by Doppler imaging. Twenty one patients underwent cardiac surgery, including left coronary artery (LCA) ligation (1/21), LCA

  16. Anomalous diffusion of epicentres

    CERN Document Server

    Sotolongo-Costa, Oscar; Posadas, A; Luzon, F

    2007-01-01

    The classification of earthquakes in main shocks and aftershocks by a method recently proposed by M. Baiesi and M. Paczuski allows to the generation of a complex network composed of clusters that group the most correlated events. The spatial distribution of epicentres inside these structures corresponding to the catalogue of earthquakes in the eastern region of Cuba shows anomalous anti-diffusive behaviour evidencing the attractive nature of the main shock and the possible description in terms of fractional kinetics.

  17. A Study of Neutron Star Structure in Strong Magnetic Fields that includes Anomalous Magnetic Moments

    Institute of Scientific and Technical Information of China (English)

    Guang-Jun Mao; Akira Iwamoto; Zhu-Xia Li

    2003-01-01

    We study the effect of strong magnetic fields on the structure of neutronstar. We find that if the interior field is on the same order as the surface fieldcurrently observed, then the influences of the field on the star's mass and radius arenegligible; if the field is as large as that estimated from the scalar virial theorem,then considerable effects will be induced. The maximum mass of the star will beincreased substantially while the central density is greatly reduced. The radius ofa magnetic star can be larger by about 10% ~ 20% than a nonmagnetic star of thesame mass.

  18. Structural features of plastic deformation in bulk metallic glasses

    Energy Technology Data Exchange (ETDEWEB)

    Scudino, S., E-mail: s.scudino@ifw-dresden.de; Shakur Shahabi, H.; Stoica, M.; Kühn, U. [IFW Dresden, Institut für Komplexe Materialien, D-01069 Dresden (Germany); Kaban, I.; Escher, B.; Eckert, J. [IFW Dresden, Institut für Komplexe Materialien, D-01069 Dresden (Germany); TU Dresden, Institut für Werkstoffwissenschaft, D-01062 Dresden (Germany); Vaughan, G. B. M. [European Synchrotron Radiation Facilities ESRF, BP220, 38043 Grenoble (France)

    2015-01-19

    Spatially resolved strain maps of a plastically deformed bulk metallic glass (BMG) have been created by using high-energy X-ray diffraction. The results reveal that plastic deformation creates a spatially heterogeneous atomic arrangement, consisting of strong compressive and tensile strain fields. In addition, significant shear strain is introduced in the samples. The analysis of the eigenvalues and eigenvectors of the strain tensor indicates that considerable structural anisotropy occurs in both the magnitude and direction of the strain. These features are in contrast to the behavior observed in elastically deformed BMGs and represent a distinctive structural sign of plastic deformation in metallic glasses.

  19. Structural features of carbon materials synthesized by different methods

    Science.gov (United States)

    Streletskii, O. A.; Ivanenko, I. P.; Khvostov, V. V.; Savchenko, N. F.; Nishchak, O. Yu.; Aleksandrov, A. F.

    2016-10-01

    This paper presents the results of investigations of three types of carbon structures synthesized by different methods, such as arc discharge plasma enhanced chemical vapor deposition of carbon in a magnetic field, chemical dehydrohalogenation of the poly(vinyl chloride)/poly(vinylidene chloride) precursor, and pulsed plasma ion assisted deposition. It has been found that the samples prepared by different methods have a common feature, i.e., the presence of three-dimensional clusters based on sp 2- or sp 3-bonds surrounded by quasi-one-dimensional carbon chains. It has been shown that the structure of carbon materials changes depending on the synthesis conditions.

  20. Trapping, anomalous transport and quasi-coherent structures in magnetically confined plasmas

    CERN Document Server

    Vlad, Madalina

    2009-01-01

    Strong electrostatic turbulence in magnetically confined plasmas is characterized by trapping or eddying of particle trajectories produced by the $E\\times B$ stochastic drift. Trapping is shown to produce strong effects on test particles and on test modes. It determines non-standard statistics of trajectories: non-Gaussian distribution, memory effects and coherence. Trapped trajectories form quasi-coherent structure. Trajectory trapping has strong nonlinear effects on the test modes on turbulent plasmas. We determine the growth rate of drift modes as function of the statistical characteristics of the background turbulence. We show that trapping provides the physical mechanism for the inverse cascade observed in drift turbulence and for the zonal flow generation.

  1. Feature Analysis and Modeling of the Network Community Structure

    Institute of Scientific and Technical Information of China (English)

    袁超; 柴毅; 魏善碧

    2012-01-01

    Community structure has an important influence on the structural and dynamic characteristics of the complex systems.So it has attracted a large number of researchers.However,due to its complexity,the mechanism of action of the community structure is still not clear to this day.In this paper,some features of the community structure have been discussed.And a constraint model of the community has been deduced.This model is effective to identify the communities.And especially,it is effective to identify the overlapping nodes between the communities.Then a community detection algorithm,which has linear time complexity,is proposed based on this constraint model,a proposed node similarity model and the Modularity Q.Through some experiments on a series of real-world and synthetic networks,the high performances of the algorithm and the constraint model have been illustrated.

  2. Structural properties of prokaryotic promoter regions correlate with functional features.

    Directory of Open Access Journals (Sweden)

    Pieter Meysman

    Full Text Available The structural properties of the DNA molecule are known to play a critical role in transcription. In this paper, the structural profiles of promoter regions were studied within the context of their diversity and their function for eleven prokaryotic species; Escherichia coli, Klebsiella pneumoniae, Salmonella Typhimurium, Pseudomonas auroginosa, Geobacter sulfurreducens Helicobacter pylori, Chlamydophila pneumoniae, Synechocystis sp., Synechoccocus elongates, Bacillus anthracis, and the archaea Sulfolobus solfataricus. The main anchor point for these promoter regions were transcription start sites identified through high-throughput experiments or collected within large curated databases. Prokaryotic promoter regions were found to be less stable and less flexible than the genomic mean across all studied species. However, direct comparison between species revealed differences in their structural profiles that can not solely be explained by the difference in genomic GC content. In addition, comparison with functional data revealed that there are patterns in the promoter structural profiles that can be linked to specific functional loci, such as sigma factor regulation or transcription factor binding. Interestingly, a novel structural element clearly visible near the transcription start site was found in genes associated with essential cellular functions and growth in several species. Our analyses reveals the great diversity in promoter structural profiles both between and within prokaryotic species. We observed relationships between structural diversity and functional features that are interesting prospects for further research to yet uncharacterized functional loci defined by DNA structural properties.

  3. Critical Features of Fragment Libraries for Protein Structure Prediction.

    Science.gov (United States)

    Trevizani, Raphael; Custódio, Fábio Lima; Dos Santos, Karina Baptista; Dardenne, Laurent Emmanuel

    2017-01-01

    The use of fragment libraries is a popular approach among protein structure prediction methods and has proven to substantially improve the quality of predicted structures. However, some vital aspects of a fragment library that influence the accuracy of modeling a native structure remain to be determined. This study investigates some of these features. Particularly, we analyze the effect of using secondary structure prediction guiding fragments selection, different fragments sizes and the effect of structural clustering of fragments within libraries. To have a clearer view of how these factors affect protein structure prediction, we isolated the process of model building by fragment assembly from some common limitations associated with prediction methods, e.g., imprecise energy functions and optimization algorithms, by employing an exact structure-based objective function under a greedy algorithm. Our results indicate that shorter fragments reproduce the native structure more accurately than the longer. Libraries composed of multiple fragment lengths generate even better structures, where longer fragments show to be more useful at the beginning of the simulations. The use of many different fragment sizes shows little improvement when compared to predictions carried out with libraries that comprise only three different fragment sizes. Models obtained from libraries built using only sequence similarity are, on average, better than those built with a secondary structure prediction bias. However, we found that the use of secondary structure prediction allows greater reduction of the search space, which is invaluable for prediction methods. The results of this study can be critical guidelines for the use of fragment libraries in protein structure prediction.

  4. Critical Features of Fragment Libraries for Protein Structure Prediction

    Science.gov (United States)

    dos Santos, Karina Baptista

    2017-01-01

    The use of fragment libraries is a popular approach among protein structure prediction methods and has proven to substantially improve the quality of predicted structures. However, some vital aspects of a fragment library that influence the accuracy of modeling a native structure remain to be determined. This study investigates some of these features. Particularly, we analyze the effect of using secondary structure prediction guiding fragments selection, different fragments sizes and the effect of structural clustering of fragments within libraries. To have a clearer view of how these factors affect protein structure prediction, we isolated the process of model building by fragment assembly from some common limitations associated with prediction methods, e.g., imprecise energy functions and optimization algorithms, by employing an exact structure-based objective function under a greedy algorithm. Our results indicate that shorter fragments reproduce the native structure more accurately than the longer. Libraries composed of multiple fragment lengths generate even better structures, where longer fragments show to be more useful at the beginning of the simulations. The use of many different fragment sizes shows little improvement when compared to predictions carried out with libraries that comprise only three different fragment sizes. Models obtained from libraries built using only sequence similarity are, on average, better than those built with a secondary structure prediction bias. However, we found that the use of secondary structure prediction allows greater reduction of the search space, which is invaluable for prediction methods. The results of this study can be critical guidelines for the use of fragment libraries in protein structure prediction. PMID:28085928

  5. Unsupervised Anomalous Vertices Detection Utilizing Link Prediction Algorithms

    CERN Document Server

    Kagan, Dima; Elovici, amd Yuval

    2016-01-01

    In the past decade, complex network structures have penetrated nearly every aspect of our lives. The detection of anomalous vertices in these networks can uncover important insights, such as exposing intruders in a computer network. In this study, we present a novel unsupervised two-layered meta classifier that can be employed to detect irregular vertices in complex networks using solely features extracted from the network topology. Our method is based on the hypothesis that a vertex having many links with low probabilities of existing has a higher likelihood of being anomalous. We evaluated our method on ten networks, using three fully simulated, five semi-simulated, and two real world datasets. In all the scenarios, our method was able to identify anomalous and irregular vertices with low false positive rates and high AUCs. Moreover, we demonstrated that our method can be applied to security-related use cases and is able to detect malicious profiles in online social networks.

  6. Anomalous Hall effect in epitaxially grown ferromagnetic FeGa/Fe3Ga hybrid structure: Evidence of spin carrier polarized by clusters

    Science.gov (United States)

    Duc Dung, Dang; Cho, Sunglae

    2013-05-01

    The anomalous Hall resistance relative with magnetic anisotropy of clusters Fe3Ga in Fe3Ga/Fe-Ga hybrid structural epitaxial was reported. The out-of-plane magnetic anisotropy was obtained for Fe3Ga/Fe-Ga hybrid structure, while in-plane magnetic anisotropy is shown in the single Fe-Ga phase epitaxial on GaAs(001). The observation of trend of saturation Hall resistance in Fe3Ga/Fe-Ga hybrid structural is compared with the Fe-Ga single crystal, which is solid evidence for spin polarization by local magnetic clusters.

  7. Nanoscale structural features determined by AFM for single virus particles.

    Science.gov (United States)

    Chen, Shu-wen W; Odorico, Michael; Meillan, Matthieu; Vellutini, Luc; Teulon, Jean-Marie; Parot, Pierre; Bennetau, Bernard; Pellequer, Jean-Luc

    2013-11-21

    In this work, we propose "single-image analysis", as opposed to multi-image averaging, for extracting valuable information from AFM images of single bio-particles. This approach allows us to study molecular systems imaged by AFM under general circumstances without restrictions on their structural forms. As feature exhibition is a resolution correlation, we have performed AFM imaging on surfaces of tobacco mosaic virus (TMV) to demonstrate variations of structural patterns with probing resolution. Two AFM images were acquired with the same tip at different probing resolutions in terms of pixel width, i.e., 1.95 and 0.49 nm per pixel. For assessment, we have constructed an in silico topograph based on the three-dimensional crystal structure of TMV as a reference. The prominent artifacts observed in the AFM-determined shape of TMV were attributed to tip convolutions. The width of TMV rod was systematically overestimated by ~10 nm at both probing resolutions of AFM. Nevertheless, the effects of tip convolution were less severe in vertical orientation so that the estimated height of TMV by AFM imaging was in close agreement with the in silico X-ray topograph. Using dedicated image processing algorithms, we found that at low resolution (i.e., 1.95 nm per pixel), the extracted surface features of TMV can be interpreted as a partial or full helical repeat (three complete turns with ~7.0 nm in length), while individual protein subunits (~2.5 nm) were perceivable only at high resolution. The present study shows that the scales of revealed structural features in AFM images are subject to both probing resolution and processing algorithms for image analysis.

  8. Feature and Statistical Model Development in Structural Health Monitoring

    Science.gov (United States)

    Kim, Inho

    All structures suffer wear and tear because of impact, excessive load, fatigue, corrosion, etc. in addition to inherent defects during their manufacturing processes and their exposure to various environmental effects. These structural degradations are often imperceptible, but they can severely affect the structural performance of a component, thereby severely decreasing its service life. Although previous studies of Structural Health Monitoring (SHM) have revealed extensive prior knowledge on the parts of SHM processes, such as the operational evaluation, data processing, and feature extraction, few studies have been conducted from a systematical perspective, the statistical model development. The first part of this dissertation, the characteristics of inverse scattering problems, such as ill-posedness and nonlinearity, reviews ultrasonic guided wave-based structural health monitoring problems. The distinctive features and the selection of the domain analysis are investigated by analytically searching the conditions of the uniqueness solutions for ill-posedness and are validated experimentally. Based on the distinctive features, a novel wave packet tracing (WPT) method for damage localization and size quantification is presented. This method involves creating time-space representations of the guided Lamb waves (GLWs), collected at a series of locations, with a spatially dense distribution along paths at pre-selected angles with respect to the direction, normal to the direction of wave propagation. The fringe patterns due to wave dispersion, which depends on the phase velocity, are selected as the primary features that carry information, regarding the wave propagation and scattering. The following part of this dissertation presents a novel damage-localization framework, using a fully automated process. In order to construct the statistical model for autonomous damage localization deep-learning techniques, such as restricted Boltzmann machine and deep belief network

  9. Facilitating best practices in collecting anomalous scattering data for de novo structure solution at the ESRF Structural Biology Beamlines

    Science.gov (United States)

    de Sanctis, Daniele; Oscarsson, Marcus; Popov, Alexander; Svensson, Olof; Leonard, Gordon

    2016-01-01

    The constant evolution of synchrotron structural biology beamlines, the viability of screening protein crystals for a wide range of heavy-atom derivatives, the advent of efficient protein labelling and the availability of automatic data-processing and structure-solution pipelines have combined to make de novo structure solution in macromolecular crystallography a less arduous task. Nevertheless, the collection of diffraction data of sufficient quality for experimental phasing is still a difficult and crucial step. Here, some examples of good data-collection practice for projects requiring experimental phasing are presented and recent developments at the ESRF Structural Biology beamlines that have facilitated these are illustrated. PMID:26960128

  10. Understanding Protein-Protein Interactions Using Local Structural Features

    DEFF Research Database (Denmark)

    Planas-Iglesias, Joan; Bonet, Jaume; García-García, Javier;

    2013-01-01

    Protein-protein interactions (PPIs) play a relevant role among the different functions of a cell. Identifying the PPI network of a given organism (interactome) is useful to shed light on the key molecular mechanisms within a biological system. In this work, we show the role of structural features...... (loops and domains) to comprehend the molecular mechanisms of PPIs. A paradox in protein-protein binding is to explain how the unbound proteins of a binary complex recognize each other among a large population within a cell and how they find their best docking interface in a short timescale. We use...

  11. Nonlocal Anomalous Hall Effect.

    Science.gov (United States)

    Zhang, Steven S-L; Vignale, Giovanni

    2016-04-01

    The anomalous Hall (AH) effect is deemed to be a unique transport property of ferromagnetic metals, caused by the concerted action of spin polarization and spin-orbit coupling. Nevertheless, recent experiments have shown that the effect also occurs in a nonmagnetic metal (Pt) in contact with a magnetic insulator [yttrium iron garnet (YIG)], even when precautions are taken to ensure that there is no induced magnetization in the metal. We propose a theory of this effect based on the combined action of spin-dependent scattering from the magnetic interface and the spin-Hall effect in the bulk of the metal. At variance with previous theories, we predict the effect to be of first order in the spin-orbit coupling, just as the conventional anomalous Hall effect-the only difference being the spatial separation of the spin-orbit interaction and the magnetization. For this reason we name this effect the nonlocal anomalous Hall effect and predict that its sign will be determined by the sign of the spin-Hall angle in the metal. The AH conductivity that we calculate from our theory is in order of magnitude agreement with the measured values in Pt/YIG structures.

  12. Nonlocal Anomalous Hall Effect

    Science.gov (United States)

    Zhang, Steven S.-L.; Vignale, Giovanni

    2016-04-01

    The anomalous Hall (AH) effect is deemed to be a unique transport property of ferromagnetic metals, caused by the concerted action of spin polarization and spin-orbit coupling. Nevertheless, recent experiments have shown that the effect also occurs in a nonmagnetic metal (Pt) in contact with a magnetic insulator [yttrium iron garnet (YIG)], even when precautions are taken to ensure that there is no induced magnetization in the metal. We propose a theory of this effect based on the combined action of spin-dependent scattering from the magnetic interface and the spin-Hall effect in the bulk of the metal. At variance with previous theories, we predict the effect to be of first order in the spin-orbit coupling, just as the conventional anomalous Hall effect—the only difference being the spatial separation of the spin-orbit interaction and the magnetization. For this reason we name this effect the nonlocal anomalous Hall effect and predict that its sign will be determined by the sign of the spin-Hall angle in the metal. The AH conductivity that we calculate from our theory is in order of magnitude agreement with the measured values in Pt /YIG structures.

  13. Xenoestrogenic gene expression: structural features of active polycyclic aromatic hydrocarbons.

    Science.gov (United States)

    Schultz, T Wayne; Sinks, Glendon D

    2002-04-01

    Estrogenicity was assessed using the Saccharomyces cerevisiae-based Lac-Z reporter assay and was reported as the logarithm of the inverse of the 50% molar beta-galactosidase activity (log[EC50(-1)]). In an effort to quantify the relationship between molecular structure of polycyclic aromatic hydrocarbons (PAHs) and estrogenic gene expression, a series of PAHs were evaluated. With noted exceptions, the results of these studies indicate that the initial two-dimensional structural warning for estrogenicity, the superpositioning of a hydroxylated aromatic system on the phenolic A-ring of 17-beta-estradiol, can be extended to the PAHs. This two-dimensional-alignment criterion correctly identified estrogenicity of 22 of the 29 PAHs evaluated. Moreover, the estrogenic potency of these compounds was directly related to the size of the hydrophobic backbone. The seven compounds classified incorrectly by this structural feature were either dihydroxylated naphthalenes or aromatic nitrogen-heterocyclic compounds; all such compounds were false positives. Results with dihydroxylated naphthalenes reveal derivatives that were nonestrogenic when superimposed on the phenolic A-ring of 17-beta-estradiol had the second hydroxyl group in the position of the C-ring or were catechol-like in structure. Structural alerts for nitrogen-heterocyclic compounds must take into account the position of the hydroxyl group and the in-ring nitrogen atom; compounds with the hydroxyl group and nitrogen atom involved with the same ring were observed to be nonactive.

  14. The 3-Loop Pure Singlet Heavy Flavor Contributions to the Structure Function $F_2(x,Q^2)$ and the Anomalous Dimension

    CERN Document Server

    Ablinger, J; Blümlein, J; De Freitas, A; von Manteuffel, A; Schneider, C

    2014-01-01

    The pure singlet asymptotic heavy flavor corrections to 3-loop order for the deep-inelastic scattering structure function $F_2(x,Q^2)$ and the corresponding transition matrix element $A_{Qq}^{(3), \\sf PS}$ in the variable flavor number scheme are computed. In Mellin-$N$ space these inclusive quantities depend on generalized harmonic sums. We also recalculate the complete 3-loop pure singlet anomalous dimension for the first time. Numerical results for the Wilson coefficients, the operator matrix element and the contribution to the structure function $F_2(x,Q^2)$ are presented.

  15. The 3-loop pure singlet heavy flavor contributions to the structure function F2(x,Q2 and the anomalous dimension

    Directory of Open Access Journals (Sweden)

    J. Ablinger

    2015-01-01

    Full Text Available The pure singlet asymptotic heavy flavor corrections to 3-loop order for the deep-inelastic scattering structure function F2(x,Q2 and the corresponding transition matrix element AQq(3,PS in the variable flavor number scheme are computed. In Mellin-N space these inclusive quantities depend on generalized harmonic sums. We also recalculate the complete 3-loop pure singlet anomalous dimension for the first time. Numerical results for the Wilson coefficients, the operator matrix element and the contribution to the structure function F2(x,Q2 are presented.

  16. Incorporating secondary structural features into sequence information for predicting protein structural class.

    Science.gov (United States)

    Liao, Bo; Peng, Ting; Chen, Haowen; Lin, Yaping

    2013-10-01

    Knowledge of structural classes is applied in numerous important predictive tasks that address structural and functional features of proteins, although the prediction accuracy of the protein structural classes is not high. In this study, 45 different features were rationally designed to model the differences between protein structural classes, among which, 30 of them reflect the combined protein sequence information. In terms of correlation function, the protein sequence can be converted to a digital signal sequence, from which we can generate 20 discrete Fourier spectrum numbers. According to the segments of amino with different characteristics occurring in protein sequences, the frequencies of the 10 kinds of segments of amino acid (motifs) in protein are calculated. Other features include the secondary structural information :10 features were proposed to model the strong adjacent correlations in the secondary structural elements and capture the long-range spatial interactions between secondary structures, other 5 features were designed to differentiate α/β from α+β classes , which is a major problem of the existing algorithm. The methods were proposed based on a large set of low-identity sequences for which secondary structure is predicted from their sequence (based on PSI-PRED). By means of this method, the overall prediction accuracy of four benchmark datasets were all improved. Especially for the dataset FC699, 25PDB and D1189 which are 1.26%, 1% and 0.85% higher than the best previous method respectively.

  17. Microfabricated structures and devices featuring nanostructured titania thin films

    Science.gov (United States)

    Monkowski, Adam J.

    2007-05-01

    When titanium reacts with hydrogen peroxide at 80°C--100°C, a nanostructured titania (NST) thin film is formed on the titanium surface. This nanostructured film is particularly suited for integration with thin film and bulk microfabrication techniques. The ability to manufacture devices in a batch format is a principal advantage of microfabrication-based production. To reliably produce arrays of micro-patterned NST thin films on the wafer scale, a patterning guideline must be considered. The formation of NST relies on a re-deposition process; adequate ti-peroxo species must be generated and remain at the solid-solution interface. Numerical analysis of the characteristic transient diffusion behavior for various micro-patterns has been compared with experimental data to generate a criterion to guide the design of NST micro-patterns. Wafer scale arrays of NST micro gas-sensors have been fabricated using standard thin film techniques. Sensing elements are 20 mum on a side. High sensitivity to hydrogen is achieved by modification of the sensors with platinum nanoparticles. When exposed to a 10 mT partial pressure of hydrogen at 250°C, the functionalized devices exhibit more than one order of magnitude resistance decrease with a response time of approximately 7 sec. Titanium microstructures formed using the titanium ICP deep etch (TIDE) process have been integrated with NST films to produce an ordered nanostructure-microstructure composite (3D-NST). The process developed allows for the incorporation of a planar top surface, advantageous for bonding and sealing applications, in which the nanostructured thin film is formed only on feature sidewalls and floors. When titanium microstructures are spaced less than 1 mum apart, titania nanostructures bridge adjacent features. NST and 3D-NST structures have been assembled and tested in a dye-sensitized solar cell (DSSC) device. The NST film is approximately 900nm thick; this yielded a DSSC with an efficiency of 1.8%, similar

  18. Anomalous ionic conductivity of Sc sub 2 (WO sub 4) sub 3 mediated by structural changes at high pressures and temperatures

    CERN Document Server

    Secco, R A; Imanaka, N; Adachi, G

    2002-01-01

    The ionic conductivity of Sc sub 2 (WO sub 4) sub 3 at 400 deg. C shows a normal decrease with increase in pressure up to 2.9 GPa but then increases anomalously at pressures up to 4.3 GPa. Synchrotron in situ x-ray diffraction results show that Sc sub 2 (WO sub 4) sub 3 undergoes pressure-induced amorphization at pressures coincident with the reversal in conductivity behaviour. The loss of crystal structure at high pressure may be associated with the property of negative thermal expansion in Sc sub 2 (WO sub 4) sub 3.

  19. Nano-structured titanium and aluminium nitride coatings: Study by grazing incidence X-ray diffraction and X-ray absorption and anomalous diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Tuilier, M.-H., E-mail: marie-helene.tuilier@uha.fr [Universite de Haute Alsace (UHA), Laboratoire Physique et Mecanique Textile (LPMT), EA 4365 -conventionnee au CNRS, Equipe PPMR, F-68093 Mulhouse (France); Pac, M.-J. [Universite de Haute Alsace (UHA), Laboratoire Physique et Mecanique Textile (LPMT), EA 4365 - conventionnee au CNRS, Equipe PPMR, F-68093 Mulhouse (France); Anokhin, D.V. [Universite de Haute Alsace (UHA), CNRS, Institut de Science des Materiaux de Mulhouse (IS2M), LRC 7228, F-68093 Mulhouse (France); Moscow State University, Faculty of Fundamental Physical and Chemical Engineering, 119991, Moscow, GSP-1, 1-51 Leninskie Gory (Russian Federation); Ivanov, D.A. [Universite de Haute Alsace (UHA), CNRS, Institut de Science des Materiaux de Mulhouse (IS2M), LRC 7228, F-68093 Mulhouse (France); Rousselot, C. [Universite de Franche-Comte, FEMTO-ST (UMR CNRS 6174), F-25211 Montbeliard (France); Thiaudiere, D. [Synchrotron Soleil, Saint Aubin, F-91192 Gif sur Yvette (France)

    2012-12-30

    Titanium and aluminium nitride thin films, Ti{sub 1-x}Al{sub x}N (x = 0, x = 0.5, x = 0.68), deposited by reactive magnetron sputtering on silicon substrates are investigated by combining two different X-ray diffraction experiments carried out using synchrotron radiation. Grazing-incidence X-ray diffraction and Ti K-edge diffraction anomalous near edge structure spectroscopy provide information on the micro- and nano-structure of the films respectively, which play a crucial role in the functionality of coatings. The spectroscopic data of Ti{sub 0.50}Al{sub 0.50}N film show that Ti atoms in crystallized domains and grain boundaries are all in octahedral cubic local order, but their growth mode is quite different. It is found that the crystallized part of the Ti{sub 0.50}Al{sub 0.50}N film has a single-crystalline nature, whereas the TiN one presents a fibrillar microstructure. For Ti{sub 0.32}Al{sub 0.68}N film, grazing-incidence X-ray diffraction provides information on the uniaxial texture along the [001] direction of the hexagonal lattice. A sharp Ti K pre-edge peak is observed in diffraction anomalous near edge spectrum that definitely shows that Ti atoms are incorporated in the hexagonal lattice of those fibrillar domains. Moreover, the difference observed between Ti K-edge diffraction anomalous and X-ray absorption pre-edge regions proves that a significant part of Ti atoms is located in nanocrystallites with cubic symmetry outside of the crystallized domains. - Highlights: Black-Right-Pointing-Pointer We study nano and micro-structures of TiN, Ti{sub 0.50}Al{sub 0.50}N and Ti{sub 0.32}Al{sub 0.68}N films. Black-Right-Pointing-Pointer Anomalous diffraction solves the crystallized part regardless of grain boundaries. Black-Right-Pointing-Pointer TiN microstructure is fibrillar, Ti{sub 0.5}Al{sub 0.5}N presents single crystalline domains. Black-Right-Pointing-Pointer For Ti{sub 0.32}Al{sub 0.68}N, Ti atoms are located in nanocrystallites with cubic symmetry

  20. Structural diversity in bacterial ribosomes: mycobacterial 70S ribosome structure reveals novel features.

    Directory of Open Access Journals (Sweden)

    Manidip Shasmal

    Full Text Available Here we present analysis of a 3D cryo-EM map of the 70S ribosome from Mycobacterium smegmatis, a saprophytic cousin of the etiological agent of tuberculosis in humans, Mycobacterium tuberculosis. In comparison with the 3D structures of other prokaryotic ribosomes, the density map of the M. smegmatis 70S ribosome reveals unique structural features and their relative orientations in the ribosome. Dramatic changes in the periphery due to additional rRNA segments and extra domains of some of the peripheral ribosomal proteins like S3, S5, S16, L17, L25, are evident. One of the most notable features appears in the large subunit near L1 stalk as a long helical structure next to helix 54 of the 23S rRNA. The sharp upper end of this structure is located in the vicinity of the mRNA exit channel. Although the M. smegmatis 70S ribosome possesses conserved core structure of bacterial ribosome, the new structural features, unveiled in this study, demonstrates diversity in the 3D architecture of bacterial ribosomes. We postulate that the prominent helical structure related to the 23S rRNA actively participates in the mechanisms of translation in mycobacteria.

  1. Structural features of DNA interaction with caffeine and theophylline

    Science.gov (United States)

    Nafisi, Shohreh; Manouchehri, Firouzeh; Tajmir-Riahi, Heidar-Ali; Varavipour, Maryam

    2008-03-01

    Caffeine and theophylline are strong antioxidants that prevent DNA damage. The anticancer and antiviral activities of these natural products are implicated in their mechanism of actions. However, there has been no information on the interactions of these xanthine derivatives with individual DNA at molecular level. The aim of this study was to examine the stability and structural features of calf-thymus DNA complexes with caffeine and theophylline in aqueous solution, using constant DNA concentration (6.25 mM) and various caffeine or theophylline/DNA(P) ratios of 1/80, 1/40, 1/20, 1/10, 1/5, 1/2 and 1/1. FTIR, UV-visible spectroscopic methods were used to determine the ligand external binding modes, the binding constant and the stability of caffeine, theophylline-DNA complexes in aqueous solution. Spectroscopic evidence showed that the complexation of caffeine and theophylline with DNA occurred via G-C and A-T and PO 2 group with overall binding constants of K(caffeine-DNA) = 9.7 × 10 3 M -1 and K(theophylline-DNA) = 1.7 × 10 4 M -1. The affinity of ligand-DNA binding is in the order of theophylline > caffeine. A partial B to A-DNA transition occurs upon caffeine and theophylline complexation.

  2. Relevance of echo-structure and texture features

    DEFF Research Database (Denmark)

    Karemore, Gopal; Mullick, Jhinuk Basu; KV, Dr. Rajagopal;

    2010-01-01

    Aim: Echostructure is an essential parameter for the evaluation of circumscribed lesions and can be described as a texture feature on ultrasound images. Present study evaluates the possibility of distinguishing between benign and malignant breast tumors using various texture features. Materials a...

  3. Weighted Feature Significance: A Simple, Interpretable Model of Compound Toxicity Based on the Statistical Enrichment of Structural Features

    OpenAIRE

    Huang, Ruili; Southall, Noel; Xia, Menghang; Cho, Ming-Hsuang; Jadhav, Ajit; Nguyen, Dac-Trung; Inglese, James; Tice, Raymond R.; Austin, Christopher P.

    2009-01-01

    In support of the U.S. Tox21 program, we have developed a simple and chemically intuitive model we call weighted feature significance (WFS) to predict the toxicological activity of compounds, based on the statistical enrichment of structural features in toxic compounds. We trained and tested the model on the following: (1) data from quantitative high–throughput screening cytotoxicity and caspase activation assays conducted at the National Institutes of Health Chemical Genomics Center, (2) dat...

  4. Electrical features of deep structures of Southern Tuscany (Italy)

    Energy Technology Data Exchange (ETDEWEB)

    Fiordelist, A. [ENEL-VDTG, Pisa (Italy); Mackie, R. [Geosystem, S.Francisco, CA (United States); Manzella, A. [Centro Nazionale delle Ricerche, Pisa (Italy). Istituto Internazionale per le Ricerche Geotermiche; Watts, D. [Geosystem, Milan (Italy); Zaja, A. [Padua Univ. (Italy). Dip. di Geologia, Paleontologia e Geofisica

    1998-08-01

    Over the last new years, magnetotelluric data were acquired at 86 sites covering much of Southern Tuscany. Twenty-four of these sites were acquired in single-site or local-reference mode, whereas 62 were acquired in very-remote-reference mode, with a remote site located on Capraia Island - 40 Km from the cost - where the cultural noise is very low. The data modelling showed that Southern Tuscany is characterized by a fairly uniform middle-lower crust that has a resistivity of a few thousand {Omega}centre dotm. The uniformity is interrupted only below the Larderello and Mt. Amiata geothermal fields where deep conductive bodies are believed to exist. A general anomalous condition can hence be depicted for this region, with low resistivity values typical of those in tectonically active areas as opposed to more resistive values typical in continental areas. These data and those from other geophysical techniques suggest that these conductive zones may be associated with hot material coming from deeper sources below the geothermal areas.

  5. Feature-based Design of Welded Structure for Robotic Arc Welding Off-line Programming

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Feature modeler of welded structure provides both 3D-geographical and non-geographical features for the off-line programming of arc welded robot. Welded structure is regarded as an assembly, the design of welded structure consists of three aspects: plane, joint, and groove design. Each aspect corresponds to a category of features. The plane features are defined by interactive feature definition. A method analogous to the “mating feature” is introduced to represent the joint features. Based on AutoCAD 2000, a B-rep solid modeler, a prototype system is implemented.

  6. Effect of processing on structural features of anodic aluminum oxides

    Science.gov (United States)

    Erdogan, Pembe; Birol, Yucel

    2012-09-01

    Morphological features of the anodic aluminum oxide (AAO) templates fabricated by electrochemical oxidation under different processing conditions were investigated. The selection of the polishing parameters does not appear to be critical as long as the aluminum substrate is polished adequately prior to the anodization process. AAO layers with a highly ordered pore distribution are obtained after anodizing in 0.6 M oxalic acid at 20 °C under 40 V for 5 minutes suggesting that the desired pore features are attained once an oxide layer develops on the surface. While the pore features are not affected much, the thickness of the AAO template increases with increasing anodization treatment time. Pore features are better and the AAO growth rate is higher at 20 °C than at 5 °C; higher under 45 V than under 40 V; higher with 0.6 M than with 0.3 M oxalic acid.

  7. Improving the performance of link prediction by adaptively exploiting multiple structural features of networks

    CERN Document Server

    Ma, Chuang; Zhang, Hai-Feng

    2016-01-01

    So far, many network-structure-based link prediction methods have been proposed. However, these traditional methods were proposed by highlighting one or two structural features of networks, and then use the methods to implement link prediction in different networks. In many cases, the performance is not ideal since each network has its unique underlying structural features. In this article, by analyzing different real networks, we find that the structural features of different networks are remarkably different. In particular, even in the same networks, their inner structural features are utterly different. Inspired by these facts, an \\emph{adaptive} link prediction method is proposed to incorporate multiple structural features from the perspective of combination optimization. In the model, the weight of each structural feature is \\emph{adaptively } determined by logistic regression but not be artificially given in advance. According to our experimental results, we find that the logistic regression based link ...

  8. Improving protein structural class prediction using novel combined sequence information and predicted secondary structural features.

    Science.gov (United States)

    Dai, Qi; Wu, Li; Li, Lihua

    2011-12-01

    Protein structural class prediction solely from protein sequences is a challenging problem in bioinformatics. Numerous efficient methods have been proposed for protein structural class prediction, but challenges remain. Using novel combined sequence information coupled with predicted secondary structural features (PSSF), we proposed a novel scheme to improve prediction of protein structural classes. Given an amino acid sequence, we first transformed it into a reduced amino acid sequence and calculated its word frequencies and word position features to combine novel sequence information. Then we added the PSSF to the combine sequence information to predict protein structural classes. The proposed method was tested on four benchmark datasets in low homology and achieved the overall prediction accuracies of 83.1%, 87.0%, 94.5%, and 85.2%, respectively. The comparison with existing methods demonstrates that the overall improvements range from 2.3% to 27.5%, which indicates that the proposed method is more efficient, especially for low-homology amino acid sequences.

  9. Process Features in Writing: Internal Structure and Incremental Value over Product Features. Research Report. ETS RR-15-27

    Science.gov (United States)

    Zhang, Mo; Deane, Paul

    2015-01-01

    In educational measurement contexts, essays have been evaluated and formative feedback has been given based on the end product. In this study, we used a large sample collected from middle school students in the United States to investigate the factor structure of the writing process features gathered from keystroke logs and the association of that…

  10. Features for Exploiting Black-Box Optimization Problem Structure

    DEFF Research Database (Denmark)

    Tierney, Kevin; Malitsky, Yuri; Abell, Tinus

    2013-01-01

    Black-box optimization (BBO) problems arise in numerous scientic and engineering applications and are characterized by compu- tationally intensive objective functions, which severely limit the number of evaluations that can be performed. We present a robust set of features that analyze the tness...... landscape of BBO problems and show how an algorithm portfolio approach can exploit these general, problem indepen- dent features and outperform the utilization of any single minimization search strategy. We test our methodology on data from the GECCO Workshop on BBO Benchmarking 2012, which contains 21...

  11. Investigating the interplay between mechanisms of anomalous diffusion via fractional Brownian walks on a comb-like structure

    CERN Document Server

    Ribeiro, H V; Alves, L G A; Zola, R S; Lenzi, E L

    2014-01-01

    The comb model is a simplified description for anomalous diffusion under geometric constraints. It represents particles spreading out in a two-dimensional space where the motions in the x-direction are allowed only when the y coordinate of the particle is zero. Here, we propose an extension for the comb model via Langevin-like equations driven by fractional Gaussian noises (long-range correlated). By carrying out computer simulations, we show that the correlations in the y-direction affect the diffusive behavior in the x-direction in a non-trivial fashion, resulting in a quite rich diffusive scenario characterized by usual, superdiffusive or subdiffusive scaling of second moment in the x-direction. We further show that the long-range correlations affect the probability distribution of the particle positions in the x-direction, making their tails longer when noise in the y-direction is persistent and shorter for anti-persistent noise. Our model thus combines and allows the study/analysis of the interplay betwe...

  12. Structural Features of the Lymphoid Tissue of Newborns’ Gastric Mucosa

    OpenAIRE

    Kliuchko, S. S.

    2015-01-01

    72 Wistar rats’ stomachs were examined in order to study the features of the dynamics of the lymphoid cells content and distribution in the newborns rats’ gastric mucosa in normal. Morphometric, histological and statistical methods were used. The most significant changes in the composition of different populations of immune cells of the gastric mucosa lymphoid tissue was found to occur within the first three weeks after birth, when antigen load on the stomach increases in the form of new food...

  13. The defining features of the modern entrepreneurship network structures

    Directory of Open Access Journals (Sweden)

    R.V. Kochubey

    2011-03-01

    Full Text Available In the article the various forms of network enterprises are analyzed, the key characteristics of network structures are identified. The relationship between network types and forms of business organization is shown. The studies of different types of network structures are systematized.

  14. Structural features of free and covalently bound glycans

    NARCIS (Netherlands)

    Blanchard, Véronique

    2006-01-01

    Carbohydrates act in many cellular functions and biological processes such as cell-cell recognition and adhesion, inflammation, fertilization, signal transduction, and development. In this context, structural information is required to understand molecular mechanisms involving carbohydrates. The pla

  15. Molecular modeling of mechanosensory ion channel structural and functional features.

    Science.gov (United States)

    Gessmann, Renate; Kourtis, Nikos; Petratos, Kyriacos; Tavernarakis, Nektarios

    2010-09-16

    The DEG/ENaC (Degenerin/Epithelial Sodium Channel) protein family comprises related ion channel subunits from all metazoans, including humans. Members of this protein family play roles in several important biological processes such as transduction of mechanical stimuli, sodium re-absorption and blood pressure regulation. Several blocks of amino acid sequence are conserved in DEG/ENaC proteins, but structure/function relations in this channel class are poorly understood. Given the considerable experimental limitations associated with the crystallization of integral membrane proteins, knowledge-based modeling is often the only route towards obtaining reliable structural information. To gain insight into the structural characteristics of DEG/ENaC ion channels, we derived three-dimensional models of MEC-4 and UNC-8, based on the available crystal structures of ASIC1 (Acid Sensing Ion Channel 1). MEC-4 and UNC-8 are two DEG/ENaC family members involved in mechanosensation and proprioception respectively, in the nematode Caenorhabditis elegans. We used these models to examine the structural effects of specific mutations that alter channel function in vivo. The trimeric MEC-4 model provides insight into the mechanism by which gain-of-function mutations cause structural alterations that result in increased channel permeability, which trigger cell degeneration. Our analysis provides an introductory framework to further investigate the multimeric organization of the DEG/ENaC ion channel complex.

  16. Molecular modeling of mechanosensory ion channel structural and functional features.

    Directory of Open Access Journals (Sweden)

    Renate Gessmann

    Full Text Available The DEG/ENaC (Degenerin/Epithelial Sodium Channel protein family comprises related ion channel subunits from all metazoans, including humans. Members of this protein family play roles in several important biological processes such as transduction of mechanical stimuli, sodium re-absorption and blood pressure regulation. Several blocks of amino acid sequence are conserved in DEG/ENaC proteins, but structure/function relations in this channel class are poorly understood. Given the considerable experimental limitations associated with the crystallization of integral membrane proteins, knowledge-based modeling is often the only route towards obtaining reliable structural information. To gain insight into the structural characteristics of DEG/ENaC ion channels, we derived three-dimensional models of MEC-4 and UNC-8, based on the available crystal structures of ASIC1 (Acid Sensing Ion Channel 1. MEC-4 and UNC-8 are two DEG/ENaC family members involved in mechanosensation and proprioception respectively, in the nematode Caenorhabditis elegans. We used these models to examine the structural effects of specific mutations that alter channel function in vivo. The trimeric MEC-4 model provides insight into the mechanism by which gain-of-function mutations cause structural alterations that result in increased channel permeability, which trigger cell degeneration. Our analysis provides an introductory framework to further investigate the multimeric organization of the DEG/ENaC ion channel complex.

  17. An automated approach to network features of protein structure ensembles.

    Science.gov (United States)

    Bhattacharyya, Moitrayee; Bhat, Chanda R; Vishveshwara, Saraswathi

    2013-10-01

    Network theory applied to protein structures provides insights into numerous problems of biological relevance. The explosion in structural data available from PDB and simulations establishes a need to introduce a standalone-efficient program that assembles network concepts/parameters under one hood in an automated manner. Herein, we discuss the development/application of an exhaustive, user-friendly, standalone program package named PSN-Ensemble, which can handle structural ensembles generated through molecular dynamics (MD) simulation/NMR studies or from multiple X-ray structures. The novelty in network construction lies in the explicit consideration of side-chain interactions among amino acids. The program evaluates network parameters dealing with topological organization and long-range allosteric communication. The introduction of a flexible weighing scheme in terms of residue pairwise cross-correlation/interaction energy in PSN-Ensemble brings in dynamical/chemical knowledge into the network representation. Also, the results are mapped on a graphical display of the structure, allowing an easy access of network analysis to a general biological community. The potential of PSN-Ensemble toward examining structural ensemble is exemplified using MD trajectories of an ubiquitin-conjugating enzyme (UbcH5b). Furthermore, insights derived from network parameters evaluated using PSN-Ensemble for single-static structures of active/inactive states of β2-adrenergic receptor and the ternary tRNA complexes of tyrosyl tRNA synthetases (from organisms across kingdoms) are discussed. PSN-Ensemble is freely available from http://vishgraph.mbu.iisc.ernet.in/PSN-Ensemble/psn_index.html.

  18. Coherent quantum transport features in carbon superlattice structures

    Science.gov (United States)

    McIntosh, R.; Henley, S. J.; Silva, S. R. P.; Bhattacharyya, S.

    2016-10-01

    Whilst resonant transmission is well understood and can be fully harnessed for crystalline superlattices, a complete picture has not yet emerged for disordered superlattices. It has proven difficult to tune resonant transmission in disordered diamond-like carbon (DLC) superlattices as conventional models are not equipped to incorporate significant structural disorder. In this work, we present concurrent experimental and theoretical analysis which addresses resonant transmission in DLC superlattices. Devices were fabricated by growing alternate layers of DLC with different percentages of sp3 hybridized carbon.Coherent quantum transport effects were demonstrated in these structurally disordered DLC superlattices through distinct current modulation with negative differential resistance (NDR) in the current-voltage (I-V) measurements. A model was developed using tight-binding calculations assuming a random variation of the hopping integral to simulate structural (bond-length) disorder. Calculations of the I-V characteristics compliment the interpretation of the measurements and illustrate that while DLC superlattice structures are unlike their classical counterparts, the near-field structural order will help with the confinement of quantised states. The present model provides an empirical guide for tailoring the properties of future devices, giving rise to much hope that carbon electronics operating at high frequencies over large areas can now be developed.

  19. Structural Features and Healthy Properties of Polysaccharides Occurring in Mushrooms

    Directory of Open Access Journals (Sweden)

    Eva Guillamón

    2012-12-01

    Full Text Available Polysaccharides from mushrooms have attracted a great deal of attention due to the many healthy benefits they have demonstrated, such as immunomodulation, anticancer activity, prevention and treatment of cardiovascular diseases, antiviral and antimicrobial effects, among others. Isolation and purification of polysaccharides commonly involve several steps, and different techniques are actually available in order to increase extraction yield and purity. Studies have demonstrated that the molecular structure and arrangement significantly influence the biological activity; therefore, there is a wide range of analytical techniques for the elucidation of chemical structures. Different polysaccharides have been isolated from mushrooms, most of them consisting of β-linked glucans, such as lentinan from Lentinus edodes, pleuran from Pleurotus species, schizophyllan from Schizophyllum commune, calocyban from Calocybe indica, or ganoderan and ganopoly from Ganoderma lucidum. This article reviews the main methods of polysaccharide isolation and structural characterization, as well as some of the most important polysaccharides isolated from mushrooms and the healthy benefits they provide.

  20. DHPC: a new tool to express genome structural features.

    Science.gov (United States)

    Deng, Xuegong; Deng, Xuemei; Rayner, Simon; Liu, Xiangdong; Zhang, Qingling; Yang, Yupu; Li, Ning

    2008-05-01

    The DHPC (DNA Hilbert-Peano curve) is a new tool for visualizing large-scale genome sequences by mapping sequences into a two-dimensional square. It utilizes the space-filling function of Hilbert-Peano mapping. By applying a Gauss smoothing technique and a user-defined color function, a large-scale genome sequence can be mapped into a two-dimensional color image. In the calculated DHPCs, many genome characteristics are revealed. In this article we introduce the method and show how DHPCs may be used to identify regions of different base composition. The power of the method is demonstrated by presenting multiple examples such as repeating sequences, degree of base bias, regions of homogeneity and their boundaries, and mark of annotated segments. We also present several genome curves generated by DHPC to demonstrate how DHPC can be used to find previously unidentified sequence features in these genomes.

  1. Structural feature of cast Al-base composite

    Energy Technology Data Exchange (ETDEWEB)

    Ji, S.; Li, Y.; Wang, G.

    1986-02-01

    An observation was carried out on the features of microstructure, fracture, and worn surface of an Al-base composite prepared by rheocasting with graphite, SiC, and SiO/sub 2/. The alpha solid solution, Si, CuAl/sub 2/, and allied eutectics are found to nucleate and to grow up along the surface of particulates added during solidification of the compslurry. The short-range movement of the particulates may distribute more uniformly in matrix owing to rapidly raising temperature of the compslurry before casting. Over the particulate, a transition layer connects with the matrix, and the active element Mg accumulates more or less. Thus, a firm bond is joined between the particulate and matrix, and no more pores and cracks form on the microstructure of fractured or worn surface. 11 references.

  2. STRUCTURAL AND SEMANTIC FEATURES OF ONLINE INFORMATION RESOURCES

    Directory of Open Access Journals (Sweden)

    Ivan Georgievich Zubkov

    2014-07-01

    Full Text Available Information society is a global economic, political, technological and antroposocial project involving controlled civilizational transition to the world social system in which the dominant role in all spheres of life will play a mass communication system, implemented with the help of computer technology, particularly Internet technology. The question of formation and presentation of information is highly relevant today. The world community has entered a transitional stage from its post-industrial state to the informational. At this stage of the development, society is increasingly dependent on the quality, availability, reliability, timeliness of information, which is created by its own representatives. Especially clearly it is evident in the Internet space, where all information flows merge into a single closed and continuously update system that has its own characteristics, features and qualities.DOI: http://dx.doi.org/10.12731/2218-7405-2014-4-7

  3. Unusual Features of Crystal Structures of Some Simple Copper Compounds

    Science.gov (United States)

    Douglas, Bodie

    2009-01-01

    Some simple copper compounds have unusual crystal structures. Cu[subscript 3]N is cubic with N atoms at centers of octahedra formed by 6 Cu atoms. Cu[subscript 2]O (cuprite) is also cubic; O atoms are in tetrahedra formed by 4 Cu atoms. These tetrahedra are linked by sharing vertices forming two independent networks without linkages between them.…

  4. Radiographic features of mandibular trabecular bone structure in hypodontia

    NARCIS (Netherlands)

    M. Créton; W. Geraets; J.W. Verhoeven; P.F. van der Stelt; H. Verhey; M. Cune

    2012-01-01

    Purpose: Radiographic parameters of mandibular trabecular bone structure between 67 subjects having hypodontia and those without were studied on digital panoramic radiographs. Materials and Methods: Three regions of interest (ROI) were defined: the ascending ramus, apical of the mandibular molar and

  5. Radiographic Features of Mandibular Trabecular Bone Structure in Hypodontia

    NARCIS (Netherlands)

    Creton, Marijn; Geraets, Wil; Verhoeven, Jan Willem; van der Stelt, Paul F.; Verhey, Hans; Cune, Marco

    2012-01-01

    Purpose: Radiographic parameters of mandibular trabecular bone structure between 67 subjects having hypodontia and those without were studied on digital panoramic radiographs. Materials and Methods: Three regions of interest (ROI) were defined: the ascending ramus, apical of the mandibular molar and

  6. Organizational structure and features of Sports Committee of Ukraine

    Directory of Open Access Journals (Sweden)

    Oleksandr Tomenko

    2015-12-01

    Full Text Available Purpose: in order to improve the management of non-Olympic sports in Ukraine to determine the structure and functions of the Sports Committee of Ukraine. Material and Methods: analysis and synthesis of scientific literature; analysis of documentary materials; sociological methods. Results: we find the structure of the Sports Committee of Ukraine as hierarchical with complexity traits. Local management bodies are: the General Assembly, the Executive Committee, the Bureau and the President. The decisions of the governing bodies implementation shall exercise the Executive Directorate and four commissions. It is shown that the strategic resource of the Sports Committee of Ukraine are knowledge and exclusive experience; capability perspective of reforming the sphere of physical culture and sports, work on the development of the Academy of Sports Committee of Ukraine

  7. Structural characteristics and petroliferous features of Tarim Basin

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Using the modern tectonic geology theories and methods such as the plate tectonic analysis, the paleo-struc- ture analysis, the structural-lithofacies analysis, and the fault related fold and petroleum system, and combining with the seismic data, well drilling data and the circumferential field geology, study on the structural characteristics and petroleum prospect in the Tarim Basin has been carried out. Results show that the Tarim Basin is a large superimposition and combination basin with continental crustal basement, composed of a Paleozoic craton and Meso-Cenozoic foreland basins. The characteristics of the basin are: the kernel part of the basin is the marine facies Paleozoic craton, superimposed 4 continental facies foreland basins. Though the scale of the paleozoic craton of the Tarim Basin is relatively small, the structure is steady. The petroleum prospect of the Paleozoic craton is: multiphase pool-generation and accumulation controlled by ancient uplift. The Meso-Cenozoic foreland basins in the Tarim Basin, which are distributed on the cratonic circumference and are a long-term subsidence, turned into rejuvenated foreland basins after the Meso-Cenozoic period. The petroleum prospects are: coal-bed generating hydrocarbon, abundant natural gas, pool-generation in later and recent periods, the oil and gas distribution controlled by the foreland thrust belt. The structural characteristics of Tarim provide it with a superimposition and combination petroleum system of multiple resources, multiple reservoirs and multiphase pool-generation. The oil and gas exploration prospect covers two large fields: the Paleozoic craton and the Meso-Cenozoic foreland thrust belt.

  8. Structural features of the regulatory ACT domain of phenylalanine hydroxylase.

    Directory of Open Access Journals (Sweden)

    Carla Carluccio

    Full Text Available Phenylalanine hydroxylase (PAH catalyzes the conversion of L-Phe to L-Tyr. Defects in PAH activity, caused by mutations in the human gene, result in the autosomal recessively inherited disease hyperphenylalaninemia. PAH activity is regulated by multiple factors, including phosphorylation and ligand binding. In particular, PAH displays positive cooperativity for L-Phe, which is proposed to bind the enzyme on an allosteric site in the N-terminal regulatory domain (RD, also classified as an ACT domain. This domain is found in several proteins and is able to bind amino acids. We used molecular dynamics simulations to obtain dynamical and structural insights into the isolated RD of PAH. Here we show that the principal motions involve conformational changes leading from an initial open to a final closed domain structure. The global intrinsic motions of the RD are correlated with exposure to solvent of a hydrophobic surface, which corresponds to the ligand binding-site of the ACT domain. Our results strongly suggest a relationship between the Phe-binding function and the overall dynamic behaviour of the enzyme. This relationship may be affected by structure-disturbing mutations. To elucidate the functional implications of the mutations, we investigated the structural effects on the dynamics of the human RD PAH induced by six missense hyperphenylalaninemia-causing mutations, namely p.G46S, p.F39C, p.F39L, p.I65S, p.I65T and p.I65V. These studies showed that the alterations in RD hydrophobic interactions induced by missense mutations could affect the functionality of the whole enzyme.

  9. Structural features of the regulatory ACT domain of phenylalanine hydroxylase.

    Science.gov (United States)

    Carluccio, Carla; Fraternali, Franca; Salvatore, Francesco; Fornili, Arianna; Zagari, Adriana

    2013-01-01

    Phenylalanine hydroxylase (PAH) catalyzes the conversion of L-Phe to L-Tyr. Defects in PAH activity, caused by mutations in the human gene, result in the autosomal recessively inherited disease hyperphenylalaninemia. PAH activity is regulated by multiple factors, including phosphorylation and ligand binding. In particular, PAH displays positive cooperativity for L-Phe, which is proposed to bind the enzyme on an allosteric site in the N-terminal regulatory domain (RD), also classified as an ACT domain. This domain is found in several proteins and is able to bind amino acids. We used molecular dynamics simulations to obtain dynamical and structural insights into the isolated RD of PAH. Here we show that the principal motions involve conformational changes leading from an initial open to a final closed domain structure. The global intrinsic motions of the RD are correlated with exposure to solvent of a hydrophobic surface, which corresponds to the ligand binding-site of the ACT domain. Our results strongly suggest a relationship between the Phe-binding function and the overall dynamic behaviour of the enzyme. This relationship may be affected by structure-disturbing mutations. To elucidate the functional implications of the mutations, we investigated the structural effects on the dynamics of the human RD PAH induced by six missense hyperphenylalaninemia-causing mutations, namely p.G46S, p.F39C, p.F39L, p.I65S, p.I65T and p.I65V. These studies showed that the alterations in RD hydrophobic interactions induced by missense mutations could affect the functionality of the whole enzyme.

  10. Computing Posterior Probabilities of Structural Features in Bayesian Networks

    CERN Document Server

    Tian, Jin

    2012-01-01

    We study the problem of learning Bayesian network structures from data. Koivisto and Sood (2004) and Koivisto (2006) presented algorithms that can compute the exact marginal posterior probability of a subnetwork, e.g., a single edge, in O(n2n) time and the posterior probabilities for all n(n-1) potential edges in O(n2n) total time, assuming that the number of parents per node or the indegree is bounded by a constant. One main drawback of their algorithms is the requirement of a special structure prior that is non uniform and does not respect Markov equivalence. In this paper, we develop an algorithm that can compute the exact posterior probability of a subnetwork in O(3n) time and the posterior probabilities for all n(n-1) potential edges in O(n3n) total time. Our algorithm also assumes a bounded indegree but allows general structure priors. We demonstrate the applicability of the algorithm on several data sets with up to 20 variables.

  11. Anomalous flows in a sunspot penumbra

    CERN Document Server

    Louis, Rohan E; Mathew, Shibu K; Venkatakrishnan, P

    2014-01-01

    High-resolution spectropolarimetric observations of active region NOAA 11271 were obtained with the spectro-polarimeter on board Hinode to analyze the properties of an anomalous flow in the photosphere in a sunspot penumbra. We detect a blue-shifted feature that appeared on the limb-side penumbra of a sunspot and that was present intermittently during the next two hours. It exhibited a maximum blue-shift of 1.6 km/s, an area of 5.2 arcsec^2, and an uninterrupted lifetime of 1 hr. The blue-shifted feature, when present, lies parallel to red-shifts. Both blue and red shifts flank a highly inclined/horizontal magnetic structure that is radially oriented in the penumbra. The low-cadence SP maps reveal changes in size, radial position in the penumbra and line-of-sight velocity of the blue-shifted feature, from one scan to the other. There was an increase of nearly 500 G in the field strength and a marginal reduction in the field inclination of about 10 deg with the onset of the blue-shifts. In the chromosphere, in...

  12. The competitive growth of cubic domains in Ti(1-x)AlxN films studied by diffraction anomalous near-edge structure spectroscopy.

    Science.gov (United States)

    Pinot, Y; Tuilier, M-H; Pac, M-J; Rousselot, C; Thiaudière, D

    2015-11-01

    Titanium and aluminium nitride films deposited by magnetron sputtering generally grow as columnar domains made of oriented nanocrystallites with cubic or hexagonal symmetry depending on Al content, which are embedded in more disordered grain boundaries. The substitution of Al atoms for Ti in the cubic lattice of the films improves their resistance to wear and oxidation, allowing their use as protective coatings. Ti K-edge X-ray absorption spectroscopy, which probes both crystallized and more disordered grain boundaries, and X-ray diffraction anomalous fine structure, which is sensitive to short- and long-range order within a given crystallized domain, are carried out on a set of Ti(1-x)AlxN films deposited by magnetron sputtering on Si substrates. Attention is paid to the shape of the pre-edge region, which is sensitive to the symmetry of the site occupied by Ti atoms, either octahedral in face-centred-cubic Ti-rich (TiN, Ti0.54Al0.46N) samples or tetrahedral in hexagonal-close-packed Al-rich (Ti0.32Al0.68N) films. In order to obain information on the titanium environment in the well crystallized areas, subtraction of the smooth part of the energy-dependent structure factor for the Bragg reflections is applied to the pre-edge region of the diffraction anomalous data in order to restore their spectroscopic appearance. A flat pre-edge is related to the typical octahedral environment of Ti atoms for cubic reflections. The difference observed between pre-edge spectra associated with face-centred-cubic 200 and 111 Bragg reflections of Ti0.54Al0.46N is assigned to Ti enrichment of 111 large well ordered domains compared with the more disordered 200 ones. The sharp peak observed in the spectrum recorded from the hexagonal 002 peak of Ti0.32Al0.68N can be regarded as a standard for the pure tetrahedral Ti environment in hexagonal-close-packed nitride.

  13. Some special features of formation of manyfunctional powders steels structure

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    It has been studied connection between composition, structure and properties of powder steels using technology of their own. Nitrogen containing powders were obtained by mechanical allowing (MA) of Fe-Cr and Fe Cr Ni-C mixtures in a high-energy planetary mill in the gaseous nitrogen environment. The contents of nitrogen after MA was 0. 7 % in Fe-Cr-N and 2.1% in Fe-Cr-Ni-C-N mixes. Phase composition after the mechanical alloying was: in system Fe-Cr-N - solid solution of chrome in iron and α - Fe, in system Fe-Cr-Ni-C-N-40% γ-phase (vol. fraction) , α - Fe and solid solution Cr-Fe.There are investigated physical-mechanical, tribo-technical and specify properties of the nitrous steels,are fixed the base dependences between parameters of process of MA and structure of steels. Introduction of nitrogen by rather new method of MA, as against saturation of melts, allows to run phase composition - to generate structure with more dispersible and uniform nitrides or with the nitrous austenite (depending on purpose of steel).It is demonstrated by means of X-ray diffraction and method of Raman spectrum analysis, that in a sintering process of powder steels, obtained by introduction of carbon in the form of cast-iron powder, a formation of metallofullerite phase Fex C60 at determined conditions. The possibility of fullerenes conception in powder carbon steels, diffusion of iron atoms at fullerite lattice and formation of metallofullerites during contact interaction of fullerene with iron is confirmed experimentally.Dependence of synthesis activity of fullerences from temperature of sintering, type and quantity of alloy elements is determined.

  14. Cluster Features in Reactions and Structure of Heavy Nuclei

    CERN Document Server

    Adamian, G G; Jolos, R V; Scheid, W; Shneidman, T M

    2003-01-01

    Cluster effects in the structure of heavy nuclei are considered. The properties of the states of the alternating parity bands in Ra, Th, U and Pu isotopes are analyzed within a cluster model. The model is based on the assumption that cluster type shapes are produced by the motion of the nuclear system in the mass asymmetry coordinate. The results of calculations of the spin dependence of the parity splitting and of the electric multipole transition moments are in agreement with the experimental data.

  15. Mapping the structural and dynamical features of kinesin motor domains.

    Directory of Open Access Journals (Sweden)

    Guido Scarabelli

    Full Text Available Kinesin motor proteins drive intracellular transport by coupling ATP hydrolysis to conformational changes that mediate directed movement along microtubules. Characterizing these distinct conformations and their interconversion mechanism is essential to determining an atomic-level model of kinesin action. Here we report a comprehensive principal component analysis of 114 experimental structures along with the results of conventional and accelerated molecular dynamics simulations that together map the structural dynamics of the kinesin motor domain. All experimental structures were found to reside in one of three distinct conformational clusters (ATP-like, ADP-like and Eg5 inhibitor-bound. These groups differ in the orientation of key functional elements, most notably the microtubule binding α4-α5, loop8 subdomain and α2b-β4-β6-β7 motor domain tip. Group membership was found not to correlate with the nature of the bound nucleotide in a given structure. However, groupings were coincident with distinct neck-linker orientations. Accelerated molecular dynamics simulations of ATP, ADP and nucleotide free Eg5 indicate that all three nucleotide states could sample the major crystallographically observed conformations. Differences in the dynamic coupling of distal sites were also evident. In multiple ATP bound simulations, the neck-linker, loop8 and the α4-α5 subdomain display correlated motions that are absent in ADP bound simulations. Further dissection of these couplings provides evidence for a network of dynamic communication between the active site, microtubule-binding interface and neck-linker via loop7 and loop13. Additional simulations indicate that the mutations G325A and G326A in loop13 reduce the flexibility of these regions and disrupt their couplings. Our combined results indicate that the reported ATP and ADP-like conformations of kinesin are intrinsically accessible regardless of nucleotide state and support a model where neck

  16. Features of structural response of mechanically loaded crystallites to irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Korchuganov, Aleksandr V., E-mail: avkor@ispms.ru [Institute of Strength Physics and Materials Science SB RAS, Tomsk, 634055 (Russian Federation); National Research Tomsk State University, Tomsk, 634050 (Russian Federation)

    2015-10-27

    A molecular dynamics method is employed to investigate the origin and evolution of plastic deformation in elastically deformed iron and vanadium crystallites due to atomic displacement cascades. Elastic stress states of crystallites result from different degrees of specimen deformation. Crystallites are deformed under constant-volume conditions. Atomic displacement cascades with the primary knock-on atom energy up to 50 keV are generated in loaded specimens. It is shown that irradiation may cause not only the Frenkel pair formation but also large-scale structural rearrangements outside the irradiated area, which prove to be similar to rearrangements proceeding by the twinning mechanism in mechanically loaded specimens.

  17. ANOMALOUS MAGNETIC FILMS,

    Science.gov (United States)

    Three types of anomalous nickel-iron magnetic films characterized by hysteresigraph and torque-magnetometer measurements; bitter-pattern observations; reprint from ’ Journal of Applied Physics .’

  18. Structural features of ZnxOy/nanosilica composites

    Science.gov (United States)

    Gun'ko, V. M.; Bogatyrov, V. M.; Oranska, O. I.; Borysenko, L. I.; Skubiszewska-Zięba, J.; Książek, A.; Leboda, R.

    2013-07-01

    Nanocomposites with nanosilica A380 (SBET = 378 m2/g) and grafted ZnO or/and zinc silicate were prepared using zinc acetate adsorbed onto nanosilica and then treated at 600-900 °C. The samples studied using a variety of methods demonstrated the dependences of the textural and structural characteristics and phase transformations on the amounts of adsorbed precursor and treatment conditions. Thermodestruction of zinc acetate Zn(ac)2 at 600 °C results in the formation of ZnO which is amorphous according to XRD data. However, HRTEM images show the presence of a small amount of ZnO crystallites of 2-5 nm in size. A portion of surface silanols interacts with adsorbed Zn-containing compounds to form Sisbnd Osbnd Zn bonds, a number of which increases with increasing Zn(ac)2 content and heating temperature. Heating at 800-900 °C leads to transformation of ZnO and other structures into crystalline zinc silicate β-Zn2SiO4 with larger particles more strongly packed in aggregates. The specific surface area of the composites decreases with increasing zinc content and heating temperature.

  19. Crystalline Structure of Accretion Disks: Features of the Global Model

    CERN Document Server

    Montani, Giovanni

    2012-01-01

    In this paper, we develop the analysis of a two-dimensional magnetohydrodynamical configuration for an axially symmetric and rotating plasma (embedded in a dipole like magnetic field), modeling the structure of a thin accretion disk around a compact astrophysical object. Our study investigates the global profile of the disk plasma, in order to fix the conditions for the existence of a crystalline morphology and ring sequence, as outlined by the local analysis pursued in [1, 2]. In the linear regime, when the electromagnetic back-reaction of the plasma is small enough, we show the existence of an oscillating radial behavior for the flux surface function which very closely resembles the one outlined in the local model, apart from a radial modulation of the amplitude. In the opposite limit, corresponding to a dominant back-reaction in the magnetic structure over the field of central object, we can recognize the existence of a ring-like decomposition of the disk, according to the same modulation of the magnetic f...

  20. Features of transport in ultrathin gold nanowire structures.

    Science.gov (United States)

    Pud, Sergii; Kisner, Alexandre; Heggen, Marc; Belaineh, Dagmawi; Temirov, Ruslan; Simon, Ulrich; Offenhäusser, Andreas; Mourzina, Yulia; Vitusevich, Svetlana

    2013-03-25

    The origin of the interface formation appearing due to the realization of contacts to ultrathin gold nanowire devices is revealed. Such interfaces play an important role in transport mechanisms in nanowire structures and can determine the electrical and operating parameters of a nanodevice. Based on experimental results, the specific electrical properties of bundles of ultrathin gold nanowires fabricated by wet chemical synthesis and subsequently assembled and contacted with gold electrodes are reported. It is demonstrated that these properties are strongly affected by the monolayers of organic molecules inevitably present on the surface of the nanowires due to synthetic conditions. In particular, such layers form a potential barrier to tunneling of the electrons from contacts to the nanowires. The electric transport behavior of the investigated nanowire structures in the temperature range from 500 mK to 300 K obeys the model of thermal fluctuation-induced tunneling conduction through the nanowire-metal electrode molecular junction. Application of this model allows calculation of the parameters of the molecular potential barrier. The formation of such a molecular barrier is verified by scanning tunneling microscope (STM) and transmission electron microscope (TEM) measurements performed using a supporting graphene layer. These findings are important for designing novel nanodevices for molecular electronics on the basis of ultrathin nanowires.

  1. Structural features of the tmRNA-ribosome interaction.

    Science.gov (United States)

    Bugaeva, Elizaveta Y; Surkov, Serhiy; Golovin, Andrey V; Ofverstedt, Lars-Göran; Skoglund, Ulf; Isaksson, Leif A; Bogdanov, Alexey A; Shpanchenko, Olga V; Dontsova, Olga A

    2009-12-01

    Trans-translation is a process which switches the synthesis of a polypeptide chain encoded by a nonstop messenger RNA to the mRNA-like domain of a transfer-messenger RNA (tmRNA). It is used in bacterial cells for rescuing the ribosomes arrested during translation of damaged mRNA and directing this mRNA and the product polypeptide for degradation. The molecular basis of this process is not well understood. Earlier, we developed an approach that allowed isolation of tmRNA-ribosomal complexes arrested at a desired step of tmRNA passage through the ribosome. We have here exploited it to examine the tmRNA structure using chemical probing and cryo-electron microscopy tomography. Computer modeling has been used to develop a model for spatial organization of the tmRNA inside the ribosome at different stages of trans-translation.

  2. Structural features of the tmRNA–ribosome interaction

    Science.gov (United States)

    Bugaeva, Elizaveta Y.; Surkov, Serhiy; Golovin, Andrey V.; Öfverstedt, Lars-Göran; Skoglund, Ulf; Isaksson, Leif A.; Bogdanov, Alexey A.; Shpanchenko, Olga V.; Dontsova, Olga A.

    2009-01-01

    Trans-translation is a process which switches the synthesis of a polypeptide chain encoded by a nonstop messenger RNA to the mRNA-like domain of a transfer-messenger RNA (tmRNA). It is used in bacterial cells for rescuing the ribosomes arrested during translation of damaged mRNA and directing this mRNA and the product polypeptide for degradation. The molecular basis of this process is not well understood. Earlier, we developed an approach that allowed isolation of tmRNA–ribosomal complexes arrested at a desired step of tmRNA passage through the ribosome. We have here exploited it to examine the tmRNA structure using chemical probing and cryo-electron microscopy tomography. Computer modeling has been used to develop a model for spatial organization of the tmRNA inside the ribosome at different stages of trans-translation. PMID:19861420

  3. Detecting Key Structural Features within Highly Recombined Genes

    Science.gov (United States)

    Wertz, John E; McGregor, Karen F; Bessen, Debra E

    2007-01-01

    Many microorganisms exhibit high levels of intragenic recombination following horizontal gene transfer events. Furthermore, many microbial genes are subject to strong diversifying selection as part of the pathogenic process. A multiple sequence alignment is an essential starting point for many of the tools that provide fundamental insights on gene structure and evolution, such as phylogenetics; however, an accurate alignment is not always possible to attain. In this study, a new analytic approach was developed in order to better quantify the genetic organization of highly diversified genes whose alleles do not align. This BLAST-based method, denoted BLAST Miner, employs an iterative process that places short segments of highly similar sequence into discrete datasets that are designated “modules.” The relative positions of modules along the length of the genes, and their frequency of occurrence, are used to identify sequence duplications, insertions, and rearrangements. Partial alleles of sof from Streptococcus pyogenes, encoding a surface protein under host immune selection, were analyzed for module content. High-frequency Modules 6 and 13 were identified and examined in depth. Nucleotide sequences corresponding to both modules contain numerous duplications and inverted repeats, whereby many codons form palindromic pairs. Combined with evidence for a strong codon usage bias, data suggest that Module 6 and 13 sequences are under selection to preserve their nucleic acid secondary structure. The concentration of overlapping tandem and inverted repeats within a small region of DNA is highly suggestive of a mechanistic role for Module 6 and 13 sequences in promoting aberrant recombination. Analysis of pbp2X alleles from Streptococcus pneumoniae, encoding cell wall enzymes that confer antibiotic resistance, supports the broad applicability of this tool in deciphering the genetic organization of highly recombined genes. BLAST Miner shares with phylogenetics the

  4. Properties and structural features of iron doped BABAL glasses

    Directory of Open Access Journals (Sweden)

    Reis Signo Tadeu dos

    2003-01-01

    Full Text Available The chemical durability, density and structure of the BABAL glasses with batch compositions (100-x(0.30BaO·0.50B2O3·0.20Al2O3·xFe 2O3 (1 < x < 10 mol%, were investigated using Mössbauer spectroscopy, electron paramagnetic resonance (EPR, X-ray diffraction, Raman and differential thermal analysis (DTA. The chemical durability for the glass of composition 27BaO·45B2O3·18Al 2O3·10Fe2O3 (mol% at 90 °C in distilled water was 700 times lower than that of iron phosphate glass 40Fe2O3·60P2O 5 (mol%. The Mössbauer spectra indicate the presence of iron (II and iron (III in tetrahedral or octahedral coordination. The results obtained from the g ef = 4.3 EPR line are typical of the occurrence of iron (III occupying substitutional sites and the line g ef = 2.0 is related to the association of two or more Fe ions found in the interstices (or holes occupied by the glass modifier cations of the glass network. The paths of X-ray diffraction are typical for glasses based in borate glasses. The Raman spectra showed that the boroxol ring disappears with the increase of iron content, concomitant with the appearance of BO4 and tetraborate structural units. At these conditions, an increase of dissolution rate and clustering of iron ions is observed.

  5. Crystalline structure of accretion disks: features of a global model.

    Science.gov (United States)

    Montani, Giovanni; Benini, Riccardo

    2011-08-01

    In this paper, we develop the analysis of a two-dimensional magnetohydrodynamical configuration for an axially symmetric and rotating plasma (embedded in a dipolelike magnetic field), modeling the structure of a thin accretion disk around a compact astrophysical object. Our study investigates the global profile of the disk plasma, in order to fix the conditions for the existence of a crystalline morphology and ring sequence, as outlined by the local analysis pursued in Coppi [Phys. Plasmas 12, 7302 (2005)] and Coppi and Rousseau [Astrophys. J. 641, 458 (2006)]. In the linear regime, when the electromagnetic back-reaction of the plasma is small enough, we show the existence of an oscillating radial behavior for the flux surface function, which very closely resembles the one outlined in the local model, apart from a radial modulation of the amplitude. In the opposite limit, corresponding to a dominant back-reaction in the magnetic structure over the field of central object, we can recognize the existence of a ringlike decomposition of the disk, according to the same modulation of the magnetic flux surface, and a smoother radial decay of the disk density, with respect to the linear case. In this extreme nonlinear regime, the global model seems to predict a configuration very close to that of the local analysis, but here the thermostatic pressure, crucial for the equilibrium setting, is also radially modulated. Among the conditions requested for the validity of such a global model, the confinement of the radial coordinate within a given value sensitive to the disk temperature and to the mass of the central objet, stands; however, this condition corresponds to dealing with a thin disk configuration.

  6. Structural and functional features of central nervous system lymphatic vessels.

    Science.gov (United States)

    Louveau, Antoine; Smirnov, Igor; Keyes, Timothy J; Eccles, Jacob D; Rouhani, Sherin J; Peske, J David; Derecki, Noel C; Castle, David; Mandell, James W; Lee, Kevin S; Harris, Tajie H; Kipnis, Jonathan

    2015-07-16

    One of the characteristics of the central nervous system is the lack of a classical lymphatic drainage system. Although it is now accepted that the central nervous system undergoes constant immune surveillance that takes place within the meningeal compartment, the mechanisms governing the entrance and exit of immune cells from the central nervous system remain poorly understood. In searching for T-cell gateways into and out of the meninges, we discovered functional lymphatic vessels lining the dural sinuses. These structures express all of the molecular hallmarks of lymphatic endothelial cells, are able to carry both fluid and immune cells from the cerebrospinal fluid, and are connected to the deep cervical lymph nodes. The unique location of these vessels may have impeded their discovery to date, thereby contributing to the long-held concept of the absence of lymphatic vasculature in the central nervous system. The discovery of the central nervous system lymphatic system may call for a reassessment of basic assumptions in neuroimmunology and sheds new light on the aetiology of neuroinflammatory and neurodegenerative diseases associated with immune system dysfunction.

  7. Chaotic features of nuclear structure and dynamics: selected topics

    Science.gov (United States)

    Zelevinsky, Vladimir; Volya, Alexander

    2016-03-01

    Quantum chaos has become an important element of our knowledge about physics of complex systems. In typical mesoscopic systems of interacting particles the dynamics invariably become chaotic when the level density, growing by combinatorial reasons, leads to the increasing probability of mixing simple mean-field (particle-hole) configurations. The resulting stationary states have exceedingly complicated structures that are comparable to those in random matrix theory. We discuss the main properties of mesoscopic quantum chaos and show that it can serve as a justification for application of statistical mechanics to mesoscopic systems. We show that quantum chaos becomes a powerful instrument for experimental, theoretical and computational work. The generalization to open systems and effects in the continuum are discussed with the help of the effective non-Hermitian Hamiltonian; it is shown how to formulate this approach for numerous problems of quantum signal transmission. The artificially introduced randomness can also be helpful for a deeper understanding of physics. We indicate the problems that require more investigation so as to be understood further.

  8. The structural feature surrounding glycated lysine residues in human hemoglobin.

    Science.gov (United States)

    Ito, Shigenori; Nakahari, Takashi; Yamamoto, Daisuke

    2011-06-01

    Complications derived from diabetes mellitus are caused by nonenzymatic protein glycation at the specific sites. LC/MS/MS was performed for the identification of the tryptic peptides of glycated hemoglobins using glyceraldehyde. After the identification of the glycation or non-glycation site, computer analysis of the structure surrounding the sites was carried out using PDB data (1BZ0). Five glycated lysine residues (Lys-16(α), -56(α), -8(β), -82(β), and -144(β)) and four non-glycated lysine residues (Lys-7(α), -40(α), -99(α), and -132(β)) were identified. The non-glycated lysine residues, Lys-7(α), -40(α), and -132(β), are most likely to form electrostatic interactions with the β carboxyl group of Asp-74(α), C-terminal His-146(β), and Glu-7(β) by virtue of their proximity, which is 2.67-2.91 Å (N-O). Additionally, there are histidine residues within 4.55-7.38 Å (N-N) around eight sites except for Lys-7(α). We conclude that the following factors seem to be necessary for glycation of lysine residues: (i) the apparent absence of aspartate or glutamate residues to inhibit the glycation reaction by forming an electrostatic interaction, (ii) the presence of histidine residues for acid-base catalysis of the Amadori rearrangement, and (iii) the presence of an amino acid residue capable of stabilizing a phosphate during proton transfer.

  9. Proceedings of a one-week course on exploiting anomalous scattering in macromolecular structure determination (EMBO'07)

    Energy Technology Data Exchange (ETDEWEB)

    Weiss, M.S.; Shepard, W.; Dauter, Z.; Leslie, A.; Diederichs, K.; Evans, G.; Svensson, O.; Schneider, T.; Bricogne, G.; Dauter, Z.; Flensburg, C.; Terwilliger, T.; Lamzin, V.; Leslie, A.; Kabsch, W.; Flensburg, C.; Terwilliger, T.; Lamzin, V.; Read, R.; Panjikar, S.; Pannu, N.S.; Dauter, Z.; Weiss, M.S.; McSweeney, S

    2007-07-01

    This course, which was directed to young scientists, illustrated both theoretical and practical aspects of macromolecular crystal structure solution using synchrotron radiation. Some software dedicated to data collection, processing and analysis were presented. This document gathers only the slides of the presentations.

  10. Observation of Anomalous Properties associated with the Low Temperature Structural Distortion in β-FeSe and Related Superconductorsa

    Directory of Open Access Journals (Sweden)

    Wu M. K.

    2012-03-01

    Full Text Available The discovery of Superconductivity in the tetragonal phase FeSe provides a unique platform for the detailed investigation of the correlation between the physical properties and crystal structure to better understand the possible origin of superconductivity in the new iron-based superconductors. We have carried out a series of properties characterizations by measuring magnetic susceptibility, Raman, NMR and femtosecond spectroscopy on single crystals and epitaxial thin films of the FeSe and Te-doped Fe(SeTe samples. Our results show clearly the presence of anomalies in all the characterized properties at the temperature where a structural distortion from tetragonal to orthorhombic (or monoclinic appears for all superconducting samples, but not in the non-superconducting ones. This structural distortion was observed not accompanied by a magnetic ordering as commonly occurs in the parent compounds of FeAs-based superconductors. All the observations suggest that the low temperature structural distortion is essential for the occurrence of superconductivity in the FeSe and related compounds. Details of the experimental results will be presented and discussed.

  11. The 3-loop non-singlet heavy flavor contributions and anomalous dimensions for the structure function F2(x,Q2) and transversity

    Science.gov (United States)

    Ablinger, J.; Behring, A.; Blümlein, J.; De Freitas, A.; Hasselhuhn, A.; von Manteuffel, A.; Round, M.; Schneider, C.; Wißbrock, F.

    2014-09-01

    We calculate the massive flavor non-singlet Wilson coefficient for the heavy flavor contributions to the structure function F2(x,Q2) in the asymptotic region Q2≫m2 and the associated operator matrix element Aqq,Q(3),NS(N) to 3-loop order in Quantum Chromodynamics at general values of the Mellin variable N. This matrix element is associated with the vector current and axial vector current for the even and the odd moments N, respectively. We also calculate the corresponding operator matrix elements for transversity, compute the contributions to the 3-loop anomalous dimensions to O(NF) and compare to results in the literature. The 3-loop matching of the flavor non-singlet distribution in the variable flavor number scheme is derived. All results can be expressed in terms of nested harmonic sums in N space and harmonic polylogarithms in x-space. Numerical results are presented for the non-singlet charm quark contribution to F2(x,Q2).

  12. The 3-loop non-singlet heavy flavor contributions and anomalous dimensions for the structure function F2(x,Q2 and transversity

    Directory of Open Access Journals (Sweden)

    J. Ablinger

    2014-09-01

    Full Text Available We calculate the massive flavor non-singlet Wilson coefficient for the heavy flavor contributions to the structure function F2(x,Q2 in the asymptotic region Q2≫m2 and the associated operator matrix element Aqq,Q(3,NS(N to 3-loop order in Quantum Chromodynamics at general values of the Mellin variable N. This matrix element is associated with the vector current and axial vector current for the even and the odd moments N, respectively. We also calculate the corresponding operator matrix elements for transversity, compute the contributions to the 3-loop anomalous dimensions to O(NF and compare to results in the literature. The 3-loop matching of the flavor non-singlet distribution in the variable flavor number scheme is derived. All results can be expressed in terms of nested harmonic sums in N space and harmonic polylogarithms in x-space. Numerical results are presented for the non-singlet charm quark contribution to F2(x,Q2.

  13. The 3-loop non-singlet heavy flavor contributions and anomalous dimensions for the structure function F{sub 2}(x,Q{sup 2}) and transversity

    Energy Technology Data Exchange (ETDEWEB)

    Ablinger, J.; Hasselhuhn, A.; Schneider, C. [Johannes Kepler Univ., Linz (Austria). Research Inst. for Symbolic Computation; Behring, A.; Bluemlein, J.; Freitas, A. de [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany); Manteuffel, A. von [Mainz Univ. (Germany). PRISMA Cluster of Excellence; Mainz Univ. (Germany). Inst. fuer Physik; Round, M.; Wissbrock, F. [Johannes Kepler Univ., Linz (Austria). Research Inst. for Symbolic Computation; Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany)

    2014-06-15

    We calculate the massive flavor non-singlet Wilson coefficient for the heavy flavor contributions to the structure function F{sub 2}(x,Q{sup 2}) in the asymptotic region Q{sup 2}>>m{sup 2} and the associated operator matrix element A{sup (3),NS}{sub qq,Q} (N) to 3-loop order in Quantum Chromodynamics at general values of the Mellin variable N. This matrix element is associated to the vector current and axial vector current for the even and the odd moments N, respectively. We also calculate the corresponding operator matrix elements for transversity, compute the contributions to the 3-loop anomalous dimensions to O(N{sub F}) and compare to results in the literature. The 3-loop matching of the flavor non-singlet distribution in the variable flavor number scheme is derived. All results can be expressed in terms of nested harmonic sums in N space and harmonic polylogarithms in x-space. Numerical results are presented for the non-singlet charm quark contribution to F{sub 2}(x,Q{sup 2}).

  14. The 3-loop non-singlet heavy flavor contributions and anomalous dimensions for the structure function F{sub 2}(x,Q{sup 2}) and transversity

    Energy Technology Data Exchange (ETDEWEB)

    Ablinger, J. [Research Institute for Symbolic Computation (RISC), Johannes Kepler University, Altenbergerstraße 69, A-4040 Linz (Austria); Behring, A.; Blümlein, J.; De Freitas, A. [Deutsches Elektronen-Synchrotron, DESY, Platanenallee 6, D-15738 Zeuthen (Germany); Hasselhuhn, A. [Research Institute for Symbolic Computation (RISC), Johannes Kepler University, Altenbergerstraße 69, A-4040 Linz (Austria); Manteuffel, A. von [PRISMA Cluster of Excellence and Institute of Physics, J. Gutenberg University, D-55099 Mainz (Germany); Round, M. [Research Institute for Symbolic Computation (RISC), Johannes Kepler University, Altenbergerstraße 69, A-4040 Linz (Austria); Deutsches Elektronen-Synchrotron, DESY, Platanenallee 6, D-15738 Zeuthen (Germany); Schneider, C. [Research Institute for Symbolic Computation (RISC), Johannes Kepler University, Altenbergerstraße 69, A-4040 Linz (Austria); Wißbrock, F. [Research Institute for Symbolic Computation (RISC), Johannes Kepler University, Altenbergerstraße 69, A-4040 Linz (Austria); Deutsches Elektronen-Synchrotron, DESY, Platanenallee 6, D-15738 Zeuthen (Germany)

    2014-09-15

    We calculate the massive flavor non-singlet Wilson coefficient for the heavy flavor contributions to the structure function F{sub 2}(x,Q{sup 2}) in the asymptotic region Q{sup 2}≫m{sup 2} and the associated operator matrix element A{sub qq,Q}{sup (3),NS}(N) to 3-loop order in Quantum Chromodynamics at general values of the Mellin variable N. This matrix element is associated with the vector current and axial vector current for the even and the odd moments N, respectively. We also calculate the corresponding operator matrix elements for transversity, compute the contributions to the 3-loop anomalous dimensions to O(N{sub F}) and compare to results in the literature. The 3-loop matching of the flavor non-singlet distribution in the variable flavor number scheme is derived. All results can be expressed in terms of nested harmonic sums in N space and harmonic polylogarithms in x-space. Numerical results are presented for the non-singlet charm quark contribution to F{sub 2}(x,Q{sup 2})

  15. The 3-Loop Non-Singlet Heavy Flavor Contributions and Anomalous Dimensions for the Structure Function $F_2(x,Q^2)$ and Transversity

    CERN Document Server

    Ablinger, J; Blümlein, J; De Freitas, A; Hasselhuhn, A; von Manteuffel, A; Round, M; Schneider, C; Wißbrock, F

    2014-01-01

    We calculate the massive flavor non-singlet Wilson coefficient for the heavy flavor contributions to the structure function $F_2(x,Q^2)$ in the asymptotic region $Q^2 \\gg m^2$ and the associated operator matrix element $A_{qq,Q}^{(3), \\rm NS}(N)$ to 3-loop order in Quantum Chromodynamics at general values of the Mellin variable $N$. This matrix element is associated to the vector current and axial vector current for the even and the odd moments $N$, respectively. We also calculate the corresponding operator matrix elements for transversity, compute the contributions to the 3-loop anomalous dimensions to $O(N_F)$ and compare to results in the literature. The 3-loop matching of the flavor non-singlet distribution in the variable flavor number scheme is derived. All results can be expressed in terms of nested harmonic sums in $N$ space and harmonic polylogarithms in $x$-space. Numerical results are presented for the non-singlet charm quark contribution to $F_2(x,Q^2)$.

  16. Structural Origin of the Anomalous Temperature Dependence of the Local Magnetic Moments in the CaFe2As2 Family of Materials

    Science.gov (United States)

    Ortenzi, L.; Gretarsson, H.; Kasahara, S.; Matsuda, Y.; Shibauchi, T.; Finkelstein, K. D.; Wu, W.; Julian, S. R.; Kim, Young-June; Mazin, I. I.; Boeri, L.

    2015-01-01

    We report a combination of Fe K β x-ray emission spectroscopy and density functional reduced Stoner theory calculations to investigate the correlation between structural and magnetic degrees of freedom in CaFe2(As1-xPx) 2 . The puzzling temperature behavior of the local moment found in rare earth-doped CaFe2As2 [H. Gretarsson et al., Phys. Rev. Lett. 110, 047003 (2013)] is also observed in CaFe2(As1-xPx) 2 . We explain this phenomenon based on first-principles calculations with scaled magnetic interaction. One scaling parameter is sufficient to describe quantitatively the magnetic moments in both CaFe2(As1-xPx) 2 (x =0.055 ) and Ca0.78La0.22Fe2As2 at all temperatures. The anomalous growth of the local moments with increasing temperature can be understood from the observed large thermal expansion of the c -axis lattice parameter combined with strong magnetoelastic coupling. These effects originate from the strong tendency to form As-As dimers across the Ca layer in the CaFe2As2 family of materials. Our results emphasize the dual local-itinerant character of magnetism in Fe pnictides.

  17. Direct phase selection of initial phases from single-wavelength anomalous dispersion (SAD) for the improvement of electron density and ab initio structure determination

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Chung-De [National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu 30076, Taiwan (China); National Tsing Hua University, Hsinchu, Taiwan (China); Huang, Yen-Chieh [National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu 30076, Taiwan (China); Chiang, Hsin-Lin [National Tsing Hua University, Hsinchu, Taiwan (China); Hsieh, Yin-Cheng; Guan, Hong-Hsiang; Chuankhayan, Phimonphan [National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu 30076, Taiwan (China); Chen, Chun-Jung, E-mail: cjchen@nsrrc.org.tw [National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu 30076, Taiwan (China); National Tsing Hua University, Hsinchu, Taiwan (China); National Cheng Kung University, Tainan City 701, Taiwan (China); National Cheng Kung University, Tainan City 701, Taiwan (China)

    2014-09-01

    A novel direct phase-selection method to select optimized phases from the ambiguous phases of a subset of reflections to replace the corresponding initial SAD phases has been developed. With the improved phases, the completeness of built residues of protein molecules is enhanced for efficient structure determination. Optimization of the initial phasing has been a decisive factor in the success of the subsequent electron-density modification, model building and structure determination of biological macromolecules using the single-wavelength anomalous dispersion (SAD) method. Two possible phase solutions (ϕ{sub 1} and ϕ{sub 2}) generated from two symmetric phase triangles in the Harker construction for the SAD method cause the well known phase ambiguity. A novel direct phase-selection method utilizing the θ{sub DS} list as a criterion to select optimized phases ϕ{sub am} from ϕ{sub 1} or ϕ{sub 2} of a subset of reflections with a high percentage of correct phases to replace the corresponding initial SAD phases ϕ{sub SAD} has been developed. Based on this work, reflections with an angle θ{sub DS} in the range 35–145° are selected for an optimized improvement, where θ{sub DS} is the angle between the initial phase ϕ{sub SAD} and a preliminary density-modification (DM) phase ϕ{sub DM}{sup NHL}. The results show that utilizing the additional direct phase-selection step prior to simple solvent flattening without phase combination using existing DM programs, such as RESOLVE or DM from CCP4, significantly improves the final phases in terms of increased correlation coefficients of electron-density maps and diminished mean phase errors. With the improved phases and density maps from the direct phase-selection method, the completeness of residues of protein molecules built with main chains and side chains is enhanced for efficient structure determination.

  18. Features of biomorphological structure of the steppe phytocenosises of Opuk Natural Reserve

    Directory of Open Access Journals (Sweden)

    Valentina Kobechinskaya

    2014-04-01

    Full Text Available Analysis of biomorphological structure of the steppe phytocenosises of Opuksky Natural Reserve revealed regional characteristics of vegetation which were based on adaptive features of growing species. On the basis of contingency coefficients between the groups of biomorphological features were marked eco-biomorphological types of plants, which allow complete investigation on the features of individual ecobiomorphs, identification of ecological identity of steppe landscape and planning of further environmental activities.

  19. Electroweak Baryogenesis with Anomalous Higgs Couplings

    CERN Document Server

    Kobakhidze, Archil; Yue, Jason

    2015-01-01

    We investigate feasibility of efficient baryogenesis at the electroweak scale within the effective field theory framework based on a non-linear realisation of the electroweak gauge symmetry. In this framework the LHC Higgs boson is described by a singlet scalar field, which, therefore, admits new interactions. Assuming that Higgs couplings with the eletroweak gauge bosons are as in the Standard Model, we demonstrate that the Higgs cubic coupling and the CP-violating Higgs-top quark anomalous couplings alone may drive the a strongly first-order phase transition. The distinguished feature of this transition is that the anomalous Higgs vacuum expectation value is generally non-zero in both phases. We identify a range of anomalous couplings, consistent with current experimental data, where sphaleron rates are sufficiently fast in the 'symmetric' phase and are suppressed in the 'broken' phase and demonstrate that the desired baryon asymmetry can indeed be generated in this framework. This range of the Higgs anomal...

  20. Structural features that predict real-value fluctuations of globular proteins.

    Science.gov (United States)

    Jamroz, Michal; Kolinski, Andrzej; Kihara, Daisuke

    2012-05-01

    It is crucial to consider dynamics for understanding the biological function of proteins. We used a large number of molecular dynamics (MD) trajectories of nonhomologous proteins as references and examined static structural features of proteins that are most relevant to fluctuations. We examined correlation of individual structural features with fluctuations and further investigated effective combinations of features for predicting the real value of residue fluctuations using the support vector regression (SVR). It was found that some structural features have higher correlation than crystallographic B-factors with fluctuations observed in MD trajectories. Moreover, SVR that uses combinations of static structural features showed accurate prediction of fluctuations with an average Pearson's correlation coefficient of 0.669 and a root mean square error of 1.04 Å. This correlation coefficient is higher than the one observed in predictions by the Gaussian network model (GNM). An advantage of the developed method over the GNMs is that the former predicts the real value of fluctuation. The results help improve our understanding of relationships between protein structure and fluctuation. Furthermore, the developed method provides a convienient practial way to predict fluctuations of proteins using easily computed static structural features of proteins.

  1. Handwritten Digit Recognition Using Structural, Statistical Features and K-nearest Neighbor Classifier

    Directory of Open Access Journals (Sweden)

    U Ravi Babu

    2014-02-01

    Full Text Available This paper presents a new approach to off-line handwritten numeral recognition based on structural and statistical features. Five different types of skeleton features: (horizontal, vertical crossings, end, branch, and cross points, number of contours in the image, Width-to-Height ratio, and distribution features are used for the recognition of numerals. We create two vectors Sample Feature Vector (SFV is a vector which contains Structural and Statistical features of MNIST sample data base of handwritten numerals and Test Feature Vector (TFV is a vector which contains Structural and Statistical features of MNIST test database of handwritten numerals. The performance of digit recognition system depends mainly on what kind of features are being used. The objective of this paper is to provide efficient and reliable techniques for recognition of handwritten numerals. A Euclidian minimum distance criterion is used to find minimum distances and k-nearest neighbor classifier is used to classify the numerals. MNIST database is used for both training and testing the system. A total 5000 numeral images are tested, and the overall accuracy is found to be 98.42%.

  2. Anomalous law of cooling

    Science.gov (United States)

    Lapas, Luciano C.; Ferreira, Rogelma M. S.; Rubí, J. Miguel; Oliveira, Fernando A.

    2015-03-01

    We analyze the temperature relaxation phenomena of systems in contact with a thermal reservoir that undergoes a non-Markovian diffusion process. From a generalized Langevin equation, we show that the temperature is governed by a law of cooling of the Newton's law type in which the relaxation time depends on the velocity autocorrelation and is then characterized by the memory function. The analysis of the temperature decay reveals the existence of an anomalous cooling in which the temperature may oscillate. Despite this anomalous behavior, we show that the variation of entropy remains always positive in accordance with the second law of thermodynamics.

  3. Anomalous chiral superfluidity

    Energy Technology Data Exchange (ETDEWEB)

    Lublinsky, Michael, E-mail: lublinsky@phys.uconn.ed [Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794 (United States); Physics Department, Ben-Gurion University, Beer Sheva 84105 (Israel); Zahed, Ismail [Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794 (United States)

    2010-02-08

    We discuss both the anomalous Cartan currents and the energy-momentum tensor in a left chiral theory with flavor anomalies as an effective theory for flavored chiral phonons in a chiral superfluid with the gauged Wess-Zumino-Witten term. In the mean-field (leading tadpole) approximation the anomalous Cartan currents and the energy-momentum tensor take the form of constitutive currents in the chiral superfluid state. The pertinence of higher order corrections and the Adler-Bardeen theorem is briefly noted.

  4. Anomalous law of cooling.

    Science.gov (United States)

    Lapas, Luciano C; Ferreira, Rogelma M S; Rubí, J Miguel; Oliveira, Fernando A

    2015-03-14

    We analyze the temperature relaxation phenomena of systems in contact with a thermal reservoir that undergoes a non-Markovian diffusion process. From a generalized Langevin equation, we show that the temperature is governed by a law of cooling of the Newton's law type in which the relaxation time depends on the velocity autocorrelation and is then characterized by the memory function. The analysis of the temperature decay reveals the existence of an anomalous cooling in which the temperature may oscillate. Despite this anomalous behavior, we show that the variation of entropy remains always positive in accordance with the second law of thermodynamics.

  5. Anomalous pion decay revisited

    CERN Document Server

    Battistel, O A; Nemes, M C; Hiller, B

    1999-01-01

    An implicit four dimensional regularization is applied to calculate the axial-vector-vector anomalous amplitude. The present technique always complies with results of Dimensional Regularization and can be easily applied to processes involving odd numbers of $\\gamma_5$ matrices. This is illustrated explicitely in the example of this letter.

  6. Structural phase transition causing anomalous photoluminescence behavior in perovskite (C{sub 6}H{sub 11}NH{sub 3}){sub 2}[PbI{sub 4}

    Energy Technology Data Exchange (ETDEWEB)

    Yangui, A. [Groupe d’Etudes de la Matière Condensée, UMR CNRS 8653-Université de Versailles Saint Quentin En Yvelines, 45 Avenue des Etats-Unis, 78035 Versailles (France); Laboratoire de Physique Appliquée, Faculté des Sciences de Sfax, Route de Soukra km 3.5 BP 1171, 3018 Sfax (Tunisia); Pillet, S. [Laboratoire de Cristallographie, Résonance Magnétique et Modélisations, UMR-CNRS 7036, Institut Jean Barriol, Université de Lorraine, BP 239, 54506 Vandoeuvre-lès-Nancy (France); Mlayah, A. [Centre d’Elaboration de Matériaux et d’Etudes Structurales (CEMES), CNRS UPR 8011-Université de Toulouse, 29 rue Jeanne Marvig 31055, Toulouse, Cedex 4 (France); Lusson, A.; Bouchez, G.; Boukheddaden, K., E-mail: Younes.abid@fss.rnu.tn, E-mail: kbo@physique.uvsq.fr [Groupe d’Etudes de la Matière Condensée, UMR CNRS 8653-Université de Versailles Saint Quentin En Yvelines, 45 Avenue des Etats-Unis, 78035 Versailles (France); Triki, S. [Laboratoire de Chimie, Electrochimie Moléculaires, Chimie Analytique, UMR CNRS 6521-Université de Bretagne Occidentale, BP 809, 29285 Brest (France); Abid, Y., E-mail: Younes.abid@fss.rnu.tn, E-mail: kbo@physique.uvsq.fr [Laboratoire de Physique Appliquée, Faculté des Sciences de Sfax, Route de Soukra km 3.5 BP 1171, 3018 Sfax (Tunisia)

    2015-12-14

    Optical and structural properties of the organic-inorganic hybrid perovskite-type (C{sub 6}H{sub 11}NH{sub 3}){sub 2}[PbI{sub 4}] (abbreviated as C{sub 6}PbI{sub 4}) were investigated using optical absorption, photoluminescence (PL), and x-ray diffraction measurements. Room temperature, optical absorption measurements, performed on spin-coated films of C{sub 6}PbI{sub 4}, revealed two absorption bands at 2.44 and 3.21 eV. Upon 325 nm (3.815 eV) laser irradiation, strong green PL emission peaks were observed at 2.41 eV (P1) and 2.24 eV (P2) and assigned to free and localized excitons, respectively. The exciton binding energy was estimated at 356 meV. At low temperature, two additional emission bands were detected at 2.366 eV (P3) and a large band (LB) at 1.97 eV. The former appeared only below 40 K and the latter emerged below 130 K. The thermal dependence of the PL spectra revealed an abnormal behavior accompanied by singularities in the peak positions and intensities at 40 and 130 K. X-ray diffraction studies performed on powder and single crystals as a function of temperature evidenced significant changes of the interlayer spacing at 50 K and ∼138 K. Around 138 K, a commensurate to incommensurate structural phase transition occurred on cooling. It involves a symmetry breaking leading to a distortion of the PbI{sub 6} octahedron. The resulting incommensurate spatial modulation of the Pb–I distances (and Pb–I–Pb angles) causes a spatial modulation of the band gap, which is at the origin of the emergence of the LB below ∼130 K and the anomalous behavior of the position of P1 below 130 K. The change of the interlayer spacing in the 40-50 K range may in turn be related to the significant decrease of the intensity of P2 and the maximum emission of the LB. These results underline the intricate character of the structural and the PL properties of the hybrid perovskites; understanding such properties should benefit to the design of optoelectronic devices with

  7. Prediction of protein secondary structure using probability based features and a hybrid system.

    Science.gov (United States)

    Ghanty, Pradip; Pal, Nikhil R; Mudi, Rajani K

    2013-10-01

    In this paper, we propose some co-occurrence probability-based features for prediction of protein secondary structure. The features are extracted using occurrence/nonoccurrence of secondary structures in the protein sequences. We explore two types of features: position-specific (based on position of amino acid on fragments of protein sequences) as well as position-independent (independent of amino acid position on fragments of protein sequences). We use a hybrid system, NEUROSVM, consisting of neural networks and support vector machines for classification of secondary structures. We propose two schemes NSVMps and NSVM for protein secondary structure prediction. The NSVMps uses position-specific probability-based features and NEUROSVM classifier whereas NSVM uses the same classifier with position-independent probability-based features. The proposed method falls in the single-sequence category of methods because it does not use any sequence profile information such as position specific scoring matrices (PSSM) derived from PSI-BLAST. Two widely used datasets RS126 and CB513 are used in the experiments. The results obtained using the proposed features and NEUROSVM classifier are better than most of the existing single-sequence prediction methods. Most importantly, the results using NSVMps that are obtained using lower dimensional features, are comparable to those by other existing methods. The NSVMps and NSVM are finally tested on target proteins of the critical assessment of protein structure prediction experiment-9 (CASP9). A larger dataset is used to compare the performance of the proposed methods with that of two recent single-sequence prediction methods. We also investigate the impact of presence of different amino acid residues (in protein sequences) that are responsible for the formation of different secondary structures.

  8. The crystal structure of phosphorylated MAPK13 reveals common structural features and differences in p38 MAPK family activation

    OpenAIRE

    Yurtsever, Zeynep; Scheaffer, Suzanne M.; Romero, Arthur G.; Holtzman, Michael J.; Brett, Tom J.

    2015-01-01

    The p38 MAP kinases are an important family of drug targets for a myriad of inflammatory, as well as other, diseases. Presented here is the crystal structure of the active form of MAPK13 (p38d) as well as a comprehensive analysis of all known apo inactive and active p38 MAPK structures, revealing a common mode of activation as well as some unique structural features.

  9. The Future of Primordial Features with Large-Scale Structure Surveys

    CERN Document Server

    Chen, Xingang; Huang, Zhiqi; Namjoo, Mohammad Hossein; Verde, Licia

    2016-01-01

    Primordial features are one of the most important extensions of the Standard Model of cosmology, providing a wealth of information on the primordial universe, ranging from discrimination between inflation and alternative scenarios, new particle detection, to fine structures in the inflationary potential. We study the prospects of future large-scale structure (LSS) surveys on the detection and constraints of these features. We classify primordial feature models into several classes, and for each class we present a simple template of power spectrum that encodes the essential physics. We study how well the most ambitious LSS surveys proposed to date, including both spectroscopic and photometric surveys, will be able to improve the constraints with respect to the current Planck data. We find that these LSS surveys will significantly improve the experimental sensitivity on features signals that are oscillatory in scales, due to the 3D information. For a broad range of models, these surveys will be able to reduce t...

  10. Common Features in Electronic Structure of the Oxypnictide Superconductors from Photoemission Spectroscopy

    Institute of Scientific and Technical Information of China (English)

    JIA Xiao-Wen; CHEN Xian-Hui; REN Zhi-An; YI Wei; CHE Guang-Can; CHEN Gen-Fu; WANG Nan-Lin; WANG Gui-Ling; ZHOU Yong; ZHU Yong; WANG Xiao-Yang; LIU Hai-Yun; ZHAO Zhong-Xian; XU Zu-Yan; CHEN Chuang-Tian; ZHOU Xing-Jiang; ZHANG Wen-Wao; ZHAO Lin; MENG Jian-Qiao; LIU Guo-Dong; DONG Xiao-Li; WU Gang; LIU Rong-Hua

    2008-01-01

    High resolution photoemission measurements are carried out on non-superconducting LaFeAsO parent compound and various superconducting RFeAs(O1-xFx) (R=La, Ce and Pr) compounds. It is found that the parent LaFeAsO compound shows a metallic character. By extensive measurements, several common features are identified in the electronic structure of these Fe-based compounds: (1) 0.2eV feature in the valence band, (2) a universal 13-16meV feature, (3) near EF spectral weight suppression with decreasing temperature. These universal features can provide important information about band structure, superconducting gap and pseudogap in these Fe-based materials.

  11. ON THE SOURCE OF ASTROMETRIC ANOMALOUS REFRACTION

    Energy Technology Data Exchange (ETDEWEB)

    Taylor, M. Suzanne [Department of Natural and Environmental Sciences, Western State Colorado University, 128 Hurst Hall, Gunnison, CO 81230 (United States); McGraw, John T.; Zimmer, Peter C. [Department of Physics and Astronomy, University of New Mexico, MSC07 4220, Albuquerque, NM 87131 (United States); Pier, Jeffrey R., E-mail: mstaylor@western.edu [Division of Astronomical Sciences, NSF 4201 Wilson Blvd, Arlington, VA 22230 (United States)

    2013-03-15

    More than a century ago, astronomers using transit telescopes to determine precise stellar positions were hampered by an unexplained periodic shifting of the stars they were observing. With the advent of CCD transit telescopes in the past three decades, this unexplained motion, termed 'anomalous refraction' by these early astronomers, is again being observed. Anomalous refraction is described as a low-frequency, large angular scale ({approx}2 Degree-Sign ) motion of the entire image plane with respect to the celestial coordinate system as observed and defined by astrometric catalogs. These motions, of typically several tenths of an arcsecond amplitude with timescales on the order of 10 minutes, are ubiquitous to ground-based drift-scan astrometric measurements regardless of location or telescopes used and have been attributed to the effect of tilting of equal-density layers of the atmosphere. The cause of this tilting has often been attributed to atmospheric gravity waves, but this cause has never been confirmed. Although theoretical models of atmospheric refraction show that atmospheric gravity waves are a plausible cause of anomalous refraction, an observational campaign specifically directed at defining this relationship provides clear evidence that anomalous refraction is not consistent with the passage of atmospheric gravity waves. The source of anomalous refraction is found to be meter-scale, slowly evolving quasi-coherent dynamical structures in the boundary layer below 60 m above ground level.

  12. On the Source of Astrometric Anomalous Refraction

    Science.gov (United States)

    Taylor, M. Suzanne; McGraw, John T.; Zimmer, Peter C.; Pier, Jeffrey R.

    2013-03-01

    More than a century ago, astronomers using transit telescopes to determine precise stellar positions were hampered by an unexplained periodic shifting of the stars they were observing. With the advent of CCD transit telescopes in the past three decades, this unexplained motion, termed "anomalous refraction" by these early astronomers, is again being observed. Anomalous refraction is described as a low-frequency, large angular scale (~2°) motion of the entire image plane with respect to the celestial coordinate system as observed and defined by astrometric catalogs. These motions, of typically several tenths of an arcsecond amplitude with timescales on the order of 10 minutes, are ubiquitous to ground-based drift-scan astrometric measurements regardless of location or telescopes used and have been attributed to the effect of tilting of equal-density layers of the atmosphere. The cause of this tilting has often been attributed to atmospheric gravity waves, but this cause has never been confirmed. Although theoretical models of atmospheric refraction show that atmospheric gravity waves are a plausible cause of anomalous refraction, an observational campaign specifically directed at defining this relationship provides clear evidence that anomalous refraction is not consistent with the passage of atmospheric gravity waves. The source of anomalous refraction is found to be meter-scale, slowly evolving quasi-coherent dynamical structures in the boundary layer below 60 m above ground level.

  13. Influence of culture medium growth variables on Ganoderma lucidum exopolysaccharides structural features.

    Science.gov (United States)

    Fraga, Irene; Coutinho, João; Bezerra, Rui M; Dias, Albino A; Marques, Guilhermina; Nunes, Fernando M

    2014-10-13

    In this work the effect of carbon and nitrogen levels and initial pH of the wheat extract culture medium of submerged culture of Ganoderma lucidum on the amount, purity and structural features of exopolysaccharides (EPS) were studied. A low peptone level (1.65 g L(-1)) favored mycelium biomass, EPS purity, but a higher supply of peptone (4.80 g L(-1)) is needed for maximum EPS production. The carbohydrate composition of the EPS and structural features also changed significantly according to the different growing conditions, being observed significant differences in the (1 → 3)/(1 → 4)-Glcp ratio and also on the branching degree of EPS. As the biological activities of EPS are highly dependent on the polysaccharide structural features, this variability can have implications on the EPS biological activities, but can also be used advantageously to produce tailor made polysaccharides with specific applications.

  14. Anomalous pulmonary venous return: A case report

    Energy Technology Data Exchange (ETDEWEB)

    Park, Gyeong Min; Kang, MinJin; Lee, Han Bee; Bae, Kyung Eun; Lee, Jaehe; Kim, Jae Hyung; Jeong, Myeong Ja; Kang, Tae Kyung [Sanggye Paik Hospital, Inje University College of Medicine, Seoul (Korea, Republic of)

    2013-10-15

    Partial anomalous pulmonary venous return is a type of congenital pulmonary venous anomaly. We present a rare type of partial pulmonary venous return, subaortic vertical vein drains left lung to superior vena cava, accompanying hypoplasia of the ipsilateral lung and pulmonary artery. We also review the previous report and relationship of these structures.

  15. Anomalous atomic volume of alpha-Pu

    DEFF Research Database (Denmark)

    Kollar, J.; Vitos, Levente; Skriver, Hans Lomholt

    1997-01-01

    .3%. The comparison between the LDA and GGA results show that the anomalously large atomic volume of alpha-Pu relative to alpha-Np can be ascribed to exchange-correlation effects connected with the presence of low coordinated sites in the structure where the f electrons are close to the onset of localization...

  16. Novel structural features in the GMC family of oxidoreductases revealed by the crystal structure of fungal aryl-alcohol oxidase.

    Science.gov (United States)

    Fernández, Israel S; Ruíz-Dueñas, Francisco J; Santillana, Elena; Ferreira, Patricia; Martínez, María Jesús; Martínez, Angel T; Romero, Antonio

    2009-11-01

    Lignin biodegradation, a key step in carbon recycling in land ecosystems, is carried out by white-rot fungi through an H(2)O(2)-dependent process defined as enzymatic combustion. Pleurotus eryngii is a selective lignin-degrading fungus that produces H(2)O(2) during redox cycling of p-anisylic compounds involving the secreted flavoenzyme aryl-alcohol oxidase (AAO). Here, the 2.4 A resolution X-ray crystal structure of this oxidoreductase, which catalyzes dehydrogenation reactions on various primary polyunsaturated alcohols, yielding the corresponding aldehydes, is reported. The AAO crystal structure was solved by single-wavelength anomalous diffraction of a selenomethionine derivative obtained by Escherichia coli expression and in vitro folding. This monomeric enzyme is composed of two domains, the overall folding of which places it into the GMC (glucose-methanol-choline oxidase) oxidoreductase family, and a noncovalently bound FAD cofactor. However, two additional structural elements exist in the surroundings of its active site that modulate the access of substrates; these are absent in the structure of the model GMC oxidoreductase glucose oxidase. The folding of these novel elements gives rise to a funnel-like hydrophobic channel that connects the solvent region to the buried active-site cavity of AAO. This putative active-site cavity is located in front of the re side of the FAD isoalloxazine ring and near two histidines (His502 and His546) that could contribute to alcohol activation as catalytic bases. Moreover, three aromatic side chains from two phenylalanines (Phe397 and Phe502) and one tyrosine (Tyr92) at the inner region of the channel form an aromatic gate that may regulate the access of the enzyme substrates to the active site as well as contribute to the recognition of the alcohols that can effectively be oxidized by AAO.

  17. Feature Selection Combined with Neural Network Structure Optimization for HIV-1 Protease Cleavage Site Prediction

    Directory of Open Access Journals (Sweden)

    Hui Liu

    2015-01-01

    Full Text Available It is crucial to understand the specificity of HIV-1 protease for designing HIV-1 protease inhibitors. In this paper, a new feature selection method combined with neural network structure optimization is proposed to analyze the specificity of HIV-1 protease and find the important positions in an octapeptide that determined its cleavability. Two kinds of newly proposed features based on Amino Acid Index database plus traditional orthogonal encoding features are used in this paper, taking both physiochemical and sequence information into consideration. Results of feature selection prove that p2, p1, p1′, and p2′ are the most important positions. Two feature fusion methods are used in this paper: combination fusion and decision fusion aiming to get comprehensive feature representation and improve prediction performance. Decision fusion of subsets that getting after feature selection obtains excellent prediction performance, which proves feature selection combined with decision fusion is an effective and useful method for the task of HIV-1 protease cleavage site prediction. The results and analysis in this paper can provide useful instruction and help designing HIV-1 protease inhibitor in the future.

  18. Features Of Household Lexics, Their Characteristics And Structural Analysis In The Modern English Language

    Directory of Open Access Journals (Sweden)

    Aygun Yusifova

    2014-04-01

    Full Text Available The present paper aims to analyze the most inherent features and characteristics of household lexis in English. Special emphasis has been placed on their names of the objects used in everyday life, kitchen utensils, animal and birds. Lexical units concerning ceremonies, habits and traditions are also among the scope of the paper. Moreover, the study deals with the structural features of the units under consideration. It is believed that the thematic-semantic characterization of every-day lexis can have both pedagogical and linguistic implications, especially when dealing with comparative structures.

  19. Model-based defect detection on structured surfaces having optically unresolved features.

    Science.gov (United States)

    O'Connor, Daniel; Henning, Andrew J; Sherlock, Ben; Leach, Richard K; Coupland, Jeremy; Giusca, Claudiu L

    2015-10-20

    In this paper, we demonstrate, both numerically and experimentally, a method for the detection of defects on structured surfaces having optically unresolved features. The method makes use of synthetic reference data generated by an observational model that is able to simulate the response of the selected optical inspection system to the ideal structure, thereby providing an ideal measure of deviation from nominal geometry. The method addresses the high dynamic range challenge faced in highly parallel manufacturing by enabling the use of low resolution, wide field of view optical systems for defect detection on surfaces containing small features over large regions.

  20. Anomalous law of cooling

    OpenAIRE

    Lapas, Luciano C.; Ferreira, Rogelma M. S.; Oliveira, Fernando A.; Rubí, J. Miguel

    2014-01-01

    We analyze the temperature relaxation phenomena of systems in contact with a thermal reservoir that undergo a non-Markovian diffusion process. From a generalized Langevin equation, we show that the temperature is governed by a law of cooling of the Newton's law type in which the relaxation time depends on the velocity autocorrelation and is then characterized by the memory function. The analysis of the temperature decay reveals the existence of an anomalous cooling in which the temperature ma...

  1. Automatic classification of hepatocellular carcinoma images based on nuclear and structural features

    Science.gov (United States)

    Kiyuna, Tomoharu; Saito, Akira; Marugame, Atsushi; Yamashita, Yoshiko; Ogura, Maki; Cosatto, Eric; Abe, Tokiya; Hashiguchi, Akinori; Sakamoto, Michiie

    2013-03-01

    Diagnosis of hepatocellular carcinoma (HCC) on the basis of digital images is a challenging problem because, unlike gastrointestinal carcinoma, strong structural and morphological features are limited and sometimes absent from HCC images. In this study, we describe the classification of HCC images using statistical distributions of features obtained from image analysis of cell nuclei and hepatic trabeculae. Images of 130 hematoxylin-eosin (HE) stained histologic slides were captured at 20X by a slide scanner (Nanozoomer, Hamamatsu Photonics, Japan) and 1112 regions of interest (ROI) images were extracted for classification (551 negatives and 561 positives, including 113 well-differentiated positives). For a single nucleus, the following features were computed: area, perimeter, circularity, ellipticity, long and short axes of elliptic fit, contour complexity and gray level cooccurrence matrix (GLCM) texture features (angular second moment, contrast, homogeneity and entropy). In addition, distributions of nuclear density and hepatic trabecula thickness within an ROI were also extracted. To represent an ROI, statistical distributions (mean, standard deviation and percentiles) of these features were used. In total, 78 features were extracted for each ROI and a support vector machine (SVM) was trained to classify negative and positive ROIs. Experimental results using 5-fold cross validation show 90% sensitivity for an 87.8% specificity. The use of statistical distributions over a relatively large area makes the HCC classifier robust to occasional failures in the extraction of nuclear or hepatic trabecula features, thus providing stability to the system.

  2. Venus volcanism - Classification of volcanic features and structures, associations, and global distribution from Magellan data

    Science.gov (United States)

    Head, James W.; Crumpler, L. S.; Aubele, Jayne C.; Guest, John E.; Saunders, R. S.

    1992-01-01

    A classification and documentation of the range of morphologic features and structures of volcanic origin on Venus, their size distribution, and their global distribution and associations are presented based on a preliminary analysis of Magellan data. Some of the major questions about volcanism on Venus are addressed.

  3. Students' Demand for Smartphones: Structural Relationships of Product Features, Brand Name, Product Price and Social Infuence

    Science.gov (United States)

    Suki, Norazah Mohd

    2013-01-01

    Purpose: The study aims to examine structural relationships of product features, brand name, product price and social influence with demand for Smartphones among Malaysian students'. Design/methodology/approach: Data collected from 320 valid pre-screened university students studying at the pubic higher learning institution in Federal Territory of…

  4. [Experience in simulating the structural and dynamic features of small proteins using table supercomputers].

    Science.gov (United States)

    Kondrat'ev, M S; Kabanov, A V; Komarov, V M; Khechinashvili, N N; Samchenko, A A

    2011-01-01

    The results of theoretical studies of the structural and dynamic features of peptides and small proteins have been presented that were carried out by quantum chemical and molecular dynamics methods in high-performance graphic stations, "table supercomputers", using distributed calculations by the CUDA technology.

  5. THE GEOMORPHOLOGIC FEATURES OF INTRUSIVE MAGMATIC STRUCTURES FROM BÂRGĂU MOUNTAINS (EASTERN CARPATHIANS, ROMANIA

    Directory of Open Access Journals (Sweden)

    Ioan Bâca

    2016-08-01

    Full Text Available Igneous intrusive structures from Bârgău Mountains belong to the group of central Neogene volcanic chain of the Eastern Carpathians of Romania. The evolution of the relief developed on these structures are three main stages: the stage of injection of structures (Pannonian, the stage of uncovering of igneous intrusive bodies from Oligo-Miocene sedimentary cover (Pliocene, and the stage of subaerial modeling of magmatic bodies (Pliocene-current.In those circumstances, the geodiversity of intrusive magmatic structures from Bârgău Mountains is represented by several types of landforms such as: polycyclic landforms (erosional levels, structural landforms (the configuration of igneous intrusive structures, petrographic landforms (andesites, lithological contact, fluvial landforms (valleys, slopes, ridges, periglacial landforms (cryogenic and crionival landforms, biogenic and anthropogenic landforms. This study highlights certain features of the landforms modeled on igneous intrusive bodies with the aim of developing some strategy for tourism recovery by local and county authorities.

  6. Nonlocal sparse model with adaptive structural clustering for feature extraction of aero-engine bearings

    Science.gov (United States)

    Zhang, Han; Chen, Xuefeng; Du, Zhaohui; Li, Xiang; Yan, Ruqiang

    2016-04-01

    Fault information of aero-engine bearings presents two particular phenomena, i.e., waveform distortion and impulsive feature frequency band dispersion, which leads to a challenging problem for current techniques of bearing fault diagnosis. Moreover, although many progresses of sparse representation theory have been made in feature extraction of fault information, the theory also confronts inevitable performance degradation due to the fact that relatively weak fault information has not sufficiently prominent and sparse representations. Therefore, a novel nonlocal sparse model (coined NLSM) and its algorithm framework has been proposed in this paper, which goes beyond simple sparsity by introducing more intrinsic structures of feature information. This work adequately exploits the underlying prior information that feature information exhibits nonlocal self-similarity through clustering similar signal fragments and stacking them together into groups. Within this framework, the prior information is transformed into a regularization term and a sparse optimization problem, which could be solved through block coordinate descent method (BCD), is formulated. Additionally, the adaptive structural clustering sparse dictionary learning technique, which utilizes k-Nearest-Neighbor (kNN) clustering and principal component analysis (PCA) learning, is adopted to further enable sufficient sparsity of feature information. Moreover, the selection rule of regularization parameter and computational complexity are described in detail. The performance of the proposed framework is evaluated through numerical experiment and its superiority with respect to the state-of-the-art method in the field is demonstrated through the vibration signals of experimental rig of aircraft engine bearings.

  7. Structural details of the Orion Nebula - Detection of a network of stringlike ionized features

    Science.gov (United States)

    Yusef-Zadeh, F.

    1990-09-01

    Continuum observations of the Orion Nebula, obtained at 20 cm using the A, B, C, and D configurations of the VLA during 1986-1987, are reported. Radio images of resolution 1.8 x 1.6 arcsec are presented and analyzed, with a focus on (1) the complex cone structure of M 42 and (2) an extended network of bright stringlike features concentrated near the Trapezium cluster. Possible theoretical explanations of these features are explored, starting from the blister model of H II regions developed by Tenorio and Tagle (1979).

  8. Structural Features of Human Memapsin 2 (β-Secretase) and Their Biological and Pathological Implications

    Institute of Scientific and Technical Information of China (English)

    Lin HONG; Xiangyuan HE; Xiangping HUANG; Wanpin CHANG; Jordan TANG

    2004-01-01

    Memapsin 2 (β-secretase) is the membrane-anchored aspartic protease that initiates the cleavage of β-amyloid precursor protein (APP) leading to the production of amyloid-β (Aβ), a major factor in the pathogenesis of Alzheimer's disease (AD). Since memapsin 2 is a major target for the development of inhibitor drugs for AD, it has been intensively studied during the past five years. Here we discuss the structural features of the catalytic/specificity apparatus, transmembrane domain, cytosolic domain and the implications of these features in the physiological and pathological roles of this protease.

  9. Beta Function and Anomalous Dimensions

    CERN Document Server

    Pica, Claudio

    2010-01-01

    We demonstrate that it is possible to determine the coefficients of an all-order beta function linear in the anomalous dimensions using as data the two-loop coefficients together with the first one of the anomalous dimensions which are universal. The beta function allows to determine the anomalous dimension of the fermion masses at the infrared fixed point, and the resulting values compare well with the lattice determinations.

  10. Anomalous Dimensions of Conformal Baryons

    CERN Document Server

    Pica, Claudio

    2016-01-01

    We determine the anomalous dimensions of baryon operators for the three color theory as function of the number of massless flavours within the conformal window to the maximum known order in perturbation theory. We show that the anomalous dimension of the baryon is controllably small for a wide range of number of flavours. We also find that this is always smaller than the anomalous dimension of the fermion mass operator. These findings challenge the partial compositeness paradigm.

  11. Anomalous radiative transitions

    CERN Document Server

    Ishikawa, Kenzo; Tobita, Yutaka

    2014-01-01

    Anomalous transitions involving photons derived by many-body interaction of the form, $\\partial_{\\mu} G^{\\mu}$, in the standard model are studied. This does not affect the equation of motion in the bulk, but makes wave functions modified, and causes the unusual transition characterized by the time-independent probability. In the transition probability at a time-interval T expressed generally in the form $P=T \\Gamma_0 +P^{(d)}$, now with $\\Gamma_0=0, P^{(d)} \

  12. Accurate Prediction of One-Dimensional Protein Structure Features Using SPINE-X.

    Science.gov (United States)

    Faraggi, Eshel; Kloczkowski, Andrzej

    2017-01-01

    Accurate prediction of protein secondary structure and other one-dimensional structure features is essential for accurate sequence alignment, three-dimensional structure modeling, and function prediction. SPINE-X is a software package to predict secondary structure as well as accessible surface area and dihedral angles ϕ and ψ. For secondary structure SPINE-X achieves an accuracy of between 81 and 84 % depending on the dataset and choice of tests. The Pearson correlation coefficient for accessible surface area prediction is 0.75 and the mean absolute error from the ϕ and ψ dihedral angles are 20(∘) and 33(∘), respectively. The source code and a Linux executables for SPINE-X are available from Research and Information Systems at http://mamiris.com .

  13. Seismicity in the platform regions of Ukraine in the zones of anomalous electrical conductivity

    Science.gov (United States)

    Kushnir, A. N.; Kulik, S. N.; Burakhovich, T. K.

    2013-05-01

    It is established for the first time that there are several regions in Ukraine, in which the earthquakes occurring within platform territory are correlated to the anomalous conductive structures in the Earth's crust and upper mantle. These regions are identified as (1) Donbass and the eastern part of the Dnieper-Donetsk Depression (DDD); (2) eastern margin of the Ingulets-Krivoi Rog suture zone in the area of the Krivoi Rog-Kremenchug fault zone; (3) the western part of the Cis-Azov megablock; (4) the western boundary of the Ukrainian Shield and its slope; (5) North Dobruja and Pre-Dobrujan Depression. The reconstructed tree-dimensional (3D) geoelectrical models of the Earth's crust and upper mantle feature anomalously low values of electric resistivity. The earthquake sources in the platform areas of Ukraine are localized above the top and in the upper parts of the crustal anomalies of electrical conductivity.

  14. Spatial structure and scale feature of the atmospheric pollution source impact of city agglomeration

    Institute of Scientific and Technical Information of China (English)

    XU; Xiangde; ZHOU; Xiuji; SHI; Xiaohui

    2005-01-01

    The spatial structure and multi-scale feature of the atmospheric pollution influence domain of Beijing and its peripheral areas (a rapidly developed city agglomeration) is dissected and analyzed in this paper on the basis of the atmospheric pollution dynamic-chemical process observation data of the urban building ensemble boundary layer of the Beijing City Air Pollution Observation Experiment (BECAPEX) in winter (February) and summer (August) 2003, and relevant meteorological elements and satellite retrieval aerosol optical depth (AOD), etc. comprehensive data with the dynamic-statistical integrated analysis of "point-surface" spatial structure. Results show that there existed significant difference in the contribution of winter/summer different pollution emission sources to the component character of atmospheric pollution, and the principal component analysis (PCA) results of statistical model also indicate that SO2 and NOX dominated in the component structure of winter aerosol particle; instead, CO and NOX dominated in summer. Surface layer atmospheric dynamic and thermal structures and various pollutant species at the upper boundary of building ensembles at urban different observational sites of Beijing in winter and summer showed an "in-phase" variation and its spatial scale feature of "influence domain". The power spectrum analysis (PSA) shows that the period spectrum of winter/summer particle concentration accorded with those of atmospheric wind field: the longer period was dominative in winter, but the shorter period in summer, revealing the impact of the seasonal scale feature of winter/summer atmospheric general circulation on the period of atmospheric pollution variations. It is found that from analyzing urban area thermal heterogeneity that the multiscale effect of Beijing region urban heat island (UHI) was associated with the heterogeneous expansion of tall buildings area. In urban atmospheric dynamical and thermal characteristic spatial structures, the

  15. Structuring feature space: a non-parametric method for volumetric transfer function generation.

    Science.gov (United States)

    Maciejewski, Ross; Woo, Insoo; Chen, Wei; Ebert, David S

    2009-01-01

    The use of multi-dimensional transfer functions for direct volume rendering has been shown to be an effective means of extracting materials and their boundaries for both scalar and multivariate data. The most common multi-dimensional transfer function consists of a two-dimensional (2D) histogram with axes representing a subset of the feature space (e.g., value vs. value gradient magnitude), with each entry in the 2D histogram being the number of voxels at a given feature space pair. Users then assign color and opacity to the voxel distributions within the given feature space through the use of interactive widgets (e.g., box, circular, triangular selection). Unfortunately, such tools lead users through a trial-and-error approach as they assess which data values within the feature space map to a given area of interest within the volumetric space. In this work, we propose the addition of non-parametric clustering within the transfer function feature space in order to extract patterns and guide transfer function generation. We apply a non-parametric kernel density estimation to group voxels of similar features within the 2D histogram. These groups are then binned and colored based on their estimated density, and the user may interactively grow and shrink the binned regions to explore feature boundaries and extract regions of interest. We also extend this scheme to temporal volumetric data in which time steps of 2D histograms are composited into a histogram volume. A three-dimensional (3D) density estimation is then applied, and users can explore regions within the feature space across time without adjusting the transfer function at each time step. Our work enables users to effectively explore the structures found within a feature space of the volume and provide a context in which the user can understand how these structures relate to their volumetric data. We provide tools for enhanced exploration and manipulation of the transfer function, and we show that the initial

  16. Structural Features That Stabilize ZnO Clusters: An Electronic Structure Approach

    Directory of Open Access Journals (Sweden)

    Csaba E. Szakacs

    2013-05-01

    Full Text Available We show that a simple approach to building small computationally inexpensive clusters offers insights on specific structural motifs that stabilize the electronic structure of ZnO. All-electron calculations on ZniOi needle (i = 6, 9, 12, 15, and 18 and plate (i = 9 and 18 clusters within the density functional theory (DFT formalism show a higher stability for ZnO needles that increases with length. Puckering of the rings to achieve a more wurtzite-like structure destabilizes the needles, although this destabilization is reduced by going to infinite needles (calculated using periodic boundary conditions. Calculations of density of states (DOS curves and band gaps for finite clusters and infinite needles highlight opportunities for band-gap tuning through kinetic control of nanocrystal growth.

  17. Anomalous electromagnetism of pions and magnons

    Energy Technology Data Exchange (ETDEWEB)

    Wiese, U.-J. [Institute for Theoretical Physics, Bern University Sidlerstrasse 5, CH-3012 Bern (Switzerland)

    2005-04-15

    Pions and magnons - the Goldstone bosons of the strong interactions and of magnetism - share a number of common features. Pion and magnon fields couple anomalously to electromagnetism through the conserved Goldstone-Wilczek current of their topological Skyrmion excitations. In the pion case, this coupling gives rise to the decay of the neutral pion into two photons. In the magnon case, the anomalous coupling leads to photonmagnon conversion in an external magnetic field. A measurement of the conversion rate in quantum Hall ferromagnets determines the anyon statistics angle of baby-Skyrmions. If photon-magnon conversion also occurs in antiferromagnets, baby-Skyrmions carry electric charge and may represent the Cooper-pairs of high-temperature superconductors.

  18. Anomalous Microwave Emission

    CERN Document Server

    Kogut, A J

    1999-01-01

    Improved knowledge of diffuse Galactic emission is important to maximize the scientific return from scheduled CMB anisotropy missions. Cross-correlation of microwave maps with maps of the far-IR dust continuum show a ubiquitous microwave emission component whose spatial distribution is traced by far-IR dust emission. The spectral index of this emission, beta_{radio} = -2.2 (+0.5 -0.7) is suggestive of free-free emission but does not preclude other candidates. Comparison of H-alpha and microwave results show that both data sets have positive correlations with the far-IR dust emission. Microwave data, however, are consistently brighter than can be explained solely from free-free emission traced by H-alpha. This ``anomalous'' microwave emission can be explained as electric dipole radiation from small spinning dust grains. The anomalous component at 53 GHz is 2.5 times as bright as the free-free emission traced by H-alpha, providing an approximate normalization for models with significant spinning dust emission.

  19. Fickian dispersion is anomalous

    Science.gov (United States)

    Cushman, John H.; O'Malley, Dan

    2015-12-01

    The thesis put forward here is that the occurrence of Fickian dispersion in geophysical settings is a rare event and consequently should be labeled as anomalous. What people classically call anomalous is really the norm. In a Lagrangian setting, a process with mean square displacement which is proportional to time is generally labeled as Fickian dispersion. With a number of counter examples we show why this definition is fraught with difficulty. In a related discussion, we show an infinite second moment does not necessarily imply the process is super dispersive. By employing a rigorous mathematical definition of Fickian dispersion we illustrate why it is so hard to find a Fickian process. We go on to employ a number of renormalization group approaches to classify non-Fickian dispersive behavior. Scaling laws for the probability density function for a dispersive process, the distribution for the first passage times, the mean first passage time, and the finite-size Lyapunov exponent are presented for fixed points of both deterministic and stochastic renormalization group operators. The fixed points of the renormalization group operators are p-self-similar processes. A generalized renormalization group operator is introduced whose fixed points form a set of generalized self-similar processes. Power-law clocks are introduced to examine multi-scaling behavior. Several examples of these ideas are presented and discussed.

  20. The role of emotion in musical improvisation: an analysis of structural features.

    Directory of Open Access Journals (Sweden)

    Malinda J McPherson

    Full Text Available One of the primary functions of music is to convey emotion, yet how music accomplishes this task remains unclear. For example, simple correlations between mode (major vs. minor and emotion (happy vs. sad do not adequately explain the enormous range, subtlety or complexity of musically induced emotions. In this study, we examined the structural features of unconstrained musical improvisations generated by jazz pianists in response to emotional cues. We hypothesized that musicians would not utilize any universal rules to convey emotions, but would instead combine heterogeneous musical elements together in order to depict positive and negative emotions. Our findings demonstrate a lack of simple correspondence between emotions and musical features of spontaneous musical improvisation. While improvisations in response to positive emotional cues were more likely to be in major keys, have faster tempos, faster key press velocities and more staccato notes when compared to negative improvisations, there was a wide distribution for each emotion with components that directly violated these primary associations. The finding that musicians often combine disparate features together in order to convey emotion during improvisation suggests that structural diversity may be an essential feature of the ability of music to express a wide range of emotion.

  1. The role of emotion in musical improvisation: an analysis of structural features.

    Science.gov (United States)

    McPherson, Malinda J; Lopez-Gonzalez, Monica; Rankin, Summer K; Limb, Charles J

    2014-01-01

    One of the primary functions of music is to convey emotion, yet how music accomplishes this task remains unclear. For example, simple correlations between mode (major vs. minor) and emotion (happy vs. sad) do not adequately explain the enormous range, subtlety or complexity of musically induced emotions. In this study, we examined the structural features of unconstrained musical improvisations generated by jazz pianists in response to emotional cues. We hypothesized that musicians would not utilize any universal rules to convey emotions, but would instead combine heterogeneous musical elements together in order to depict positive and negative emotions. Our findings demonstrate a lack of simple correspondence between emotions and musical features of spontaneous musical improvisation. While improvisations in response to positive emotional cues were more likely to be in major keys, have faster tempos, faster key press velocities and more staccato notes when compared to negative improvisations, there was a wide distribution for each emotion with components that directly violated these primary associations. The finding that musicians often combine disparate features together in order to convey emotion during improvisation suggests that structural diversity may be an essential feature of the ability of music to express a wide range of emotion.

  2. Hyperhomocysteinemia disrupts retinal pigment epithelial structure and function with features of age-related macular degeneration.

    Science.gov (United States)

    Ibrahim, Ahmed S; Mander, Suchreet; Hussein, Khaled A; Elsherbiny, Nehal M; Smith, Sylvia B; Al-Shabrawey, Mohamed; Tawfik, Amany

    2016-02-23

    The disruption of retinal pigment epithelial (RPE) function and the degeneration of photoreceptors are cardinal features of age related macular degeneration (AMD); however there are still gaps in our understanding of underlying biological processes. Excess homocysteine (Hcy) has been reported to be elevated in plasma of patients with AMD. This study aimed to evaluate the direct effect of hyperhomocysteinemia (HHcy) on structure and function of RPE. Initial studies in a mouse model of HHcy, in which cystathionine-β-synthase (cbs) was deficient, revealed abnormal RPE cell morphology with features similar to that of AMD upon optical coherence tomography (OCT), fluorescein angiography (FA), histological, and electron microscopic examinations. These features include atrophy, vacuolization, hypopigmentation, thickened basal laminar membrane, hyporeflective lucency, choroidal neovascularization (CNV), and disturbed RPE-photoreceptor relationship. Furthermore, intravitreal injection of Hcy per se in normal wild type (WT) mice resulted in diffuse hyper-fluorescence, albumin leakage, and CNV in the area of RPE. In vitro experiments on ARPE-19 showed that Hcy dose-dependently reduced tight junction protein expression, increased FITC dextran leakage, decreased transcellular electrical resistance, and impaired phagocytic activity. Collectively, our results demonstrated unreported effects of excess Hcy levels on RPE structure and function that lead to the development of AMD-like features.

  3. Adaptive cellular structures and devices with internal features for enhanced structural performance

    Science.gov (United States)

    Pontecorvo, Michael Eugene

    This dissertation aims to develop a family of cellular and repeatable devices that exhibit a variety of force-displacement behaviors. It is envisioned that these cellular structures might be used either as stand-alone elements, or combined and repeated to create multiple types of structures (i.e. buildings, ship hulls, vehicle subfloors, etc.) with the ability to passively or actively perform multiple functions (harmonic energy dissipation, impact mitigation, modulus change) over a range of loading types, amplitudes, and frequencies. To accomplish this goal, this work combines repeatable structural frameworks, such as that provided by a hexagonal cellular structure, with internal structural elements such as springs, viscous dampers, buckling plates, bi-stable von Mises trusses (VMTs), and pneumatic artificial muscles (PAMs). The repeatable framework serves to position damping and load carrying elements throughout the structure, and the configuration of the internal elements allow each cell to be tuned to exhibit a desired force-displacement response. Therefore, gradient structures or structures with variable load paths can be created for an optimal global response to a range of loads. This dissertation focuses on the development of cellular structures for three functions: combined load-carrying capability with harmonic energy dissipation, impact mitigation, and cell modulus variation. One or more conceptual designs are presented for devices that can perform each of these functions, and both experimental measurements and simulations are used to gain a fundamental understanding of each device. Chapter 2 begins with a presentation of a VMT model that is the basis for many of the elements. The equations of motion for the VMT are derived and the static and dynamic behavior of the VMT are discussed in detail. Next, two metrics for the energy dissipation of the VMT - hysteresis loop area and loss factor - are presented. The responses of the VMT to harmonic displacement

  4. Discriminant features and temporal structure of nonmanuals in American Sign Language.

    Science.gov (United States)

    Benitez-Quiroz, C Fabian; Gökgöz, Kadir; Wilbur, Ronnie B; Martinez, Aleix M

    2014-01-01

    To fully define the grammar of American Sign Language (ASL), a linguistic model of its nonmanuals needs to be constructed. While significant progress has been made to understand the features defining ASL manuals, after years of research, much still needs to be done to uncover the discriminant nonmanual components. The major barrier to achieving this goal is the difficulty in correlating facial features and linguistic features, especially since these correlations may be temporally defined. For example, a facial feature (e.g., head moves down) occurring at the end of the movement of another facial feature (e.g., brows moves up), may specify a Hypothetical conditional, but only if this time relationship is maintained. In other instances, the single occurrence of a movement (e.g., brows move up) can be indicative of the same grammatical construction. In the present paper, we introduce a linguistic-computational approach to efficiently carry out this analysis. First, a linguistic model of the face is used to manually annotate a very large set of 2,347 videos of ASL nonmanuals (including tens of thousands of frames). Second, a computational approach is used to determine which features of the linguistic model are more informative of the grammatical rules under study. We used the proposed approach to study five types of sentences--Hypothetical conditionals, Yes/no questions, Wh-questions, Wh-questions postposed, and Assertions--plus their polarities--positive and negative. Our results verify several components of the standard model of ASL nonmanuals and, most importantly, identify several previously unreported features and their temporal relationship. Notably, our results uncovered a complex interaction between head position and mouth shape. These findings define some temporal structures of ASL nonmanuals not previously detected by other approaches.

  5. Classification of EEG with structural feature dictionaries in a brain computer interface.

    Science.gov (United States)

    Göksu, Fikri; Ince, Nuri Firat; Tadipatri, Vijay Aditya; Tewfik, Ahmed H

    2008-01-01

    We present a new method for the classification of EEG in a brain computer interface by adapting subject specific features in spectral, temporal and spatial domain. For this particular purpose we extend our previous work on ECoG classification based on structural feature dictionary and apply it to extract the spectro-temporal patterns of multichannel EEG recordings related to a motor imagery task. The construction of the feature dictionary based on undecimated wavelet packet transform is extended to block FFT. We evaluate several subset selection algorithms to select a small number of features for final classification. We tested our proposed approach on five subjects of BCI Competition 2005 dataset- IVa. By adapting the wavelet filter for each subject, the algorithm achieved an average classification accuracy of 91.4% The classification results and characteristic of selected features indicate that the proposed algorithm can jointly adapt to EEG patterns in spectro-spatio-temporal domain and provide classification accuracies as good as existing methods used in the literature.

  6. Ht-Index for Quantifying the Fractal or Scaling Structure of Geographic Features

    CERN Document Server

    Jiang, Bin

    2013-01-01

    Although geographic features, such as mountains and coastlines, are fractal, some studies have claimed that the fractal property is not universal. This claim, which is false, is mainly attributed to the strict definition of fractal dimension as a measure or index for characterizing the complexity of fractals. In this paper, we propose an alternative, the ht-index, to quantify the fractal or scaling structure of geographic features. A geographic feature has ht-index h if the pattern of far more small things than large ones recurs (h-1) times at different scales. The higher the ht-index, the more complex the geographic feature. We conduct three case studies to illustrate how the computed ht-indices capture the complexity of different geographic features. We further discuss how the ht-index is complementary to fractal dimension, and elaborate on a dynamic view behind the ht-index that enables better understanding of geographic forms and processes. Keywords: Scaling of geographic space, fractal dimension, Richard...

  7. Summarization based on physical features and logical structure of multi documents

    Institute of Scientific and Technical Information of China (English)

    Qin Bing; Liu Ting; Li Sheng

    2005-01-01

    With the rapid development of the Internet, multi documents summarization is becoming a very hot research topic. In order to generate a summarization that can effectively characterize the original information from documents, this paper proposes a multi documents summarization approach based on the physical features and logical structure of the document set. This method firstly clusterssimilar sentences into several Logical Topics (LTs), and then orders these topics according to their physical features of multi documents. After that, sentences used for the summarization are extracted from these LTs, and finally the summarization is generated via certain sorting algorithms. Our experiments show that the information coverage rate of our method is 8.83% higher than those methods based solely on logical structures, and 14.31% higher than Top-N method.

  8. On the structural features of fiber suspensions in converging channel flow

    Institute of Scientific and Technical Information of China (English)

    林建忠; 张凌新

    2003-01-01

    The structural features of fiber suspensions are dependent on the fiber alignment in the flows. In this work the orientation distribution function and orientation tensors for semi-concentrated fiber suspensions in converging channel flow were calculated, and the evolutions of the fiber alignment and the bulk effective viscosity were analyzed. The results showed that the bulk stress and the effective viscosity were functions of the rate-of-strain tensor and the fiber orientation state; and that the fiber suspensions evolved to steady alignment and tended to concentrate to some preferred directions close to but not same as the directions of local streamlines. The bulk effective viscosity depended on the product of Reynolds number and time. The decrease of effective viscosity near the boundary benefited the increase of the rate of flow. Finally when the fiber alignment went into steady state, the structural features of fiber suspensions were not dependent on the Reynolds number but on the converging channel angle.

  9. Structural Features and In-service Inspection of the LTNHR-200 Pressure Vessel

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    The pressure vessel of 200 MW low temperature nuclear heating reactor (LTNHR-200) is the main part of primary pressure boundary and its reasonable and reliable structural design is the key point to assure the safe operation of LTNHR-200. The double-shell pressure vessels were designed. LTNHR-200 pressure vessel meets the condition of Leak Before Break and has a relatively low failure probability. Metal containment (outer pressure vessel) has the similar features to LTNHR-200 pressure vessel. There exists no LOCA and core melting with the double vessel. The in-service inspection of the pressure vessel can be simplified greatly because of the safety and structural features of the reactor.

  10. Structural features affecting the enzymatic digestibility of pine wood pretreated with ionic liquids.

    Science.gov (United States)

    Torr, Kirk M; Love, Karen T; Simmons, Blake A; Hill, Stefan J

    2016-03-01

    Pretreating lignocellulosic biomass with certain ionic liquids results in structural and chemical changes that make the biomass more digestible by enzymes. In this study, pine wood was pretreated with 1-ethyl-3-methylimidazolium chloride/acetate ([C2 mim]Cl and [C2 mim][OAc]) at different temperatures to investigate the relative importance of substrate features, such as accessible surface area, cellulose crystallinity, and lignin content, on enzymatic digestibility. The ionic liquid pretreatments resulted in glucan conversions ranging from 23% to 84% on saccharification of the substrates, with [C2 mim][OAc] being more effective than [C2 mim]Cl. The pretreatments resulted in no delignification of the wood, some loss of cellulose crystallinity under certain conditions, and varying levels of increased surface area. Enzymatic digestibility closely correlated with accessible surface area and porosity measurements obtained using Simons' staining and thermoporosimetry techniques. Increased accessible surface area was identified as the principal structural feature responsible for the improved enzymatic digestibility.

  11. Large-scale oscillation of structure-related DNA sequence features in human chromosome 21

    Science.gov (United States)

    Li, Wentian; Miramontes, Pedro

    2006-08-01

    Human chromosome 21 is the only chromosome in the human genome that exhibits oscillation of the (G+C) content of a cycle length of hundreds kilobases (kb) ( 500kb near the right telomere). We aim at establishing the existence of a similar periodicity in structure-related sequence features in order to relate this (G+C)% oscillation to other biological phenomena. The following quantities are shown to oscillate with the same 500kb periodicity in human chromosome 21: binding energy calculated by two sets of dinucleotide-based thermodynamic parameters, AA/TT and AAA/TTT bi- and tri-nucleotide density, 5'-TA-3' dinucleotide density, and signal for 10- or 11-base periodicity of AA/TT or AAA/TTT. These intrinsic quantities are related to structural features of the double helix of DNA molecules, such as base-pair binding, untwisting or unwinding, stiffness, and a putative tendency for nucleosome formation.

  12. Seismically-induced structures in the Quaternary sediments of the NE Fennoscandian Shield: Features and age

    OpenAIRE

    Nikolaeva S. B.

    2016-01-01

    Results of studying secondary seismogenic deformations of the vibrational type (termed "seismites") in loose sediments of the north-eastern Baltic Shield (the Kola region) have been provided. The features, types, formation patterns and age of seismites have been considered. On the basis of previous results the major periods of the region activation in the Holocene have been defined. Criteria of identifying similar structures with widely spread glaciodislocations have been suggested. Results o...

  13. Structural features of cross-bridges in isometrically contracting skeletal muscle.

    OpenAIRE

    Kraft, Theresia; Mattei, Thomas; Radocaj, Ante; Piep, Birgit; Nocula, Christoph; Furch, Markus; Brenner, Bernhard

    2002-01-01

    Two-dimensional x-ray diffraction was used to investigate structural features of cross-bridges that generate force in isometrically contracting skeletal muscle. Diffraction patterns were recorded from arrays of single, chemically skinned rabbit psoas muscle fibers during isometric force generation, under relaxation, and in rigor. In isometric contraction, a rather prominent intensification of the actin layer lines at 5.9 and 5.1 nm and of the first actin layer line at 37 nm was found compared...

  14. Feature selection and the information content of Thematic Mapper simulator data for forest structural assessment

    Science.gov (United States)

    Spanner, M. A.; Brass, J. A.; Peterson, D. L.

    1984-01-01

    An assessment is made of the information content of Thematic Mapper Simulator (TMS) data for the case of a forested region, in order to determine the sensitivity of such data to forest crown closure and tree size class. Principal components analysis and Monte Carlo simulation indicated that channels 4, 7, 5 and 3 were optimal for four-channel forest structure analysis. As the number of channels supplied to the Monte Carlo feature selection routine increased, classification accuracy increased. The greatest sensitivity to the forest structural parameters, which included succession within clearcuts as well as crown closure and size class, was obtained from the 7-channel TMS data.

  15. Fabrication method for small-scale structures with non-planar features

    Energy Technology Data Exchange (ETDEWEB)

    Burckel, David Bruce; Ten Eyck, Gregory A.

    2016-09-20

    The fabrication of small-scale structures is disclosed. A unit-cell of a small-scale structure with non-planar features is fabricated by forming a membrane on a suitable material. A pattern is formed in the membrane and a portion of the substrate underneath the membrane is removed to form a cavity. Resonators are then directionally deposited on the wall or sides of the cavity. The cavity may be rotated during deposition to form closed-loop resonators. The resonators may be non-planar. The unit-cells can be formed in a layer that includes an array of unit-cells.

  16. Structural features of Ni-Cr-Si-B materials obtained by different technologies

    OpenAIRE

    Kornienko, E. E.; Nikulina, A. A.; Belousova, N. S.; Lazurenko, D. V.; Ivashutenko, Alexander Sergeevich; Kuzmin, V. I.

    2016-01-01

    This study considers the structural features of Ni-Cr-Si-B (Ni - base; 15.1 % Cr; 2 % Si; 2 % B; 0.4 % C) materials obtained by different methods. The self-fluxing coatings were deposited by plasma spraying on the tubes from low carbon steel. Bulk cylinder specimens of 20 mm diameter and 15 mm height were obtained by spark plasma sintering (SPS). The structure and phase composition of these materials were investigated by optical microscopy (OM), scanning electron microscopy (SEM), transmissio...

  17. Multiple linear regression model for predicting biomass digestibility from structural features.

    Science.gov (United States)

    Zhu, Li; O'Dwyer, Jonathan P; Chang, Vincent S; Granda, Cesar B; Holtzapple, Mark T

    2010-07-01

    A total of 147 model lignocellulose samples with a broad spectrum of structural features (lignin contents, acetyl contents, and crystallinity indices) were hydrolyzed with a wide range of cellulase loadings during 1-, 6-, and 72-h hydrolysis periods. Carbohydrate conversions at 1, 6, and 72 h were linearly proportional to the logarithm of cellulase loadings from approximately 10% to 90% conversion, indicating that the simplified HCH-1 model is valid for predicting lignocellulose digestibility. The HCH-1 model is a modified Michaelis-Menton model that accounts for the fraction of insoluble substrate available to bind with enzyme. The slopes and intercepts of a simplified HCH-1 model were correlated with structural features using multiple linear regression (MLR) models. The agreement between the measured and predicted 1-, 6-, and 72-h slopes and intercepts of glucan, xylan, and total sugar hydrolyses indicate that lignin content, acetyl content, and cellulose crystallinity are key factors that determine biomass digestibility. The 1-, 6-, and 72-h glucan, xylan, and total sugar conversions predicted from structural features using MLR models and the simplified HCH-1 model fit satisfactorily with the measured data (R(2) approximately 1.0). The parameter selection suggests that lignin content and cellulose crystallinity more strongly affect on digestibility than acetyl content. Cellulose crystallinity has greater influence during short hydrolysis periods whereas lignin content has more influence during longer hydrolysis periods. Cellulose crystallinity shows more influence on glucan hydrolysis whereas lignin content affects xylan hydrolysis to a greater extent.

  18. Structure and functional features of olive pollen pectin methylesterase using homology modeling and molecular docking methods.

    Science.gov (United States)

    Jimenez-Lopez, Jose C; Kotchoni, Simeon O; Rodríguez-García, María I; Alché, Juan D

    2012-12-01

    Pectin methylesterases (PMEs), a multigene family of proteins with multiple differentially regulated isoforms, are key enzymes implicated in the carbohydrates (pectin) metabolism of cell walls. Olive pollen PME has been identified as a new allergen (Ole e 11) of potential relevance in allergy amelioration, since it exhibits high prevalence among atopic patients. In this work, the structural and functional characterization of two olive pollen PME isoforms and their comparison with other PME plants was performed by using different approaches: (1) the physicochemical properties and functional-regulatory motifs characterization, (2) primary sequence analysis, 2D and 3D comparative structural features study, (3) conservation and evolutionary analysis, (4) catalytic activity and regulation based on molecular docking analysis of a homologue PME inhibitor, and (5) B-cell epitopes prediction by sequence and structural based methods and protein-protein interaction tools, while T-cell epitopes by inhibitory concentration and binding score methods. Our results indicate that the structural differences and low conservation of residues, together with differences in physicochemical and posttranslational motifs might be a mechanism for PME isovariants generation, regulation, and differential surface epitopes generation. Olive PMEs perform a processive catalytic mechanism, and a differential molecular interaction with specific PME inhibitor, opening new possibilities for PME activity regulation. Despite the common function of PMEs, differential features found in this study will lead to a better understanding of the structural and functional characterization of plant PMEs and help to improve the component-resolving diagnosis and immunotherapy of olive pollen allergy by epitopes identification.

  19. Analytical techniques and computer algorithms combined for the rapid characterization of structural peptide and protein features.

    Science.gov (United States)

    Caporale, C

    1998-11-01

    The most recent algorithms based on the use of modern analytical techniques for the assessment of structural peptide and protein features have been reviewed. No algorithm devoted to the realization of predictive models or statistical analysis has been discussed, but only methods furnishing information on the real structure of the molecules. In particular, the procedures designed for handling sequence and mass spectrometric data obtained from the analysis of unfractionated digestion mixtures allow the user to get rapid information on the structure of the target polypeptide. Two classes of methods are illustrated: the first regards the determination of the amino acid sequence, whereas the second used its knowledge to supply data on the localization, function and three-dimensional structure of disulphides.

  20. Anomalous Dimensions of Conformal Baryons

    DEFF Research Database (Denmark)

    Pica, Claudio; Sannino, Francesco

    2016-01-01

    We determine the anomalous dimensions of baryon operators for the three color theory as function of the number of massless flavours within the conformal window to the maximum known order in perturbation theory. We show that the anomalous dimension of the baryon is controllably small, within...

  1. Anomalous Dimensions of Conformal Baryons

    DEFF Research Database (Denmark)

    Pica, Claudio; Sannino, Francesco

    2016-01-01

    We determine the anomalous dimensions of baryon operators for the three color theory as function of the number of massless flavours within the conformal window to the maximum known order in perturbation theory. We show that the anomalous dimension of the baryon is controllably small, within the $...

  2. Beta Function and Anomalous Dimensions

    DEFF Research Database (Denmark)

    Pica, Claudio; Sannino, Francesco

    2011-01-01

    We demonstrate that it is possible to determine the coefficients of an all-order beta function linear in the anomalous dimensions using as data the two-loop coefficients together with the first one of the anomalous dimensions which are universal. The beta function allows to determine the anomalou...

  3. Fractal model of anomalous diffusion.

    Science.gov (United States)

    Gmachowski, Lech

    2015-12-01

    An equation of motion is derived from fractal analysis of the Brownian particle trajectory in which the asymptotic fractal dimension of the trajectory has a required value. The formula makes it possible to calculate the time dependence of the mean square displacement for both short and long periods when the molecule diffuses anomalously. The anomalous diffusion which occurs after long periods is characterized by two variables, the transport coefficient and the anomalous diffusion exponent. An explicit formula is derived for the transport coefficient, which is related to the diffusion constant, as dependent on the Brownian step time, and the anomalous diffusion exponent. The model makes it possible to deduce anomalous diffusion properties from experimental data obtained even for short time periods and to estimate the transport coefficient in systems for which the diffusion behavior has been investigated. The results were confirmed for both sub and super-diffusion.

  4. Detection of anomalous events

    Energy Technology Data Exchange (ETDEWEB)

    Ferragut, Erik M.; Laska, Jason A.; Bridges, Robert A.

    2016-06-07

    A system is described for receiving a stream of events and scoring the events based on anomalousness and maliciousness (or other classification). The system can include a plurality of anomaly detectors that together implement an algorithm to identify low-probability events and detect atypical traffic patterns. The anomaly detector provides for comparability of disparate sources of data (e.g., network flow data and firewall logs.) Additionally, the anomaly detector allows for regulatability, meaning that the algorithm can be user configurable to adjust a number of false alerts. The anomaly detector can be used for a variety of probability density functions, including normal Gaussian distributions, irregular distributions, as well as functions associated with continuous or discrete variables.

  5. Optically Anomalous Crystals

    CERN Document Server

    Shtukenberg, Alexander; Kahr, Bart

    2007-01-01

    Optical anomalies in crystals are puzzles that collectively constituted the greatest unsolved problems in crystallography in the 19th Century. The most common anomaly is a discrepancy between a crystal’s symmetry as determined by its shape or by X-ray analysis, and that determined by monitoring the polarization state of traversing light. These discrepancies were perceived as a great impediment to the development of the sciences of crystals on the basis of Curie’s Symmetry Principle, the grand organizing idea in the physical sciences to emerge in the latter half of the 19th Century. Optically Anomalous Crystals begins with an historical introduction covering the contributions of Brewster, Biot, Mallard, Brauns, Tamman, and many other distinguished crystallographers. From this follows a tutorial in crystal optics. Further chapters discuss the two main mechanisms of optical dissymmetry: 1. the piezo-optic effect, and 2. the kinetic ordering of atoms. The text then tackles complex, inhomogeneous crystals, and...

  6. Identification of Characteristic Features of Structural Change in the Research and Innovation Process

    Directory of Open Access Journals (Sweden)

    Mikhail Aleksandrovich Gusakov

    2015-12-01

    Full Text Available The paper substantiates and identifies the characteristics and emerging trends of structural change in the research and innovation process in the conditions of formation of post-industrial economy and transition to post-industrial technology. The characteristics and developments concern the structure of the research and innovation process, research and development quality, the role of basic science and high technology, the place of services in research and innovation products, and the spatial context of the structure. The evolution of the concept and content (structure of the research and innovation process determines the initial trend in the specific features of structural change in the research and innovation process. The authors of the article investigate the dynamics of the main indicators of innovation activity as an integrated result of boosting the efficiency of the research and innovation process, the indicators of development of high-tech industries with special emphasis on nanotechnology and information and communication technology, the indicators of dissemination of post-industrial economic services, in the spatial context as well. The article reveals a tendency towards the implementation of the research and innovation process in the spatial dimension. The authors reveal characteristic features of structural change in the research and innovation process and several emerging shifts in the structure of the process; this helps to outline certain specific requirements to the organizational-economic mechanism, the feasibility of changing institutional conditions and institutions for the purpose of strengthening the promising trends of development of post-industrial technology and acceleration of innovation development

  7. Anomalous enthalpy relaxation in vitreous silica

    DEFF Research Database (Denmark)

    Yue, Yuanzheng

    2015-01-01

    scans. It is known that the liquid fragility (i.e., the speed of the viscous slow-down of a supercooled liquid at its Tg during cooling) has impact on enthalpy relaxation in glass. Here, we find that vitreous silica (as a strong system) exhibits striking anomalies in both glass transition and enthalpy...... the fragile ones do in a structurally independent fashion. We discuss the origin of the anomalous enthalpy relaxation in the HQ vitreous silica....

  8. Protein subcellular localization prediction based on compartment-specific features and structure conservation

    Directory of Open Access Journals (Sweden)

    Lo Allan

    2007-09-01

    Full Text Available Abstract Background Protein subcellular localization is crucial for genome annotation, protein function prediction, and drug discovery. Determination of subcellular localization using experimental approaches is time-consuming; thus, computational approaches become highly desirable. Extensive studies of localization prediction have led to the development of several methods including composition-based and homology-based methods. However, their performance might be significantly degraded if homologous sequences are not detected. Moreover, methods that integrate various features could suffer from the problem of low coverage in high-throughput proteomic analyses due to the lack of information to characterize unknown proteins. Results We propose a hybrid prediction method for Gram-negative bacteria that combines a one-versus-one support vector machines (SVM model and a structural homology approach. The SVM model comprises a number of binary classifiers, in which biological features derived from Gram-negative bacteria translocation pathways are incorporated. In the structural homology approach, we employ secondary structure alignment for structural similarity comparison and assign the known localization of the top-ranked protein as the predicted localization of a query protein. The hybrid method achieves overall accuracy of 93.7% and 93.2% using ten-fold cross-validation on the benchmark data sets. In the assessment of the evaluation data sets, our method also attains accurate prediction accuracy of 84.0%, especially when testing on sequences with a low level of homology to the training data. A three-way data split procedure is also incorporated to prevent overestimation of the predictive performance. In addition, we show that the prediction accuracy should be approximately 85% for non-redundant data sets of sequence identity less than 30%. Conclusion Our results demonstrate that biological features derived from Gram-negative bacteria translocation

  9. Inherent Structure-Based Multiview Learning With Multitemplate Feature Representation for Alzheimer's Disease Diagnosis.

    Science.gov (United States)

    Liu, Mingxia; Zhang, Daoqiang; Adeli, Ehsan; Shen, Dinggang

    2016-07-01

    Multitemplate-based brain morphometric pattern analysis using magnetic resonance imaging has been recently proposed for automatic diagnosis of Alzheimer's disease (AD) and its prodromal stage (i.e., mild cognitive impairment or MCI). In such methods, multiview morphological patterns generated from multiple templates are used as feature representation for brain images. However, existing multitemplate-based methods often simply assume that each class is represented by a specific type of data distribution (i.e., a single cluster), while in reality, the underlying data distribution is actually not preknown. In this paper, we propose an inherent structure-based multiview leaning method using multiple templates for AD/MCI classification. Specifically, we first extract multiview feature representations for subjects using multiple selected templates and then cluster subjects within a specific class into several subclasses (i.e., clusters) in each view space. Then, we encode those subclasses with unique codes by considering both their original class information and their own distribution information, followed by a multitask feature selection model. Finally, we learn an ensemble of view-specific support vector machine classifiers based on their, respectively, selected features in each view and fuse their results to draw the final decision. Experimental results on the Alzheimer's Disease Neuroimaging Initiative database demonstrate that our method achieves promising results for AD/MCI classification, compared to the state-of-the-art multitemplate-based methods.

  10. Blurred face recognition by fusing blur-invariant texture and structure features

    Science.gov (United States)

    Zhu, Mengyu; Cao, Zhiguo; Xiao, Yang; Xie, Xiaokang

    2015-10-01

    Blurred face recognition is still remaining as a challenge task, but with wide applications. Image blur can largely affect recognition performance. The local phase quantization (LPQ) was proposed to extract the blur-invariant texture information. It was used for blurred face recognition and achieved good performance. However, LPQ considers only the phase blur-invariant texture information, which is not sufficient. In addition, LPQ is extracted holistically, which cannot fully explore its discriminative power on local spatial properties. In this paper, we propose a novel method for blurred face recognition. The texture and structure blur-invariant features are extracted and fused to generate a more complete description on blurred image. For texture blur-invariant feature, LPQ is extracted in a densely sampled way and vector of locally aggregated descriptors (VLAD) is employed to enhance its performance. For structure blur-invariant feature, the histogram of oriented gradient (HOG) is used. To further enhance its blur invariance, we improve HOG by eliminating weak gradient magnitude which is more sensitive to image blur than the strong gradient. The improved HOG is then fused with the original HOG by canonical correlation analysis (CCA). At last, we fuse them together by CCA to form the final blur-invariant representation of the face image. The experiments are performed on three face datasets. The results demonstrate that our improvements and our proposition can have a good performance in blurred face recognition.

  11. Hydrovolcanic Breccia Pipe Structures-General Features and Genetic Criteria. I. Phreatomagmatic Breccias

    Directory of Open Access Journals (Sweden)

    Călin G. Tămas

    2002-04-01

    Full Text Available Two types of hydrovolcanic breccias are generally accepted: phreatomagmatic and phreatic. Due to their specific characteristics generated during the brecciation, characteristics that control the ore deposition, these breccias represent favourable hosts for mineralization. The depth of formation, the general form and dimensions, the breccia - host rock contact, as well as fragments, matrix, and open spaces altogether control the position and the size of the breccia hosted ore bodies and contribute in different degrees to the rise of the ore grades in phreatomagmatic and phreatic structures. Consequently, the recognition of the genetic type of breccia allows an appropriate strategy in mineral exploration. Describing a breccia necessarily implies a check of its general features, such as environment/depth of formation, general form/geometry, dimensions, breccia-host rock contact, fragments, matrix, alteration, mineralization, surface connection, as well as of its additional features, namely fluidization and facies changes (see Table 2. There are several characteristics with high genetic significance among the abundant descriptive features regarding breccia structures. To point out such evidences means to find out the keys for the genetic intrepretation. A complete list of genetic criteria is proposed for phreatomagmatic breccias (see Table 3.

  12. Structural-phenomenological features of the internal picture of doctors’ illnesses

    Directory of Open Access Journals (Sweden)

    Lazarenko, Victor A.

    2016-06-01

    Full Text Available The vocational activities of doctors and their social status do not ensure their health. And, falling ill, doctors don’t identify themselves with ordinary patients as they have a deep knowledge of medicine. Thus, the internal picture of a doctor’s illness is both a research and a practical problem: the problem of the psychoprevention of doctors’ illnesses at all stages of their professionalization. The purpose of the research was to study the phenomenological features of the internal picture of doctors’ illnesses using the structural approach. The total number of participants was 132. The experimental group consisted of 66 sick doctors, differentiated according to their stage of professionalization: vocational training (students, professional adaptation (interns, full professionalization (doctors. The control group consisted of 66 people who did not have any medical education. All the control subjects were hospitalized with chronic diseases during the study period. The organization of the research was carried out with the use of clinical-psychological and diagnostic methods, the methods of descriptive statistics, and comparative, multidimensional, and structural analysis. The research revealed the following phenomenological features of the internal picture of doctors’ illnesses: the prevalence of some anxiety in the doctors and high awareness of their health; the doctors’ altruistic orientation; their willingness to work despite difficulties; and their ability to achieve high results in different activities. The structural features of the doctors’ image of their own diseases on the cognitive level were the following: qualitative heterogeneity during in-service activities; a high degree of image integration during in-service activities; and stereotyped perceptions of the disease. The emotional level revealed the emotional distance between doctors and their patients, and the behavioral level revealed doctors’ disregard for the

  13. Influence of landscape features on the microgeographic genetic structure of a resident songbird.

    Science.gov (United States)

    Adams, R V; Lazerte, S E; Otter, K A; Burg, T M

    2016-08-01

    Landscape features influence individual dispersal and as a result can affect both gene flow and genetic variation within and between populations. The landscape of British Columbia, Canada, is already highly heterogeneous because of natural ecological and geological transitions, but disturbance from human-mediated processes has further fragmented continuous habitat, particularly in the central plateau region. In this study, we evaluated the effects of landscape heterogeneity on the genetic structure of a common resident songbird, the black-capped chickadee (Poecile atricapillus). Previous work revealed significant population structuring in British Columbia that could not be explained by physical barriers, so our aim was to assess the pattern of genetic structure at a microgeographic scale and determine the effect of different landscape features on genetic differentiation. A total of 399 individuals from 15 populations were genotyped for fourteen microsatellite loci revealing significant population structuring in this species. Individual- and population-based analyses revealed as many as nine genetic clusters with isolation in the north, the central plateau and the south. Moreover, a mixed modelling approach that accounted for non-independence of pairwise distance values revealed a significant effect of land cover and elevation resistance on genetic differentiation. These results suggest that barriers in the landscape influence dispersal which has led to the unexpectedly high levels of population isolation. Our study demonstrates the importance of incorporating landscape features when interpreting patterns of population differentiation. Despite taking a microgeographic approach, our results have opened up additional questions concerning the processes influencing dispersal and gene flow at the local scale.

  14. Statistical identification of syndromes feature and structure of disease of western medicine based on general latent structure model.

    Science.gov (United States)

    Yang, Wei; Yi, Dan-Hui; Xie, Yan-Ming; Tian, Feng

    2012-11-01

    Syndrome differentiation is the character of Chinese medicine (CM). Disease differentiation is the principle of Western medicine (WM). Identifying basic syndromes feature and structure of disease of WM is an important avenue for prevention and treatment of integrated Chinese and Western medicine. The idea here is first to divide all patients suffering from a disease of WM into several groups in the light of the stage of the disease, and secondly to identify basic syndromes feature in a distinct stage, and finally to achieve the purpose of syndrome differentiation. Syndrome differentiation is simply taken as a classifier that classifies patients into distinct classes primarily based on overall observation of their symptoms. Previous clustering methods are unable to cope with the complexity of CM. We therefore show a new multi-dimensional clustering method in the form of general latent structure (GLS) model, which is a suitable statistical learning technique of latent class analysis. In this paper, we learn an optimal GLS model which reflects much better model quality compared with other latent class models from the osteoporosis patient of community women (OPCW) real data including 40-65 year-old women whose bone mineral density (BMD) is less than mean-2.0 standard deviation (M-2.0SD). Further, we illustrate a case analysis of statistical identification of CM syndromes feature and structure of OPCW from qualitative and quantitative contents through the GLS model. Our analysis has discovered natural clusters and structures that correspond well to CM basic syndrome and factors of osteoporosis patients (OP). The GLS model suggests the possibility of establishing objective and quantitative diagnosis standards for syndrome differentiation on OPCW. Hence, for the future it can provide a reference for the similar study from the perspective of a combination of disease differentiation and syndrome differentiation.

  15. Influence of some structural features of a coal on its tendency to undergo reduction

    Energy Technology Data Exchange (ETDEWEB)

    Grigor' eva, E.A.; Bakirova, E.V.; Lesnikova, E.B.; Larina, N.K.; Zharova, M.N.; Dzhalyabova, L.V.

    1981-01-01

    Among the many factors determining the depth of conversion of a coal on hydrogenation, various structural features and, in particular, the nature and number of the labile oxygen-containing structures and bridge bonds, have an influence. There are statements that a direct relationship exists between the activity of a coal in destructive hydrogenation and the amount of oxygen in the ether/ester form, and also the nature of the bond of the mineral fraction of the coal with the organic constituents. The present paper is devoted to an investigation of the dependence of the tendancy of coal to undergo hydrogenation on the nature and number of the ether/ester and organomineral bonds in the structure of the coal. In experiments the researchers used the hydrolytic destruction of the coals and subsequent selective hydrogeneatin with sodium tetrahydroborate. 17 refs.

  16. Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function

    Science.gov (United States)

    Martin, O. C.; Krzywicki, A.; Zagorski, M.

    2016-07-01

    Living cells can maintain their internal states, react to changing environments, grow, differentiate, divide, etc. All these processes are tightly controlled by what can be called a regulatory program. The logic of the underlying control can sometimes be guessed at by examining the network of influences amongst genetic components. Some associated gene regulatory networks have been studied in prokaryotes and eukaryotes, unveiling various structural features ranging from broad distributions of out-degrees to recurrent "motifs", that is small subgraphs having a specific pattern of interactions. To understand what factors may be driving such structuring, a number of groups have introduced frameworks to model the dynamics of gene regulatory networks. In that context, we review here such in silico approaches and show how selection for phenotypes, i.e., network function, can shape network structure.

  17. Influence of Topological Features on Spatially-Structured Evolutionary Algorithms Dynamics

    CERN Document Server

    DeFelice, Matteo; Panzieri, Stefano

    2012-01-01

    In the last decades, complex networks theory significantly influenced other disciplines on the modeling of both static and dynamic aspects of systems observed in nature. This work aims to investigate the effects of networks' topological features on the dynamics of an evolutionary algorithm, considering in particular the ability to find a large number of optima on multi-modal problems. We introduce a novel spatially-structured evolutionary algorithm and we apply it on two combinatorial problems: ONEMAX and the multi-modal NMAX. Considering three different network models we investigate the relationships between their features, algorithm's convergence and its ability to find multiple optima (for the multi-modal problem). In order to perform a deeper analysis we investigate the introduction of weighted graphs with time-varying weights. The results show that networks with a large Average Path Length lead to an higher number of optima and a consequent slow exploration dynamics (i.e. low First Hitting Time). Further...

  18. Local appearance features for robust MRI brain structure segmentation across scanning protocols

    DEFF Research Database (Denmark)

    Achterberg, H.C.; Poot, Dirk H. J.; van der Lijn, Fedde;

    2013-01-01

    Segmentation of brain structures in magnetic resonance images is an important task in neuro image analysis. Several papers on this topic have shown the benefit of supervised classification based on local appearance features, often combined with atlas-based approaches. These methods require...... a representative annotated training set and therefore often do not perform well if the target image is acquired on a different scanner or with a different acquisition protocol than the training images. Assuming that the appearance of the brain is determined by the underlying brain tissue distribution...... and that brain tissue classification can be performed robustly for images obtained with different protocols, we propose to derive appearance features from brain-tissue density maps instead of directly from the MR images. We evaluated this approach on hippocampus segmentation in two sets of images acquired...

  19. Random forest-based protein model quality assessment (RFMQA) using structural features and potential energy terms.

    Science.gov (United States)

    Manavalan, Balachandran; Lee, Juyong; Lee, Jooyoung

    2014-01-01

    Recently, predicting proteins three-dimensional (3D) structure from its sequence information has made a significant progress due to the advances in computational techniques and the growth of experimental structures. However, selecting good models from a structural model pool is an important and challenging task in protein structure prediction. In this study, we present the first application of random forest based model quality assessment (RFMQA) to rank protein models using its structural features and knowledge-based potential energy terms. The method predicts a relative score of a model by using its secondary structure, solvent accessibility and knowledge-based potential energy terms. We trained and tested the RFMQA method on CASP8 and CASP9 targets using 5-fold cross-validation. The correlation coefficient between the TM-score of the model selected by RFMQA (TMRF) and the best server model (TMbest) is 0.945. We benchmarked our method on recent CASP10 targets by using CASP8 and 9 server models as a training set. The correlation coefficient and average difference between TMRF and TMbest over 95 CASP10 targets are 0.984 and 0.0385, respectively. The test results show that our method works better in selecting top models when compared with other top performing methods. RFMQA is available for download from http://lee.kias.re.kr/RFMQA/RFMQA_eval.tar.gz.

  20. Endotoxin Structures in the Psychrophiles Psychromonas marina and Psychrobacter cryohalolentis Contain Distinctive Acyl Features

    Directory of Open Access Journals (Sweden)

    Charles R. Sweet

    2014-07-01

    Full Text Available Lipid A is the essential component of endotoxin (Gram-negative lipopolysaccharide, a potent immunostimulatory compound. As the outer surface of the outer membrane, the details of lipid A structure are crucial not only to bacterial pathogenesis but also to membrane integrity. This work characterizes the structure of lipid A in two psychrophiles, Psychromonas marina and Psychrobacter cryohalolentis, and also two mesophiles to which they are related using MALDI-TOF MS and fatty acid methyl ester (FAME GC-MS. P. marina lipid A is strikingly similar to that of Escherichia coli in organization and total acyl size, but incorporates an unusual doubly unsaturated tetradecadienoyl acyl residue. P. cryohalolentis also shows structural organization similar to a closely related mesophile, Acinetobacter baumannii, however it has generally shorter acyl constituents and shows many acyl variants differing by single methylene (-CH2- units, a characteristic it shares with the one previously reported psychrotolerant lipid A structure. This work is the first detailed structural characterization of lipid A from an obligate psychrophile and the second from a psychrotolerant species. It reveals distinctive structural features of psychrophilic lipid A in comparison to that of related mesophiles which suggest constitutive adaptations to maintain outer membrane fluidity in cold environments.

  1. An Matching Method for Vehicle-borne Panoramic Image Sequence Based on Adaptive Structure from Motion Feature

    Directory of Open Access Journals (Sweden)

    ZHANG Zhengpeng

    2015-10-01

    Full Text Available Panoramic image matching method with the constraint condition of local structure from motion similarity feature is an important method, the process requires multivariable kernel density estimations for the structure from motion feature used nonparametric mean shift. Proper selection of the kernel bandwidth is a critical step for convergence speed and accuracy of matching method. Variable bandwidth with adaptive structure from motion feature for panoramic image matching method has been proposed in this work. First the bandwidth matrix is defined using the locally adaptive spatial structure of the sampling point in spatial domain and optical flow domain. The relaxation diffusion process of structure from motion similarity feature is described by distance weighting method of local optical flow feature vector. Then the expression form of adaptive multivariate kernel density function is given out, and discusses the solution of the mean shift vector, termination conditions, and the seed point selection method. The final fusions of multi-scale SIFT the features and structure features to establish a unified panoramic image matching framework. The sphere panoramic images from vehicle-borne mobile measurement system are chosen such that a comparison analysis between fixed bandwidth and adaptive bandwidth is carried out in detail. The results show that adaptive bandwidth is good for case with the inlier ratio changes and the object space scale changes. The proposed method can realize the adaptive similarity measure of structure from motion feature, improves the correct matching points and matching rate, experimental results have shown our method to be robust.

  2. Observational Features of Large-Scale Structures as Revealed by the Catastrophe Model of Solar Eruptions

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Large-scale magnetic structures are the main carrier of major eruptions in the solar atmosphere. These structures are rooted in the photosphere and are driven by the unceasing motion of the photospheric material through a series of equilibrium configurations. The motion brings energy into the coronal magnetic field until the system ceases to be in equilibrium. The catastrophe theory for solar eruptions indicates that loss of mechanical equilibrium constitutes the main trigger mechanism of major eruptions, usually shown up as solar flares,eruptive prominences, and coronal mass ejections (CMEs). Magnetic reconnection which takes place at the very beginning of the eruption as a result of plasma instabilities/turbulence inside the current sheet, converts magnetic energy into heating and kinetic energy that are responsible for solar flares, and for accelerating both plasma ejecta (flows and CMEs) and energetic particles. Various manifestations are thus related to one another, and the physics behind these relationships is catastrophe and magnetic reconnection. This work reports on recent progress in both theoretical research and observations on eruptive phenomena showing the above manifestations. We start by displaying the properties of large-scale structures in the corona and the related magnetic fields prior to an eruption, and show various morphological features of the disrupting magnetic fields. Then, in the framework of the catastrophe theory,we look into the physics behind those features investigated in a succession of previous works,and discuss the approaches they used.

  3. Structural damage identification using damping: a compendium of uses and features

    Science.gov (United States)

    Cao, M. S.; Sha, G. G.; Gao, Y. F.; Ostachowicz, W.

    2017-04-01

    The vibration responses of structures under controlled or ambient excitation can be used to detect structural damage by correlating changes in structural dynamic properties extracted from responses with damage. Typical dynamic properties refer to modal parameters: natural frequencies, mode shapes, and damping. Among these parameters, natural frequencies and mode shapes have been investigated extensively for their use in damage characterization by associating damage with reduction in local stiffness of structures. In contrast, the use of damping as a dynamic property to represent structural damage has not been comprehensively elucidated, primarily due to the complexities of damping measurement and analysis. With advances in measurement technologies and analysis tools, the use of damping to identify damage is becoming a focus of increasing attention in the damage detection community. Recently, a number of studies have demonstrated that damping has greater sensitivity for characterizing damage than natural frequencies and mode shapes in various applications, but damping-based damage identification is still a research direction ‘in progress’ and is not yet well resolved. This situation calls for an overall survey of the state-of-the-art and the state-of-the-practice of using damping to detect structural damage. To this end, this study aims to provide a comprehensive survey of uses and features of applying damping in structural damage detection. First, we present various methods for damping estimation in different domains including the time domain, the frequency domain, and the time-frequency domain. Second, we investigate the features and applications of damping-based damage detection methods on the basis of two predominant infrastructure elements, reinforced concrete structures and fiber-reinforced composites. Third, we clarify the influential factors that can impair the capability of damping to characterize damage. Finally, we recommend future research directions

  4. ARX model-based damage sensitive features for structural damage localization using output-only measurements

    Science.gov (United States)

    Roy, Koushik; Bhattacharya, Bishakh; Ray-Chaudhuri, Samit

    2015-08-01

    The study proposes a set of four ARX model (autoregressive model with exogenous input) based damage sensitive features (DSFs) for structural damage detection and localization using the dynamic responses of structures, where the information regarding the input excitation may not be available. In the proposed framework, one of the output responses of a multi-degree-of-freedom system is assumed as the input and the rest are considered as the output. The features are based on ARX model coefficients, Kolmogorov-Smirnov (KS) test statistical distance, and the model residual error. At first, a mathematical formulation is provided to establish the relation between the change in ARX model coefficients and the normalized stiffness of a structure. KS test parameters are then described to show the sensitivity of statistical distance of ARX model residual error with the damage location. The efficiency of the proposed set of DSFs is evaluated by conducting numerical studies involving a shear building and a steel moment-resisting frame. To simulate the damage scenarios in these structures, stiffness degradation of different elements is considered. It is observed from this study that the proposed set of DSFs is good indicator for damage location even in the presence of damping, multiple damages, noise, and parametric uncertainties. The performance of these DSFs is compared with mode shape curvature-based approach for damage localization. An experimental study has also been conducted on a three-dimensional six-storey steel moment frame to understand the performance of these DSFs under real measurement conditions. It has been observed that the proposed set of DSFs can satisfactorily localize damage in the structure.

  5. Anomalous screening in two-dimensional materials with an extremum ring in the dispersion law

    Science.gov (United States)

    Kolomeisky, Eugene B.; Straley, Joseph P.

    2016-12-01

    A variety of two-dimensional materials possess a band structure with an energy extremal ridge along a ring in momentum space. Examples are biased bilayer graphene and surfaces and interfaces with a Rashba spin-orbit interaction where at low doping the carriers fill an annulus. This topological feature causes an anomalous screening behavior, which we study using the Thomas-Fermi theory. Specifically, reducing the doping is predicted to enhance the linear screening response, whereas at zero doping the size of the screening cloud surrounding a Coulomb impurity is found to increase as the cube root of the impurity charge.

  6. Features of kinematic structure of motor actions technique in the freestyle wrestlers with different qualification

    Directory of Open Access Journals (Sweden)

    Tupeev Y.V.

    2010-02-01

    Full Text Available The sequence of educational steps in teaching basic technique elements in stance for young wrestlers at the initial training stage was determined by the expert assessment method. The biomechanical features of technique of a sprint by an inclination hold of legs for differently qualified wrestlers in freestyle were ascertained by the biomechanical videocomputer analysis. The results of research of kinematic structure of motor actions technique testify that performance duration of phases in sprint by an inclination hold of legs was characterized by the greater values for qualified wrestlers in comparison with highly skilled ones.

  7. Seismically-induced structures in the Quaternary sediments of the NE Fennoscandian Shield: Features and age

    Directory of Open Access Journals (Sweden)

    Nikolaeva S. B.

    2016-03-01

    Full Text Available Results of studying secondary seismogenic deformations of the vibrational type (termed "seismites" in loose sediments of the north-eastern Baltic Shield (the Kola region have been provided. The features, types, formation patterns and age of seismites have been considered. On the basis of previous results the major periods of the region activation in the Holocene have been defined. Criteria of identifying similar structures with widely spread glaciodislocations have been suggested. Results of studying the sections with seismites in certain areas of the region have been provided

  8. Structural Features of Boron-Doped Si(113) Surfaces Simulated by ab initio Calculations

    Institute of Scientific and Technical Information of China (English)

    LIAO Long-Zhong; LIU Zheng-Hui; ZHANG Zhao-Hui

    2008-01-01

    Based on ab initio calculations, boron-doped Si(113) surfaces have been simulated and atomic structures of the surfaces have been proposed. It has been determined that surface features of empty and filled states that are separately localized at pentamers and adatoms indicates a low surface density of B atoms, while it is attributed to heavy doping of B atoms at the second layer that pentamers and adatoms are both present in an image of scanning tunnelling microscopy. B doping at the second layer should be balanced by adsorbed B or Si atoms beside the adatoms and inserted B interstitials below the adatoms.

  9. Spatial structure and scale feature of the atmospheric pollution source impact of city agglomeration

    Institute of Scientific and Technical Information of China (English)

    XU Xiangde; ZHOU Xiuji; SHI Xiaohui

    2005-01-01

    The spatial structure and multi-scale feature of the atmospheric pollution influence domain of Beijing and its peripheral areas (a rapidly developed city agglomeration) is dissected and analyzed in this paper on the basis of the atmospheric pollution dynamic-chemical process observation data of the urban building ensemble boundary layer of the Beijing City Air Pollution Observation Experiment (BECAPEX) in winter (February) and summer (August) 2003, and relevant meteorological elements and satellite retrieval aerosol optical depth (AOD), etc. comprehensive data with the dynamic-statistical integrated analysis of "point-surface" spatial structure. Results show that there existed significant difference in the contribution of winter/summer different pollution emission sources to the component character of atmospheric pollution, and the principal component analysis (PCA) results of statistical model also indicate that SO2 and NOX dominated in the component structure of winter aerosol particle; instead, CO and NOX dominated in summer. Surface layer atmospheric dynamic and thermal structures and various pollutant species at the upper boundary of building ensembles at urban different observational sites of Beijing in winter and summer showed an "in-phase" variation and its spatial scale feature of "influence domain". The power spectrum analysis (PSA) shows that the period spectrum of winter/summer particle concentration accorded with those of atmospheric wind field: the longer period was dominative in winter, but the shorter period in summer, revealing the impact of the seasonal scale feature of winter/summer atmospheric general circulation on the period of atmospheric pollution variations. It is found that from analyzing urban area thermal heterogeneity that the multiscale effect of Beijing region urban heat island (UHI) was associated with the heterogeneous expansion of tall buildings area. In urban atmospheric dynamical and thermal characteristic spatial structures, the

  10. Automated discovery of structural features of the optic nerve head on the basis of image and genetic data

    Science.gov (United States)

    Christopher, Mark; Tang, Li; Fingert, John H.; Scheetz, Todd E.; Abramoff, Michael D.

    2014-03-01

    Evaluation of optic nerve head (ONH) structure is a commonly used clinical technique for both diagnosis and monitoring of glaucoma. Glaucoma is associated with characteristic changes in the structure of the ONH. We present a method for computationally identifying ONH structural features using both imaging and genetic data from a large cohort of participants at risk for primary open angle glaucoma (POAG). Using 1054 participants from the Ocular Hypertension Treatment Study, ONH structure was measured by application of a stereo correspondence algorithm to stereo fundus images. In addition, the genotypes of several known POAG genetic risk factors were considered for each participant. ONH structural features were discovered using both a principal component analysis approach to identify the major modes of variance within structural measurements and a linear discriminant analysis approach to capture the relationship between genetic risk factors and ONH structure. The identified ONH structural features were evaluated based on the strength of their associations with genotype and development of POAG by the end of the OHTS study. ONH structural features with strong associations with genotype were identified for each of the genetic loci considered. Several identified ONH structural features were significantly associated (p genetic risk status was found to substantially increase performance of early POAG prediction. These results suggest incorporating both imaging and genetic data into ONH structural modeling significantly improves the ability to explain POAG-related changes to ONH structure.

  11. Influence of multilayer modulation on structural and magnetic features in the Pt/Sm-Co system

    Science.gov (United States)

    Angelakeris, M.; Siskos, I.; Simeonidis, K.; Tsiaoussis, I.; Delimitis, A.; Kalogirou, O.

    2009-10-01

    In this work, we study the influence of Pt underlayer in Pt/Sm-Co/Pt trilayers and in Pt/Sm-Co multilayers. In both cases, Pt underlayer seems to impose better crystallinity to Sm-Co layer and certainly promotes the evolution of the hard-magnetic SmCo 5 phase. Particularly, in the case of multilayer form, where multiple interlayers of Pt each one serving as a dedicated underlayer for the deposition of a specific Sm-Co layer, enhanced crystallinity is observed. Moreover, post-deposition annealing facilitates these features at relatively lower temperatures (˜400 °C) than those met in thin-film cases. This behavior is also followed by enhancement of saturation magnetization, while higher temperature post-deposition thermal treatment seems to deteriorate structural and magnetic features. If annealing temperature gets over 550 °C macroscopic magnetic features depress, probably due to domination of annealing-activated processes such as Sm oxidation and formation of non-magnetic phases since Pt diffuses throughout the whole magnetic layer.

  12. Novel structural features of the immunocompetent ceramide phospho-inositol glycan core from Trichomonas vaginalis.

    Science.gov (United States)

    Heiss, Christian; Wang, Zhirui; Black, Ian; Azadi, Parastoo; Fichorova, Raina N; Singh, Bibhuti N

    2016-01-01

    The ceramide phosphoinositol glycan core (CPI-GC) of the lipophosphoglycan of Trichomonas vaginalis is a major virulent factor of this common genitourinary parasite. While its carbohydrate composition has been reported before, its structure has remained largely unknown. We isolated the glycan portions of CPI-GC by nitrous acid deamination and hydrofluoric acid treatment and investigated their structures by methylation analysis and 1- and 2-D NMR. We found that the α-anomer of galactose is a major constituent of CPI-GC. The β-anomer was found exclusively at the non-reducing end of CPI-GC side chains. Furthermore the data showed that the rhamnan backbone is more complex than previously thought and that the inositol residue at the reducing end is linked to a 4-linked α-glucuronic acid (GlcA) residue. This appears to be the most striking and novel feature of this GPI-anchor type molecule.

  13. Structural features of anodic oxide films formed on aluminum substrate coated with self-assembled microspheres

    Energy Technology Data Exchange (ETDEWEB)

    Asoh, Hidetaka [Department of Applied Chemistry, Faculty of Engineering, Kogakuin University, 2665-1 Nakano, Hachioji, Tokyo 192-0015 (Japan)], E-mail: asoh@cc.kogakuin.ac.jp; Uchibori, Kota; Ono, Sachiko [Department of Applied Chemistry, Faculty of Engineering, Kogakuin University, 2665-1 Nakano, Hachioji, Tokyo 192-0015 (Japan)

    2009-07-15

    The structural features of anodic oxide films formed on an aluminum substrate coated with self-assembled microspheres were investigated by scanning electron microscopy and atomic force microscopy. In the first anodization in neutral solution, the growth of a barrier-type film was partially suppressed in the contact area between the spheres and the underlying aluminum substrate, resulting in the formation of ordered dimple arrays in an anodic oxide film. After the subsequent second anodization in acid solution at a voltage lower than that of the first anodization, nanopores were generated only within each dimple. The nanoporous region could be removed selectively by post-chemical etching using the difference in structural dimensions between the porous region and the surrounding barrier region. The mechanism of anodic oxide growth on the aluminum substrate coated with microspheres through multistep anodization is discussed.

  14. The features of finite-element modeling of a structural element of flexible woven composites

    Directory of Open Access Journals (Sweden)

    Dmitry A. Kozhanov

    2016-03-01

    Full Text Available The features of finite-element modeling of both an element itself and its behavior under uniaxial tension have been demonstrated with a structural element of flexible woven composites. The main components of the material, such as reinforcing fabric and material's matrix were examined in modeling. The reinforcing fabric is a plain weave. These yarns were taken as an elastic material. The matrix of the material was considered to be a soft polymer with the possible occurrence of irreversible elastic-plastic deformations. Moreover, the possible occurrence of damages in the structure of the material under high loads was taken into account in modeling. The fields of stresses and strains were built; the zones of the material's internal damages under uniaxial tension were demonstrated. The risk zones of weave were revealed.

  15. On the structural features of fiber suspensions in converging channel flow

    Institute of Scientific and Technical Information of China (English)

    林建忠; 张凌新

    2003-01-01

    The structural features of fiber suspensions are dependent on the fiber alignment in the flows. In this work the orientation distribution function and orientation tensors for semi-concentrated fiber suspensions in converging channel flow were calculated, and the evolutions of the fiber alignment and the bulk effective vis-cosity were analyzed. The results showed that the bulk stress and the effective viscosity were functions of therate-of-strain tensor and the fiber orientation state ; and that the fiber suspensions evolved to steady alignment and tended to concentrate to some preferred directions close to but not same as the directions of local stream-lines. The bulk effective viscosity depended on the product of Reynolds number and time. The decrease of ef-fective viscosity near the boundary benefited the increase of the rate of flow. Finally when the fiber alignment went into steady state, the structural features of fiber suspensions were not dependent on the Reynolds numberbut on the converging channel angle.

  16. Identifying structural features of fibrillar islet amyloid polypeptide using site-directed spin labeling.

    Science.gov (United States)

    Jayasinghe, Sajith A; Langen, Ralf

    2004-11-12

    Pancreatic amyloid deposits, composed primarily of the 37-residue islet amyloid polypeptide (IAPP), are a characteristic feature found in more than 90% of patients with type II diabetes. Although IAPP amyloid deposits are associated with areas of pancreatic islet beta-cell dysfunction and depletion and are thought to play a role in disease, their structure is unknown. We used electron paramagnetic resonance spectroscopy to analyze eight spin-labeled derivatives of IAPP in an effort to determine structural features of the peptide. In solution, all eight derivatives gave rise to electron paramagnetic resonance spectra with sharp lines indicative of rapid motion on the sub-nanosecond time scale. These spectra are consistent with a rapidly tumbling and highly dynamic peptide. In contrast, spectra for the fibrillar form exhibit reduced mobility and the presence of strong intermolecular spin-spin interactions. The latter implies that the peptide subunits are ordered and that the same residues from neighboring peptides are in close proximity to one another. Our data are consistent with a parallel arrangement of IAPP peptides within the amyloid fibril. Analysis of spin label mobility indicates a high degree of order throughout the peptide, although the N-terminal region is slightly less ordered. Possible similarities with respect to the domain organization and parallelism of Alzheimer's amyloid beta peptide fibrils are discussed.

  17. SoftSearch: integration of multiple sequence features to identify breakpoints of structural variations.

    Directory of Open Access Journals (Sweden)

    Steven N Hart

    Full Text Available BACKGROUND: Structural variation (SV represents a significant, yet poorly understood contribution to an individual's genetic makeup. Advanced next-generation sequencing technologies are widely used to discover such variations, but there is no single detection tool that is considered a community standard. In an attempt to fulfil this need, we developed an algorithm, SoftSearch, for discovering structural variant breakpoints in Illumina paired-end next-generation sequencing data. SoftSearch combines multiple strategies for detecting SV including split-read, discordant read-pair, and unmated pairs. Co-localized split-reads and discordant read pairs are used to refine the breakpoints. RESULTS: We developed and validated SoftSearch using real and synthetic datasets. SoftSearch's key features are 1 not requiring secondary (or exhaustive primary alignment, 2 portability into established sequencing workflows, and 3 is applicable to any DNA-sequencing experiment (e.g. whole genome, exome, custom capture, etc.. SoftSearch identifies breakpoints from a small number of soft-clipped bases from split reads and a few discordant read-pairs which on their own would not be sufficient to make an SV call. CONCLUSIONS: We show that SoftSearch can identify more true SVs by combining multiple sequence features. SoftSearch was able to call clinically relevant SVs in the BRCA2 gene not reported by other tools while offering significantly improved overall performance.

  18. CFD Simulation of Flow Features and Vorticity Structures in Tuna-Like Swimming

    Institute of Scientific and Technical Information of China (English)

    YANG Liang; SU Yu-min

    2011-01-01

    The theoretical research on the propulsive principle of aquatic animal becomes more important and attracted more researchers to make efforts on it.In the present study,a computational fluid dynamic(CFD)simulation of a three-dimensional traveling-wave undulations body of tuna has been developed to investigate the fluid flow features and vorticity structures around this body when moving in a straight line.The undulation only takes place in the posterior half of the fish,and the tuna-tail is considered as a lunate fin oscillating with the mode combined swaying with yawing.A Reynolds-averaged Navier-Stokes(BANS)equation is developed,employing a control-volume method and a k-omega SST turbulent model;meanwhile an unstructured tetrahedral grid,which is generated for the three-dimensional geometry,is used based on the deformation of the hind parts of the body and corresponding movement of the tail.We calculated the hydrodynamic performance of tuna-like body when a tuna swims in a uniform velocity,and compared the input power coefficient,output power coefficient and propulsive efficiency of the oscillating tuna-tail with or without body vortex shedding.Additionally,the load distribution on the body,flow features and vorticity structures around the body were demonstrated.The effect of interaction between the body-generated vortices and the tail-generated vorticity on the hydrodynamic performance can be obtained.

  19. Structural and ultrastructural features of the agouti tongue (Dasyprocta aguti Linnaeus, 1766).

    Science.gov (United States)

    Ciena, Adriano Polican; de Sousa Bolina, Cristina; de Almeida, Sonia Regina Yokomizo; Rici, Rose Eli Grassi; de Oliveira, Moacir Franco; da Silva, Marcelo Cavenaghi Pereira; Miglino, Maria Angélica; Watanabe, Ii-sei

    2013-08-01

    The agouti (Dasyprocta aguti Linnaeus, 1766) is a wild rodent belonging to the family Dasyproctidae that is found throughout Brazil and feeds on fruits and seeds. The aim of the present study was to describe the following features of the tongue of agouti: its morphological structures, the three-dimensional characteristics of the lingual papillae surface, the connective tissue cores (CTCs) and the epithelial cell ultrastructure. Four types of papillae were observed on the dorsal surface of the tongue with a triangular shape: filiform, fungiform, foliate and vallate. Filiform papillae were distributed throughout the tongue surface, and removal of the epithelial surface revealed conical CTCs and multifilaments. Fungiform papillae were observed in the rostral and middle regions, whereas foliate papillae developed in pairs on the lateral margin of the caudal region. Removal of the epithelium in these regions revealed CTCs with parallel laminar conformation. Vallate papillae were arranged in a V-shape in the caudal region, and their CTCs ranged in shape from elongate to ovoid. The ultrastructural components of the dorsal epithelium were the basal, spinous, granular and keratinised layers. A broad area with cytoplasmic projections was identified in the interface region between the lamina propria and the basal layer. Flattened cells with intermediate filaments were observed in the transitional region between spinous and granular layers. The keratinised layer was composed of superimposed epithelial cells where desmosomes and cell-surface microridges were observed. These structural features, including the three-dimensional aspects of the lingual papillae, the CTCs and the epithelial ultrastructure, indicate that when compared with other animals, particularly other rodent species, the morphological features of the tongue of agouti are relatively well developed, especially regarding foliate and vallate papillae.

  20. Structural features of the pore formed by Staphylococcus aureus alpha-toxin inferred from chemical modification and primary structure analysis.

    Science.gov (United States)

    Menestrina, G; Belmonte, G; Parisi, V; Morante, S

    1992-09-01

    Staphylococcus aureus alpha-toxin makes cells and model membranes permeable to ions and uncharged molecules by opening oligomeric pores of uniform size. Its primary sequence reveals peculiar features which give some hints on the structure of the pore. A flexible region separating the toxin into two halves, several amphiphilic beta-strands and two amphiphilic alpha-helices long enough to span the hydrophobic core of the lipid bilayer are predicted. In analogy to bacterial porins, we propose that the inner walls of the pore are, at least in part, built by an amphiphilic beta-barrel. The model is consistent with circular dichroism data and with the electrophysiological properties of the pore. Functional information on this toxin were obtained by chemical modification of its four histidine residues. Specific carbethoxylation suggested they have different roles: one is required for specific receptor binding, one for oligomerisation and two for unspecific lipid binding. A tentative assignment of each histidine to its specific role is done on the basis of the structural predictions. A functionally related hemolysin, Aeromonas hydrophyla aerolysin, reveals remarkably similar features including the presence and location of histidines involved in receptor binding and oligomerisation.

  1. Expanded potential of seleno-carbohydrates as a molecular tool for X-ray structural determination of a carbohydrate-protein complex with single/multi-wavelength anomalous dispersion phasing.

    Science.gov (United States)

    Suzuki, Tatsuya; Makyio, Hisayoshi; Ando, Hiromune; Komura, Naoko; Menjo, Masanori; Yamada, Yusuke; Imamura, Akihiro; Ishida, Hideharu; Wakatsuki, Soichi; Kato, Ryuichi; Kiso, Makoto

    2014-04-01

    Seleno-lactoses have been successfully synthesized as candidates for mimicking carbohydrate ligands for human galectin-9 N-terminal carbohydrate recognition domain (NCRD). Selenium was introduced into the mono- or di-saccharides using p-methylselenobenzoic anhydride (Tol2Se) as a novel selenating reagent. The TolSe-substituted monosaccharides were converted into selenoglycosyl donors or acceptors, which were reacted with coupling partners to afford seleno-lactoses. The seleno-lactoses were converted to the target compounds. The structure of human galectin-9 NCRD co-crystallized with 6-MeSe-lactose was determined with single/multi-wavelength anomalous dispersion (SAD/MAD) phasing and was similar to that of the co-crystal with natural lactose.

  2. The Structure of Neurexin 1[alpha] Reveals Features Promoting a Role as Synaptic Organizer

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Fang; Venugopal, Vandavasi; Murray, Beverly; Rudenko, Gabby (Michigan)

    2014-10-02

    {alpha}-Neurexins are essential synaptic adhesion molecules implicated in autism spectrum disorder and schizophrenia. The {alpha}-neurexin extracellular domain consists of six LNS domains interspersed by three EGF-like repeats and interacts with many different proteins in the synaptic cleft. To understand how {alpha}-neurexins might function as synaptic organizers, we solved the structure of the neurexin 1{alpha} extracellular domain (n1{alpha}) to 2.65 {angstrom}. The L-shaped molecule can be divided into a flexible repeat I (LNS1-EGF-A-LNS2), a rigid horseshoe-shaped repeat II (LNS3-EGF-B-LNS4) with structural similarity to so-called reelin repeats, and an extended repeat III (LNS5-EGF-B-LNS6) with controlled flexibility. A 2.95 {angstrom} structure of n1{alpha} carrying splice insert SS3 in LNS4 reveals that SS3 protrudes as a loop and does not alter the rigid arrangement of repeat II. The global architecture imposed by conserved structural features enables {alpha}-neurexins to recruit and organize proteins in distinct and variable ways, influenced by splicing, thereby promoting synaptic function.

  3. Topological features in crystal structures: a quotient graph assisted analysis of underlying nets and their embeddings.

    Science.gov (United States)

    Eon, Jean Guillaume

    2016-05-01

    Topological properties of crystal structures may be analysed at different levels, depending on the representation and the topology that has been assigned to the crystal. Considered here is the combinatorial or bond topology of the structure, which is independent of its realization in space. Periodic nets representing one-dimensional complexes, or the associated graphs, characterize the skeleton of chemical bonds within the crystal. Since periodic nets can be faithfully represented by their labelled quotient graphs, it may be inferred that their topological features can be recovered by a direct analysis of the labelled quotient graph. Evidence is given for ring analysis and structure decomposition into building units and building networks. An algebraic treatment is developed for ring analysis and thoroughly applied to a description of coesite. Building units can be finite or infinite, corresponding to 1-, 2- or even 3-periodic subnets. The list of infinite units includes linear chains or sheets of corner- or edge-sharing polyhedra. Decomposing periodic nets into their building units relies on graph-theoretical methods classified as surgery techniques. The most relevant operations are edge subdivision, vertex identification, edge contraction and decoration. Instead, these operations can be performed on labelled quotient graphs, evidencing in almost a mechanical way the nature and connection mode of building units in the derived net. Various examples are discussed, ranging from finite building blocks to 3-periodic subnets. Among others, the structures of strontium oxychloride, spinel, lithiophilite and garnet are addressed.

  4. Oxide-ion and proton conducting electrolyte materials for clean energy applications: structural and mechanistic features.

    Science.gov (United States)

    Malavasi, Lorenzo; Fisher, Craig A J; Islam, M Saiful

    2010-11-01

    This critical review presents an overview of the various classes of oxide materials exhibiting fast oxide-ion or proton conductivity for use as solid electrolytes in clean energy applications such as solid oxide fuel cells. Emphasis is placed on the relationship between structural and mechanistic features of the crystalline materials and their ion conduction properties. After describing well-established classes such as fluorite- and perovskite-based oxides, new materials and structure-types are presented. These include a variety of molybdate, gallate, apatite silicate/germanate and niobate systems, many of which contain flexible structural networks, and exhibit different defect properties and transport mechanisms to the conventional materials. It is concluded that the rich chemistry of these important systems provides diverse possibilities for developing superior ionic conductors for use as solid electrolytes in fuel cells and related applications. In most cases, a greater atomic-level understanding of the structures, defects and conduction mechanisms is achieved through a combination of experimental and computational techniques (217 references).

  5. Structural features of a potential gas hydrate area in the Pointer Ridge off southwest Taiwan

    Science.gov (United States)

    Wang, Hsueh-Fen; Hsu, Shu-Kun; Tsai, Ching-Hui; Chen, Song-Chuen; Liu, Char-Shine; Lin, Hsiao-Shan

    2015-04-01

    The offshore area of the southwest Taiwan is located in the oblique convergence zone between the northern continental margin of South China Sea and the Manila accretionary wedge. To the west of the deformation front offshore southwestern Taiwan, the Pointer Ridge is located in the passive South China Sea continental margin. The continental margin is compose of extensional horst-and-graben structures. There are numerous submarine channels and linear ridge, formed due to the submarine erosion across the continental slope region. According to geophysical research off SW Taiwan, abundant gas hydrate may exist. In this study, our purpose is to understand the relationship between the near-seafloor structures of the Pointer Ridge and the gas hydrate formation off SW Taiwan. The data we used include multi-beam echo sounder (MBES), side-scan sonar (SSS), sub-bottom profiler (SBP) and the multi-channel reflection seismic (MCS) data. Our results show the pockmark and gas seepage structures mainly appear in the place where the gradient of the BSR thickness is maximum. Those sites contain authigenic carbonate signature shown in the sub-bottom profiler. We also observe several folds and faults structures in this extensional background; however, these compressional features need further studies.

  6. CDK1 structures reveal conserved and unique features of the essential cell cycle CDK

    Science.gov (United States)

    Brown, Nicholas R.; Korolchuk, Svitlana; Martin, Mathew P.; Stanley, Will A.; Moukhametzianov, Rouslan; Noble, Martin E. M.; Endicott, Jane A.

    2015-04-01

    CDK1 is the only essential cell cycle CDK in human cells and is required for successful completion of M-phase. It is the founding member of the CDK family and is conserved across all eukaryotes. Here we report the crystal structures of complexes of CDK1-Cks1 and CDK1-cyclin B-Cks2. These structures confirm the conserved nature of the inactive monomeric CDK fold and its ability to be remodelled by cyclin binding. Relative to CDK2-cyclin A, CDK1-cyclin B is less thermally stable, has a smaller interfacial surface, is more susceptible to activation segment dephosphorylation and shows differences in the substrate sequence features that determine activity. Both CDK1 and CDK2 are potential cancer targets for which selective compounds are required. We also describe the first structure of CDK1 bound to a potent ATP-competitive inhibitor and identify aspects of CDK1 structure and plasticity that might be exploited to develop CDK1-selective inhibitors.

  7. Petrology of Anomalous Eucrites

    Science.gov (United States)

    Mittlefehldt, D. W.; Peng, Z. X.; Ross, D. K.

    2015-01-01

    Most mafic achondrites can be broadly categorized as being "eucritic", that is, they are composed of a ferroan low-Ca clinopyroxene, high-Ca plagioclase and a silica phase. They are petrologically distinct from angritic basalts, which are composed of high-Ca, Al-Ti-rich clinopyroxene, Carich olivine, nearly pure anorthite and kirschsteinite, or from what might be called brachinitic basalts, which are composed of ferroan orthopyroxene and high-Ca clinopyroxene, intermediate-Ca plagioclase and ferroan olivine. Because of their similar mineralogy and composition, eucrite-like mafic achondrites formed on compositionally similar asteroids under similar conditions of temperature, pressure and oxygen fugacity. Some of them have distinctive isotopic compositions and petrologic characteristics that demonstrate formation on asteroids different from the parent of the HED clan (e.g., Ibitira, Northwest Africa (NWA) 011). Others show smaller oxygen isotopic distinctions but are otherwise petrologically and compositionally indistinguishable from basaltic eucrites (e.g., Pasamonte, Pecora Escarpment (PCA) 91007). The degree of uniformity in delta O-17 of eucrites and diogenites is one piece of evidence considered to favor of a magma-ocean scenario for their petrogenesis. Given that the O isotopic differences separating Pasamonte and PCA 91007 from other eucrites are small, and that there is an absence of other distinguishing characteristics, a legitimate question is: Did the HED parent asteroid fail to homogenize via a magma-ocean stage, thus explaining outliers like Pasamonte? We are initiating a program of study of anomalous eucrite-like achondrites as one part of our effort to seek a resolution of this issue. Here we present preliminary petrologic information on Asuka (A-) 881394, Elephant Moraine (EET) 87520 and EET 87542. We will have studied several more by conference time.

  8. Light-harvesting features revealed by the structure of plant Photosystem I

    CERN Document Server

    Ben-Shem, A; Nelson, N; 10.1023/B:PRES.0000036881.23512.42

    2004-01-01

    Oxygenic photosynthesis is driven by two multi-subunit membrane protein complexes, Photosystem I and Photosystem II. In plants and green algae, both complexes are composed of two moieties: a reaction center (RC), where light-induced charge translocation occurs, and a peripheral antenna that absorbs light and funnels its energy to the reaction center. The peripheral antenna of PS I (LHC I) is composed of four gene products (Lhca 1-4) that are unique among the chlorophyll a/b binding proteins in their pronounced long-wavelength absorbance and in their assembly into dimers. The recently determined structure of plant Photosystem I provides the first relatively high- resolution structural model of a super-complex containing a reaction center and its peripheral antenna. We describe some of the structural features responsible for the unique properties of LHC I and discuss the advantages of the particular LHC I dimerization mode over monomeric or trimeric forms. In addition, we delineate some of the interactions betw...

  9. Influence of structural features on immunostimulating activity of glucans extracted from Agaricus blazei mushroom

    Directory of Open Access Journals (Sweden)

    Kozarski Maja S.

    2009-01-01

    Full Text Available High molecular weight b-D-glucans derived from Basidiomycetes cell walls are able to specifically activate cellular and humoral components of the host immune system. The aim of this paper was to examine immunomodulating activity of native, chemically and enzimatically modified glucans from Agaricus blazei mushroom and to determine which structural features are of primary importance for their stimulation referring to humane immune cells. The immunomodulating activities were tested in vitro, by stimulation of peripheral blood mononuclear cells (PBMCs and measuring of interferon-gamma (IFN-g production by enzyme linked immunosorbent assay (ELISA. Measurements of immunomodulatory capacity of Agaricus blazei native glucans showed their expressive immunostimulating effect on activated PBMCs and synthesis of IFN-g. The results obtained after the stimulation of cells with 1M H2SO4 and 1M NaOH, the treated glucans showed that primary structure is of more importance than the tertiary structure of the triple helix for their immunostimulating activity and synthesis of IFN-g. Glucans of lower molecular weight obtained after acid hydrolysis appeared as effective immunostimulators of PBMC's. The results obtained after the incubation of cells with 1,6 b-glucanase modified glucans suggest that b-(1,6 binding of glucose monomers probably has no importance for the production of imunostimulating effects, in vitro. This confirmed that b-(1,3 bonds are the primary determinants of immunomodulatory activities and stimulation of IFN-g synthesis.

  10. Novel RNA structural features of an alternatively splicing group II intron from Clostridium tetani.

    Science.gov (United States)

    McNeil, Bonnie A; Zimmerly, Steven

    2014-06-01

    Group II introns are ribozymes in bacterial and organellar genomes that function as self-splicing introns and as retroelements. Previously, we reported that the group II intron C.te.I1 of Clostridium tetani alternatively splices in vivo to produce five distinct coding mRNAs. Accurate fusion of upstream and downstream reading frames requires a shifted 5' splice site located 8 nt upstream of the usual 5' GUGYG motif. This site is specified by the ribozyme through an altered intron/exon-binding site 1 (IBS1-EBS1) pairing. Here we use mutagenesis and self-splicing assays to investigate in more detail the significance of the structural features of the C.te.I1 ribozyme. The shifted 5' splice site is shown to be affected by structures in addition to IBS1-EBS1, and unlike other group II introns, C.te.I1 appears to require a spacer between IBS1 and the GUGYG motif. In addition, the mechanism of 3' exon recognition is modified from the ancestral IIB mechanism to a IIA-like mechanism that appears to be longer than the typical single base-pair interaction and may extend up to 4 bp. The novel ribozyme properties that have evolved for C.te.I1 illustrate the plasticity of group II introns in adapting new structural and catalytic properties that can be utilized to affect gene expression.

  11. Non-iridescent Transmissive Structural Color Filter Featuring Highly Efficient Transmission and High Excitation Purity

    Science.gov (United States)

    Shrestha, Vivek Raj; Lee, Sang-Shin; Kim, Eun-Soo; Choi, Duk-Yong

    2014-05-01

    Nanostructure based color filtering has been considered an attractive replacement for current colorant pigmentation in the display technologies, in view of its increased efficiencies, ease of fabrication and eco-friendliness. For such structural filtering, iridescence relevant to its angular dependency, which poses a detrimental barrier to the practical development of high performance display and sensing devices, should be mitigated. We report on a non-iridescent transmissive structural color filter, fabricated in a large area of 76.2 × 25.4 mm2, taking advantage of a stack of three etalon resonators in dielectric films based on a high-index cavity in amorphous silicon. The proposed filter features a high transmission above 80%, a high excitation purity of 0.93 and non-iridescence over a range of 160°, exhibiting no significant change in the center wavelength, dominant wavelength and excitation purity, which implies no change in hue and saturation of the output color. The proposed structure may find its potential applications to large-scale display and imaging sensor systems.

  12. Non-iridescent transmissive structural color filter featuring highly efficient transmission and high excitation purity.

    Science.gov (United States)

    Shrestha, Vivek Raj; Lee, Sang-Shin; Kim, Eun-Soo; Choi, Duk-Yong

    2014-05-12

    Nanostructure based color filtering has been considered an attractive replacement for current colorant pigmentation in the display technologies, in view of its increased efficiencies, ease of fabrication and eco-friendliness. For such structural filtering, iridescence relevant to its angular dependency, which poses a detrimental barrier to the practical development of high performance display and sensing devices, should be mitigated. We report on a non-iridescent transmissive structural color filter, fabricated in a large area of 76.2 × 25.4 mm(2), taking advantage of a stack of three etalon resonators in dielectric films based on a high-index cavity in amorphous silicon. The proposed filter features a high transmission above 80%, a high excitation purity of 0.93 and non-iridescence over a range of 160°, exhibiting no significant change in the center wavelength, dominant wavelength and excitation purity, which implies no change in hue and saturation of the output color. The proposed structure may find its potential applications to large-scale display and imaging sensor systems.

  13. Structure, Ferromagnetic, Dielectric and Electronic Features of the LaBiFe2O6 Material

    Science.gov (United States)

    Cuervo Farfán, J. A.; Aljure García, D. M.; Cardona, R.; Arbey Rodríguez, J.; Landínez Téllez, D. A.; Roa-Rojas, J.

    2016-12-01

    In this paper, the synthesis and study of the structural, morphological, electrical, magnetic and electronic properties of the LaBiFe2O6 novel material are reported. The material was produced using the standard ceramic method. The Rietveld analysis of experimental data of X-ray diffraction showed that it synthesizes in an orthorhombic perovskite structure (Pnma space group, # 62). Two types of grain, micro and sub-micrometric, with the LaBiFe2O6 stoichiometry were identified by scanning electron microscopy and X-ray dispersive spectroscopy. Results of electrical polarization and dielectric constant reveal the occurrence of hysteretic loops of polarization with evidences of dielectric loss. At room temperature, the material is ferromagnetic and exhibits an anomaly at T = 258 K, which is attributed to anisotropy effects. Results of diffuse reflectance suggest a semiconductor feature with energy gap Eg=2.17 eV, which is in agreement with calculations of band structure and density of states for one spin orientation, while for the other spin configuration from the calculations a conductor behavior is expected.

  14. Structure, Ferromagnetic, Dielectric and Electronic Features of the LaBiFe2O6 Material

    Science.gov (United States)

    Cuervo Farfán, J. A.; Aljure García, D. M.; Cardona, R.; Arbey Rodríguez, J.; Landínez Téllez, D. A.; Roa-Rojas, J.

    2017-03-01

    In this paper, the synthesis and study of the structural, morphological, electrical, magnetic and electronic properties of the LaBiFe2O6 novel material are reported. The material was produced using the standard ceramic method. The Rietveld analysis of experimental data of X-ray diffraction showed that it synthesizes in an orthorhombic perovskite structure ( Pnma space group, # 62). Two types of grain, micro and sub-micrometric, with the LaBiFe2O6 stoichiometry were identified by scanning electron microscopy and X-ray dispersive spectroscopy. Results of electrical polarization and dielectric constant reveal the occurrence of hysteretic loops of polarization with evidences of dielectric loss. At room temperature, the material is ferromagnetic and exhibits an anomaly at T = 258 K, which is attributed to anisotropy effects. Results of diffuse reflectance suggest a semiconductor feature with energy gap Eg=2.17 eV, which is in agreement with calculations of band structure and density of states for one spin orientation, while for the other spin configuration from the calculations a conductor behavior is expected.

  15. Structural and Functional Features of Peroxidases with a Potential as Industrial Biocatalysts

    Science.gov (United States)

    Ruiz-Dueñas, Francisco J.; Martínez, Angel T.

    This chapter begins with a description of the main structural features of heme peroxidases representative of the two large superfamilies of plant-fungal-bacterial and animal peroxidases, and the four additional (super)families described to date. Then, we focus on several fungal peroxidases of high biotechnological potential as industrial biocatalysts. These include (1) ligninolytic peroxidases from white-rot basidiomycetes being able to oxidize high redox-potential substrates at an exposed protein radical; (2) heme-thiolate peroxidases that are structural hybrids of typical peroxidases and cytochrome P450 enzymes and, after their discovery in sooty molds, are being described in basidiomycetes with even more interesting catalytic properties, such as selective aromatic oxygenation; and (3) the so-called dye-decolorizing peroxidases that are still to be thoroughly investigated but have been identified in different basidiomycete genomes. The structural-functional description of these peroxidases includes an analysis of the heme environment and a description of their substrate oxidation sites, with the purpose of understanding their interesting catalytic properties and biotechnological potential.

  16. GeneViTo: Visualizing gene-product functional and structural features in genomic datasets

    Directory of Open Access Journals (Sweden)

    Promponas Vasilis J

    2003-10-01

    Full Text Available Abstract Background The availability of increasing amounts of sequence data from completely sequenced genomes boosts the development of new computational methods for automated genome annotation and comparative genomics. Therefore, there is a need for tools that facilitate the visualization of raw data and results produced by bioinformatics analysis, providing new means for interactive genome exploration. Visual inspection can be used as a basis to assess the quality of various analysis algorithms and to aid in-depth genomic studies. Results GeneViTo is a JAVA-based computer application that serves as a workbench for genome-wide analysis through visual interaction. The application deals with various experimental information concerning both DNA and protein sequences (derived from public sequence databases or proprietary data sources and meta-data obtained by various prediction algorithms, classification schemes or user-defined features. Interaction with a Graphical User Interface (GUI allows easy extraction of genomic and proteomic data referring to the sequence itself, sequence features, or general structural and functional features. Emphasis is laid on the potential comparison between annotation and prediction data in order to offer a supplement to the provided information, especially in cases of "poor" annotation, or an evaluation of available predictions. Moreover, desired information can be output in high quality JPEG image files for further elaboration and scientific use. A compilation of properly formatted GeneViTo input data for demonstration is available to interested readers for two completely sequenced prokaryotes, Chlamydia trachomatis and Methanococcus jannaschii. Conclusions GeneViTo offers an inspectional view of genomic functional elements, concerning data stemming both from database annotation and analysis tools for an overall analysis of existing genomes. The application is compatible with Linux or Windows ME-2000-XP operating

  17. Statistical quantification of the uncertainty in transmissibility feature for structural condition binary classification

    Science.gov (United States)

    Mao, Zhu; Todd, Michael

    2011-04-01

    Transmissibility-related features are one class of indicators used to detect structural defects, especially because of their sensitivity to local changes. In this paper, we consider a SIMO identification model and regard the change in transmissibility as a feature indicating damage occurrence. Both inherent randomness in the system identification process and the noise contamination (or other types of measurement/sampling/quantization variabilities) are included as the sources of transmissibility uncertainty. The uncertainty quantification is necessary to group-classify the measurements into either undamaged or damaged (binary) conditions with a better understanding of Type I/II trade-offs. A sensitivity research is deployed in this paper, where Receiver Operating Characteristic (ROC) curves for individual frequency lines are given with different damage levels and extraneous noise levels, and Area Under Curve (AUC) will be evaluated as the key performance metric across the entire frequency domain. The paper concludes that regions near resonance will have the best hypothesis test performance in terms of sensitivity and specificity.

  18. Automatic registration of Iphone images to LASER point clouds of the urban structures using shape features

    Science.gov (United States)

    Sirmacek, B.; Lindenbergh, R. C.; Menenti, M.

    2013-10-01

    Fusion of 3D airborne laser (LIDAR) data and terrestrial optical imagery can be applied in 3D urban modeling and model up-dating. The most challenging aspect of the fusion procedure is registering the terrestrial optical images on the LIDAR point clouds. In this article, we propose an approach for registering these two different data from different sensor sources. As we use iPhone camera images which are taken in front of the interested urban structure by the application user and the high resolution LIDAR point clouds of the acquired by an airborne laser sensor. After finding the photo capturing position and orientation from the iPhone photograph metafile, we automatically select the area of interest in the point cloud and transform it into a range image which has only grayscale intensity levels according to the distance from the image acquisition position. We benefit from local features for registering the iPhone image to the generated range image. In this article, we have applied the registration process based on local feature extraction and graph matching. Finally, the registration result is used for facade texture mapping on the 3D building surface mesh which is generated from the LIDAR point cloud. Our experimental results indicate possible usage of the proposed algorithm framework for 3D urban map updating and enhancing purposes.

  19. Structural Features of the Telomerase RNA Gene in the Naked Mole Rat Heterocephalus glaber

    Science.gov (United States)

    Evfratov, S. A.; Smekalova, E. M.; Golovin, A. V.; Logvina, N. A.; Zvereva, M. I.; Dontsova, O. A.

    2014-01-01

    Telomere length, an important feature of life span control, is dependent on the activity of telomerase (a key enzyme of the telomere-length-maintaining system). Telomerase RNA is a component of telomerase and, thus, is crucial for its activity. The structures of telomerase RNA genes and their promoter regions were compared for the long-living naked mole rat and different organisms. Two rare polymorphisms in Heterocephalus glaber telomerase RNA (hgTER) were identified: A→G in the first loop of pseudoknot P2b-p3 (an equivalent of 111nt in hTR) and G→A in the scaRNA domain CR7-p8b (an equivalent of 421nt in hTR). Analysis of TER promoter regions allowed us to identify two new transcription factor binding sites. The first one is the ETS family site, which was found to be a conserved element for all the analyzed TER promoters. The second site is unique for the promoter region of TER of the naked mole rat and is a binding site for the SOX17 transcription factor. The absence of one Sp1 site in the TER promoter region of the naked small rat is an additional specific feature of the promoter area of hgTER. Such variation in the hgTER transcription regulation region and hgTER itself could provide increased telomerase activity in stem cells and an extended lifespan to H. glaber. PMID:25093110

  20. Probabilistic uncertainty quantification of wavelet-transform-based structural health monitoring features

    Science.gov (United States)

    Sarrafi, Aral; Mao, Zhu

    2016-04-01

    In the application of Structural Health Monitoring (SHM), processing the online-acquired data plays a very important role, among which wavelet transform is an outstanding tool and compared to Fourier transform, it handles the nonstationary behaviors in the time series in an adaptive fashion. When dealing with time-variant data, there are uncertainties from numerous resources inherent to the feature estimation, such as measurement noise, operational and environmental variability, hardware limitation, etc. The corruption from uncertainty will make the data interpretation ambiguous and thereby dramatically degrades the decision quality with regard to the occurrence, location, severity, and extent of damages. This paper derives a probabilistic model to quantify analytically the uncertainty of wavelet transform feature as a random variable, and variance is derived analytically in this work. Considering central limit theorem, Gaussian probability density function characterizes the distribution and this has been validated via Monte Carlo testing. By fully characterizing the uncertainty, the damage detection implementations may be facilitated with a quantified false alarm rate and miss catch rate.

  1. IR spectroscopic features of gaseous C7H7O+ ions: benzylium versus tropylium ion structures.

    Science.gov (United States)

    Chiavarino, Barbara; Crestoni, Maria Elisa; Fornarini, Simonetta; Dopfer, Otto; Lemaire, Joel; Maître, Philippe

    2006-08-03

    Gaseous [C7H7O]+ ions have been formed by protonation of benzaldehyde or tropone (2,4,6-cycloheptatrienone) in the cell of an FT-ICR mass spectrometer using C2H5(+) as a Brønsted acid. The so-formed species have been assayed by infrared multiphoton dissociation (IRMPD) using the free electron laser (FEL) at the CLIO (Centre Laser Infrarouge Orsay) facility. The IRMPD features are quite distinct for ions from the two different precursors, pointing to two different isomers. A number of potential structures for [C7H7O]+ ions have been optimized at the B3LYP/6-31+G(d,p) level of theory, and their relative energies and IR spectra are reported. On this basis, the IRMPD spectra of [C7H7O]+ ions are found to display features characteristic of O-protonated species, with no evidence of any further skeletal rearrangements. The so-formed ions are thus hydroxy-substituted benzylium and tropylium ions, respectively, representative members of the benzylium/tropylium ion family. The IRMPD assay using the FEL laser light has allowed their unambiguous discrimination where other mass spectrometric techniques have yielded a less conclusive answer.

  2. Low-frequency features of the ultrasound echo from an adhesively bonded layer-substrate structure

    Institute of Scientific and Technical Information of China (English)

    WANG Xiaomin; LI Mingxuan; MAO Jie; LIAN Guoxuan

    2005-01-01

    The low-frequency features of the ultrasound reflection spectra from the structure of a single layer on a substrate bonded by a thin adhesive layer are theoretically studied; the low-frequency here means the frequency of the interrogating ultrasonic wave is less than the quart-wavelength resonance frequency of the adhesive layer. The possibility of the inversion of the thickness and the evaluation of the cohesion strength of the adhesive layer from the resonance frequency shifts of the layered system is indicated. An analytic solution to the nonlinear equation satisfied by the resonance frequency is presented by Taylor expansion method showing satisfactory agreement with the numerical results by Newton iterative method. The results indicate larger range for application than the traditional spring model for the thin adhesive layer. In a much lower frequency range the thin adhesive layer may be regarded to be a spring.

  3. Multi-font Multi-size Kannada Numeral Recognition Based on Structural Features

    CERN Document Server

    Dhandra, B V; Hangarge, Mallikarjun

    2011-01-01

    In this paper a fast and novel method is proposed for multi-font multi-size Kannada numeral recognition which is thinning free and without size normalization approach. The different structural feature are used for numeral recognition namely, directional density of pixels in four directions, water reservoirs, maximum profile distances, and fill hole density are used for the recognition of Kannada numerals. A Euclidian minimum distance criterion is used to find minimum distances and K-nearest neighbor classifier is used to classify the Kannada numerals by varying the size of numeral image from 16 to 50 font sizes for the 20 different font styles from NUDI and BARAHA popular word processing Kannada software. The total 1150 numeral images are tested and the overall accuracy of classification is found to be 100%. The average time taken by this method is 0.1476 seconds.

  4. Novel Fluorinated Indanone, Tetralone and Naphthone Derivatives: Synthesis and Unique Structural Features

    Directory of Open Access Journals (Sweden)

    Joseph C. Sloop

    2012-02-01

    Full Text Available Several fluorinated and trifluoromethylated indanone, tetralone and naphthone derivatives have been prepared via Claisen condensations and selective fluorinations in yields ranging from 22–60%. In addition, we report the synthesis of new, selectively fluorinated bindones in yields ranging from 72–92%. Of particular interest is the fluorination and trifluoroacetylation regiochemistry observed in these fluorinated products. We also note unusual transformations including a novel one pot, dual trifluoroacetylation, trifluoroacetylnaphthone synthesis via a deacetylation as well as an acetyl-trifluoroacetyl group exchange. Solid-state structural features exhibited by these compounds were investigated using crystallographic methods. Crystallographic results, supported by spectroscopic data, show that trifluoroacetylated ketones prefer a chelated cis-enol form whereas fluorinated bindone products exist primarily as the cross-conjugated triketo form.

  5. Multipotent natural agents to combat Alzheimer's disease. Functional spectrum and structural features

    Institute of Scientific and Technical Information of China (English)

    Hong-fang JI; Hong-yu ZHANG

    2008-01-01

    With the accelerated aging of human society, Alzheimer's disease (AD) is becoming one of the biggest threats to human health. Since multiple pathogenetic factors are implicated in the disease, the current hitting-one-target therapeutic strategy has proved inefficient to AD. As a result, finding multipotent agents that aim at multiple targets is attracting more and more attention. Although multifunc-tional anti-AD agents can be created by incorporating two or more pharmacophores in one scaffold, naturally occurring multipotent agents also attracted much attention. In this review, we first describe the functions of some typical naturally originated multipotent anti-AD compounds, then summarize their structural fea-tures and reveal that phenolics with certain flexibility predominate in these agents, which are of significance to find novel multipotent drugs to combat AD and other neurodegenerative diseases as well.

  6. Raman imaging to study structural and chemical features of the dentin enamel junction

    Science.gov (United States)

    Alebrahim, M. Anwar; Krafft, C.; Popp, J.

    2015-10-01

    The structure and chemical features of the human dentin enamel junction (DEJ) were characterized using Raman spectroscopic imaging. Slices were prepared from 10 German, and 10 Turkish teeth. Raman images were collected at 785 nm excitation and the average Raman spectra were calculated for analysis. Univariate and multivariate spectral analysis were applied for investigation. Raman images were obtained based on the intensity ratios of CH at 1450 cm-1 (matrix) to phosphate at 960 cm-1 (mineral), and carbonate to phosphate (1070/960) ratios. Different algorithms (HCA, K-means cluster and VCA) also used to study the DEJ. The obtained results showed that the width of DEJ is about 5 pm related to univariate method while it varies from 6 to 12 μm based on multivariate spectral technique. Both spectral analyses showed increasing in carbonate content inside the DEJ compared to the dentin, and the amide I (collagen) peak in dentin spectra is higher than DEJ spectra peak.

  7. 基于视觉与结构谱特征融合的视频检索%Video retrieval based on visual feature and structural spectral feature

    Institute of Scientific and Technical Information of China (English)

    翟素兰; 查到丽

    2012-01-01

    The time series structure is one of key characters of videos. In the paper, the method of abstraction and presentation video series feature is discussed which is based on DTW and graph spectral. DTW is used to extract some key frame images on the frame difference curves; the structure graph of video shot is constructed with the vertex set of the key frame images and edge set of the relation of these images. The video structure spectral is extracted by analyzing the the video structural graph's adjacent matrix. Visual feature and structral featrue are taken into consideration to rank the simility of the selected video clips. Experimental results show that the structrual spectral is able to present the video structural feature efficiently and can be used to retrieval the vido.%视频的时序结构特征是视频的重要特征.提出了一种基于DTW和图谱理论的视频结构特征提取与表示方法,并将这种结构特征融合视觉特征用于视频的镜头检索.根据镜头分割中的帧差曲线,使用DTW原理得到视频镜头特征帧,以镜头特征帧作为图的顶点,以特征帧间的关系作为图的边,生成镜头关系图,分解图的邻接矩阵,得到镜头结构谱,融合镜头的视觉特征得到最终的检索结果.实验结果表明,视频的结构谱特征可以有效地表示视频的结构特征,在视频检索中也是有效的.

  8. Characterization of structural features controlling the receptiveness of empty class II MHC molecules.

    Directory of Open Access Journals (Sweden)

    Bernd Rupp

    Full Text Available MHC class II molecules (MHC II play a pivotal role in the cell-surface presentation of antigens for surveillance by T cells. Antigen loading takes place inside the cell in endosomal compartments and loss of the peptide ligand rapidly leads to the formation of a non-receptive state of the MHC molecule. Non-receptiveness hinders the efficient loading of new antigens onto the empty MHC II. However, the mechanisms driving the formation of the peptide inaccessible state are not well understood. Here, a combined approach of experimental site-directed mutagenesis and computational modeling is used to reveal structural features underlying "non-receptiveness." Molecular dynamics simulations of the human MHC II HLA-DR1 suggest a straightening of the α-helix of the β1 domain during the transition from the open to the non-receptive state. The movement is mostly confined to a hinge region conserved in all known MHC molecules. This shift causes a narrowing of the two helices flanking the binding site and results in a closure, which is further stabilized by the formation of a critical hydrogen bond between residues αQ9 and βN82. Mutagenesis experiments confirmed that replacement of either one of the two residues by alanine renders the protein highly susceptible. Notably, loading enhancement was also observed when the mutated MHC II molecules were expressed on the surface of fibroblast cells. Altogether, structural features underlying the non-receptive state of empty HLA-DR1 identified by theoretical means and experiments revealed highly conserved residues critically involved in the receptiveness of MHC II. The atomic details of rearrangements of the peptide-binding groove upon peptide loss provide insight into structure and dynamics of empty MHC II molecules and may foster rational approaches to interfere with non-receptiveness. Manipulation of peptide loading efficiency for improved peptide vaccination strategies could be one of the applications profiting

  9. On the quantum mechanics of consciousness, with application to anomalous phenomena

    Science.gov (United States)

    Jahn, Robert G.; Dunne, Brenda J.

    1986-08-01

    Theoretical explication of a growing body of empirical data on consciousness-related anomalous phenomena is unlikely to be achieved in terms of known physical processes. Rather, it will first be necessary to formulate the basic role of consciousness in the definition of reality before such anomalous experience can adequately be represented. This paper takes the position that reality is constituted only in the interaction of consciousness with its environment, and therefore that any scheme of conceptual organization developed to represent that reality must reflect the processes of consciousness as well as those of its environment. In this spirit, the concepts and formalisms of elementary quantum mechanics, as originally proposed to explain anomalous atomic-scale physical phenomena, are appropriated via metaphor to represent the general characteristics of consciousness interacting with any environment. More specifically, if consciousness is represented by a quantum mechanical wave function, and its environment by an appropriate potential profile, Schrödinger wave mechanics defines eigenfunctions and eigenvalues that can be associated with the cognitive and emotional experiences of that consciousness in that environment. To articulate this metaphor it is necessary to associate certain aspects of the formalism, such as the coordinate system, the quantum numbers, and even the metric itself, with various impressionistic descriptors of consciousness, such as its intensity, perspective, approach/avoidance attitude, balance between cognitive and emotional activity, and receptive/assertive disposition. With these established, a number of the generic features of quantum mechanics, such as the wave/particle duality, and the uncertainty, indistinguishability, and exclusion principles, display metaphoric relevance to familiar individual and collective experiences. Similarly, such traditional quantum theoretic exercises as the central force field and atomic structure, covalent

  10. Structural features of Ni-Cr-Si-B materials obtained by different technologies

    Science.gov (United States)

    Kornienko, E. E.; Nikulina, A. A.; Belousova, N. S.; Lazurenko, D. V.; Ivashutenko, A. S.; Kuz'min, V. I.

    2016-11-01

    This study considers the structural features of Ni-Cr-Si-B (Ni - base; 15.1 % Cr; 2 % Si; 2 % B; 0.4 % C) materials obtained by different methods. The self-fluxing coatings were deposited by plasma spraying on the tubes from low carbon steel. Bulk cylinder specimens of 20 mm diameter and 15 mm height were obtained by spark plasma sintering (SPS). The structure and phase composition of these materials were investigated by optical microscopy (OM), scanning electron microscopy (SEM), transmission electron microscopy (TEM) and X-ray diffractometry (XRD). The major phases of coatings and sintered materials are γ-Ni, Ni3B, CrB and Cr7C3. We demonstrate that the particle unmelted in the process of plasma spraying or SPS consist of γ-Ni-NEB eutectic and also CrB and Cr7C3 inclusions. The prolonged exposure of powder to high temperatures as well as slow cooling rates by SPS provide for the growth of the structural components as compared to those of plasma coatings materials. High cooling rates at the plasma spraying by melted particles contribute to the formation of supersaturated solid solution of Cr, Si and Fe in γ-Ni. The structure of the melted particles in sintering material has gradient composition: the core constituted of Ni grains of 10 μm with γ-Ni-Ni3B eutectic on the edges. The results of the experiment demonstrate that the sintering material has a smaller microhardness in comparison with plasma coatings (650 and 850 MPa, respectively), but at the same time the material has higher density (porosity less than 1 %) than plasma coatings (porosity about 2.. .3 %).

  11. Medicinal properties of mangiferin, structural features, derivative synthesis, pharmacokinetics and biological activities.

    Science.gov (United States)

    Benard, Outhiriaradjou; Chi, Yuling

    2015-01-01

    The identification of biologically active and potentially therapeutically useful pharmacophores from natural products has been a long-term focus in the pharmaceutical industry. The recent emergence of a worldwide obesity and Type II diabetes epidemic has increased focus upon small molecules that can modulate energy metabolism, insulin sensitivity and fat biology. Interesting preliminary work done on mangiferin (MGF), the predominant constituent of extracts of the mango plant Mangifera indica L., portends potential for this pharmacophore as a novel parent compound for treating metabolic disorders. MGF is comprised of a C-glucosylated xanthone. Owing to the xanthone chemical structure, MGF has a redox active aromatic system and has antioxidant properties. MGF exerts varied and impressive metabolic effects in animals, improving metabolic disorders. For example we have discovered that MGF is a novel activator of the mammalian pyruvate dehydrogenase complex, leading to enhancement of carbohydrate utilization in oxidative metabolism, and leading to increased insulin sensitivity in animal models of obesity and insulin resistance. In addition, recent unbiased proteomics studies revealed that MGF upregulates proteins pivotal for mitochondrial bioenergetics and downregulates proteins controlling de novo lipogenesis in liver, helping to explain protective effects of MGF in prevention of liver steatosis. Several chemical studies have achieved synthesis of MGF, suggesting possible synthetic strategies to alter its chemical structure for development of structure-activity relationship (SAR) information. Ultimately, chemical derivatization studies could lead to the eventual development of novel therapeutics based upon the parent pharmacophore structure. Here we provide comprehensive review on chemical features of MGF, synthesis of its derivatives, its pharmacokinetics and biological activities.

  12. Discrete and polymeric Cu(II) complexes featuring substituted indazole ligands: their synthesis and structural chemistry.

    Science.gov (United States)

    Hawes, Chris S; Kruger, Paul E

    2014-11-21

    Reported here are the syntheses of four indazole-based ligands and the structural characterisation of four Cu(II) complexes derived from them. The ligands 1-(2-pyridyl)-1H-indazole, L1, and 2-(2-pyridyl)-2H-indazole, L2, have been characterised by single crystal X-ray diffraction methods for the first time. The intramolecular structural changes within L1 and L2 that result from the transition from the 1H to the 2H electronic configuration have been delineated. The synthesis of 1H-indazole-6-carboxylic acid, H2L3, and 1H-indazole-7-carboxylic acid, H2L4, is fully described and the structure of H2L4·H2O determined. The structures of two discrete mononuclear complexes {[Cu(L1)2(NO3)]·NO3·1.5H2O}, 1, and {[Cu(L2)2(NO3)]·NO3}, 2, have been determined and their molecular compositions corroborated by solution-based methods. Reaction of Cu(II) with H2L3 generates a 2D coordination polymer, [Cu3(HL3)4(NO3)2(EtOH)2]·3(C6H6)·2(H2O), 3, that features the archetypal [Cu2(OAc)4] paddlewheel motif and 1D channels; whereas reaction with H2L4 gives a discrete complex [Cu(HL4)2]·H2O·MeOH, 4, in which hydrogen bonding interactions link indazole dimers via a water molecule to yield a 1D network.

  13. A set-theoretic approach to linguistic feature structures and unification algorithms (I

    Directory of Open Access Journals (Sweden)

    N. Curteanu

    2000-10-01

    Full Text Available The paper proposes formal inductive definitions for linguistic feature structures (FSs taking values within a class of value types or sorts: single, disjunctive, (ordered lists, multisets (or bags, po-multisets (multisets embedded into a partially ordered set, and indexed (re-entrance values. The linguistic realization (semantics of the considered sorts is proposed. The FSs having these multi-sort values are organized as (rooted directed acyclic graphs. The concrete model of the FSs we had in mind for our set-theoretic definitions are the FSs used within the well-known HPSG linguistic theory. Set-theoretic general definitions for the proposed multi-sort FSs are defined. These constructive definitions start from atomic values and build recurrently multi-sorted values and structures, providing naturally a fixed-point semantics of the obtained FSs as a counterpart to the large class of logical semantics models on FSs. The linguistic unification algorithm based on tableau-subsumption is outlined. The Prolog code of the unification algorithm is provided and results of running it on some of the main multi-sort FSs is enclosed in the appendices. We consider the proposed formal approach to FS definitions and unification as necessary steps to set-theoretical implementations of natural language processing systems.

  14. A set-theoretic approach to linguistic feature structures and unification algorithms (II

    Directory of Open Access Journals (Sweden)

    N.Curteanu

    2001-02-01

    Full Text Available The paper proposes formal inductive definitions for linguistic feature structures (FSs taking values within a class of value types or sorts: single, disjunctive, (ordered lists, multisets (or bags, po-multisets (multisets embedded into a partially ordered set, and indexed (re-entrance values. The linguistic realization (semantics of the considered sorts is proposed. The FSs having these multi-sort values are organized as (rooted directed acyclic graphs. The concrete model of the FSs we had in mind for our set-theoretic definitions are the FSs used within the well-known HPSG linguistic theory. Set-theoretic general definitions for the proposed multi-sort FSs are defined. These constructive definitions start from atomic values and build recurrent multi-sorted values and structures, providing naturally a fixed-point semantics of the obtained FSs as a counterpart to the large class of logical semantics models on FSs. The linguistic unification algorithm based on tableau-subsumption is outlined. The Prolog code of the unification algorithm is provided and results of running it on some of the main multi-sort FSs is enclosed in the appendices. We consider the proposed formal approach to FSs definitions and unification as necessary steps to set-theoretical implementations of natural language processing systems.

  15. Hsp60, a novel target for antitumor therapy: structure-function features and prospective drugs design.

    Science.gov (United States)

    Pace, Andrea; Barone, Giampaolo; Lauria, Antonino; Martorana, Annamaria; Piccionello, Antonio Palumbo; Pierro, Paola; Terenzi, Alessio; Almerico, Anna Maria; Buscemi, Silvestre; Campanella, Claudia; Angileri, Francesca; Carini, Francesco; Zummo, Giovanni; de Macario, Everly Conway; Cappello, Francesco; Macario, Alberto J L

    2013-01-01

    Heat shock protein 60 kDa (Hsp60) is a chaperone classically believed to be involved in assisting the correct folding of other mitochondrial proteins. Hsp60 also plays a role in cytoprotection against cell stressors, displaying for example, antiapoptotic potential. Despite the plethora of studies devoted to the mechanism of Hsp60's function, especially in prokaryotes, fundamental issues still remain unexplored, including the definition of its role in cancer. Key questions still unanswered pertain to the differences in structure-function features that might exist between the well-studied prokaryotic GroEL and the largely unexplored eukaryotic Hsp60 proteins. In this article we discuss these differences in sequence, structure, and roles of Hsp60, focusing on the human ortholog with the view of devising compounds to block its ability to favour tumor-cell growth and survival. Compounds currently known to directly or indirectly affect Hsp60 functions, such as protein folding, HIF-1α accumulation, or Hsp60-induced cell proliferation, are discussed along with strategies that might prove effective for developing Hsp60-targeting drugs for anticancer therapy.

  16. Mode of formation and structural features of DNA-cationic liposome complexes used for transfection.

    Science.gov (United States)

    Gershon, H; Ghirlando, R; Guttman, S B; Minsky, A

    1993-07-20

    Complexes formed between cationic liposomes and nucleic acids represent a highly efficient vehicle for delivery of DNA and RNA molecules into a large variety of eukaryotic cells. By using fluorescence, gel electrophoresis, and metal-shadowing electron microscopy techniques, the factors that affect the, yet unclear, interactions between DNA and cationic liposomes as well as the structural features of the resulting complexes have been elucidated. A model is suggested according to which cationic liposomes bind initially to DNA molecules to form clusters of aggregated vesicles along the nucleic acids. At a critical liposome density, two processes occur, namely, DNA-induced membrane fusion, indicated by lipid mixing studies, and liposome-induced DNA collapse, pointed out by the marked cooperativity of the encapsulation processes, by their modulations by DNA-condensing agents, and also by their conspicuous independence upon DNA length. The DNA collapse leads to the formation of condensed structures which can be completely encapsulated within the fused lipid bilayers in a fast, highly cooperative process since their exposed surface is substantially smaller than that of extended DNA molecules. The formation of the transfecting DNA-liposome complexes in which the nucleic acids are fully encapsulated within a positively-charged lipid bilayer is proposed, consequently, to be dominated by mutual effects exerted by the DNA and the cationic liposomes, leading to interrelated lipid fusion and DNA collapse.

  17. Anomalous Hall Effect in a Kagome Ferromagnet

    Science.gov (United States)

    Ye, Linda; Wicker, Christina; Suzuki, Takehito; Checkelsky, Joseph; Joseph Checkelsky Team

    The ferromagnetic kagome lattice is theoretically known to possess topological band structures. We have synthesized large single crystals of a kagome ferromagnet Fe3Sn2 which orders ferromagnetically well above room temperature. We have studied the electrical and magnetic properties of these crystals over a broad temperature and magnetic field range. Both the scaling relation of anomalous Hall effect and anisotropic magnetic susceptibility show that the ferromagnetism of Fe3Sn2 is unconventional. We discuss these results in the context of magnetism in kagome systems and relevance to the predicted topological properties in this class of compounds. This research is supported by DMR-1231319.

  18. Characterizing structural features of cuticle-degrading proteases from fungi by molecular modeling

    Directory of Open Access Journals (Sweden)

    Fu Yun-Xin

    2007-05-01

    Full Text Available Abstract Background Serine proteases secreted by nematode and insect pathogenic fungi are bio-control agents which have commercial potential for developing into effective bio-pesticides. A thorough understanding of the structural and functional features of these proteases would significantly assist with targeting the design of efficient bio-control agents. Results Structural models of serine proteases PR1 from entomophagous fungus, Ver112 and VCP1 from nematophagous fungi, have been modeled using the homology modeling technique based on the crystal coordinate of the proteinase K. In combination with multiple sequence alignment, these models suggest one similar calcium-binding site and two common disulfide bridges in the three cuticle-degrading enzymes. In addition, the predicted models of the three cuticle-degrading enzymes present an essentially identical backbone topology and similar geometric properties with the exception of a limited number of sites exhibiting relatively large local conformational differences only in some surface loops and the N-, C termini. However, they differ from each other in the electrostatic surface potential, in hydrophobicity and size of the S4 substrate-binding pocket, and in the number and distribution of hydrogen bonds and salt bridges within regions that are part of or in close proximity to the S2-loop. Conclusion These differences likely lead to variations in substrate specificity and catalytic efficiency among the three enzymes. Amino acid polymorphisms in cuticle-degrading enzymes were discussed with respect to functional effects and host preference. It is hoped that these structural models would provide a further basis for exploitation of these serine proteases from pathogenic fungi as effective bio-control agents.

  19. Analysis on Features of Agricultural Structure Change and Agricultural Competitiveness in Hubei Province

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The output data of crop farming,forestry,animal husbandry and fishery in the Hubei Statistical Yearbook-2009 is used to analyze the features of agricultural structure change in Hubei Province since 1983;according to the relevant data in Hubei Statistical Yearbook and China Statistical Yearbook in 2005 and 2009,and adopting the shift-share analysis model,the difference in agricultural economic growth between Hubei and other provinces in Central China as well as the difference among the 17 regions of Hubei Province during 2004-2008 are analyzed.Results show that,the agriculture in Hubei Province shows significant overall advantages in central China and has stronger competitiveness,but its crop farming and fishery structure are not quite reasonable,and the competitive advantages of its fishery and agricultural services still need to be strengthened;the agricultural structure within Hubei Province sees an obvious regional differences,viewed from the total deviation,Huanggang,Jingmen and Yichang enjoy competitive edge in the whole province,from the viewpoint of industrial sectors,Huanggang is the most competitive in its planting,forestry and animal husbandry,while Jingmen is the strongest in fishery and Xiangfan has a competitive edge over others in its agricultural services.Based on those results above,it is proposed that Hubei Province should fully recognize its natural conditions,resources endowment and current differences in the economic status of each places,work out measures to suit local conditions,take full use of its advantages,extend its production chain and go on the development road with regional characteristics.

  20. Contrasted structuring effects of mesoscale features on the seabird community in the Mozambique Channel

    Science.gov (United States)

    Jaquemet, S.; Ternon, J. F.; Kaehler, S.; Thiebot, J. B.; Dyer, B.; Bemanaja, E.; Marteau, C.; Le Corre, M.

    2014-02-01

    of mescoscale features in structuring the tropical seabird community in the Mozambique Channel, in addition to segregating tropical and non-tropical species. The mechanisms underlying the segregation of tropical seabirds seem to partially differ from that of other tropical regions, and this may be a consequence of the strong local mesoscale activity, affecting prey size and availability schemes. Beyond characterising the foraging habitats of the seabird community of the Mozambique Channel, this study highlights the importance of this region as a hot spot for seabirds; especially the southern part, where several endangered sub-Antarctic species over-winter.

  1. Anomalous Dynamical Responses in a Driven System

    CERN Document Server

    Dutta, Suman

    2016-01-01

    The interplay between structure and dynamics in non-equilibrium steady-state is far from understood. We address this interplay by tracking Brownian Dynamics trajectories of particles in a binary colloid of opposite charges in an external electric field, undergoing cross-over from homogeneous to lane state, a prototype of heterogeneous structure formation in non-equilibrium systems. We show that the length scale of structural correlations controls heterogeneity in diffusion and consequent anomalous dynamic responses, like the exponential tail in probability distributions of particle displacements and stretched exponential structural relaxation. We generalise our observations using equations for steady state density which may aid to understand microscopic basis of heterogeneous diffusion in condensed matter systems.

  2. Superconductivity in an anomalously tetragonal YB2C3O6.62 single crystal: A possible singularity in the structural phase diagram

    DEFF Research Database (Denmark)

    Frello, T.; Andersen, N.H.; Baziljevich, M.

    2003-01-01

    During systematic studies of the structural phase diagram of YBa2Cu3O6+x (YBCO), a YBCO single crystal of oxygen concentration x=0.62 turned out to have a tetragonal crystal structure. By magneto-optical imaging of the expulsion of an applied magnetic field, it was shown that the sample was bulk ...

  3. Filtering and counting of extended connectivity fingerprint features maximizes compound recall and the structural diversity of hits.

    Science.gov (United States)

    Hu, Ye; Lounkine, Eugen; Bajorath, Jürgen

    2009-07-01

    Extended connectivity fingerprints produce variable numbers of structural features for molecules and quantitative comparison of feature ensembles is typically carried out as a measure of molecular similarity. As an alternative way to utilize the information content of extended connectivity fingerprint features, we have introduced a compound class-directed feature filtering technique. In combination with a simple feature counting protocol, feature filtering significantly improves the performance of extended connectivity fingerprint similarity searching compared with state-of-the-art fingerprint search methods. Subsets of extended connectivity fingerprint features that are unique to active compounds are found to be responsible for high compound recall. Moreover, feature filtering and counting is shown to result in significantly higher scaffold hopping potential than data fusion or fingerprint averaging methods. Extended connectivity fingerprint feature filtering and counting represents one of the simplest similarity search methods introduced to date, yet it produces top compound recall and maximizes the scaffold diversity of hits, which is a longstanding goal of similarity searching.

  4. A structural feature of the non-peptide ligand interactions with mice mu-opioid receptors.

    Science.gov (United States)

    Noori, Hamid R; Mucksch, Christian; Urbassek, Herbert M

    2014-01-01

    By binding to and activating the G-protein coupled μ-, κ- and δ-opioid receptors in the central nervous system, opiates are known to induce analgesic and sedative effects. In particular, non-peptide opioid ligands are often used in clinical applications to induce these therapeutically beneficial effects, due to their superior pharmacokinetics and bioavailability in comparison to endogenous neuropeptides. However, since opioid alkaloids are highly addictive substances, it is necessary to understand the exact mechanisms of their actions, specifically the ligand-binding properties of the target receptors, in order to safely apply opiates for therapeutic purposes. Using an in silico molecular docking approach (AutoDock Vina) combined with two-step cluster analysis, we have computationally obtained the docking scores and the ligand-binding pockets of twelve representative non-peptide nonendogenous agonists and antagonists at the crystallographically identified μ-opioid receptor. Our study predicts the existence of two main binding sites that are congruently present in all opioid receptor types. Interestingly, in terms of the agonist or antagonist properties of the substances on the receptors, the clustering analysis suggests a relationship with the position of the ligand-binding pockets, particularly its depth within the receptor structure. Furthermore, the binding affinity of the substances is directly correlated to the proximity of the binding pockets to the extracellular space. In conclusion, the results provide further insights into the structural features of the functional pharmacology of opioid receptors, suggesting the importance of the binding position of non-peptide agonists and antagonists- specifically the distance and the level of exposure to the extracellular space- to their dissociation kinetics and subsequent potency.

  5. PEG-induced osmotic stress in Mentha x piperita L.: Structural features and metabolic responses.

    Science.gov (United States)

    Búfalo, Jennifer; Rodrigues, Tatiane Maria; de Almeida, Luiz Fernando Rolim; Tozin, Luiz Ricardo Dos Santos; Marques, Marcia Ortiz Mayo; Boaro, Carmen Silvia Fernandes

    2016-08-01

    The present study investigated whether osmotic stress induced by the exposure of peppermint (Mentha x piperita L.) to moderate and severe stress for short periods of time changes the plant's physiological parameters, leaf anatomy and ultrastructure and essential oil. Plants were exposed to two levels of polyethyleneglycol (50 g L(-1) and 100 g L(-1) of PEG) in a hydroponic experiment. The plants exposed to 50 g L(-1) maintained metabolic functions similar to those of the control group (0 g L(-1)) without changes in gas exchange or structural characteristics. The increase in antioxidant enzyme activity reduced the presence of free radicals and protected membranes, including chloroplasts and mitochondria. In contrast, the osmotic stress caused by 100 g L(-1) of PEG inhibited leaf gas exchange, reduced the essential oil content and changed the oil composition, including a decrease in menthone and an increase in menthofuran. These plants also showed an increase in peroxidase activity, but this increase was not sufficient to decrease the lipid peroxidation level responsible for damaging the membranes of organelles. Morphological changes were correlated with the evaluated physiological features: plants exposed to 100 g L(-1) of PEG showed areas with collapsed cells, increases in mesophyll thickness and the area of the intercellular space, cuticle shrinkage, morphological changes in plastids, and lysis of mitochondria. In summary, our results revealed that PEG-induced osmotic stress in M. x piperita depends on the intensity level of the osmotic stress applied; severe osmotic stress changed the structural characteristics, caused damage at the cellular level, and reduced the essential oil content and quality.

  6. Crystal structures and inhibitor binding properties of plant class V chitinases: the cycad enzyme exhibits unique structural and functional features.

    Science.gov (United States)

    Umemoto, Naoyuki; Kanda, Yuka; Ohnuma, Takayuki; Osawa, Takuo; Numata, Tomoyuki; Sakuda, Shohei; Taira, Toki; Fukamizo, Tamo

    2015-04-01

    A class V (glycoside hydrolase family 18) chitinase from the cycad Cycas revoluta (CrChiA) is a plant chitinase that has been reported to possess efficient transglycosylation (TG) activity. We solved the crystal structure of CrChiA, and compared it with those of class V chitinases from Nicotiana tabacum (NtChiV) and Arabidopsis thaliana (AtChiC), which do not efficiently catalyze the TG reaction. All three chitinases had a similar (α/β)8 barrel fold with an (α + β) insertion domain. In the acceptor binding site (+1, +2 and +3) of CrChiA, the Trp168 side chain was found to stack face-to-face with the +3 sugar. However, this interaction was not found in the identical regions of NtChiV and AtChiC. In the DxDxE motif, which is essential for catalysis, the carboxyl group of the middle Asp (Asp117) was always oriented toward the catalytic acid Glu119 in CrChiA, whereas the corresponding Asp in NtChiV and AtChiC was oriented toward the first Asp. These structural features of CrChiA appear to be responsible for the efficient TG activity. When binding of the inhibitor allosamidin was evaluated using isothermal titration calorimetry, the changes in binding free energy of the three chitinases were found to be similar to each other, i.e. between -9.5 and -9.8 kcal mol(-1) . However, solvation and conformational entropy changes in CrChiA were markedly different from those in NtChiV and AtChiC, but similar to those of chitinase A from Serratia marcescens (SmChiA), which also exhibits significant TG activity. These results provide insight into the molecular mechanism underlying the TG reaction and the molecular evolution from bacterial chitinases to plant class V chitinases.

  7. Segmentation of anatomical branching structures based on texture features and conditional random field

    Science.gov (United States)

    Nuzhnaya, Tatyana; Bakic, Predrag; Kontos, Despina; Megalooikonomou, Vasileios; Ling, Haibin

    2012-02-01

    This work is a part of our ongoing study aimed at understanding a relation between the topology of anatomical branching structures with the underlying image texture. Morphological variability of the breast ductal network is associated with subsequent development of abnormalities in patients with nipple discharge such as papilloma, breast cancer and atypia. In this work, we investigate complex dependence among ductal components to perform segmentation, the first step for analyzing topology of ductal lobes. Our automated framework is based on incorporating a conditional random field with texture descriptors of skewness, coarseness, contrast, energy and fractal dimension. These features are selected to capture the architectural variability of the enhanced ducts by encoding spatial variations between pixel patches in galactographic image. The segmentation algorithm was applied to a dataset of 20 x-ray galactograms obtained at the Hospital of the University of Pennsylvania. We compared the performance of the proposed approach with fully and semi automated segmentation algorithms based on neural network classification, fuzzy-connectedness, vesselness filter and graph cuts. Global consistency error and confusion matrix analysis were used as accuracy measurements. For the proposed approach, the true positive rate was higher and the false negative rate was significantly lower compared to other fully automated methods. This indicates that segmentation based on CRF incorporated with texture descriptors has potential to efficiently support the analysis of complex topology of the ducts and aid in development of realistic breast anatomy phantoms.

  8. Structural features of Fab fragments of rheumatoid factor IgM-RF in solution

    Energy Technology Data Exchange (ETDEWEB)

    Volkov, V. V., E-mail: vvo@ns.crys.ras.ru [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation); Lapuk, V. A. [Russian Academy of Sciences, Zelinskii Institute of Organic Chemistry (Russian Federation); Shtykova, E. V.; Stepina, N. D.; Dembo, K. A.; Sokolova, A. V.; Amarantov, S. V. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation); Timofeev, V. P. [Russian Academy of Sciences, Engelhardt Institute of Molecular Biology (Russian Federation); Ziganshin, R. Kh. [Russian Academy of Sciences, Shemyakin Ovchinnikov Institute of Bioorganic Chemistry (Russian Federation); Varlamova, E. Yu. [Russian Academy of Medical Sciences, Hematology Research Center (Russian Federation)

    2008-05-15

    The structural features of the Fab fragments of monoclonal (Waldenstroem's disease) immunoglobulin M (IgM) and rheumatoid immunoglobulin M (IgM-RF) were studied by a complex of methods, including small-angle X-ray scattering (SAXS), electron spin resonance (ESR), and mass spectrometry (MS). The Fab-RF fragment was demonstrated to be much more flexible in the region of interdomain contacts, the molecular weights and the shapes of the Fab and Fab-RF macromolecules in solution being only slightly different. According to the ESR data, the rotational correlation time for a spin label introduced into the peptide sequence for Fab is twice as large as that for Fab-RF (21{+-}2 and 11{+-}1 ns, respectively), whereas the molecular weights of these fragments differ by only 0.5% (mass-spectrometric data), which correlates with the results of molecular-shape modeling by small-angle X-ray scattering. The conclusion about the higher flexibility of the Fab-RF fragment contributes to an understanding of the specificity of interactions between the rheumatoid factor and the antigens of the own organism.

  9. Mental Imagery Scale: a new measurement tool to assess structural features of mental representations

    Science.gov (United States)

    D'Ercole, Martina; Castelli, Paolo; Giannini, Anna Maria; Sbrilli, Antonella

    2010-05-01

    Mental imagery is a quasi-perceptual experience which resembles perceptual experience, but occurring without (appropriate) external stimuli. It is a form of mental representation and is often considered centrally involved in visuo-spatial reasoning and inventive and creative thought. Although imagery ability is assumed to be functionally independent of verbal systems, it is still considered to interact with verbal representations, enabling objects to be named and names to evoke images. In literature, most measurement tools for evaluating imagery capacity are self-report instruments focusing on differences in individuals. In the present work, we applied a Mental Imagery Scale (MIS) to mental images derived from verbal descriptions in order to assess the structural features of such mental representations. This is a key theme for those disciplines which need to turn objects and representations into words and vice versa, such as art or architectural didactics. To this aim, an MIS questionnaire was administered to 262 participants. The questionnaire, originally consisting of a 33-item 5-step Likert scale, was reduced to 28 items covering six areas: (1) Image Formation Speed, (2) Permanence/Stability, (3) Dimensions, (4) Level of Detail/Grain, (5) Distance and (6) Depth of Field or Perspective. Factor analysis confirmed our six-factor hypothesis underlying the 28 items.

  10. The Structural Features of Sports and Race Betting Inducements: Issues for Harm Minimisation and Consumer Protection.

    Science.gov (United States)

    Hing, Nerilee; Sproston, Kerry; Brook, Kate; Brading, Richard

    2016-09-08

    Minimal research has been published about inducements for sports and race betting, despite their ready availability and aggressive advertising. This paper aimed to document the range and structural features of these inducements, and analyse their alignment with the harm minimisation and consumer protection goals of responsible gambling. A scan of all inducements offered on the websites of 30 major race and sports betting brands located 223 separate inducements which we categorised into 15 generic types, all offering financial incentives to purchase. These comprised sign-up offers, refer-a-friend offers, happy hours, mobile betting bonuses, multi-bet offers, refund/stake-back offers, matching stakes/deposits, winnings paid for 'close calls', bonus or better odds, bonus or better winnings, competitions, reduced commission, free bets to selected punters, cash rebates and other free bets. All inducements were subject to numerous terms and conditions which were complex, difficult to find, and obscured by legalistic language. Play-through conditions of bonus bets were particularly difficult to interpret and failed basic requirements for informed choice. Website advertisements for inducements were prominently promoted but few contained a responsible gambling message. The results were analysed to generate 12 research propositions considered worthy of empirical research to inform much needed regulatory reform in this area.

  11. Anomalous magnetic moment of anyons

    CERN Document Server

    Gat, G; Gat, Gil; Ray, Rashmi

    1994-01-01

    The anomalous magnetic moment of anyons is calculated to leading order in a 1/N expansion. It is shown that the gyromagnetic ratio g remains 2 to the leading order in 1/N. This result strongly supports that obtained in \\cite{poly}, namely that g=2 is in fact exact.

  12. Nonclassical light in coupled optical systems: anomalous power distribution, Fock space dynamics and supersymmetry

    CERN Document Server

    El-Ganainy, Ramy; Christodoulides, Demetrios N

    2013-01-01

    We investigate the dynamics of nonclassical states of light in coupled optical structures and we demonstrate a number of intriguing features associated with such arrangements. By diagonalizing the system's Hamiltonian, we show that these geometries can support eigenstates having anomalous optical intensity distribution with no classical counterpart. These features may provide new avenues towards manipulating light flow at the quantum level. By projecting the Hamiltonian operator on Hilbert subspaces spanning different numbers of photon excitations, we demonstrate that processes such as coherent transport, state localization and surface Bloch oscillations can take place in Fock space. Furthermore, we show that Hamiltonian representations of Fock space manifolds differing by one photon obey a discrete supersymmetry relation

  13. How do 2D fingerprints detect structurally diverse active compounds? Revealing compound subset-specific fingerprint features through systematic selection.

    Science.gov (United States)

    Heikamp, Kathrin; Bajorath, Jürgen

    2011-09-26

    In independent studies it has previously been demonstrated that two-dimensional (2D) fingerprints have scaffold hopping ability in virtual screening, although these descriptors primarily emphasize structural and/or topological resemblance of reference and database compounds. However, the mechanism by which such fingerprints enrich structurally diverse molecules in database selection sets is currently little understood. In order to address this question, similarity search calculations on 120 compound activity classes of varying structural diversity were carried out using atom environment fingerprints. Two feature selection methods, Kullback-Leibler divergence and gain ratio analysis, were applied to systematically reduce these fingerprints and generate alternative versions for searching. Gain ratio is a feature selection method from information theory that has thus far not been considered in fingerprint analysis. However, it is shown here to be an effective fingerprint feature selection approach. Following comparative feature selection and similarity searching, the compound recall characteristics of original and reduced fingerprint versions were analyzed in detail. Small sets of fingerprint features were found to distinguish subsets of active compounds from other database molecules. The compound recall of fingerprint similarity searching often resulted from a cumulative detection of distinct compound subsets by different fingerprint features, which provided a rationale for the scaffold hopping potential of these 2D fingerprints.

  14. Anomalous properties and the liquid-liquid phase transition in gallium

    Science.gov (United States)

    Li, Renzhong; Sun, Gang; Xu, Limei

    2016-08-01

    A group of materials including water and silicon exhibit many anomalous behaviors, e.g., density anomaly and diffusivity anomaly (increase upon compression). These materials are hypothesized to have a liquid-liquid phase transition (LLPT) and the critical fluctuation in the vicinity of the liquid-liquid critical point is considered as the origin of different anomalies. Liquid gallium was also reported to have a LLPT, yet whether it shows similar water-like anomalies is not yet studied. Using molecular dynamics simulations on a modified embedded-atom model, we study the thermodynamic, dynamic, and structural properties of liquid gallium as well as its LLPT. We find that, similar to water-like materials predicted to have the LLPT, gallium also shows different anomalous behaviors (e.g., density anomaly, diffusivity anomaly, and structural anomaly). We also find that its thermodynamic and structural response functions are continuous and show maxima in the supercritical region, the loci of which asymptotically approach to the other and merge to the Widom line. These phenomena are consistent with the supercritical phenomenon in a category of materials with a liquid-liquid critical point, which could be common features in most materials with a LLPT.

  15. Anomalous Enthalpy Relaxation in Vitreous Silica

    Directory of Open Access Journals (Sweden)

    Yuanzheng eYue

    2015-08-01

    Full Text Available It is a challenge to calorimetrically determine the glass transition temperature (Tg of vitreous silica. Here we demonstrate that this challenge mainly arises from the extreme sensitivity of the Tg to the hydroxyl content in vitreous silica, but also from the irreversibility of its glass transition when repeating the calorimetric scans. It is known that the liquid fragility (i.e., the speed of the viscous slow-down of a supercooled liquid at its Tg during cooling has impact on enthalpy relaxation in glass. Here we find that vitreous silica (as a strong system exhibits striking anomalies in both glass transition and enthalpy relaxation compared to fragile oxide systems. The anomalous enthalpy relaxation of vitreous silica is discovered by performing the hperquenching-annealing-calorimetry experiments. We argue that the strong systems like vitreous silica and vitreous Germania relax in a structurally cooperative manner, whereas the fragile ones do in a structurally independent fashion. We discuss the origin of the anomalous enthalpy relaxation in the HQ vitreous silica.

  16. Robust action recognition using multi-scale spatial-temporal concatenations of local features as natural action structures.

    Directory of Open Access Journals (Sweden)

    Xiaoyuan Zhu

    Full Text Available Human and many other animals can detect, recognize, and classify natural actions in a very short time. How this is achieved by the visual system and how to make machines understand natural actions have been the focus of neurobiological studies and computational modeling in the last several decades. A key issue is what spatial-temporal features should be encoded and what the characteristics of their occurrences are in natural actions. Current global encoding schemes depend heavily on segmenting while local encoding schemes lack descriptive power. Here, we propose natural action structures, i.e., multi-size, multi-scale, spatial-temporal concatenations of local features, as the basic features for representing natural actions. In this concept, any action is a spatial-temporal concatenation of a set of natural action structures, which convey a full range of information about natural actions. We took several steps to extract these structures. First, we sampled a large number of sequences of patches at multiple spatial-temporal scales. Second, we performed independent component analysis on the patch sequences and classified the independent components into clusters. Finally, we compiled a large set of natural action structures, with each corresponding to a unique combination of the clusters at the selected spatial-temporal scales. To classify human actions, we used a set of informative natural action structures as inputs to two widely used models. We found that the natural action structures obtained here achieved a significantly better recognition performance than low-level features and that the performance was better than or comparable to the best current models. We also found that the classification performance with natural action structures as features was slightly affected by changes of scale and artificially added noise. We concluded that the natural action structures proposed here can be used as the basic encoding units of actions and may hold

  17. Robust Speech Recognition Using Temporal Pattern Feature Extracted From MTMLP Structure

    Directory of Open Access Journals (Sweden)

    Yasser Shekofteh

    2014-10-01

    Full Text Available Temporal Pattern feature of a speech signal could be either extracted from the time domain or via their front-end vectors. This feature includes long-term information of variations in the connected speech units. In this paper, the second approach is followed, i.e. the features which are the cases of temporal computations, consisting of Spectral-based (LFBE and Cepstrum-based (MFCC feature vectors, are considered. To extract these features, we use posterior probability-based output of the proposed MTMLP neural networks. The combination of the temporal patterns, which represents the long-term dynamics of the speech signal, together with some traditional features, composed of the MFCC and its first and second derivatives are evaluated in an ASR task. It is shown that the use of such a combined feature vector results in the increase of the phoneme recognition accuracy by more than 1 percent regarding the results of the baseline system, which does not benefit from the long-term temporal patterns. In addition, it is shown that the use of extracted features by the proposed method gives robust recognition under different noise conditions (by 13 percent and, therefore, the proposed method is a robust feature extraction method.

  18. Chiral magnetic plasmons in anomalous relativistic matter

    CERN Document Server

    Gorbar, E V; Shovkovy, I A; Sukhachov, P O

    2016-01-01

    The chiral plasmon modes of relativistic matter in background magnetic and strain-induced pseudomagnetic fields are studied in detail using the consistent chiral kinetic theory. The results reveal a number of anomalous features of these chiral magnetic and pseudomagnetic plasmons that could be used to identify them in experiment. In a system with nonzero electric (chiral) chemical potential, the background magnetic (pseudomagnetic) fields not only modify the values of the plasmon frequencies in the long wavelength limit, but also affect the qualitative dependence on the wave-vector. Similar modifications can be also induced by the chiral shift parameter in Weyl materials. Interestingly, even in the absence of the chiral shift and external fields, the chiral chemical potential alone leads to a splitting of plasmon energies at linear order in the wave vector.

  19. Examination of anomalous self-experience

    DEFF Research Database (Denmark)

    Raballo, Andrea; Parnas, Josef

    2012-01-01

    -disorders [SDs]), has been shown to constitute a core feature of both clinically overt and latent (schizotaxic) spectrum phenotypes. However, a major limitation for the translational implementation of this research evidence has been a lack of assessment tools capable of encompassing the clinical richness of SDs....... Here, we present the initial normative data and psychometric properties of a newly developed instrument (Examination of Anomalous Self-experience [EASE]), specifically designed to support the psychopathological exploration of SDs in both research and "real world" clinical settings. Our results support...... the clinical validity of the EASE as a tool for assessing anomalies of self-awareness (SDs) and lend credit to the translational potential of a phenomenological exploration of the subjective experience of vulnerability to schizophrenia....

  20. Stable feature selection for clinical prediction: exploiting ICD tree structure using Tree-Lasso.

    Science.gov (United States)

    Kamkar, Iman; Gupta, Sunil Kumar; Phung, Dinh; Venkatesh, Svetha

    2015-02-01

    Modern healthcare is getting reshaped by growing Electronic Medical Records (EMR). Recently, these records have been shown of great value towards building clinical prediction models. In EMR data, patients' diseases and hospital interventions are captured through a set of diagnoses and procedures codes. These codes are usually represented in a tree form (e.g. ICD-10 tree) and the codes within a tree branch may be highly correlated. These codes can be used as features to build a prediction model and an appropriate feature selection can inform a clinician about important risk factors for a disease. Traditional feature selection methods (e.g. Information Gain, T-test, etc.) consider each variable independently and usually end up having a long feature list. Recently, Lasso and related l1-penalty based feature selection methods have become popular due to their joint feature selection property. However, Lasso is known to have problems of selecting one feature of many correlated features randomly. This hinders the clinicians to arrive at a stable feature set, which is crucial for clinical decision making process. In this paper, we solve this problem by using a recently proposed Tree-Lasso model. Since, the stability behavior of Tree-Lasso is not well understood, we study the stability behavior of Tree-Lasso and compare it with other feature selection methods. Using a synthetic and two real-world datasets (Cancer and Acute Myocardial Infarction), we show that Tree-Lasso based feature selection is significantly more stable than Lasso and comparable to other methods e.g. Information Gain, ReliefF and T-test. We further show that, using different types of classifiers such as logistic regression, naive Bayes, support vector machines, decision trees and Random Forest, the classification performance of Tree-Lasso is comparable to Lasso and better than other methods. Our result has implications in identifying stable risk factors for many healthcare problems and therefore can

  1. Structural features of sugars that trigger or support conidial germination in the filamentous fungus Aspergillus niger.

    Science.gov (United States)

    Hayer, Kimran; Stratford, Malcolm; Archer, David B

    2013-11-01

    The asexual spores (conidia) of Aspergillus niger germinate to produce hyphae under appropriate conditions. Germination is initiated by conidial swelling and mobilization of internal carbon and energy stores, followed by polarization and emergence of a hyphal germ tube. The effects of different pyranose sugars, all analogues of d-glucose, on the germination of A. niger conidia were explored, and we define germination as the transition from a dormant conidium into a germling. Within germination, we distinguish two distinct stages, the initial swelling of the conidium and subsequent polarized growth. The stage of conidial swelling requires a germination trigger, which we define as a compound that is sensed by the conidium and which leads to catabolism of d-trehalose and isotropic growth. Sugars that triggered germination and outgrowth included d-glucose, d-mannose, and d-xylose. Sugars that triggered germination but did not support subsequent outgrowth included d-tagatose, d-lyxose, and 2-deoxy-d-glucose. Nontriggering sugars included d-galactose, l-glucose, and d-arabinose. Certain nontriggering sugars, including d-galactose, supported outgrowth if added in the presence of a complementary triggering sugar. This division of functions indicates that sugars are involved in two separate events in germination, triggering and subsequent outgrowth, and the structural features of sugars that support each, both, or none of these events are discussed. We also present data on the uptake of sugars during the germination process and discuss possible mechanisms of triggering in the absence of apparent sugar uptake during the initial swelling of conidia.

  2. Structural Features and Molecular Evolution of Bowman-Birk Protease Inhibitors and Their Potential Application

    Institute of Scientific and Technical Information of China (English)

    Rui-Feng QI; Zhan-Wu SONG; Cheng-Wu CHI

    2005-01-01

    The Bowman-Birk inhibitors (BBIs) are well-studied serine protease inhibitors that are abundant in dicotyledonous and monocotyledonous plants. BBIs from dicots usually have a molecular weight of 8k and are double-headed with two reactive sites, whereas those from monocots can be divided into two classes, one approximately 8 kDa in size with one reactive site (another reactive site was lost) and the other approximately 16 kDa in size with two reactive sites. The reactive site is located at unique exposed surfaces formed by a disulfide-linked β-sheet loop that is highly conserved, rigid and mostly composed of nine residues. The structural features and molecular evolution of inhibitors are described, focusing on the conserved disulfide bridges. The sunflower trypsin inhibitor-1 (SFTI-1), with 14 amino acid residues, is a recently discovered bicyclic inhibitor, and is the most small and potent naturally occurring Bowman-Birk inhibitor.Recently, BBIs have become a hot topic because of their potential applications. BBIs are now used for defense against pathogens and insects in transgenic plants, which has advantages over using toxic and polluting insecticides. BBIs could also be applied in the prevention of cancer, Dengue fever, and inflammatory and allergic disorders, because of their inhibitory activity with respect to the serine proteases that play a pivotal role in the development and pathogenesis of these diseases. The canonical nine-residue loop of BBIs/STFI-1 provides an ideal template for drug design of specific inhibitors to target their respective proteases.

  3. Structural features of cross-bridges in isometrically contracting skeletal muscle.

    Science.gov (United States)

    Kraft, Theresia; Mattei, Thomas; Radocaj, Ante; Piep, Birgit; Nocula, Christoph; Furch, Markus; Brenner, Bernhard

    2002-05-01

    Two-dimensional x-ray diffraction was used to investigate structural features of cross-bridges that generate force in isometrically contracting skeletal muscle. Diffraction patterns were recorded from arrays of single, chemically skinned rabbit psoas muscle fibers during isometric force generation, under relaxation, and in rigor. In isometric contraction, a rather prominent intensification of the actin layer lines at 5.9 and 5.1 nm and of the first actin layer line at 37 nm was found compared with those under relaxing conditions. Surprisingly, during isometric contraction, the intensity profile of the 5.9-nm actin layer line was shifted toward the meridian, but the resulting intensity profile was different from that observed in rigor. We particularly addressed the question whether the differences seen between rigor and active contraction might be due to a rigor-like configuration of both myosin heads in the absence of nucleotide (rigor), whereas during active contraction only one head of each myosin molecule is in a rigor-like configuration and the second head is weakly bound. To investigate this question, we created different mixtures of weak binding myosin heads and rigor-like actomyosin complexes by titrating MgATPgammaS at saturating [Ca2+] into arrays of single muscle fibers. The resulting diffraction patterns were different in several respects from patterns recorded under isometric contraction, particularly in the intensity distribution along the 5.9-nm actin layer line. This result indicates that cross-bridges present during isometric force generation are not simply a mixture of weakly bound and single-headed rigor-like complexes but are rather distinctly different from the rigor-like cross-bridge. Experiments with myosin-S1 and truncated S1 (motor domain) support the idea that for a force generating cross-bridge, disorder due to elastic distortion might involve a larger part of the myosin head than for a nucleotide free, rigor cross-bridge.

  4. Observations of Anomalous Refraction with Co-housed Telescopes

    Science.gov (United States)

    Taylor, Malinda S.; McGraw, J. T.; Zimmer, P. C.

    2013-01-01

    Anomalous refraction is described as a low frequency, large angular scale motion of the entire image plane with respect to the celestial coordinate system as observed and defined by previous astrometric catalogs. These motions of typically several tenths of an arcsecond with timescales on the order of ten minutes are ubiquitous to drift-scan ground-based astrometric measurements regardless of location or telescopes used and have been attributed to meter scale slowly evolving coherent dynamical structures in the boundary-layer below 60 meters. The localized nature of the effect and general inconsistency of the motions seen by even closely spaced telescopes in individual domes has led to the hypothesis that the dome or other type of telescope housing may be responsible. This hypothesis is tested by observing anomalous refraction using two telescopes housed in a single roll-off roof observatory building with the expected outcome that the two telescopes will see correlated anomalous refraction induced motions.

  5. A variable-order fractal derivative model for anomalous diffusion

    Directory of Open Access Journals (Sweden)

    Liu Xiaoting

    2017-01-01

    Full Text Available This paper pays attention to develop a variable-order fractal derivative model for anomalous diffusion. Previous investigations have indicated that the medium structure, fractal dimension or porosity may change with time or space during solute transport processes, results in time or spatial dependent anomalous diffusion phenomena. Hereby, this study makes an attempt to introduce a variable-order fractal derivative diffusion model, in which the index of fractal derivative depends on temporal moment or spatial position, to characterize the above mentioned anomalous diffusion (or transport processes. Compared with other models, the main advantages in description and the physical explanation of new model are explored by numerical simulation. Further discussions on the dissimilitude such as computational efficiency, diffusion behavior and heavy tail phenomena of the new model and variable-order fractional derivative model are also offered.

  6. Anomalous N-glycan structures with an internal fucose branched to GlcA and GlcN residues isolated from a mollusk shell-forming fluid.

    Science.gov (United States)

    Zhou, Hui; Hanneman, Andrew J; Chasteen, N Dennis; Reinhold, Vernon N

    2013-10-01

    This report describes the structural details of a unique N-linked valence epitope on the major protein within the extrapallial (EP) fluid of the mollusk, Mytilus edulis. Fluids from this area are considered to be responsible for shell expansion by a self-assembly process that provides an organic framework for the growth of CaCO3 crystals. Previous reports from our laboratories have described the purification and amino acid sequence of this EP protein, which was found to be a glycoprotein (EPG) of approximately 28 KDa with 14.3% carbohydrate on a single N-linked consensus site. Described herein is the de novo sequence of the major glycan and its glycomers. The sequence was determined by ion trap sequential mass spectrometry (ITMS(n)) resolving structure by tracking precursor-product relationships through successive rounds of collision induced disassociation (CID), thereby spatially resolving linkage and branching details within the confines of the ion trap. Three major glycomers were detected, each possessing a 6-linked fucosylated N-linked core. Two glycans possessed four and five identical antennae, while the third possessed four antennas, but with an additional methylfucose 2-linked to the glucuronic acid moiety, forming a pentasaccharide. The tetrasaccharide structure was: 4-O-methyl-GlcA(1-4)[GlcNAc(1-3)]Fuc(1-4)GlcNAc, while the pentasaccharide was shown to be as follows: mono-O-methyl-Fuc(1-2)-4-O-methyl-GlcA(1-4)[GlcNAc(1-3)]Fuc(1-4)GlcNAc. Samples were differentially deuteriomethylated (CD3/CH3) to localize indigenous methylation, further analyzed by high resolution mass spectrometry (HRMS) to confirm monomer compositions, and finally gas chromatography mass spectrometry (GC-MS) to assign structural and stereoisomers. The interfacial shell surface location of this major extrapallial glycoprotein, its calcium and heavy metal binding properties and unique structure suggests a probable role in shell formation and possibly metal ion detoxification. A closely

  7. Isolation, structural features and antitumor activities of sixpolysaccharides from Angelica sinensis (Oliv.) diels in vitro

    Institute of Scientific and Technical Information of China (English)

    WeiCAO; Xiao-qiangLI; Tie-hongYANG; Hui-tingFAN; Qi-bingMEI

    2005-01-01

    AIM The previous work has demonstrated that the polysaccharides of Angelica sinensis (Oliv.) Diels have significantly antitumor activity and indicated that the activity is strongly dependent on their structures. However, the relationships between the structure and the activities are still ambiguous. Thus, at present, more efforts are being expended in seeking to isolate the polysaccharides from Angelica sinensis(Oliv.) Diels, measure their structural features and antitumor activities, and elucidate structure - activity relationships of polysaccharides. METHODS The roots of Angelica sinensis ( Oliv. ) Diels were extracted With water, separated by Sephacryl S-400 and DEAE-sephadex A-25 columns and further purifled on Sephadex G-100 column.

  8. DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale

    Science.gov (United States)

    Zhou, Tianyin; Yang, Lin; Lu, Yan; Dror, Iris; Dantas Machado, Ana Carolina; Ghane, Tahereh; Di Felice, Rosa; Rohs, Remo

    2013-01-01

    We present a method and web server for predicting DNA structural features in a high-throughput (HT) manner for massive sequence data. This approach provides the framework for the integration of DNA sequence and shape analyses in genome-wide studies. The HT methodology uses a sliding-window approach to mine DNA structural information obtained from Monte Carlo simulations. It requires only nucleotide sequence as input and instantly predicts multiple structural features of DNA (minor groove width, roll, propeller twist and helix twist). The results of rigorous validations of the HT predictions based on DNA structures solved by X-ray crystallography and NMR spectroscopy, hydroxyl radical cleavage data, statistical analysis and cross-validation, and molecular dynamics simulations provide strong confidence in this approach. The DNAshape web server is freely available at http://rohslab.cmb.usc.edu/DNAshape/. PMID:23703209

  9. Visual Odometry Based on Structural Matching of Local Invariant Features Using Stereo Camera Sensor

    Directory of Open Access Journals (Sweden)

    Antonio Bandera

    2011-07-01

    Full Text Available This paper describes a novel sensor system to estimate the motion of a stereo camera. Local invariant image features are matched between pairs of frames and linked into image trajectories at video rate, providing the so-called visual odometry, i.e., motion estimates from visual input alone. Our proposal conducts two matching sessions: the first one between sets of features associated to the images of the stereo pairs and the second one between sets of features associated to consecutive frames. With respect to previously proposed approaches, the main novelty of this proposal is that both matching algorithms are conducted by means of a fast matching algorithm which combines absolute and relative feature constraints. Finding the largest-valued set of mutually consistent matches is equivalent to finding the maximum-weighted clique on a graph. The stereo matching allows to represent the scene view as a graph which emerge from the features of the accepted clique. On the other hand, the frame-to-frame matching defines a graph whose vertices are features in 3D space. The efficiency of the approach is increased by minimizing the geometric and algebraic errors to estimate the final displacement of the stereo camera between consecutive acquired frames. The proposed approach has been tested for mobile robotics navigation purposes in real environments and using different features. Experimental results demonstrate the performance of the proposal, which could be applied in both industrial and service robot fields.

  10. Visual odometry based on structural matching of local invariant features using stereo camera sensor.

    Science.gov (United States)

    Núñez, Pedro; Vázquez-Martín, Ricardo; Bandera, Antonio

    2011-01-01

    This paper describes a novel sensor system to estimate the motion of a stereo camera. Local invariant image features are matched between pairs of frames and linked into image trajectories at video rate, providing the so-called visual odometry, i.e., motion estimates from visual input alone. Our proposal conducts two matching sessions: the first one between sets of features associated to the images of the stereo pairs and the second one between sets of features associated to consecutive frames. With respect to previously proposed approaches, the main novelty of this proposal is that both matching algorithms are conducted by means of a fast matching algorithm which combines absolute and relative feature constraints. Finding the largest-valued set of mutually consistent matches is equivalent to finding the maximum-weighted clique on a graph. The stereo matching allows to represent the scene view as a graph which emerge from the features of the accepted clique. On the other hand, the frame-to-frame matching defines a graph whose vertices are features in 3D space. The efficiency of the approach is increased by minimizing the geometric and algebraic errors to estimate the final displacement of the stereo camera between consecutive acquired frames. The proposed approach has been tested for mobile robotics navigation purposes in real environments and using different features. Experimental results demonstrate the performance of the proposal, which could be applied in both industrial and service robot fields.

  11. First Numerical Simulations of Anomalous Hydrodynamics

    CERN Document Server

    Hongo, Masaru; Hirano, Tetsufumi

    2013-01-01

    Anomalous hydrodynamics is a low-energy effective theory that captures effects of quantum anomalies. We develop a numerical code of anomalous hydrodynamics and apply it to dynamics of heavy-ion collisions, where anomalous transports are expected to occur. This is the first attempt to perform fully non-linear numerical simulations of anomalous hydrodynamics. We discuss implications of the simulations for possible experimental observations of anomalous transport effects. From analyses of the charge-dependent elliptic flow parameters ($v_2^\\pm$) as a function of the net charge asymmetry $A_\\pm$, we quantitatively verify that the linear dependence of $\\Delta v_2 \\equiv v_2^- - v_2^+$ on the net charge asymmetry $A_\\pm$ cannot be regarded as a sensitive signal of anomalous transports, contrary to previous studies. We, however, find that the intercept $\\Delta v_2(A_\\pm=0)$ is sensitive to anomalous transport effects.

  12. Anomalous Thermalization in Ergodic Systems

    Science.gov (United States)

    Luitz, David J.; Bar Lev, Yevgeny

    2016-10-01

    It is commonly believed that quantum isolated systems satisfying the eigenstate thermalization hypothesis (ETH) are diffusive. We show that this assumption is too restrictive since there are systems that are asymptotically in a thermal state yet exhibit anomalous, subdiffusive thermalization. We show that such systems satisfy a modified version of the ETH ansatz and derive a general connection between the scaling of the variance of the off-diagonal matrix elements of local operators, written in the eigenbasis of the Hamiltonian, and the dynamical exponent. We find that for subdiffusively thermalizing systems the variance scales more slowly with system size than expected for diffusive systems. We corroborate our findings by numerically studying the distribution of the coefficients of the eigenfunctions and the off-diagonal matrix elements of local operators of the random field Heisenberg chain, which has anomalous transport in its thermal phase. Surprisingly, this system also has non-Gaussian distributions of the eigenfunctions, thus, directly violating Berry's conjecture.

  13. Faraday anomalous dispersion optical tuners

    Science.gov (United States)

    Wanninger, P.; Valdez, E. C.; Shay, T. M.

    1992-01-01

    Common methods for frequency stabilizing diode lasers systems employ gratings, etalons, optical electric double feedback, atomic resonance, and a Faraday cell with low magnetic field. Our method, the Faraday Anomalous Dispersion Optical Transmitter (FADOT) laser locking, is much simpler than other schemes. The FADOT uses commercial laser diodes with no antireflection coatings, an atomic Faraday cell with a single polarizer, and an output coupler to form a compound cavity. This method is vibration insensitive, thermal expansion effects are minimal, and the system has a frequency pull in range of 443.2 GHz (9A). Our technique is based on the Faraday anomalous dispersion optical filter. This method has potential applications in optical communication, remote sensing, and pumping laser excited optical filters. We present the first theoretical model for the FADOT and compare the calculations to our experimental results.

  14. Minimal flavor violation and anomalous top decays

    Science.gov (United States)

    Faller, Sven; Mannel, Thomas; Gadatsch, Stefan

    2013-08-01

    Top-quark physics at the LHC may open a window to physics beyond the Standard Model and even lead us to an understanding of the phenomenon of “flavor.” However, current flavor data is a strong hint that no “new physics” with a generic flavor structure can be expected at the TeV scale. In turn, if there is “new physics” at the TeV scale, it must be “minimally flavor violating.” This has become a widely accepted assumption for “new physics” models. In this paper we propose a model-independent scheme to test minimal flavor violation for the anomalous charged Wtq, q∈{d,s,b} and flavor-changing Vtq, q∈{u,c} and V∈{Z,γ,g} couplings within an effective field theory framework, i.e., in a model-independent way. We perform a spurion analysis of our effective field theory approach and calculate the decay rates for the anomalous top-quark decays in terms of the effective couplings for different helicities by using a two-Higgs doublet model of type II, under the assumption that the top-quark is produced at a high-energy collision and decays as a quasi-free particle.

  15. Minimal Flavour Violation and Anomalous Top Decays

    CERN Document Server

    Faller, Sven; Mannel, Thomas

    2013-01-01

    Top quark physics at the LHC may open a window to physics beyond the standard model and even lead us to an understanding of the phenomenon "flavour". However, current flavour data is a strong hint that no "new physics" with a generic flavour structure can be expected in the TeV scale. In turn, if there is "new physics" at the TeV scale, it must be "minimally flavour violating". This has become a widely accepted assumption for "new physics" models. In this paper we propose a way to test the concept of minimal flavour violation for the anomalous charged $Wtq$, $q\\in\\{d,s,b\\}$, and flavour-changing $Vtq$, $q\\in\\{u,c\\}$ and $V\\in\\{Z,\\gamma,g\\}$, couplings within an effective field theory framework, i.e. in a model independent way. We perform a spurion analysis of our effective field theory approach and calculate the decay rates for the anomalous top-quark decays in terms of the effective couplings for different helicities by using a two-Higgs doublet model of type II (2HDM-II), under the assumption that the top-q...

  16. Anomalous Magnetic Excitations of Cooperative Tetrahedral Spin Clusters

    DEFF Research Database (Denmark)

    Prsa, K.; Rønnow, H.M.; Zaharko, O.;

    2009-01-01

    An inelastic neutron scattering study of Cu2Te2O5X2 (X=Cl, Br) shows strong dispersive modes with large energy gaps persisting far above T-N, notably in Cu2Te2O5Br2. The anomalous features: a coexisting unusually weak Goldstone-like mode observed in Cu2Te2O5Cl2 and the size of the energy gaps can...

  17. Structural features of piperazinyl-linked ciprofloxacin dimers required for activity against drug-resistant strains of Staphylococcus aureus.

    Science.gov (United States)

    Kerns, Robert J; Rybak, Michael J; Kaatz, Glenn W; Vaka, Flamur; Cha, Raymond; Grucz, Richard G; Diwadkar, Veena U

    2003-07-07

    We previously demonstrated that piperazinyl-linked fluoroquinolone dimers possess potent antibacterial activity against drug-resistant strains of Staphylococcus aureus. In this study, we report the preparation and evaluation of a series of incomplete dimers toward ascertaining structural features of piperazinyl-linked ciprofloxacin dimers that render these agents refractory to fluoroquinolone-resistance mechanisms in Staphylococcus aureus.

  18. Linguistic Features and Schematic Textual Structure in Look-Good Advertisements in the Indian Print Media in English

    Science.gov (United States)

    Singh, Sukhdev; Bedi, Navkiran Kaur

    2013-01-01

    Every text has a communicative purpose that it performs by dividing itself into generic stages. These stages are assigned specific goals and have differing linguistic structures. This paper makes an attempt to investigate whether there is a definable co-relation between linguistic features and stages in the genre of look-good advertisements. It…

  19. Analysis on anomalous degradation in silicon solar cell designed for space use

    Energy Technology Data Exchange (ETDEWEB)

    Ohshima, Takeshi; Morita, Yousuke; Nashiyama, Isamu [Japan Atomic Energy Research Inst., Takasaki, Gunma (Japan). Takasaki Radiation Chemistry Research Establishment; Kawasaki, Osamu; Hisamatsu, Tadashi; Yamamoto, Yasunari; Matsuda, Sumio; Nakao, Tetsuya; Wakow, Yoshihito

    1997-03-01

    Recently, we have found the anomalous degradation of electrical performance in silicon solar cells irradiated with charged particles in a high-fluence region. This anomalous phenomenon has two typical features, which are sudden-drop-down of electrical performances in a high-fluence region and slight recovery of the short circuit current I{sub SC} just before the sudden-drop-down. These features cannot be understood by a conventional model coming from the decrease of minority-carriers life-time. We introduce this anomalous degradation of the electrical performance in Si solar cells irradiated with electrons or protons. We also report the result of simulation for the fluence dependence of the I{sub SC}, and discuss the mechanism of this anomalous phenomenon. (author)

  20. Faraday anomalous dispersion optical filters

    Science.gov (United States)

    Shay, T. M.; Yin, B.; Alvarez, L. S.

    1993-01-01

    The effect of Faraday anomalous dispersion optical filters on infrared and blue transitions of some alkali atoms is calculated. A composite system is designed to further increase the background noise rejection. The measured results of the solar background rejection and image quality through the filter are presented. The results show that the filter may provide high transmission and high background noise rejection with excellent image quality.

  1. Anomalously Weak Solar Convection

    Science.gov (United States)

    Hanasoge, Shravan M.; Duvall, Thomas L.; Sreenivasan, Katepalli R.

    2012-01-01

    Convection in the solar interior is thought to comprise structures on a spectrum of scales. This conclusion emerges from phenomenological studies and numerical simulations, though neither covers the proper range of dynamical parameters of solar convection. Here, we analyze observations of the wavefield in the solar photosphere using techniques of time-distance helioseismology to image flows in the solar interior. We downsample and synthesize 900 billion wavefield observations to produce 3 billion cross-correlations, which we average and fit, measuring 5 million wave travel times. Using these travel times, we deduce the underlying flow systems and study their statistics to bound convective velocity magnitudes in the solar interior, as a function of depth and spherical- harmonic degree l..Within the wavenumber band l convective velocities are 20-100 times weaker than current theoretical estimates. This constraint suggests the prevalence of a different paradigm of turbulence from that predicted by existing models, prompting the question: what mechanism transports the heat flux of a solar luminosity outwards? Advection is dominated by Coriolis forces for wavenumbers l convection may be quasi-geostrophic. The fact that isorotation contours in the Sun are not coaligned with the axis of rotation suggests the presence of a latitudinal entropy gradient.

  2. Does my face FIT?: a face image task reveals structure and distortions of facial feature representation.

    Directory of Open Access Journals (Sweden)

    Christina T Fuentes

    Full Text Available Despite extensive research on face perception, few studies have investigated individuals' knowledge about the physical features of their own face. In this study, 50 participants indicated the location of key features of their own face, relative to an anchor point corresponding to the tip of the nose, and the results were compared to the true location of the same individual's features from a standardised photograph. Horizontal and vertical errors were analysed separately. An overall bias to underestimate vertical distances revealed a distorted face representation, with reduced face height. Factor analyses were used to identify separable subconfigurations of facial features with correlated localisation errors. Independent representations of upper and lower facial features emerged from the data pattern. The major source of variation across individuals was in representation of face shape, with a spectrum from tall/thin to short/wide representation. Visual identification of one's own face is excellent, and facial features are routinely used for establishing personal identity. However, our results show that spatial knowledge of one's own face is remarkably poor, suggesting that face representation may not contribute strongly to self-awareness.

  3. A spectral-structural bag-of-features scene classifier for very high spatial resolution remote sensing imagery

    Science.gov (United States)

    Zhao, Bei; Zhong, Yanfei; Zhang, Liangpei

    2016-06-01

    Land-use classification of very high spatial resolution remote sensing (VHSR) imagery is one of the most challenging tasks in the field of remote sensing image processing. However, the land-use classification is hard to be addressed by the land-cover classification techniques, due to the complexity of the land-use scenes. Scene classification is considered to be one of the expected ways to address the land-use classification issue. The commonly used scene classification methods of VHSR imagery are all derived from the computer vision community that mainly deal with terrestrial image recognition. Differing from terrestrial images, VHSR images are taken by looking down with airborne and spaceborne sensors, which leads to the distinct light conditions and spatial configuration of land cover in VHSR imagery. Considering the distinct characteristics, two questions should be answered: (1) Which type or combination of information is suitable for the VHSR imagery scene classification? (2) Which scene classification algorithm is best for VHSR imagery? In this paper, an efficient spectral-structural bag-of-features scene classifier (SSBFC) is proposed to combine the spectral and structural information of VHSR imagery. SSBFC utilizes the first- and second-order statistics (the mean and standard deviation values, MeanStd) as the statistical spectral descriptor for the spectral information of the VHSR imagery, and uses dense scale-invariant feature transform (SIFT) as the structural feature descriptor. From the experimental results, the spectral information works better than the structural information, while the combination of the spectral and structural information is better than any single type of information. Taking the characteristic of the spatial configuration into consideration, SSBFC uses the whole image scene as the scope of the pooling operator, instead of the scope generated by a spatial pyramid (SP) commonly used in terrestrial image classification. The experimental

  4. Distill: a suite of web servers for the prediction of one-, two- and three-dimensional structural features of proteins

    Directory of Open Access Journals (Sweden)

    Walsh Ian

    2006-09-01

    Full Text Available Abstract Background We describe Distill, a suite of servers for the prediction of protein structural features: secondary structure; relative solvent accessibility; contact density; backbone structural motifs; residue contact maps at 6, 8 and 12 Angstrom; coarse protein topology. The servers are based on large-scale ensembles of recursive neural networks and trained on large, up-to-date, non-redundant subsets of the Protein Data Bank. Together with structural feature predictions, Distill includes a server for prediction of Cα traces for short proteins (up to 200 amino acids. Results The servers are state-of-the-art, with secondary structure predicted correctly for nearly 80% of residues (currently the top performance on EVA, 2-class solvent accessibility nearly 80% correct, and contact maps exceeding 50% precision on the top non-diagonal contacts. A preliminary implementation of the predictor of protein Cα traces featured among the top 20 Novel Fold predictors at the last CASP6 experiment as group Distill (ID 0348. The majority of the servers, including the Cα trace predictor, now take into account homology information from the PDB, when available, resulting in greatly improved reliability. Conclusion All predictions are freely available through a simple joint web interface and the results are returned by email. In a single submission the user can send protein sequences for a total of up to 32k residues to all or a selection of the servers. Distill is accessible at the address: http://distill.ucd.ie/distill/.

  5. The evaluation of multi-structure, multi-atlas pelvic anatomy features in a prostate MR lymphography CAD system

    Science.gov (United States)

    Meijs, M.; Debats, O.; Huisman, H.

    2015-03-01

    In prostate cancer, the detection of metastatic lymph nodes indicates progression from localized disease to metastasized cancer. The detection of positive lymph nodes is, however, a complex and time consuming task for experienced radiologists. Assistance of a two-stage Computer-Aided Detection (CAD) system in MR Lymphography (MRL) is not yet feasible due to the large number of false positives in the first stage of the system. By introducing a multi-structure, multi-atlas segmentation, using an affine transformation followed by a B-spline transformation for registration, the organ location is given by a mean density probability map. The atlas segmentation is semi-automatically drawn with ITK-SNAP, using Active Contour Segmentation. Each anatomic structure is identified by a label number. Registration is performed using Elastix, using Mutual Information and an Adaptive Stochastic Gradient optimization. The dataset consists of the MRL scans of ten patients, with lymph nodes manually annotated in consensus by two expert readers. The feature map of the CAD system consists of the Multi-Atlas and various other features (e.g. Normalized Intensity and multi-scale Blobness). The voxel-based Gentleboost classifier is evaluated using ROC analysis with cross validation. We show in a set of 10 studies that adding multi-structure, multi-atlas anatomical structure likelihood features improves the quality of the lymph node voxel likelihood map. Multiple structure anatomy maps may thus make MRL CAD more feasible.

  6. Structural and phylogenetic analysis of Rhodobacter capsulatus NifF: uncovering general features of nitrogen-fixation (nif)-flavodoxins.

    Science.gov (United States)

    Pérez-Dorado, Inmaculada; Bortolotti, Ana; Cortez, Néstor; Hermoso, Juan A

    2013-01-09

    Analysis of the crystal structure of NifF from Rhodobacter capsulatus and its homologues reported so far reflects the existence of unique structural features in nif flavodoxins: a leucine at the re face of the isoalloxazine, an eight-residue insertion at the C-terminus of the 50's loop and a remarkable difference in the electrostatic potential surface with respect to non-nif flavodoxins. A phylogenetic study on 64 sequences from 52 bacterial species revealed four clusters, including different functional prototypes, correlating the previously defined as "short-chain" with the firmicutes flavodoxins and the "long-chain" with gram-negative species. The comparison of Rhodobacter NifF structure with other bacterial flavodoxin prototypes discloses the concurrence of specific features of these functional electron donors to nitrogenase.

  7. Structural and Phylogenetic Analysis of Rhodobacter capsulatus NifF: Uncovering General Features of Nitrogen-fixation (nif-Flavodoxins

    Directory of Open Access Journals (Sweden)

    Inmaculada Pérez-Dorado

    2013-01-01

    Full Text Available Analysis of the crystal structure of NifF from Rhodobacter capsulatus and its homologues reported so far reflects the existence of unique structural features in nif flavodoxins: a leucine at the re face of the isoalloxazine, an eight-residue insertion at the C-terminus of the 50’s loop and a remarkable difference in the electrostatic potential surface with respect to non-nif flavodoxins. A phylogenetic study on 64 sequences from 52 bacterial species revealed four clusters, including different functional prototypes, correlating the previously defined as “short-chain” with the firmicutes flavodoxins and the “long-chain” with gram-negative species. The comparison of Rhodobacter NifF structure with other bacterial flavodoxin prototypes discloses the concurrence of specific features of these functional electron donors to nitrogenase.

  8. Structural coherence and temporal stability of psychopathic personality features during emerging adulthood.

    Science.gov (United States)

    Hawes, Samuel W; Mulvey, Edward P; Schubert, Carol A; Pardini, Dustin A

    2014-08-01

    Psychopathy is a complex personality disorder characterized by affective, interpersonal, and behavioral dimensions. Although features of psychopathy have been extended downwardly to earlier developmental periods, there is a discerning lack of studies that have focused on critically important issues such as longitudinal invariance and stability/change in these features across time. The current study examines these issues using a large sample of male adolescent offenders (N = 1,170) assessed across 7 annual time points during the transition into emerging adulthood (ages ∼17 to 24 years). Findings demonstrated that features of psychopathy remained longitudinally invariant across this developmental period, and showed temporally consistent and theoretically coherent associations with other measures of personality, psychopathology, and criminal behaviors. Results also demonstrated that mean levels of psychopathic personality features tended to decrease into emerging adulthood and showed relatively modest rank-order stability across assessments with 7-year lags. These findings suggest that reductions in maladaptive personality features seem to parallel the well-documented decreases in offending that occur during the early 20s.

  9. Control-group feature normalization for multivariate pattern analysis of structural MRI data using the support vector machine.

    Science.gov (United States)

    Linn, Kristin A; Gaonkar, Bilwaj; Satterthwaite, Theodore D; Doshi, Jimit; Davatzikos, Christos; Shinohara, Russell T

    2016-05-15

    Normalization of feature vector values is a common practice in machine learning. Generally, each feature value is standardized to the unit hypercube or by normalizing to zero mean and unit variance. Classification decisions based on support vector machines (SVMs) or by other methods are sensitive to the specific normalization used on the features. In the context of multivariate pattern analysis using neuroimaging data, standardization effectively up- and down-weights features based on their individual variability. Since the standard approach uses the entire data set to guide the normalization, it utilizes the total variability of these features. This total variation is inevitably dependent on the amount of marginal separation between groups. Thus, such a normalization may attenuate the separability of the data in high dimensional space. In this work we propose an alternate approach that uses an estimate of the control-group standard deviation to normalize features before training. We study our proposed approach in the context of group classification using structural MRI data. We show that control-based normalization leads to better reproducibility of estimated multivariate disease patterns and improves the classifier performance in many cases.

  10. Understanding Legacy Features with Featureous

    DEFF Research Database (Denmark)

    Olszak, Andrzej; Jørgensen, Bo Nørregaard

    2011-01-01

    Feature-centric comprehension of source code is essential during software evolution. However, such comprehension is oftentimes difficult to achieve due the discrepancies between structural and functional units of object-oriented programs. We present a tool for feature-centric analysis of legacy...

  11. A highly accurate protein structural class prediction approach using auto cross covariance transformation and recursive feature elimination.

    Science.gov (United States)

    Li, Xiaowei; Liu, Taigang; Tao, Peiying; Wang, Chunhua; Chen, Lanming

    2015-12-01

    Structural class characterizes the overall folding type of a protein or its domain. Many methods have been proposed to improve the prediction accuracy of protein structural class in recent years, but it is still a challenge for the low-similarity sequences. In this study, we introduce a feature extraction technique based on auto cross covariance (ACC) transformation of position-specific score matrix (PSSM) to represent a protein sequence. Then support vector machine-recursive feature elimination (SVM-RFE) is adopted to select top K features according to their importance and these features are input to a support vector machine (SVM) to conduct the prediction. Performance evaluation of the proposed method is performed using the jackknife test on three low-similarity datasets, i.e., D640, 1189 and 25PDB. By means of this method, the overall accuracies of 97.2%, 96.2%, and 93.3% are achieved on these three datasets, which are higher than those of most existing methods. This suggests that the proposed method could serve as a very cost-effective tool for predicting protein structural class especially for low-similarity datasets.

  12. Mammographic density and structural features can individually and jointly contribute to breast cancer risk assessment in mammography screening

    DEFF Research Database (Denmark)

    Winkel, Rikke Rass; von Euler-Chelpin, My; Nielsen, Mads;

    2016-01-01

    BACKGROUND: Mammographic density is a well-established risk factor for breast cancer. We investigated the association between three different methods of measuring density or parenchymal pattern/texture on digitized film-based mammograms, and examined to what extent textural features independently......-RADS alone). CONCLUSION: Our findings suggest that the (relative) amount of fibroglandular tissue (density) and mammographic structural features (texture/parenchymal pattern) jointly can improve risk segregation of screening women, using information already available from normal screening routine, in respect...... to future personalized screening strategies....

  13. Hydrothermal breccia pipe structures: general features and genetic criteria - II Phreatic breccia

    Directory of Open Access Journals (Sweden)

    Călin G. Tămas

    2003-04-01

    Full Text Available Phreatic and phreatomagmatic breccias are the two end-member styles of hydromagmatic breccias. A previous contribution deals with phreatomagmatic breccias with an emphasis on their general features and those genetic criteria that allow an accurate and rapid recognition. Phreatic breccias are presented here. Their general features, i.e. environment/ depth of formation, general form/geometry, dimensions, contacts with the host rocks, fragments, matrix, alteration, mineralization, surface connection, fluidization and facies changes were examined. Furthermore, genetic criteria, very useful in phreatic breccia recognition are summarized.

  14. Denoising of multiscale/multiresolution structural feature dictionaries for rapid training of a brain computer interface.

    Science.gov (United States)

    Ince, Nuri Firat; Tadipatri, Vijay Aditya; Göksu, Fikri; Tewfik, Ahmed H

    2009-01-01

    Multichannel neural activities such as EEG or ECoG in a brain computer interface can be classified with subset selection algorithms running on large feature dictionaries describing subject specific features in spectral, temporal and spatial domain. While providing high accuracies in classification, the subset selection techniques are associated with long training times due to the large feature set constructed from multichannel neural recordings. In this paper we study a novel denoising technique for reducing the dimensionality of the feature space which decreases the computational complexity of the subset selection step radically without causing any degradation in the final classification accuracy. The denoising procedure was based on the comparison of the energy in a particular time segment and in a given scale/level to the energy of the raw data. By setting denoising threshold a priori the algorithm removes those nodes which fail to capture the energy in the raw data in a given scale. We provide experimental studies towards the classification of motor imagery related multichannel ECoG recordings for a brain computer interface. The denoising procedure was able to reach the same classification accuracy without denoising and a computational complexity around 5 times smaller. We also note that in some cases the denoised procedure performed better classification.

  15. Anomalous delta-type electric and magnetic two-nucleon interactions

    CERN Document Server

    Mandache, Nicolae Bogdan

    2009-01-01

    Anomalous delta-type interactions, of both electric and magnetic nature, are introduced between the overlapping peripheral structures of the nucleons, which may explain the spin-triplet deuteron state and the absence of other nucleon-nucleon bound states.

  16. Anomalous Abelian symmetry in the standard model

    Energy Technology Data Exchange (ETDEWEB)

    Ramond, P.

    1995-12-31

    The observed hierarchy of quark and lepton masses can be parametrized by nonrenormalizable operators with dimensions determined by an anomalous Abelian family symmetry, a gauge extension to the minimal supersymmetric standard model. Such an Abelian symmetry is generic to compactified superstring theories, with its anomalies compensated by the Green-Schwarz mechanism. If we assume these two symmetries to be the same, we find the electroweak mixing angle to be sin {sup 2}{theta}{sub {omega}} = 3/8 at the string scale, just by setting the ratio of the product of down quark to charged lepton masses equal to one at the string scale. This assumes no GUT structure. The generality of the result suggests a superstring origin for the standard model. We generalize our analysis to massive neutrinos, and mixings in the lepton sector.

  17. Structural features of various kinds of carbon fibers as determined by small-angle X-ray scattering

    Science.gov (United States)

    Li, Denghua; Lu, Chunxiang; Du, Sujun; Wu, Gangping; Yang, Yu; Wang, Lina

    2016-11-01

    The structural features of polyacrylonitrile and pitch-based carbon fibers were analyzed from a comprehensive point of view by X-ray measurements and related techniques. The results indicated that the undulating graphite ribbon with embedded microvoid was the main structural unit for graphitic fibers. The void's parameters for these fibers could be obtained directly by small-angle X-ray scattering following the classic method deduced based on the typical two-phase system (i.e., Porod's law, Guinier's law and Debye's law). The non-graphitic fibers, however, were composed of two-dimensional turbostratic crystallites in the aggregation of microfibril and thus had a quasi two-phase structure (microfibril, interfibrillar amorphous structure and microvoid embedded within the microfibril). The extended Debye or Beaucage model in this case should be applied in order to obtain the structural parameters. It also revealed that the quasi two-phase system would complete its transformation to two-phase system during high-temperature graphitization. Therefore, the degree of graphitization was speculated to be the essential indicator distinguishing graphitic fibers from non-graphitic ones and would be helpful in understanding the transformation of structural features during the graphitization of carbon fibers.

  18. Structural features of various kinds of carbon fibers as determined by small-angle X-ray scattering

    Energy Technology Data Exchange (ETDEWEB)

    Li, Denghua; Du, Sujun [Shanxi Transportation Research Institute, National and Local Joint Engineering Laboratory of Advanced Road Materials, Taiyuan (China); Lu, Chunxiang; Wu, Gangping; Yang, Yu; Wang, Lina [Chinese Academy of Sciences, National Engineering Laboratory for Carbon Fiber Technology, Institute of Coal Chemistry, Taiyuan (China)

    2016-11-15

    The structural features of polyacrylonitrile and pitch-based carbon fibers were analyzed from a comprehensive point of view by X-ray measurements and related techniques. The results indicated that the undulating graphite ribbon with embedded microvoid was the main structural unit for graphitic fibers. The void's parameters for these fibers could be obtained directly by small-angle X-ray scattering following the classic method deduced based on the typical two-phase system (i.e., Porod's law, Guinier's law and Debye's law). The non-graphitic fibers, however, were composed of two-dimensional turbostratic crystallites in the aggregation of microfibril and thus had a quasi two-phase structure (microfibril, interfibrillar amorphous structure and microvoid embedded within the microfibril). The extended Debye or Beaucage model in this case should be applied in order to obtain the structural parameters. It also revealed that the quasi two-phase system would complete its transformation to two-phase system during high-temperature graphitization. Therefore, the degree of graphitization was speculated to be the essential indicator distinguishing graphitic fibers from non-graphitic ones and would be helpful in understanding the transformation of structural features during the graphitization of carbon fibers. (orig.)

  19. Anomalous human behavior detection: an adaptive approach

    Science.gov (United States)

    van Leeuwen, Coen; Halma, Arvid; Schutte, Klamer

    2013-05-01

    Detection of anomalies (outliers or abnormal instances) is an important element in a range of applications such as fault, fraud, suspicious behavior detection and knowledge discovery. In this article we propose a new method for anomaly detection and performed tested its ability to detect anomalous behavior in videos from DARPA's Mind's Eye program, containing a variety of human activities. In this semi-unsupervised task a set of normal instances is provided for training, after which unknown abnormal behavior has to be detected in a test set. The features extracted from the video data have high dimensionality, are sparse and inhomogeneously distributed in the feature space making it a challenging task. Given these characteristics a distance-based method is preferred, but choosing a threshold to classify instances as (ab)normal is non-trivial. Our novel aproach, the Adaptive Outlier Distance (AOD) is able to detect outliers in these conditions based on local distance ratios. The underlying assumption is that the local maximum distance between labeled examples is a good indicator of the variation in that neighborhood, and therefore a local threshold will result in more robust outlier detection. We compare our method to existing state-of-art methods such as the Local Outlier Factor (LOF) and the Local Distance-based Outlier Factor (LDOF). The results of the experiments show that our novel approach improves the quality of the anomaly detection.

  20. Powder diffraction studies using anomalous dispersion

    Energy Technology Data Exchange (ETDEWEB)

    Cox, D.E. [Brookhaven National Lab., Upton, NY (United States); Wilkinson, A.P. [California Univ., Santa Barbara, CA (United States). Dept. of Materials

    1993-05-01

    With the increasing availability and accessibility of high resolution powder diffractometers at many synchrotron radiation sources throughout the world, there is rapidly-growing interest in the exploitation of anomalous dispersion techniques for structural studies of polycrystalline materials. In conjunction with the Rietveld profile method for structure refinement, such studies are especially useful for the determination of the site distributions of two or more atoms which are near neighbors in the periodic table, or atoms which are distributed among partially occupied sites. Additionally, it is possible to (1) determine the mean-square displacements associated with different kinds of atoms distributed over a single set of sites, (2) distinguish between different oxidation states and coordination geometries of a particular atom in a compound and (3) to determine f` for a wide range of atomic species as a function of energy in the vicinity of an absorption edge. Experimental methods for making anomalous dispersion measurements are described in some detail, including data collection strategies, data analysis and correlation problems, possible systematic errors, and the accuracy of the results. Recent work in the field is reviewed, including cation site-distribution studies (e.g. doped high {Tc} superconductors, ternary alloys, FeCo{sub 2}(PO{sub 4}){sub 3}, FeNi{sub 2}BO{sub 5}), oxidation-state contrast (e.g. YBa{sub 2}Cu{sub 3}O{sub 6+x}, Eu{sub 3}O{sub 4}, GaCl{sub 2}, Fe{sub 2}PO{sub 5}), and the effect of coordination geometry (e.g. Y{sub 3}Ga{sub 5}O{sub l2}).

  1. Powder diffraction studies using anomalous dispersion

    Energy Technology Data Exchange (ETDEWEB)

    Cox, D.E. (Brookhaven National Lab., Upton, NY (United States)); Wilkinson, A.P. (California Univ., Santa Barbara, CA (United States). Dept. of Materials)

    1993-01-01

    With the increasing availability and accessibility of high resolution powder diffractometers at many synchrotron radiation sources throughout the world, there is rapidly-growing interest in the exploitation of anomalous dispersion techniques for structural studies of polycrystalline materials. In conjunction with the Rietveld profile method for structure refinement, such studies are especially useful for the determination of the site distributions of two or more atoms which are near neighbors in the periodic table, or atoms which are distributed among partially occupied sites. Additionally, it is possible to (1) determine the mean-square displacements associated with different kinds of atoms distributed over a single set of sites, (2) distinguish between different oxidation states and coordination geometries of a particular atom in a compound and (3) to determine f' for a wide range of atomic species as a function of energy in the vicinity of an absorption edge. Experimental methods for making anomalous dispersion measurements are described in some detail, including data collection strategies, data analysis and correlation problems, possible systematic errors, and the accuracy of the results. Recent work in the field is reviewed, including cation site-distribution studies (e.g. doped high [Tc] superconductors, ternary alloys, FeCo[sub 2](PO[sub 4])[sub 3], FeNi[sub 2]BO[sub 5]), oxidation-state contrast (e.g. YBa[sub 2]Cu[sub 3]O[sub 6+x], Eu[sub 3]O[sub 4], GaCl[sub 2], Fe[sub 2]PO[sub 5]), and the effect of coordination geometry (e.g. Y[sub 3]Ga[sub 5]O[sub l2]).

  2. The Vertical Structure of Major Meteorological Features on Jupiter: The Great Red Spot and White Ovals BC and DE

    Science.gov (United States)

    Baines, Kevin H.; Carlson, Robert W.

    1999-01-01

    Multi-spectral imagery of Jupiter's Great Red Spot (GRS) and two White ovals acquired by the Galileo/NIMS are used to constrain the spatial variability of the vertical aerosol structure and the distribution of ammonia in and around these most-prominent anti-cyclonic features. All three features exhibit a high-altitude core spanning about 3/4 of their visual size when viewed with moderate absorption wavelengths, indicating a bulk elliptical, "wedding cake" shape in their overall three-dimensional cloud structure. A distinctive spiral pattern within the GRS core is seen in moderate methane and hydrogen absorption bandpasses. This pattern - which has been modelled to show a 2 km variation in cloudtop pressure within the GRS - is inconsistent with a different spiral-shaped pattern observed in ammonia-sensitive wavelengths, thus indicating spatial variability not only in the column abundance of ammonia within the GRS, but in its mixing ratio as well. White Ovals BC and DE were observed in February 1997, just a year before their unusual merger into a single feature. At the time of these observations, the centers of the two anti-cyclones were about 16 degrees apart, separated by a complex cyclonic feature which exhibited unusual spatial variability in its appearance in images acquired at ammonia-sensitive wavelengths. In particular, the northern half of this feature has the largest ammonia column abundance seen within the environs around the white ovals, indicating unusual variability in either cloud structure/altitude and/or ammonia humidity within the cyclone.

  3. THE GEOMORPHOLOGIC FEATURES OF INTRUSIVE MAGMATIC STRUCTURES FROM BÂRGĂU MOUNTAINS (EASTERN CARPATHIANS, ROMANIA)

    OpenAIRE

    Ioan Bâca

    2016-01-01

    Igneous intrusive structures from Bârgău Mountains belong to the group of central Neogene volcanic chain of the Eastern Carpathians of Romania. The evolution of the relief developed on these structures are three main stages: the stage of injection of structures (Pannonian), the stage of uncovering of igneous intrusive bodies from Oligo-Miocene sedimentary cover (Pliocene), and the stage of subaerial modeling of magmatic bodies (Pliocene-current).In those circumstances, the geodiversity of int...

  4. Anomalous Transport Foundations and Applications

    CERN Document Server

    Klages, Rainer; Sokolov, Igor M

    2008-01-01

    This multi-author reference work provides a unique introduction to the currently emerging, highly interdisciplinary field of those transport processes that cannot be described by using standard methods of statistical mechanics. It comprehensively summarizes topics ranging from mathematical foundations of anomalous dynamics to the most recent experiments in this field. In so doing, this monograph extracts and emphasizes common principles and methods from many different disciplines while providing up-to-date coverage of this new field of research, considering such diverse applications as plasma

  5. The Relationship between Syntactic Structure Analysis Features, Histological Grade and High-Risk HPV DNA in Cervical Intraepithelial Neoplasia

    Directory of Open Access Journals (Sweden)

    Arnold‐Jan Kruse

    2004-01-01

    Full Text Available Aim: To assess the correlation between syntactic structure analysis (SSA features, revised dysplasia grade and the presence of high‐risk human papillomavirus DNA in cervical intraepithelial neoplasia (CIN. Materials and methods: HPV polymerase chain reaction (PCR was assessed in 101 consecutive biopsies and consensus in CIN grade between the experts occurred in 88 cases (CIN1=16, CIN2=27, CIN3=45. SSA was performed in the diagnostic histological section of the CIN lesions in these patients and SSA features were compared with the blind review CIN grade, and presence/absence of high‐risk HPV DNA. Results: One of the SSA features (points from which the surrounding surfaces has 4 edges, PECO‐4 was significantly different between all three consensus CIN grades. Many more features revealed significant differences between CIN1 and CIN2 or between CIN2 and CIN3 cases. With stepwise discriminant analysis, the best multivariate combination of features to distinguish the different CIN grades were the Maximum MST Line Length (MML and the Area Disorder. Crude overall classification of the consensus grades with these features was 69%. The MML and the Area Disorder is also the best combination to distinguish cases with and without high‐risk HPV DNA (77% correct classifications. Conclusions: SSA features are correlated with both CIN grade and presence of high‐risk HPV DNA, but the discrimination power is not good enough to be used as a routine method for quality control of subjective grade or as a surrogate marker for high‐risk HPV DNA presence.

  6. Anomalous Hall effect in polycrystalline Ni films

    KAUST Repository

    Guo, Zaibing

    2012-02-01

    We systematically studied the anomalous Hall effect in a series of polycrystalline Ni films with thickness ranging from 4 to 200 nm. It is found that both the longitudinal and anomalous Hall resistivity increased greatly as film thickness decreased. This enhancement should be related to the surface scattering. In the ultrathin films (46 nm thick), weak localization corrections to anomalous Hall conductivity were studied. The granular model, taking into account the dominated intergranular tunneling, has been employed to explain this phenomenon, which can explain the weak dependence of anomalous Hall resistivity on longitudinal resistivity as well. © 2011 Elsevier Ltd. All rights reserved.

  7. Electromagnetic turbulent structures: A ubiquitous feature of the edge region of toroidal plasma configurations

    Energy Technology Data Exchange (ETDEWEB)

    Spolaore, M., E-mail: monica.spolaore@igi.cnr.it; Vianello, N.; Agostini, M.; Cavazzana, R.; De Masi, G.; Martines, E.; Momo, B.; Scaggion, A.; Scarin, P.; Spagnolo, S.; Spizzo, G.; Zuin, M. [Consorzio RFX (CNR, ENEA, INFN, Università di Padova, Acciaierie Venete SpA), Corso Stati Uniti 4, 35127 Padova (Italy); Furno, I.; Avino, F.; Fasoli, A.; Theiler, C. [Centre de Recherches en Physique des Plasmas (CRPP), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne (Switzerland); Carralero, D. [Laboratorio Nacional de Fusion, CIEMAT, Avda. Complutense, 40 28040 Madrid (Spain); Max Planck Institute for Plasma Physics, Boltzmannstr. 2, 85748 Garching (Germany); Alonso, J. A.; Hidalgo, C. [Laboratorio Nacional de Fusion, CIEMAT, Avda. Complutense, 40 28040 Madrid (Spain)

    2015-01-15

    Electromagnetic features of turbulent filaments, emerging from a turbulent plasma background, have been studied in four different magnetic configurations: the stellarator TJ-II, the Reversed Field Pinch RFX-mod, a device that can be operated also as a ohmic tokamak, and the Simple Magnetized Torus, TORPEX. By applying an analogous diagnostic concept in all cases, direct measurements of both field-aligned current density and vorticity were performed inside the filament. The inter-machine comparison reveals a clear dependence of the filament vorticity upon the local time-averaged E × B flow shear. Furthermore, a wide range of local beta was explored allowing concluding that this parameter plays a fundamental role in the appearance of filament electromagnetic features.

  8. Constraints on the lithospheric structure of Venus from mechanical models and tectonic surface features

    Science.gov (United States)

    Zuber, Maria T.

    1987-01-01

    The evidence for the extensional or compressional origins of some prominent Venusian surface features disclosed by radar images is discussed. Using simple models, the hypothesis that the observed length scales (10-20 km and 100-300 km) of deformations are controlled by dominant wavelengths arising from unstable compression or extension of the Venus lithosphere is tested. The results show that the existence of tectonic features that exhibit both length scales can be explained if, at the time of deformation, the lithosphere consisted of a crust that was relatively strong near the surface and weak at its base, and an upper mantle that was stronger than or nearly comparable in strength to the upper crust.

  9. Structural features of colloidal species in the human fasted upper small intestine

    DEFF Research Database (Denmark)

    Mullertz, Anette; Reppas, Christos; Psachoulias, Dimitrios;

    2015-01-01

    Objectives This paper aims to study the features of colloidal species in the lumen of the upper small intestine of two healthy adults at fasted state by means of electron microscopy. Methods Samples were aspirated from a location near the ligament of Treitz 30 min (volunteer no. 1, Aspirate30min...... with previously studied samples from the lower intestine in the fasted state. Micelles and unilamellar vesicles observed in both samples closely resemble morphological characteristics of those found in fluids simulating the colloidal species in fasted upper intestinal environment. Conclusions Features...... of colloidal species in contents of fasted small intestine have similarities with fluids simulating the contents in fasted upper small intestine and with contents of lower intestine in the fasted state....

  10. The crystal structure of phosphorylated MAPK13 reveals common structural features and differences in p38 MAPK family activation.

    Science.gov (United States)

    Yurtsever, Zeynep; Scheaffer, Suzanne M; Romero, Arthur G; Holtzman, Michael J; Brett, Tom J

    2015-04-01

    The p38 MAP kinases (p38 MAPKs) represent an important family centrally involved in mediating extracellular signaling. Recent studies indicate that family members such as MAPK13 (p38δ) display a selective cellular and tissue expression and are therefore involved in specific diseases. Detailed structural studies of all p38 MAPK family members are crucial for the design of specific inhibitors. In order to facilitate such ventures, the structure of MAPK13 was determined in both the inactive (unphosphorylated; MAPK13) and active (dual phosphorylated; MAPK13/pTpY) forms. Here, the first preparation, crystallization and structure determination of MAPK13/pTpY are presented and the structure is compared with the previously reported structure of MAPK13 in order to facilitate studies for structure-based drug design. A comprehensive analysis of inactive versus active structures for the p38 MAPK family is also presented. It is found that MAPK13 undergoes a larger interlobe configurational rearrangement upon activation compared with MAPK14. Surprisingly, the analysis of activated p38 MAPK structures (MAP12/pTpY, MAPK13/pTpY and MAPK14/pTpY) reveals that, despite a high degree of sequence similarity, different side chains are used to coordinate the phosphorylated residues. There are also differences in the rearrangement of the hinge region that occur in MAPK14 compared with MAPK13 which would affect inhibitor binding. A thorough examination of all of the active (phosphorylated) and inactive (unphosphorylated) p38 MAPK family member structures was performed to reveal a common structural basis of activation for the p38 MAP kinase family and to identify structural differences that may be exploited for developing family member-specific inhibitors.

  11. Systematic analysis of non-structural protein features for the prediction of PTM function potential by artificial neural networks

    Science.gov (United States)

    2017-01-01

    Post-translational modifications (PTMs) provide an extensible framework for regulation of protein behavior beyond the diversity represented within the genome alone. While the rate of identification of PTMs has rapidly increased in recent years, our knowledge of PTM functionality encompasses less than 5% of this data. We previously developed SAPH-ire (Structural Analysis of PTM Hotspots) for the prioritization of eukaryotic PTMs based on function potential of discrete modified alignment positions (MAPs) in a set of 8 protein families. A proteome-wide expansion of the dataset to all families of PTM-bearing, eukaryotic proteins with a representational crystal structure and the application of artificial neural network (ANN) models demonstrated the broader applicability of this approach. Although structural features of proteins have been repeatedly demonstrated to be predictive of PTM functionality, the availability of adequately resolved 3D structures in the Protein Data Bank (PDB) limits the scope of these methods. In order to bridge this gap and capture the larger set of PTM-bearing proteins without an available, homologous structure, we explored all available MAP features as ANN inputs to identify predictive models that do not rely on 3D protein structural data. This systematic, algorithmic approach explores 8 available input features in exhaustive combinations (247 models; size 2–8). To control for potential bias in random sampling for holdback in training sets, we iterated each model across 100 randomized, sample training and testing sets—yielding 24,700 individual ANNs. The size of the analyzed dataset and iterative generation of ANNs represents the largest and most thorough investigation of predictive models for PTM functionality to date. Comparison of input layer combinations allows us to quantify ANN performance with a high degree of confidence and subsequently select a top-ranked, robust fit model which highlights 3,687 MAPs, including 10,933 PTMs with a

  12. One-step synthesis of mesoporous pentasil zeolite with single-unit-cell lamellar structural features

    Science.gov (United States)

    Tsapstsis, Michael; Zhang, Xueyi

    2015-11-17

    A method for making a pentasil zeolite material includes forming an aqueous solution that includes a structure directing agent and a silica precursor; and heating the solution at a sufficient temperature and for sufficient time to form a pentasil zeolite material from the silica precursor, wherein the structure directing agent includes a quaternary phosphonium ion.

  13. Ellipsis as a Diagnostic Tool of Feature Strength and the Syntactic Structure of Ilocano

    Science.gov (United States)

    Anderson, Michael Don

    2009-01-01

    This dissertation examines Ilocano, an Austronesian Filipino language, within the Minimalist Framework, in an effort to tease apart the general syntactic properties of the language. I show that Ilocano underlying structure can easily be captured within the standard syntactic structures proposed for languages generally (Universal Grammar). In my…

  14. Cruciform structures are a common DNA feature important for regulating biological processes

    Directory of Open Access Journals (Sweden)

    Arrowsmith Cheryl

    2011-08-01

    Full Text Available Abstract DNA cruciforms play an important role in the regulation of natural processes involving DNA. These structures are formed by inverted repeats, and their stability is enhanced by DNA supercoiling. Cruciform structures are fundamentally important for a wide range of biological processes, including replication, regulation of gene expression, nucleosome structure and recombination. They also have been implicated in the evolution and development of diseases including cancer, Werner's syndrome and others. Cruciform structures are targets for many architectural and regulatory proteins, such as histones H1 and H5, topoisomerase IIβ, HMG proteins, HU, p53, the proto-oncogene protein DEK and others. A number of DNA-binding proteins, such as the HMGB-box family members, Rad54, BRCA1 protein, as well as PARP-1 polymerase, possess weak sequence specific DNA binding yet bind preferentially to cruciform structures. Some of these proteins are, in fact, capable of inducing the formation of cruciform structures upon DNA binding. In this article, we review the protein families that are involved in interacting with and regulating cruciform structures, including (a the junction-resolving enzymes, (b DNA repair proteins and transcription factors, (c proteins involved in replication and (d chromatin-associated proteins. The prevalence of cruciform structures and their roles in protein interactions, epigenetic regulation and the maintenance of cell homeostasis are also discussed.

  15. Structural insights into species-specific features of the ribosome from the pathogen Staphylococcus aureus.

    Science.gov (United States)

    Eyal, Zohar; Matzov, Donna; Krupkin, Miri; Wekselman, Itai; Paukner, Susanne; Zimmerman, Ella; Rozenberg, Haim; Bashan, Anat; Yonath, Ada

    2015-10-27

    The emergence of bacterial multidrug resistance to antibiotics threatens to cause regression to the preantibiotic era. Here we present the crystal structure of the large ribosomal subunit from Staphylococcus aureus, a versatile Gram-positive aggressive pathogen, and its complexes with the known antibiotics linezolid and telithromycin, as well as with a new, highly potent pleuromutilin derivative, BC-3205. These crystal structures shed light on specific structural motifs of the S. aureus ribosome and the binding modes of the aforementioned antibiotics. Moreover, by analyzing the ribosome structure and comparing it with those of nonpathogenic bacterial models, we identified some unique internal and peripheral structural motifs that may be potential candidates for improving known antibiotics and for use in the design of selective antibiotic drugs against S. aureus.

  16. Features of the Calculation Deployment Large Transformable Structures of Different Configurations

    Directory of Open Access Journals (Sweden)

    V. N. Zimin

    2014-01-01

    Full Text Available Despite the significant progress achieved in the design of space transformable structures to ensure a smooth and reliable deployment remains an important task. This type of construction can consist of dozens, hundreds or even thousands of interconnected elements. Deployment transformable space structures in orbit to test their performance in orbital conditions are associated with high material costs. Full deploy: experimental development process transformable structures involve a number of fundamental difficulties: It is impossible to eliminate the influence of gravity and resistance forces conditions. Thus, to calculate deploy of large transformable structures of various configurations is an important stage of their creation. Simulation provides an opportunity to analyze various schemes of deploy, to reveal their advantages and possible disadvantages. For numerical analysis of deploy of such structures is necessary to use modern software modeling of the dynamics of multi-component of mechanical systems such as EULER and Adams. Simulation of deployment space transformable structures was performed taking as example folding flat antenna contours diameter of 5 m and 20 m, foldable spatial calibration reflector diameter of 3 m, deployable antenna reflector truss-type aperture 3×6 m.The results of the calculations represent following characteristics: the time of adoption of the working position structures; form intermediate positions structures during deployment; dependence of opening angles and angular velocities of the design links on the time. The parameters of these calculations can be used as input in the development of structural elements providing deployment. They can also be used to prepare stands for experimental testing of disclosure designs in ground conditions. It should be noted that the theoretical models are the only way to analyze the deployment of such structures for possible emergency situations.

  17. Structural and Phylogenetic Analysis of Rhodobacter capsulatus NifF: Uncovering General Features of Nitrogen-fixation (nif)-Flavodoxins

    OpenAIRE

    Inmaculada Pérez-Dorado; Ana Bortolotti; Néstor Cortez; Hermoso, Juan A.

    2013-01-01

    Analysis of the crystal structure of NifF from Rhodobacter capsulatus and its homologues reported so far reflects the existence of unique structural features in nif flavodoxins: a leucine at the re face of the isoalloxazine, an eight-residue insertion at the C-terminus of the 50’s loop and a remarkable difference in the electrostatic potential surface with respect to non-nif flavodoxins. A phylogenetic study on 64 sequences from 52 bacterial species revealed four clusters, including...

  18. Structural Features of Nanocrystalline Magnetite Obtained by Different Syntheses According to X-Ray Diffraction and Electron Microscopy Data

    Directory of Open Access Journals (Sweden)

    A.N. Kalinkevich

    2011-01-01

    Full Text Available Structural features of nanosized magnetite Fe3O4 synthesized in the presence of polymeric matrices (polysaccharide chitosan, etc. were studied using transmission electron microscopy (TEM and X-ray diffraction analysis. The data obtained strongly suggest the influence of the polysaccharide matrix on the magnetite nanoparticles growth inhibition and size stabilization. The controlled size decrease of Fe3O4 nanoparticles is accompanied with the increase of crystal lattice imperfection and the decrease of the unit cell size. The utility of TEM and XRD complementary use for the determination of nanosized magnetite particles structure and substructure parameters is shown in the present paper.

  19. A combination of feature extraction methods with an ensemble of different classifiers for protein structural class prediction problem.

    Science.gov (United States)

    Dehzangi, Abdollah; Paliwal, Kuldip; Sharma, Alok; Dehzangi, Omid; Sattar, Abdul

    2013-01-01

    Better understanding of structural class of a given protein reveals important information about its overall folding type and its domain. It can also be directly used to provide critical information on general tertiary structure of a protein which has a profound impact on protein function determination and drug design. Despite tremendous enhancements made by pattern recognition-based approaches to solve this problem, it still remains as an unsolved issue for bioinformatics that demands more attention and exploration. In this study, we propose a novel feature extraction model that incorporates physicochemical and evolutionary-based information simultaneously. We also propose overlapped segmented distribution and autocorrelation-based feature extraction methods to provide more local and global discriminatory information. The proposed feature extraction methods are explored for 15 most promising attributes that are selected from a wide range of physicochemical-based attributes. Finally, by applying an ensemble of different classifiers namely, Adaboost.M1, LogitBoost, naive Bayes, multilayer perceptron (MLP), and support vector machine (SVM) we show enhancement of the protein structural class prediction accuracy for four popular benchmarks.

  20. Navigation by anomalous random walks on complex networks

    Science.gov (United States)

    Weng, Tongfeng; Zhang, Jie; Khajehnejad, Moein; Small, Michael; Zheng, Rui; Hui, Pan

    2016-11-01

    Anomalous random walks having long-range jumps are a critical branch of dynamical processes on networks, which can model a number of search and transport processes. However, traditional measurements based on mean first passage time are not useful as they fail to characterize the cost associated with each jump. Here we introduce a new concept of mean first traverse distance (MFTD) to characterize anomalous random walks that represents the expected traverse distance taken by walkers searching from source node to target node, and we provide a procedure for calculating the MFTD between two nodes. We use Lévy walks on networks as an example, and demonstrate that the proposed approach can unravel the interplay between diffusion dynamics of Lévy walks and the underlying network structure. Moreover, applying our framework to the famous PageRank search, we show how to inform the optimality of the PageRank search. The framework for analyzing anomalous random walks on complex networks offers a useful new paradigm to understand the dynamics of anomalous diffusion processes, and provides a unified scheme to characterize search and transport processes on networks.

  1. Common and distinctive features of GNRA tetraloops based on a GUAA tetraloop structure at 1.4 A resolution.

    Science.gov (United States)

    Correll, Carl C; Swinger, Kerren

    2003-03-01

    GNRA tetraloops (N is A, C, G, or U; R is A or G) are basic building blocks of RNA structure that often interact with proteins or other RNA structural elements. Understanding sequence-dependent structural variation among different GNRA tetraloops is an important step toward elucidating the molecular basis of specific GNRA tetraloop recognition by proteins and RNAs. Details of the geometry and hydration of this motif have been based on high-resolution crystallographic structures of the GRRA subset of tetraloops; less is known about the GYRA subset (Y is C or U). We report here the structure of a GUAA tetraloop determined to 1.4 A resolution to better define these details and any distinctive features of GYRA tetraloops. The tetraloop is part of a 27-nt structure that mimics the universal sarcin/ricin loop from Escherichia coli 23S ribosomal RNA in which a GUAA tetraloop replaces the conserved GAGA tetraloop. The adenosines of the GUAA tetraloop form an intermolecular contact that is a commonplace RNA tertiary interaction called an A-minor motif. This is the first structure to reveal in great detail the geometry and hydration of a GUAA tetraloop and an A-minor motif. Comparison of tetraloop structures shows a common backbone geometry for each of the eight possible tetraloop sequences and suggests a common hydration. After backbone atom superposition, equivalent bases from different tetraloops unexpectedly depart from coplanarity by as much as 48 degrees. This variation displaces the functional groups of tetraloops implicated in protein and RNA binding, providing a recognition feature.

  2. [Colonization and community structural features of AM fungi in urban ecosystem: a review].

    Science.gov (United States)

    Shi, Li-jun; Diao, Zhi-kai; Liu, Run-jin

    2011-07-01

    Arbuscular mycorrhizal (AM) fungi, an important component of soil microbes, are of significance in maintaining the sustainable development of urban ecosystem. This paper summarized the characteristics of the colonization and community structure of AM fungi in urban ecosystems, and discussed the effects of urban ecological factors, e.g., human activities, vegetation re-establishment and maintenance, and urban soil status, on the colonization and community structure. It was considered that the researches on the community structure and function of AM fungi in urban ecosystems, such as the effects and mechanisms of the key urban ecological factors (e.g., water resource shortage and heat island effect) on the alternation of AM fungal community structure should be strengthened in the future.

  3. Structural and functional features of a collagen-binding matrix protein from the mussel byssus.

    Science.gov (United States)

    Suhre, Michael H; Gertz, Melanie; Steegborn, Clemens; Scheibel, Thomas

    2014-02-26

    Blue mussels adhere to surfaces by the byssus, a holdfast structure composed of individual threads representing a collagen fibre reinforced composite. Here, we present the crystal structure and function of one of its matrix proteins, the proximal thread matrix protein 1, which is present in the proximal section of the byssus. The structure reveals two von Willebrand factor type A domains linked by a two-β-stranded linker yielding a novel structural arrangement. In vitro, the protein binds heterologous collagens with high affinity and affects collagen assembly, morphology and arrangement of its fibrils. By providing charged surface clusters as well as insufficiently coordinated metal ions, the proximal thread matrix protein 1 might interconnect other byssal proteins and thereby contribute to the integrity of the byssal threads in vivo. Moreover, the protein could be used for adjusting the mechanical properties of collagen materials, a function likely important in the natural byssus.

  4. Effect of certain structural features of coal on Its tendency towards reduction

    Energy Technology Data Exchange (ETDEWEB)

    Grigor' yeva, Ye. A.; Bakirova, Ye.V.; Dzhalyabova, L.V.; Larina, N.K.; Lesnikova, Ye.B.; Zharova, M.N.,

    1981-01-01

    A study is made of the effect of easily destroyed ether groupings and organic-mineral bonds in coal structure on the tendency towards reduction with the help of hydrolytic destruction of coals and subsequent selective reduction by sodium borohydride.

  5. Structural features and thermal property of propionylated starches with different amylose/amylopectin ratio.

    Science.gov (United States)

    Zhu, Jie; Zhang, Shuyan; Zhang, Binjia; Qiao, Dongling; Pu, Huayin; Liu, Siyuan; Li, Lin

    2017-04-01

    This work concerned the effects of amylose/amylopectin ratio on the structure and thermal stability of propionylated starches with high degree of substitution (DS). Four starches with different amylose content were used to obtain propionylated starches. Acylation partly disrupted granule morphology of native starches, and the imperfection and porous structures of starch granule were intensified along with the increased amylose content. It was noted that the crystalline structure of starch was destroyed and thus intense acylation occurred in both amorphous and crystalline regions. The acylated starch with high-amylose content displayed more ordered region compared to low-amylose starch. Acylation enhanced the thermal stability of starch, and this effect became more evident as the amylose content increased. Thus, the amylose/amylopectin ratio has been confirmed capable of affecting the structure and thermal behaviors of hydrophobic propionylated starch, which is of value for the design of starchy materials with tailored thermal stability.

  6. Layout Optimization of Structures with Finite-size Features using Multiresolution Analysis

    DEFF Research Database (Denmark)

    Chellappa, S.; Diaz, A. R.; Bendsøe, Martin P.

    2004-01-01

    A scheme for layout optimization in structures with multiple finite-sized heterogeneities is presented. Multiresolution analysis is used to compute reduced operators (stiffness matrices) representing the elastic behavior of material distributions with heterogeneities of sizes that are comparable...

  7. Multiresolution Analysis Techniques to Isolate, Detect and Characterize Morphologically Diverse Features of Structured ICF Capsule Implosions

    CERN Document Server

    Afeyan, Bedros; Jones, Peter; Starck, Jean Luc; Herrmann, Mark

    2012-01-01

    In order to capture just how nonuniform and degraded the symmetry may become of an imploding inertial confinement fusion capsule one may resort to the analysis of high energy X ray point projection backlighting generated radiographs. Here we show new results for such images by using methods of modern harmonic analysis which involve different families of wavelets, curvelets and WaSP (wavelet square partition) functions from geometric measure theory. Three different methods of isolating morphologically diverse features are suggested together with statistical means of quantifying their content for the purposes of comparing the same implosion at different times, to simulations and to different implosion images.

  8. Non-iridescent Transmissive Structural Color Filter Featuring Highly Efficient Transmission and High Excitation Purity

    OpenAIRE

    2014-01-01

    Nanostructure based color filtering has been considered an attractive replacement for current colorant pigmentation in the display technologies, in view of its increased efficiencies, ease of fabrication and eco-friendliness. For such structural filtering, iridescence relevant to its angular dependency, which poses a detrimental barrier to the practical development of high performance display and sensing devices, should be mitigated. We report on a non-iridescent transmissive structural color...

  9. Novel Features of Eukaryotic Photosystem II Revealed by Its Crystal Structure Analysis from a Red Alga.

    Science.gov (United States)

    Ago, Hideo; Adachi, Hideyuki; Umena, Yasufumi; Tashiro, Takayoshi; Kawakami, Keisuke; Kamiya, Nobuo; Tian, Lirong; Han, Guangye; Kuang, Tingyun; Liu, Zheyi; Wang, Fangjun; Zou, Hanfa; Enami, Isao; Miyano, Masashi; Shen, Jian-Ren

    2016-03-11

    Photosystem II (PSII) catalyzes light-induced water splitting, leading to the evolution of molecular oxygen indispensible for life on the earth. The crystal structure of PSII from cyanobacteria has been solved at an atomic level, but the structure of eukaryotic PSII has not been analyzed. Because eukaryotic PSII possesses additional subunits not found in cyanobacterial PSII, it is important to solve the structure of eukaryotic PSII to elucidate their detailed functions, as well as evolutionary relationships. Here we report the structure of PSII from a red alga Cyanidium caldarium at 2.76 Å resolution, which revealed the structure and interaction sites of PsbQ', a unique, fourth extrinsic protein required for stabilizing the oxygen-evolving complex in the lumenal surface of PSII. The PsbQ' subunit was found to be located underneath CP43 in the vicinity of PsbV, and its structure is characterized by a bundle of four up-down helices arranged in a similar way to those of cyanobacterial and higher plant PsbQ, although helices I and II of PsbQ' were kinked relative to its higher plant counterpart because of its interactions with CP43. Furthermore, two novel transmembrane helices were found in the red algal PSII that are not present in cyanobacterial PSII; one of these helices may correspond to PsbW found only in eukaryotic PSII. The present results represent the first crystal structure of PSII from eukaryotic oxygenic organisms, which were discussed in comparison with the structure of cyanobacterial PSII.

  10. Classification of Vessels in Single-Pol COSMO-SkyMed Images Based on Statistical and Structural Features

    Directory of Open Access Journals (Sweden)

    Fan Wu

    2015-05-01

    Full Text Available Vessel monitoring is one of the most important maritime applications of Synthetic Aperture Radar (SAR data. Because of the dihedral reflections between the vessel hull and sea surface and the trihedral reflections among superstructures, vessels usually have strong backscattering in SAR images. Furthermore, in high-resolution SAR images, detailed information on vessel structures can be observed, allowing for vessel classification in high-resolution SAR images. This paper focuses on the feature analysis of merchant vessels, including bulk carriers, container ships and oil tankers, in 3 m resolution COSMO-SkyMed stripmap HIMAGE mode images and proposes a method for vessel classification. After preprocessing, a feature vector is estimated by calculating the average value of the kernel density estimation, three structural features and the mean backscattering coefficient. Support vector machine (SVM classifier is used for the vessel classification, and the results are compared with traditional methods, such as the K-nearest neighbor algorithm (K-NN and minimum distance classifier (MDC. In situ investigations are conducted during the SAR data acquisition. Corresponding Automatic Identification System (AIS reports are also obtained as ground truth to evaluate the effectiveness of the classifier. The preliminary results show that the combination of the average value of the kernel density estimation and mean backscattering coefficient has good ability for classifying the three types of vessels. When adding the three structural features, the results slightly improve. The result of the SVM classifier is better than that of K-NN and MDC. However, the SVM requires more time, when the parameters of the kernel are estimated.

  11. Structural features of indium antimonide quantum dots on the indium arsenide substrate

    Directory of Open Access Journals (Sweden)

    Liliya A. Sokura

    2015-06-01

    Full Text Available The properties of InSb/InAs quantum dots (QDs have been investigated by transmission electron microscopy (TEM. Specific features of diffraction contrast were discovered in plan-view TEM images of big (9–10 nm in height and 38–50 nm in diameter InSb QDs. To understand the origin of such distortions, a model of an InSb QD on InAs substrate containing a partial Frank dislocation (FD was developed and used for calculations of the displacement field and the subsequent diffraction image simulation of an InSb QD for the first time. The shape of the QD was established to have an insignificant influence on the magnitude of radial displacements. The insertion of a misfit defect (a partial Frank dislocation into the QD reduces the strain at the edges of the QD almost by 30%. The comparison of experimental and simulated data allowed us to explain the observed features of the moiré pattern in the image of a big InSb QD by the presence of a misfit defect at the QD-substrate interface.

  12. Structural features and kinetic characterization of alanine racemase from Staphylococcus aureus (Mu50).

    Science.gov (United States)

    Scaletti, Emma R; Luckner, Sylvia R; Krause, Kurt L

    2012-01-01

    Staphylococcus aureus is an opportunistic Gram-positive bacterium which causes a wide variety of diseases ranging from minor skin infections to potentially fatal conditions such as pneumonia, meningitis and septicaemia. The pathogen is a leading cause of nosocomial acquired infections, a problem that is exacerbated by the existence of methicillin- and glycopeptide antibiotic-resistant strains which can be challenging to treat. Alanine racemase (Alr) is a pyridoxal-5'-phosphate-dependent enzyme which catalyzes reversible racemization between enantiomers of alanine. As D-alanine is an essential component of the bacterial cell-wall peptidoglycan, inhibition of Alr is lethal to prokaryotes. Additionally, while ubiquitous amongst bacteria, this enzyme is absent in humans and most eukaryotes, making it an excellent antibiotic drug target. The crystal structure of S. aureus alanine racemase (Alr(Sas)), the sequence of which corresponds to that from the highly antibiotic-resistant Mu50 strain, has been solved to 2.15 Å resolution. Comparison of the Alr(Sas) structure with those of various alanine racemases demonstrates a conserved overall fold, with the enzyme sharing most similarity to those from other Gram-positive bacteria. Structural examination indicates that the active-site binding pocket, dimer interface and active-site entryway of the enzyme are potential targets for structure-aided inhibitor design. Kinetic constants were calculated in this study and are reported here. The potential for a disulfide bond in this structure is noted. This structural and biochemical information provides a template for future structure-based drug-development efforts targeting Alr(Sas).

  13. Structural basis for featuring of steroid isomerase activity in alpha class glutathione transferases.

    Science.gov (United States)

    Tars, Kaspars; Olin, Birgit; Mannervik, Bengt

    2010-03-19

    Glutathione transferases (GSTs) are abundant enzymes catalyzing the conjugation of hydrophobic toxic substrates with glutathione. In addition to detoxication, human GST A3-3 displays prominent steroid double-bond isomerase activity; e.g. transforming Delta(5)-androstene-3-17-dione into Delta(4)-androstene-3-17-dione (AD). This chemical transformation is a crucial step in the biosynthesis of steroids, such as testosterone and progesterone. In contrast to GST A3-3, the homologous GST A2-2 does not show significant steroid isomerase activity. We have solved the 3D structures of human GSTs A2-2 and A3-3 in complex with AD. In the GST A3-3 crystal structure, AD was bound in an orientation suitable for the glutathione (GSH)-mediated catalysis to occur. In GST A2-2, however, AD was bound in a completely different orientation with its reactive double bond distant from the GSH-binding site. The structures illustrate how a few amino acid substitutions in the active site spectacularly alter the binding mode of the steroid substrate in relation to the conserved catalytic groups and an essentially fixed polypeptide chain conformation. Furthermore, AD did not bind to the GST A2-2-GSH complex. Altogether, these results provide a first-time structural insight into the steroid isomerase activity of any GST and explain the 5000-fold difference in catalytic efficiency between GSTs A2-2 and A3-3. More generally, the structures illustrate how dramatic diversification of functional properties can arise via minimal structural alterations. We suggest a novel structure-based mechanism of the steroid isomerization reaction.

  14. Structure of the Spt16 Middle Domain Reveals Functional Features of the Histone Chaperone FACT*

    Science.gov (United States)

    Kemble, David J.; Whitby, Frank G.; Robinson, Howard; McCullough, Laura L.; Formosa, Tim; Hill, Christopher P.

    2013-01-01

    The histone chaperone FACT is an essential and abundant heterodimer found in all eukaryotes. Here we report a crystal structure of the middle domain of the large subunit of FACT (Spt16-M) to reveal a double pleckstrin homology architecture. This structure was found previously in the Pob3-M domain of the small subunit of FACT and in the related histone chaperone Rtt106, although Spt16-M is distinguished from these structures by the presence of an extended α-helix and a C-terminal addition. Consistent with our finding that the double pleckstrin homology structure is common to these three histone chaperones and reports that Pob3 and Rtt106 double pleckstrin homology domains bind histones H3-H4, we also find that Spt16-M binds H3-H4 with low micromolar affinity. Our structure provides a framework for interpreting a large body of genetic data regarding the physiological functions of FACT, including the identification of potential interaction surfaces for binding histones or other proteins. PMID:23417676

  15. Catalogue of the morphological features in the Spitzer Survey of Stellar Structure in Galaxies (S$^4$G)

    CERN Document Server

    Herrera-Endoqui, M; Laurikainen, E; Salo, H

    2015-01-01

    A catalogue of the morphological features for the complete Spitzer Survey of Stellar Structure in Galaxies (S$^4$G), including 2352 nearby galaxies, is presented. The measurements are made using 3.6 $\\mu$m images, largely tracing the old stellar population; at this wavelength the effects of dust are also minimal. The measured features are the sizes, ellipticities, and orientations of bars, rings, ringlenses, and lenses. Measured in a similar manner are also barlenses (lens-like structures embedded in the bars), which are not lenses in the usual sense, being rather the more face-on counterparts of the boxy/peanut structures in the edge-on view. In addition, pitch angles of spiral arm segments are measured for those galaxies where they can be reliably traced. More than one pitch angle may appear for a single galaxy. All measurements are made in a human-supervised manner so that attention is paid to each galaxy. We used isophotal analysis, unsharp masking, and fitting ellipses to measured structures. We find tha...

  16. The influence of contemporary and historic landscape features on the genetic structure of the sand dune endemic, Cirsium pitcheri (Asteraceae).

    Science.gov (United States)

    Fant, J B; Havens, K; Keller, J M; Radosavljevic, A; Yates, E D

    2014-05-01

    Narrow endemics are at risk from climate change because of their restricted habitat preferences, lower colonization ability and dispersal distances. Landscape genetics combines new tools and analyses that allow us to test how both past and present landscape features have facilitated or hindered previous range expansion and local migration patterns, and thereby identifying potential limitations to future range shifts. We have compared current and historic habitat corridors in Cirsium pitcheri, an endemic of the linear dune ecosystem of the Great Lakes, to determine the relative contributions of contemporary migration and post-glacial range expansion on genetic structure. We used seven microsatellite loci to characterize the genetic structure for 24 populations of Cirsium pitcheri, spanning the center to periphery of the range. We tested genetic distance against different measures of geographic distance and landscape permeability, based on contemporary and historic landscape features. We found moderate genetic structure (Fst=0.14), and a north-south pattern to the distribution of genetic diversity and inbreeding, with northern populations having the highest diversity and lowest levels of inbreeding. High allelic diversity, small average pairwise distances and mixed genetic clusters identified in Structure suggest that populations in the center of the range represent the point of entry to the Lake Michigan and a refugium of diversity for this species. A strong association between genetic distances and lake-level changes suggests that historic lake fluctuations best explain the broad geographic patterns, and sandy habitat best explains local patterns of movement.

  17. Modeling-dependent protein characterization of the rice aldehyde dehydrogenase (ALDH superfamily reveals distinct functional and structural features.

    Directory of Open Access Journals (Sweden)

    Simeon O Kotchoni

    Full Text Available The completion of the rice genome sequence has made it possible to identify and characterize new genes and to perform comparative genomics studies across taxa. The aldehyde dehydrogenase (ALDH gene superfamily encoding for NAD(P(+-dependent enzymes is found in all major plant and animal taxa. However, the characterization of plant ALDHs has lagged behind their animal- and prokaryotic-ALDH homologs. In plants, ALDHs are involved in abiotic stress tolerance, male sterility restoration, embryo development and seed viability and maturation. However, there is still no structural property-dependent functional characterization of ALDH protein superfamily in plants. In this paper, we identify members of the rice ALDH gene superfamily and use the evolutionary nesting events of retrotransposons and protein-modeling-based structural reconstitution to report the genetic and molecular and structural features of each member of the rice ALDH superfamily in abiotic/biotic stress responses and developmental processes. Our results indicate that rice-ALDHs are the most expanded plant ALDHs ever characterized. This work represents the first report of specific structural features mediating functionality of the whole families of ALDHs in an organism ever characterized.

  18. Anomalous osmosis resulting from preferential absorption

    NARCIS (Netherlands)

    Staverman, A.J.; Kruissink, C.A.; Pals, D.T.F.

    1965-01-01

    An explanation of the anomalous osmosis described in the preceding paper is given in terms of friction coefficients in the glass membrane. It is shown that anomalous osmosis may be expected when the friction coefficients are constant and positive provided that the membrane absorbs solute strongly an

  19. Features of the Masonry Structure Calculation with Vertical Ring Beams based on the European Standards

    Directory of Open Access Journals (Sweden)

    Zejak Danijela

    2016-01-01

    Full Text Available The design of masonry structures should remain a combination of traditional and modern knowledge. The Eurocodes in the field of the design of earthquake-resistant masonry structures, carry mostly acceptable and expected recommendations and requirements. This paper shows that they contain less acceptable principles, which require further experimental and analytical studies. Particularly it should be noted that Eurocode knows only a shearing mechanism by the horizontal coupling, although during the seismic load, the fracture usually occurs due to exceeding the main tensile stress, which manifests by opening diagonal cracks. The mechanism of the horizontal shearing by Eurocode is treated as critical for the seismic resistance of most masonry buildings, thus the masonry structure is attributed as sufficiently secure, although its actual seismic resistance would be far below from the required.

  20. NOBAI: a web server for character coding of geometrical and statistical features in RNA structure.

    Science.gov (United States)

    Knudsen, Vegeir; Caetano-Anollés, Gustavo

    2008-07-01

    The Numeration of Objects in Biology: Alignment Inferences (NOBAI) web server provides a web interface to the applications in the NOBAI software package. This software codes topological and thermodynamic information related to the secondary structure of RNA molecules as multi-state phylogenetic characters, builds character matrices directly in NEXUS format and provides sequence randomization options. The web server is an effective tool that facilitates the search for evolutionary history embedded in the structure of functional RNA molecules. The NOBAI web server is accessible at 'http://www.manet.uiuc.edu/nobai/nobai.php'. This web site is free and open to all users and there is no login requirement.

  1. Localized 3D-structural features of dynamic-chemical processes of urban air pollution in Beijing winter

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    The Beijing City Air Pollution Observation Field Experiment (BECAPEX) is described with emphases on the "point-surface" research approach and composite analysis. The analysis results of measurements from four observation sites across the Beijing urban area from January to March indicate that the overall impact of urban emission sources in the heating season is significant, and the staggered impact of urban emission sources has different features at observation sites over different parts of Beijing in both heating and non-heating seasons. The pollutants NOx, SO2 and CO in the urban boundary layer have the in-phase variation features over a large area. O3 concentrations at different sites have the same variation trend but its change is reversed phases with above pollutants. The pollutants over the urban area in heating and non-heating seasons also have the synchronous variation trend. The comprehensive sounding of BECAPEX indicates that pollutants and aerosol vertical profiles are closely correlated to the vertical structure of the large-scale inversion layer in the urban boundary layer over the urban area. The localized 3D-structural features of local urban polluting processes associated with the peripheral areas are discussed with a "point-surface" comprehensive sounding technique.

  2. Physical structure features of the crust at southeast region of Tibetan Plateau

    Institute of Scientific and Technical Information of China (English)

    刘宏兵; 孔祥儒; 马晓冰; 王谦身; 闫永利; 闫雅芬; 杨志强

    2001-01-01

    Research results show the obvious differences between the crustal deep physical features of each block and fault zone, and obvious inhomogeneity in longitudinal and horizontal directions. The Gandise block is especially outstanding. Squeezed by Indian Continent, the high conductive layer inclines northward, which is continuous in the Gandise block, but becomes horizontal in distribution and thick in Qiangtang and Bayan Har blocks. The Jinshajiang fault zone inclines northward near Yushu, while Lancangjiang and Nujiang fault zones present vertical distributions. Gravity Bouguer anomalies are high at the south and north edges and low in the center of the plateau. The Zayu-Shama region has not reached gravity equilibrium yet and represents obvious negative anomaly, which indicates that the region is in rapid uplift. Its geomagnetic anomaly varies evidently in different blocks and on different fault zones, and decreases obviously both in intensity and amplitude variations from south to north. The surveys and

  3. Structural features of flower trichomes in drug eyebright (Euphrasia stricta D. Wolff EX J. F. Lehm.

    Directory of Open Access Journals (Sweden)

    Weronika Haratym

    2014-01-01

    Full Text Available Euphrasia stricta D. Wolff ex J. F. Lehm. (Orobanchaceae is a representative of plants that are widely used in folk medicine, phytomedicine, and homeopathy. The medicinal raw material derived from the drug eyebright is applied primarily in treatment of ophthalmic diseases. The investigations of trichomes in drug eyebright (Euphrasia stricta D. Wolff ex J. F. Lehm were conducted in 2010–2011. Using light microscopy and scanning electron microscopy, their location and morphological and anatomical features were identified. Three types of non-glandular trichomes were found: short unicellular, long 1–2 celled, and long 2-celled with wall ornamentation. Additionally, 7 types of glandular trichomes were found; these included: unicellular clavate, 2–3-celled clavate, capitate with a unicellular head and a 3-cel- led stalk, capitate with a unicellular head and a 2-celled stalk, capitate with a 2-celled head, conical papillae, and ribbon-like trichomes with wall thickening.

  4. 飞行器结构设计特点及演变%Aircraft Structural Design Features and Evolution

    Institute of Scientific and Technical Information of China (English)

    赵智姝; 李伟; 李映红

    2014-01-01

    飞行器结构设计是飞行器设计中重要的组成部分,本文从飞行器结构设计的要求出发、详细介绍了机身、机翼、尾翼的设计特点,总结了飞行器结构设计的演变趋势,对飞行器设计人员和维修人员具有一定的参考价值。%Structural design is a very important part of aircraft design . Starting from aircraft structural design requirement , this paper introduces in detail the design features of fuselage, wing, and empennage, and summarizes evolution trends of aircraft structural design , which has a certain reference value for aircraft design and maintenance personnel .

  5. Features of morpho-anatomic structure of vegetative organs of Sedum antiquum Omelcz et Zaverucha (Crassulaceae DC.

    Directory of Open Access Journals (Sweden)

    Valentyna Berezkina

    2015-05-01

    Full Text Available The study results of biological features and morpho-anatomical structure of vegetative organs of Sedum antiquum Omelcz et Zaverucha (Crassulaceae DC. are given. S. antiquum is Eastern Carpathian-Opillia rare endemic species. It is listed in the Red Book of Ukraine and in the European Red List of Animals and Plants and is endangered in world scale. As a result of study of morpho-anatomic structure of leaves and stems of S. antiquum the anisocytic type of stomata and presence of cuticle have been determined. It was ascertained that structure of leaves is adapted to the accumulation of significant water reserves and its further gradual use. Ecological and phytocenotic conditions of growth are studied too. S. antiquum has been determined here as petrophyte, calcephyl, and succulent ephemer. This rare species need protection and control of population state in all natural habitats.

  6. Features of structure and phase transitions in pure uranium and U-Mo alloys: atomistic simulation

    Science.gov (United States)

    Kolotova, L. N.; Kuksin, A. Yu; Smirnova, D. E.; Starikov, S. V.; Tseplyaev, V. I.

    2016-11-01

    We study structural properties of cubic and tetragonal phases of U-Mo alloys using atomistic simulations: molecular dynamics and density functional theory. For pure uranium and U-Mo alloys at low temperatures we observe body-centered tetragonal (bct) structure, which is similar to the metastable γ°-phase found in the experiments. At higher temperatures bct structure transforms to a quasi body-centered cubic (q-bcc) phase that exhibits cubic symmetry just on the scale of several interatomic spacings or when averaged over time. Instantaneous pair distribution function (PDF) differs from PDF for the time-averaged atomic coordinates corresponding to the bcc lattice. The local positions of uranium atoms in q-bcc lattice correspond to the bct structure, which is energetically favourable due to formation of short U-U bonds. Transition from bct to q-bcc could be considered as ferro-to paraelastic transition of order-disorder type. The temperature of transition depends on Mo concentration. For pure uranium it is equal to about 700 K, which is well below than the upper boundary of the stability region of the α-U phase. Due to this reason, bct phase is observed only in uranium alloys containing metals with low solubility in α-U.

  7. Structural features of condensed tannins affect in vitro ruminal methane production and fermentation characteristics

    NARCIS (Netherlands)

    Huyen, N.T.; Fryganas, C.; Uittenbogaard, G.; Mueller-Harvey, I.; Verstegen, M.W.A.; Hendriks, W.H.; Pellikaan, W.F.

    2016-01-01

    An in vitro study was conducted to investigate the effects of condensed tannin (CT) structural properties, i.e. average polymer size (or mean degree of polymerization), percentage of cis flavan-3-ols and percentage of prodelphinidins in CT extracts on methane (CH4) production and ferme

  8. Structural and biochemical features of acidic α-amylase of Bacillus acidicola.

    Science.gov (United States)

    Sharma, Archana; Satyanarayana, T

    2013-10-01

    The investigation is aimed at understanding structure-function aspect of α-amylase of an acidophilic bacterium Bacillus acidicola (BAamy), which is Ca(2+)-independent and active at acidic pH of native starch, and thus, suits better in starch saccharification process. The CD spectroscopic data analysis revealed that the enzyme has 30% α-helices, 14.2% β-sheets, and 55.8% random coils at 60 °C and pH 4.0. Using Bacillus stearothermophilus α-amylase (BStA) as the template, 3-D structure of rBAamy has been proposed. A complete loss in α-amylase activity was recorded when the amino acid residues (D231, E261 and D328) were substituted that confirmed their role in catalysis. The CD studies indicated a decrease in the α-helices content below and beyond the optimum pH and temperature that suggests a critical role of α-helix in maintaining the structural conformation of the enzyme. Fluorescence-quenching by N-bromosuccinimide (NBS) suggested the role of tryptophan in maintaining structural integrity of α-amylase and that by acrylamide indicated interaction by simple collision process.

  9. Features of highly structured equatorial plasma irregularities deduced from CHAMP observations

    DEFF Research Database (Denmark)

    Xiong, C.; Luhr, H.; Ma, S. Y.;

    2012-01-01

    for different scale sizes with the global distribution of plasma vertical uplift, we have found that EPBs reaching higher altitudes are more structured than those which are sampled by CHAMP near the top side of the depleted fluxtube. Such a result is in accord with 3-D model simulations (Aveiro and Hysell, 2010...

  10. Crystal Structures of Two Transcriptional Regulators from Bacillus cereus Define the Conserved Structural Features of a PadR Subfamily

    NARCIS (Netherlands)

    Fibriansah, Guntur; Kovacs, Akos T.; Pool, Trijntje J.; Boonstra, Mirjam; Kuipers, Oscar P.; Thunnissen, Andy-Mark W. H.

    2012-01-01

    PadR-like transcriptional regulators form a structurally-related family of proteins that control the expression of genes associated with detoxification, virulence and multi-drug resistance in bacteria. Only a few members of this family have been studied by genetic, biochemical and biophysical method

  11. Sensitivity of near field GIA response with respect to rheological features of the Earth structure

    Science.gov (United States)

    Hagedoorn, Jan M.; Klemann, Volker; Sasgen, Ingo; Thomas, Maik

    2016-04-01

    One task of the German National Climate Modeling Initiative PalMod will be to couple earth system models representing the atmospere, ocean and ice dynamics during the last glacial cycle with the dynamic loading response of a viscoelastic earth model. In preparation, we discuss in this study the influence of viscosity stratification and of lateral heterogeneities in the Earth structure on the solid-earth response to glacial loading. As discussed in literature, there is a controversy about the impact of lateral heterogeneity on the prediction of present and past GIA signals. The influence of the Earth structure on the far-field response is governed by the flexural behaviour of the regional lithosphere and upper-mantle structure in response to the varying ocean load. The influence at and around the glacial ice sheets is substantial with respect to the amplitudes and also with respect to the temporal evolution of the earth's response. Depending on the region of interest, lithospheric variations are present over the extent of the glacial ice sheets varying between 40 and 200 km, and lateral variations in viscosity can vary by one or two orders of magnitude. The focus will be to what extent the behaviour of a laterally heterogeneous viscosity structure can be parameterised by an adjusted spherical earth model representation. Accordingly, we apply predefined ice-sheet histories (like ICE5G and ICE6G) and analyse ensemble runs representing the variability of relative sea-level and palaeo-topography predictions. Spatial pattern of deformation fields will be discussed as the behaviour at specific sea-level curves. Furthermore, we compare the sensitivity on earth structure during the evolution of sea level and palaeo topography during the termination phase of the last glaciation to present-day rates of relative sea-level height and radial displacement.

  12. VSA Observations of the Anomalous Microwave Emission in the Perseus Region

    OpenAIRE

    2009-01-01

    The dust feature G159.6--18.5 in the Perseus region has previously been observed with the COSMOSOMAS experiment \\citep{Watson:05} on angular scales of $\\approx$ 1$^{\\circ}$, and was found to exhibit anomalous microwave emission. We present new observations of this dust feature, performed with the Very Small Array (VSA) at 33 GHz, to help increase the understanding of the nature of this anomalous emission. On the angular scales observed with the VSA ($\\approx$ 10 -- 40$^{\\prime}$), G159.6--18....

  13. Anomalous diffraction in hyperbolic materials

    CERN Document Server

    Alberucci, Alessandro; Boardman, Allan D; Assanto, Gaetano

    2016-01-01

    We demonstrate that light is subject to anomalous (i.e., negative) diffraction when propagating in the presence of hyperbolic dispersion. We show that light propagation in hyperbolic media resembles the dynamics of a quantum particle of negative mass moving in a two-dimensional potential. The negative effective mass implies time reversal if the medium is homogeneous. Such property paves the way to diffraction compensation, spatial analogue of dispersion compensating fibers in the temporal domain. At variance with materials exhibiting standard elliptic dispersion, in inhomogeneous hyperbolic materials light waves are pulled towards regions with a lower refractive index. In the presence of a Kerr-like optical response, bright (dark) solitons are supported by a negative (positive) nonlinearity.

  14. Anomalous diffraction in hyperbolic materials

    Science.gov (United States)

    Alberucci, Alessandro; Jisha, Chandroth P.; Boardman, Allan D.; Assanto, Gaetano

    2016-09-01

    We demonstrate that light is subject to anomalous (i.e., negative) diffraction when propagating in the presence of hyperbolic dispersion. We show that light propagation in hyperbolic media resembles the dynamics of a quantum particle of negative mass moving in a two-dimensional potential. The negative effective mass implies time reversal if the medium is homogeneous. Such property paves the way to diffraction compensation, i.e., spatial analog of dispersion compensating fibers in the temporal domain. At variance with materials exhibiting standard elliptic dispersion, in inhomogeneous hyperbolic materials light waves are pulled towards regions with a lower refractive index. In the presence of a Kerr-like optical response, bright (dark) solitons are supported by a negative (positive) nonlinearity.

  15. Prediction of protein structural features by use of artificial neural networks

    DEFF Research Database (Denmark)

    Petersen, Bent

    that it is possible to predict the specificity of the HIV protease with a high performance. In the process we also identified new possible cleavage sites which will further be verified experimentally in the lab. In summary, the thesis presented in this work has greatly contributed to the development of new tools....... There is a huge over-representation of DNA sequences when comparing the amount of experimentally verified proteins with the amount of DNA sequences. The academic and industrial research community therefore has to rely on structure predictions instead of waiting for the time consuming experimentally determined...... structure data. This thesis describes the development of two new tools to study such genetic sequence data. NetSurfP was developed to predict the surface accessibility of amino acids in amino acid sequences. Knowledge of the degree of surface exposure of an amino acid is valuable and has been used...

  16. Properties and features of structure formation CuCr-contact alloys in electron beam cladding

    Energy Technology Data Exchange (ETDEWEB)

    Durakov, Vasiliy G., E-mail: electron@ispms.tsc.ru [Institute of Strength Physics and Materials Science SB RAS, Tomsk, 634055 (Russian Federation); Dampilon, Bair V., E-mail: dampilon@ispms.tsc.ru, E-mail: gnusov@rambler.ru; Gnyusov, Sergey F., E-mail: dampilon@ispms.tsc.ru, E-mail: gnusov@rambler.ru [Institute of Strength Physics and Materials Science SB RAS, Tomsk, 634055, Russia and National Research Tomsk Polytechnic University, Tomsk, 634050 (Russian Federation)

    2014-11-14

    The microstructure and properties of the contact CuCr alloy produced by electron-beam cladding have been investigated. The effect of the electron beam cladding parameters and preheating temperature of the base metal on the structure and the properties of the coatings has been determined. The bimodal structure of the cladding coating has been established. The short circuit currents tests have been carried out according to the Weil-Dobke synthetic circuit simulating procedure developed for vacuum circuit breakers (VCB) test in real electric circuits. Test results have shown that the electron beam cladding (EBC) contact material has better breaking capacity than that of commercially fabricated sintered contact material. The application of the technology of electron beam cladding for production of contact material would significantly improve specific characteristics and reliability of vacuum switching equipment.

  17. [Features of the structure of the regional lymph nodes of the duodenum in monkeys].

    Science.gov (United States)

    Rusina, A K

    1980-05-01

    By means of morphometric methods, duodenal regional lymph nodes were studied in rhesus and lapunder macaques. It was demonstrated that in monkeys the connective tissue framework, cortical plateau, medullary substance, cortical substance, sinuses and follicles are expressed differently. Cellular elements in the lymph nodes analysed in the monkeys subjected to a comparative investigation demonstrated their uneven distribution in the same structural components. Small lymphocytes were predominate cellular elements. There were rather essential differences in the number of plasmic cells, mitotically dividing cells, acidophilic granulocytes, mast cells and macrophages. Certain species differences were demonstrated to exist both in structure and cell composition of the lymph nodes that seemed to depend on some local peculiarities of immunogenic reactions.

  18. EVOLUTIONARY MODEL OF FREE ECONOMIC ZONES --Different Generations and Structural Features

    Institute of Scientific and Technical Information of China (English)

    MENG Guang-wen

    2005-01-01

    Free economic zone (FEZ) has a long history and plays a more and more important role in the world economy. Most studies, however, focused on the theoretical analysis of benefit and cost as well as the economic role of FEZ in the less developed countries and little attention has been paid to the evolution of FEZ. This paper will improve the above-mentioned studies and put forward the structural and spatial evolutionary model of FEZ by analyzing the development of objectives, preferential policy, governance structure, industrial sectors and location of FEZs based on the international economic and political development. FEZs develop towards: 1) more comprehensive and macro objectives, 2) more industry-oriented and multi-preferential policies, 3) more cross-national and combination zones with administrative areas, 4) more technology-intensive and multi-industries, 5) more flexible location and larger spatial dimensions, 6) more rapid evolution and typologies, and 7) more economic integration to the host economy.

  19. Innovative Structural Design Features for a 10 m Solar Sail Demonstrator

    Science.gov (United States)

    Laue, G.; Moore, J.; Clayton, W.

    2004-01-01

    The successful development of sail architectures will require careful attention to a number of key issues including but not limited to material strength issues, stress conditions for the membrane, load interactions between membrane and structure, and membrane material planarity. Along with the inherent challenges of fabricating and handling very large membrane structures these issues will pose real challenges for the near-term development of practical sail technologies. SRS has developed innovative technologies that deal directly with the challenges of developing very large sail membranes. Some of these technologies include edge reinforcements and innovative reinforcement attachment techniques, production of flight durable sail materials of less than 2.5 micron thicknesses and large scale fabrication techniques. SRS has employed these technologies in several large 10 m demonstrators that have been delivered to LaRC for solar vacuum testing. Details of the design of this system will be discussed.

  20. Prediction of protein structural features from sequence data based on Shannon entropy and Kolmogorov complexity.

    Science.gov (United States)

    Bywater, Robert Paul

    2015-01-01

    While the genome for a given organism stores the information necessary for the organism to function and flourish it is the proteins that are encoded by the genome that perhaps more than anything else characterize the phenotype for that organism. It is therefore not surprising that one of the many approaches to understanding and predicting protein folding and properties has come from genomics and more specifically from multiple sequence alignments. In this work I explore ways in which data derived from sequence alignment data can be used to investigate in a predictive way three different aspects of protein structure: secondary structures, inter-residue contacts and the dynamics of switching between different states of the protein. In particular the use of Kolmogorov complexity has identified a novel pathway towards achieving these goals.

  1. Influence of laser cladding regimes on structural features and mechanical properties of coatings on titanium substrates

    Energy Technology Data Exchange (ETDEWEB)

    Malyutina, Yulia N., E-mail: iuliiamaliutina@gmail.ru; Lazurenko, Daria V., E-mail: pavlyukova-87@mail.ru; Bataev, Ivan A., E-mail: ivanbataev@ngs.ru [Novosibirsk State Technical University, Novosibirsk, 630073 (Russian Federation); Movtchan, Igor A., E-mail: igor.movtchan@enise.fr [National Engineering School in Saint-Etienne, Saint-Etienne, 42000 France (France)

    2015-10-27

    In this paper an influence of the tantalum content on the structure and properties of surface layers of the titanium alloy doped using a laser treatment technology was investigated. It was found that an increase of a quantity of filler powder per one millimeter of a track length contributed to a rise of the content of undissolved particles in coatings. The maximum thickness of a cladded layer was reached at the mass of powder per the length unit equaled to 5.5 g/cm. Coatings were characterized by the formation of a dendrite structure with attributes of segregation. The width of a quenched fusion zone grew with an increase in the rate of powder feed to the treated area. Significant strengthening of the titanium surface layer alloyed with tantalum was not observed; however, the presence of undissolved tantalum particles can decrease the hardness of titanium surface layers.

  2. Elucidating features that drive the design of selective antifolates using crystal structures of human dihydrofolate reductase.

    Science.gov (United States)

    Lamb, Kristen M; G-Dayanandan, Narendran; Wright, Dennis L; Anderson, Amy C

    2013-10-15

    The pursuit of antimicrobial drugs that target dihydrofolate reductase (DHFR) exploits differences in sequence and dynamics between the pathogenic and human enzymes. Here, we present five crystal structures of human DHFR bound to a new class of antimicrobial agents, the propargyl-linked antifolates (PLAs), with a range of potency (IC50 values of 0.045-1.07 μM) for human DHFR. These structures reveal that interactions between the ligands and Asn 64, Phe 31, and Phe 34 are important for increased affinity for human DHFR and that loop residues 58-64 undergo ligand-induced conformational changes. The utility of these structural studies was demonstrated through the design of three new ligands that reduce the number of contacts with Asn 64, Phe 31, and Phe 34. Synthesis and evaluation show that one of the designed inhibitors exhibits the lowest affinity for human DHFR of any of the PLAs (2.64 μM). Comparisons of structures of human and Staphylococcus aureus DHFR bound to the same PLA reveal a conformational change in the ligand that enhances interactions with residues Phe 92 (Val 115 in huDHFR) and Ile 50 (Ile 60 in huDHFR) in S. aureus DHFR, yielding selectivity. Likewise, comparisons of human and Candida glabrata DHFR bound to the same ligand show that hydrophobic interactions with residues Ile 121 and Phe 66 (Val 115 and Asn 64 in human DHFR) yield selective inhibitors. The identification of residue substitutions that are important for selectivity and the observation of active site flexibility will help guide antimicrobial antifolate development for the inhibition of pathogenic species.

  3. STRUCTURE FEATURES OF THE SODIUM-GERMANATE GLASSES DOPED WITH YTTERBIUM ERBIUM RETRIEVED FROM RAMAN SPECTROSCOPY

    Directory of Open Access Journals (Sweden)

    I. M. Sevastianova

    2016-09-01

    Full Text Available Subject of Research.The paper deals with study of Raman spectra and luminescence spectra in the visible region of the sodium-germanate glass: 49 GeO2 – 13 Na2O – 27 Yb2O3 – 11 La2O3 - 0,25 Er2O3 and presents research results. In addition, this glass is doped with 5 mol% of the following components MgO, BaO, Al2O3, PbO, Nb2O5, TiO2, SiO2, P2O5 in order to study the effect of these additives on the structure of the glassy matrix and the anti-Stokes luminescence spectra of erbium ions. Method. Raman scatteringspectra were recorded by Renishaw inVia Raman Microscope. Excitation source is a helium neon laser (λ= 633 nm with power equal to 50Wt. Anti-Stokes luminescence of erbium ions was registered in spectral region of 450–750 nm at room temperature (excitation laser wavelength is 975 nm, power is 1Wt. Main Results. It was shown that the structure of the initial glass does not change with the introduction of niobium as Nb2O5 in any coordination plays a role of network forming, building a single mixed grid with tetrahedrons [GeO4]. Introduction of the second glass former P2O5 leads to loosening germanate structure due to the appearance of the phosphate sublattice. This leads to a redistribution of the relative intensity of up-conversion luminescence bands with maxima at 540 and 670 nm compared with the initial glass. Introduction of additives PbO, MgO, Al2O3, TiO2 results in a multicenter structure. In case of titanium oxide addition it leads to a change in the relative intensities of the erbium luminescence.

  4. Structural features of conopeptide genes inferred from partial sequences of the Conus tribblei genome.

    Science.gov (United States)

    Barghi, Neda; Concepcion, Gisela P; Olivera, Baldomero M; Lluisma, Arturo O

    2016-02-01

    The evolvability of venom components (in particular, the gene-encoded peptide toxins) in venomous species serves as an adaptive strategy allowing them to target new prey types or respond to changes in the prey field. The structure, organization, and expression of the venom peptide genes may provide insights into the molecular mechanisms that drive the evolution of such genes. Conus is a particularly interesting group given the high chemical diversity of their venom peptides, and the rapid evolution of the conopeptide-encoding genes. Conus genomes, however, are large and characterized by a high proportion of repetitive sequences. As a result, the structure and organization of conopeptide genes have remained poorly known. In this study, a survey of the genome of Conus tribblei was undertaken to address this gap. A partial assembly of C. tribblei genome was generated; the assembly, though consisting of a large number of fragments, accounted for 2160.5 Mb of sequence. A large number of repetitive genomic elements consisting of 642.6 Mb of retrotransposable elements, simple repeats, and novel interspersed repeats were observed. We characterized the structural organization and distribution of conotoxin genes in the genome. A significant number of conopeptide genes (estimated to be between 148 and 193) belonging to different superfamilies with complete or nearly complete exon regions were observed, ~60 % of which were expressed. The unexpressed conopeptide genes represent hidden but significant conotoxin diversity. The conotoxin genes also differed in the frequency and length of the introns. The interruption of exons by long introns in the conopeptide genes and the presence of repeats in the introns may indicate the importance of introns in facilitating recombination, evolution and diversification of conotoxins. These findings advance our understanding of the structural framework that promotes the gene-level molecular evolution of venom peptides.

  5. Structure of TSA2 reveals novel features of the active-site loop of peroxiredoxins

    DEFF Research Database (Denmark)

    Nielsen, Maja Holch; Kidmose, Rune Thomas; Jenner, Lasse Bohl

    2016-01-01

    stress and in hydrogen peroxide signalling. Furthermore, several 2-Cys peroxiredoxins, including S. cerevisiae TSA1 and TSA2, are able to switch to chaperone activity upon hyperoxidation of their peroxidatic cysteine. This makes the sensitivity to hyperoxidation of the peroxidatic cysteine a very...... the reactivity and the sensitivity to hyperoxidation. Furthermore, the structure also explains the observed difference in the pKa values of the peroxidatic cysteines of S. cerevisiae TSA1 and TSA2 despite their very high sequence identity....

  6. Structural Flexibility and Conformation Features of Cyclic Dinucleotides in Aqueous Solutions.

    Science.gov (United States)

    Che, Xing; Zhang, Jun; Zhu, Yanyu; Yang, Lijiang; Quan, Hui; Gao, Yi Qin

    2016-03-17

    Cyclic dinucleotides are able to trigger the innate immune system by activating STING. It was found that the binding affinity of asymmetric 2'3'-cGAMP to symmetric dimer of STING is 3 orders of magnitude higher than that of the symmetric 3'3'-cyclic dinucleotides. Such a phenomenon has not been understood yet. Here we show that the subtle changes in phosphodiester linkage of CDNs lead to their distinct structural properties which correspond to the varied binding affinities. 2'-5' and/or 3'-5' linked CDNs adopt specific while different types of ribose puckers and backbone conformations. That ribose conformations and base types have different propensities for anti or syn glycosidic conformations further affects the overall flexibility of CDNs. The counterbalance between backbone ring tension and electrostatic repulsion, both affected by the ring size, also contributes to the different flexibility of CDNs. Our calculations reveal that the free energy cost for 2'3'-cGAMP to adopt the STING-bound structure is smaller than that for 3'3'-cGAMP and cyclic-di-GMP. These findings may serve as a reference for design of CDN-analogues as vaccine adjuvants. Moreover, the cyclization pattern of CDNs closely related to their physiological roles suggests the importance of understanding structural properties in the study of protein-ligand interactions.

  7. Structure and electronic properties features of amorphous chalhogenide semiconductor films prepared by ion-plasma spraying

    Energy Technology Data Exchange (ETDEWEB)

    Korobova, N., E-mail: korobova3@mail.ru; Timoshenkov, S. [Department of Microelectronics, National Research University of Electronic Technology (MIET), Zelenograd (Russian Federation); Almasov, N.; Prikhodko, O. [al-Farabi Kazakh National University, Almaty (Kazakhstan); Tsendin, K. [Ioffe Physical-Technical Institute, Russian Academy of Sciences, St. Petersburg (Russian Federation)

    2014-10-21

    Structure of amorphous chalcogenide semiconductor glassy As-S-Se films, obtained by high-frequency (HF) ion-plasma sputtering has been investigated. It was shown that the length of the atomic structure medium order and local structure were different from the films obtained by thermal vacuum evaporation. Temperature dependence of dark conductivity, as well as the dependence of the spectral transmittance has been studied. Conductivity value was determined at room temperature. Energy activation conductivity and films optical band gap have been calculated. Temperature and field dependence of the drift mobility of charge carriers in the HF As-S-Se films have been shown. Bipolarity of charge carriers drift mobility has been confirmed. Absence of deep traps for electrons in the As{sub 40}Se{sub 30}S{sub 30} spectrum of localized states for films obtained by HF plasma ion sputtering was determined. Bipolar drift of charge carriers was found in amorphous As{sub 40}Se{sub 30}S{sub 30} films obtained by ion-plasma sputtering of high-frequency, unlike the films of these materials obtained by thermal evaporation.

  8. The molecular structural features controlling stickiness in cooked rice, a major palatability determinant

    Science.gov (United States)

    Li, Hongyan; Fitzgerald, Melissa A.; Prakash, Sangeeta; Nicholson, Timothy M.; Gilbert, Robert G.

    2017-03-01

    The stickiness of cooked rice is important for eating quality and consumer acceptance. The first molecular understanding of stickiness is obtained from leaching and molecular structural characteristics during cooking. Starch is a highly branched glucose polymer. We find (i) the molecular size of leached amylopectin is 30 times smaller than that of native amylopectin while (ii) that of leached amylose is 5 times smaller than that of native amylose, (iii) the chain-length distribution (CLD: the number of monomer units in a chain on the branched polymer) of leached amylopectin is similar to native amylopectin while (iv) the CLD of leached amylose is much narrower than that of the native amylose, and (v) mainly amylopectin, not amylose, leaches out of the granule and rice kernel during cooking. Stickiness is found to increase with decreasing amylose content in the whole grain, and, in the leachate, with increasing total amount of amylopectin, the proportion of short amylopectin chains, and amylopectin molecular size. Molecular adhesion mechanisms are put forward to explain this result. This molecular structural mechanism provides a new tool for rice breeders to select cultivars with desirable palatability by quantifying the components and molecular structure of leached starch.

  9. Specific features of quasineutral carrier transport modes in semiconductors and semiconductor structures

    Science.gov (United States)

    Mnatsakanov, T. T.; Tandoev, A. G.; Yurkov, S. N.; Levinshtein, M. E.

    2009-07-01

    It has been demonstrated that the field dependence of the electron and hole mobility strongly affects the carrier distribution in semiconductor structures under quasineutral conditions. Taking into account this phenomenon, a new equation for quasineutral carrier transport in semiconductors and semiconductor structures has been suggested. The concept of the critical current density jcr has been introduced and validated. At j Lt jcr, the suggested equation transforms to the well-known 'classical' equation of quasineutral transport. By contrast, at j > jcr, novel solutions become apparent from the suggested equation. The performed analysis gives insight into what happens in regions in which the quasineutral drift and DSQD (diffusion stimulated by quasineutral drift) modes predominate. Analytical expressions have been derived for the dependences of the voltage drops across the quasineutral drift and DQSD regions on current. It has been shown that, at high current densities, the voltage drop across the DSQD region tends to decrease as the current density increases. The results obtained enable a qualitative interpretation of the negative differential conductivity region in the current-voltage characteristic of forward-biased semiconductor structures, which arises at high current densities.

  10. Discovering New Features of Protein Complexes Structures by Small-Angle X-Ray Scattering

    Science.gov (United States)

    Oliveira, C. L. P.; Vorup-Jensen, T.; Andersen, C. B. F.; Andersen, G. R.; Pedersen, J. S.

    In spite of the recent advances in the X-Ray crystallography and nuclear magnetic resonance techniques, the determination of the quaternary structure of large protein complexes is still a challenge in molecular biology and biological sciences. In this respect, small-angle X-ray scattering (SAXS) is a key technique, enabling the determination of the possible structural conformation of complexes in an almost native state. Despite of this book being devoted to scattering techniques by synchrotron radiation, in this chapter we present two examples of application of laboratory-based SAXS to protein solution. The fundaments of the technique are obviously the same and have been deeply described in Chap. 2. In this chapter, we will introduce the application of SAXS to protein solution. Special emphasis is done on data reduction and absolute units calibration. As an example to illustrate the power of this technique, two new data sets for two protein complexes will be presented. This will show how high-quality SAXS data combined with advanced model strategies enables the determination of the quaternary structure of protein complexes.

  11. NADP-Dependent Aldehyde Dehydrogenase from Archaeon Pyrobaculum sp.1860: Structural and Functional Features

    Directory of Open Access Journals (Sweden)

    Ekaterina Yu. Bezsudnova

    2016-01-01

    Full Text Available We present the functional and structural characterization of the first archaeal thermostable NADP-dependent aldehyde dehydrogenase AlDHPyr1147. In vitro, AlDHPyr1147 catalyzes the irreversible oxidation of short aliphatic aldehydes at 60–85°С, and the affinity of AlDHPyr1147 to the NADP+ at 60°С is comparable to that for mesophilic analogues at 25°С. We determined the structures of the apo form of AlDHPyr1147 (3.04 Å resolution, three binary complexes with the coenzyme (1.90, 2.06, and 2.19 Å, and the ternary complex with the coenzyme and isobutyraldehyde as a substrate (2.66 Å. The nicotinamide moiety of the coenzyme is disordered in two binary complexes, while it is ordered in the ternary complex, as well as in the binary complex obtained after additional soaking with the substrate. AlDHPyr1147 structures demonstrate the strengthening of the dimeric contact (as compared with the analogues and the concerted conformational flexibility of catalytic Cys287 and Glu253, as well as Leu254 and the nicotinamide moiety of the coenzyme. A comparison of the active sites of AlDHPyr1147 and dehydrogenases characterized earlier suggests that proton relay systems, which were previously proposed for dehydrogenases of this family, are blocked in AlDHPyr1147, and the proton release in the latter can occur through the substrate channel.

  12. Bio-inspired device: a novel smart MR spring featuring tendril structure

    Science.gov (United States)

    Kaluvan, Suresh; Park, Chun-Yong; Choi, Seung-Bok

    2016-01-01

    Smart materials such as piezoelectric patches, shape memory alloy, electro and magneto rheological fluid, magnetostrictive materials, etc are involved by far to design intelligent and high performance smart devices like injectors, dental braces, dampers, actuators and sensors. In this paper, an interesting smart device is proposed by inspiring on the structure of the bio climber plant. The key enabling concept of this proposed work is to design the smart spring damper as a helical shaped tendril structure using magneto-rheological (MR) fluid. The proposed smart spring consists of a hollow helical structure filled with MR fluid. The viscosity of the MR fluid decides the damping force of helical shaped smart spring, while the fluid intensity in the vine decides the strength of the tendril in the climber plant. Thus, the proposed smart spring can provide a new concept design of the damper which can be applicable to various damping system industries with tuneable damping force. The proposed smart spring damper has several advantageous such as cost effective, easy implementation compared with the conventional damper. In addition, the proposed spring damper can be easily designed to adapt different damping force levels without any alteration.

  13. Structural Features Essential to the Antimicrobial Functions of Human SPLUNC1.

    Science.gov (United States)

    Walton, William G; Ahmad, Saira; Little, Michael S; Kim, Christine S K; Tyrrell, Jean; Lin, Qiao; Di, Y Peter; Tarran, Robert; Redinbo, Matthew R

    2016-05-31

    SPLUNC1 is an abundantly secreted innate immune protein in the mammalian respiratory tract that exerts bacteriostatic and antibiofilm effects, binds to lipopolysaccharide (LPS), and acts as a fluid-spreading surfactant. Here, we unravel the structural elements essential for the surfactant and antimicrobial functions of human SPLUNC1 (short palate lung nasal epithelial clone 1). A unique α-helix (α4) that extends from the body of SPLUNC1 is required for the bacteriostatic, surfactant, and LPS binding activities of this protein. Indeed, we find that mutation of just four leucine residues within this helical motif to alanine is sufficient to significantly inhibit the fluid spreading abilities of SPLUNC1, as well as its bacteriostatic actions against Gram-negative pathogens Burkholderia cenocepacia and Pseudomonas aeruginosa. Conformational flexibility in the body of SPLUNC1 is also involved in the bacteriostatic, surfactant, and LPS binding functions of the protein as revealed by disulfide mutants introduced into SPLUNC1. In addition, SPLUNC1 exerts antibiofilm effects against Gram-negative bacteria, although α4 is not involved in this activity. Interestingly, though, the introduction of surface electrostatic mutations away from α4 based on the unique dolphin SPLUNC1 sequence, and confirmed by crystal structure, is shown to impart antibiofilm activity against Staphylococcus aureus, the first SPLUNC1-dependent effect against a Gram-positive bacterium reported to date. Together, these data pinpoint SPLUNC1 structural motifs required for the antimicrobial and surfactant actions of this protective human protein.

  14. Establishing whether the structural feature controlling the mechanical properties of starch films is molecular or crystalline.

    Science.gov (United States)

    Li, Ming; Xie, Fengwei; Hasjim, Jovin; Witt, Torsten; Halley, Peter J; Gilbert, Robert G

    2015-03-06

    The effects of molecular and crystalline structures on the tensile mechanical properties of thermoplastic starch (TPS) films from waxy, normal, and high-amylose maize were investigated. Starch structural variations were obtained through extrusion and hydrothermal treatment (HTT). The molecular and crystalline structures were characterized using size-exclusion chromatography and X-ray diffractometry, respectively. TPS from high-amylose maize showed higher elongation at break and tensile strength than those from normal maize and waxy maize starches when processed with 40% plasticizer. Within the same amylose content, the mechanical properties were not affected by amylopectin molecular size or the crystallinity of TPS prior to HTT. This lack of correlation between the molecular size, crystallinity and mechanical properties may be due to the dominant effect of the plasticizer on the mechanical properties. Further crystallization of normal maize TPS by HTT increased the tensile strength and Young's modulus, while decreasing the elongation at break. The results suggest that the crystallinity from the remaining ungelatinized starch granules has less significant effect on the mechanical properties than that resulting from starch recrystallization, possibly due to a stronger network from leached-out amylose surrounding the remaining starch granules.

  15. Predictive models of biohydrogen and biomethane production based on the compositional and structural features of lignocellulosic materials.

    Science.gov (United States)

    Monlau, Florian; Sambusiti, Cecilia; Barakat, Abdellatif; Guo, Xin Mei; Latrille, Eric; Trably, Eric; Steyer, Jean-Philippe; Carrere, Hélène

    2012-11-01

    In an integrated biorefinery concept, biological hydrogen and methane production from lignocellulosic substrates appears to be one of the most promising alternatives to produce energy from renewable sources. However, lignocellulosic substrates present compositional and structural features that can limit their conversion into biohydrogen and methane. In this study, biohydrogen and methane potentials of 20 lignocellulosic residues were evaluated. Compositional (lignin, cellulose, hemicelluloses, total uronic acids, proteins, and soluble sugars) as well as structural features (crystallinity) were determined for each substrate. Two predictive partial least square (PLS) models were built to determine which compositional and structural parameters affected biohydrogen or methane production from lignocellulosic substrates, among proteins, total uronic acids, soluble sugars, crystalline cellulose, amorphous holocelluloses, and lignin. Only soluble sugars had a significant positive effect on biohydrogen production. Besides, methane potentials correlated negatively to the lignin contents and, to a lower extent, crystalline cellulose showed also a negative impact, whereas soluble sugars, proteins, and amorphous hemicelluloses showed a positive impact. These findings will help to develop further pretreatment strategies for enhancing both biohydrogen and methane production.

  16. Oxide cathode mechanisms: Electronic and structural features of oxide cathode surfaces

    Science.gov (United States)

    Cunningham, J.; Nunan, J.

    1985-01-01

    This report describes studies made upon systems selected for their ability to model various important features of oxide cathodes and the mechanisms which enable them to function as efficient thermionic emitters at moderate temperatures. An account is given of experiments which aimed to simulate conditions upon the surfaces of polycrystalline samples of alkaline earth oxides (e.g., SrO and BaO/SrO or MgO and BaO/MgO) at various stages of their preparation in similiar fashion to that used in the thermal activation of oxide cathodes. Accounts are given of experiments which examined the interaction between the gases O2, N2O, H2 or Ch4 and appropriately preactivated surface of pure and mixed alkaline earth oxide samples. Accounts are given of experiments involving the controlled deposition in UHV conditions of zero-valent Ba ad-atoms-in amounts ranging from submonolayer to multilayer coverage - upon layers of SrO or BaO previously prepared in UHV conditions by evaporation of the corresponding metal and its subsequent oxidation. UPS spectra have been undertaken in order to examine surfaces of samples prepared by evaporation of barium metal or strontium metal and to study effects upon the UPS spectra by exposures to the gases N20, O2 and CH4.

  17. Two-loop anomalous dimensions for currents of baryons with two heavy quarks in NRQCD

    CERN Document Server

    Kiselev, V V

    1998-01-01

    We present analytical results on the two-loop anomalous dimensions of currents for baryons, containing two heavy quarks $J = [Q^{iT}C\\Gamma\\tau Q^j]\\Gamma' q^k\\epsilon_{ijk}$ with arbitrary Dirac matrices $\\Gamma$ and velocity of heavy quarks and the inverse heavy quark mass. It is shown, that in this approximation the anomalous dimensions do not depend on the Dirac structure of the current under consideration.

  18. Electronic Origins of Anomalous Twin Boundary Energies in Hexagonal Close Packed Transition Metals

    OpenAIRE

    de Jong, M.; Kacher, J.; Sluiter, M.H.F.; L. Qi; Olmsted, D. L.; van de Walle, A.; Morris, J. W., Jr.; Minor, A. M.; Asta, M.

    2015-01-01

    Density-functional-theory calculations of twin-boundary energies in hexagonal close packed metals reveal anomalously low values for elemental Tc and Re, which can be lowered further by alloying with solutes that reduce the electron per atom ratio. The anomalous behavior is linked to atomic geometries in the interface similar to those observed in bulk tetrahedrally close packed phases. The results establish a link between twin-boundary energetics and the theory of bulk structural stability in ...

  19. Structural Features and Chaperone Activity of the NudC Protein Family

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, Meiying; Cierpicki, Tomasz; Burdette, Alexander J.; Utepbergenov, Darkhan; Janczyk, Pawe; #322; ; #321; .; Derewenda, Urszula; Stukenberg, P. Todd; Caldwell, Kim A.; Derewenda, Zygmunt S. (UV); (UAT)

    2012-05-25

    The NudC family consists of four conserved proteins with representatives in all eukaryotes. The archetypal nudC gene from Aspergillus nidulans is a member of the nud gene family that is involved in the maintenance of nuclear migration. This family also includes nudF, whose human orthologue, Lis1, codes for a protein essential for brain cortex development. Three paralogues of NudC are known in vertebrates: NudC, NudC-like (NudCL), and NudC-like 2 (NudCL2). The fourth distantly related member of the family, CML66, contains a NudC-like domain. The three principal NudC proteins have no catalytic activity but appear to play as yet poorly defined roles in proliferating and dividing cells. We present crystallographic and NMR studies of the human NudC protein and discuss the results in the context of structures recently deposited by structural genomics centers (i.e., NudCL and mouse NudCL2). All proteins share the same core CS domain characteristic of proteins acting either as cochaperones of Hsp90 or as independent small heat shock proteins. However, while NudC and NudCL dimerize via an N-terminally located coiled coil, the smaller NudCL2 lacks this motif and instead dimerizes as a result of unique domain swapping. We show that NudC and NudCL, but not NudCL2, inhibit the aggregation of several target proteins, consistent with an Hsp90-independent heat shock protein function. Importantly, and in contrast to several previous reports, none of the three proteins is able to form binary complexes with Lis1. The availability of structural information will be of help in further studies on the cellular functions of the NudC family.

  20. Unique Structural and Nucleotide Exchange Features of the Rho1 GTPase of Entamoeba histolytica

    Energy Technology Data Exchange (ETDEWEB)

    Bosch, Dustin E.; Wittchen, Erika S.; Qiu, Connie; Burridge, Keith; Siderovski, David P. (UNC)

    2012-08-10

    The single-celled human parasite Entamoeba histolytica possesses a dynamic actin cytoskeleton vital for its intestinal and systemic pathogenicity. The E. histolytica genome encodes several Rho family GTPases known to regulate cytoskeletal dynamics. EhRho1, the first family member identified, was reported to be insensitive to the Rho GTPase-specific Clostridium botulinum C3 exoenzyme, raising the possibility that it may be a misclassified Ras family member. Here, we report the crystal structures of EhRho1 in both active and inactive states. EhRho1 is activated by a conserved switch mechanism, but diverges from mammalian Rho GTPases in lacking a signature Rho insert helix. EhRho1 engages a homolog of mDia, EhFormin1, suggesting a role in mediating serum-stimulated actin reorganization and microtubule formation during mitosis. EhRho1, but not a constitutively active mutant, interacts with a newly identified EhRhoGDI in a prenylation-dependent manner. Furthermore, constitutively active EhRho1 induces actin stress fiber formation in mammalian fibroblasts, thereby identifying it as a functional Rho family GTPase. EhRho1 exhibits a fast rate of nucleotide exchange relative to mammalian Rho GTPases due to a distinctive switch one isoleucine residue reminiscent of the constitutively active F28L mutation in human Cdc42, which for the latter protein, is sufficient for cellular transformation. Nonconserved, nucleotide-interacting residues within EhRho1, revealed by the crystal structure models, were observed to contribute a moderating influence on fast spontaneous nucleotide exchange. Collectively, these observations indicate that EhRho1 is a bona fide member of the Rho GTPase family, albeit with unique structural and functional aspects compared with mammalian Rho GTPases.

  1. STRUCTURAL FEATURE AND EXCHANGE KINETICS OF CARBOXYLATED POLYPROPYLENE ION EXCHANGE RESIN

    Institute of Scientific and Technical Information of China (English)

    WU Chinyung; YANG Chaoshiung; YANG Chong

    1987-01-01

    The present article deals with the exchange process of bivalent metal ions, such as Zn2 +, Cd2 + and Hg2+, etc., taken up by non-crosslinked carboxylated polypropylene (CPP) resin. The control factor of the exchange rate deduced from the kinetic data is governed basically by the chemical reaction rather than the mass transfer effect particle diffusion and/or liquid film diffusion. In solution, all the graft chains in the outer shell ofa CPP resin could form a "quasi-macromolecular solution" domain. This opinion further demonstrates the structural pattern of CPP resin proposed in earlier paper[1].

  2. Structural features in GaN grown on a Ge(111) substrate

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Y.; McAleese, C.; Xiu, H.; Humphreys, C.J. [Department of Materials Science and Metallurgy, University of Cambridge (United Kingdom); Lieten, R.R.; Degroote, S.; Borghs, G. [Interuniversity Microelectronics Center, Leuven (Belgium)

    2008-07-01

    Using electron microscopy, structural characterisation has been carried out on a GaN epilayer grown directly on a Ge(111) substrate using plasma assisted molecular beam epitaxy (PAMBE) without any intermediate buffer layers. It was determined that a defect with a triangular shape, initially observed with optical microscopy, is essentially a faceted void in the Ge extending from the interface into the substrate. Both hexagonal and cubic phase GaN were observed in the epilayer which may be due to temperature variation during growth. (copyright 2008 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  3. Crystal structures of two transcriptional regulators from Bacillus cereus define the conserved structural features of a PadR subfamily.

    Directory of Open Access Journals (Sweden)

    Guntur Fibriansah

    Full Text Available PadR-like transcriptional regulators form a structurally-related family of proteins that control the expression of genes associated with detoxification, virulence and multi-drug resistance in bacteria. Only a few members of this family have been studied by genetic, biochemical and biophysical methods, and their structure/function relationships are still largely undefined. Here, we report the crystal structures of two PadR-like proteins from Bacillus cereus, which we named bcPadR1 and bcPadR2 (products of gene loci BC4206 and BCE3449 in strains ATCC 14579 and ATCC 10987, respectively. BC4206, together with its neighboring gene BC4207, was previously shown to become significantly upregulated in presence of the bacteriocin AS-48. DNA mobility shift assays reveal that bcPadR1 binds to a 250 bp intergenic region containing the putative BC4206-BC4207 promoter sequence, while in-situ expression of bcPadR1 decreases bacteriocin tolerance, together suggesting a role for bcPadR1 as repressor of BC4206-BC4207 transcription. The function of bcPadR2 (48% identical in sequence to bcPadR1 is unknown, but the location of its gene just upstream from genes encoding a putative antibiotic ABC efflux pump, suggests a role in regulating antibiotic resistance. The bcPadR proteins are structurally similar to LmrR, a PadR-like transcription regulator in Lactococcus lactis that controls expression of a multidrug ABC transporter via a mechanism of multidrug binding and induction. Together these proteins define a subfamily of conserved, relatively small PadR proteins characterized by a single C-terminal helix for dimerization. Unlike LmrR, bcPadR1 and bcPadR2 lack a central pore for ligand binding, making it unclear whether the transcriptional regulatory roles of bcPadR1 and bcPadR2 involve direct ligand recognition and induction.

  4. Crystal structures of two transcriptional regulators from Bacillus cereus define the conserved structural features of a PadR subfamily.

    Science.gov (United States)

    Fibriansah, Guntur; Kovács, Ákos T; Pool, Trijntje J; Boonstra, Mirjam; Kuipers, Oscar P; Thunnissen, Andy-Mark W H

    2012-01-01

    PadR-like transcriptional regulators form a structurally-related family of proteins that control the expression of genes associated with detoxification, virulence and multi-drug resistance in bacteria. Only a few members of this family have been studied by genetic, biochemical and biophysical methods, and their structure/function relationships are still largely undefined. Here, we report the crystal structures of two PadR-like proteins from Bacillus cereus, which we named bcPadR1 and bcPadR2 (products of gene loci BC4206 and BCE3449 in strains ATCC 14579 and ATCC 10987, respectively). BC4206, together with its neighboring gene BC4207, was previously shown to become significantly upregulated in presence of the bacteriocin AS-48. DNA mobility shift assays reveal that bcPadR1 binds to a 250 bp intergenic region containing the putative BC4206-BC4207 promoter sequence, while in-situ expression of bcPadR1 decreases bacteriocin tolerance, together suggesting a role for bcPadR1 as repressor of BC4206-BC4207 transcription. The function of bcPadR2 (48% identical in sequence to bcPadR1) is unknown, but the location of its gene just upstream from genes encoding a putative antibiotic ABC efflux pump, suggests a role in regulating antibiotic resistance. The bcPadR proteins are structurally similar to LmrR, a PadR-like transcription regulator in Lactococcus lactis that controls expression of a multidrug ABC transporter via a mechanism of multidrug binding and induction. Together these proteins define a subfamily of conserved, relatively small PadR proteins characterized by a single C-terminal helix for dimerization. Unlike LmrR, bcPadR1 and bcPadR2 lack a central pore for ligand binding, making it unclear whether the transcriptional regulatory roles of bcPadR1 and bcPadR2 involve direct ligand recognition and induction.

  5. Combining EEG Microstates with fMRI Structural Features for Modeling Brain Activity.

    Science.gov (United States)

    Michalopoulos, Kostas; Bourbakis, Nikolaos

    2015-12-01

    Combining information from Electroencephalography (EEG) and Functional Magnetic Resonance Imaging (fMRI) has been a topic of increased interest recently. The main advantage of the EEG is its high temporal resolution, in the scale of milliseconds, while the main advantage of fMRI is the detection of functional activity with good spatial resolution. The advantages of each modality seem to complement each other, providing better insight in the neuronal activity of the brain. The main goal of combining information from both modalities is to increase the spatial and the temporal localization of the underlying neuronal activity captured by each modality. This paper presents a novel technique based on the combination of these two modalities (EEG, fMRI) that allow a better representation and understanding of brain activities in time. EEG is modeled as a sequence of topographies, based on the notion of microstates. Hidden Markov Models (HMMs) were used to model the temporal evolution of the topography of the average Event Related Potential (ERP). For each model the Fisher score of the sequence is calculated by taking the gradient of the trained model parameters. The Fisher score describes how this sequence deviates from the learned HMM. Canonical Partial Least Squares (CPLS) were used to decompose the two datasets and fuse the EEG and fMRI features. In order to test the effectiveness of this method, the results of this methodology were compared with the results of CPLS using the average ERP signal of a single channel. The presented methodology was able to derive components that co-vary between EEG and fMRI and present significant differences between the two tasks.

  6. Role of water on formation and structural features of Maya blue

    Science.gov (United States)

    Mondelli, C.; Sánchez del Río, M.; González, M. A.; Magazzú, A.; Cavallari, C.; Suárez, M.; García-Romero, E.; Romano, P.

    2012-02-01

    The Maya blue (MB) is an artificial pigment created between 500-800 A.D. and used in murals, pottery and sculptures by Mayas and other people in Mesoamerica. MB is resistant to age, acid, weathering, biodegradation and even modern chemical solvents, but the chemical reasons behind the resistance to chemical aggressions are still under debate. Water plays a fundamental role in the interactions between indigo and clay. The dynamics of the clay's zeolitic and structural water molecules during the formation of MB, usually stabilized by moderate heating, has been monitored by means of neutron inelastic scattering. Neutron incoherent scattering in these samples is only due to the hydrogen atoms, so the signal is very sensitive to the amount of released water, providing detailed information on the dehydration process. A simultaneous analysis of the coherent elastic scattering and the incoherent scattering allows observing and quantifying how the structure of the clay is affected by dehydration. Here we show that a quite resistant pigment can be obtained at room temperature simply by dehydrating a palygorskite-indigo mixture employing only vacuum, without any thermal treatment.

  7. Structural features of the Nogo receptor signaling complexes at the neuron/myelin interface.

    Science.gov (United States)

    Saha, Nayanendu; Kolev, Momchil; Nikolov, Dimitar B

    2014-10-01

    Upon spinal cord injury, the central nervous system axons are unable to regenerate, partially due to the repulsive action of myelin inhibitors, such as the myelin-associated glycoprotein (MAG), Nogo-A and the oligodendrocyte myelin glycoprotein (OMgp). These inhibitors bind and signal through a single receptor/co-receptor complex that comprises of NgR1/LINGO-1 and either p75 or TROY, triggering intracellular downstream signaling that impedes the re-growth of axons. Structure-function analysis of myelin inhibitors and their neuronal receptors, particularly the NgRs, have provided novel information regarding the molecular details of the inhibitor/receptor/co-receptor interactions. Structural and biochemical studies have revealed the architecture of many of these proteins and identified the molecular regions important for assembly of the inhibitory signaling complexes. It was also recently shown that gangliosides, such as GT1b, mediate receptor/co-receptor binding. In this review, we highlight these studies and summarize our current understanding of the multi-protein cell-surface complexes mediating inhibitory signaling events at the neuron/myelin interface.

  8. Novel structural and regulatory features of rhoptry secretory kinases in Toxoplasma gondii

    Energy Technology Data Exchange (ETDEWEB)

    Qiu, Wei; Wernimont, Amy; Tang, Keliang; Taylor, Sonya; Lunin, Vladimir; Schapira, Matthieu; Fentress, Sarah; Hui, Raymond; Sibley, L. David; (Toronto); (WU-MED)

    2009-09-29

    Serine/threonine kinases secreted from rhoptry organelles constitute important virulence factors of Toxoplasma gondii. Rhoptry kinases are highly divergent and their structures and regulatory mechanism are hitherto unknown. Here, we report the X-ray crystal structures of two related pseudokinases named ROP2 and ROP8, which differ primarily in their substrate-binding site. ROP kinases contain a typical bilobate kinase fold and a novel N-terminal extension that both stabilizes the N-lobe and provides a unique means of regulation. Although ROP2 and ROP8 were catalytically inactive, they provided a template for homology modelling of the active kinase ROP18, a major virulence determinant of T. gondii. Autophosphorylation of key residues in the N-terminal extension resulted in ROP18 activation, which in turn phosphorylated ROP2 and ROP8. Mutagenesis and mass spectrometry experiments revealed that ROP18 was maximally activated when this phosphorylated N-terminus relieved autoinhibition resulting from extension of aliphatic side chains into the ATP-binding pocket. This novel means of regulation governs ROP kinases implicated in parasite virulence.

  9. One common structural feature of "words" in protein sequences and human texts.

    Science.gov (United States)

    Zemková, M; Trifonov, E N; Zahradník, D

    2014-01-01

    Frequently discussed analogy between genetic and human texts is explored by comparison of alternation of polar and non-polar amino-acid residues in proteins and alternation of consonants and vowels in human texts. In human languages, the usage of possible combinations of consonants and vowels is influenced by pronounceability of the combinations. Similarly, oligopeptide composition of proteins is influenced by requirements of protein folding and stability. One special type of structure often present in proteins is amphipathic α-helices in which polar and non-polar amino acids alternate with the period 3.5 residues, not unlike alternation of consonants and vowels. In this study, we evaluated the contribution made by amphipathic alternations to the protein sequence texts (20-24%). Their proportion is lower than respective values for alternating words in human texts (57-89%). The proteomes (full sets of proteins for selected organisms) were transformed into ranked sequences of n-grams (words of length n), including periodical amphipathic structures. Similarly, human texts were transformed into sequences of alternating consonants and vowels. Analysis of the vocabularies shows that in both types of texts (human languages and proteins) the alternating words are dominant or highly preferred, thus, strengthening the analogy between these two types of texts. The contribution of amphipathic words in the upper parts of the ranked lists for 10 analyzed proteomes varies between 58 and 74%. In human texts respective values range between 90 and 100%.

  10. The structural, compositional and mechanical features of the calcite shell of the barnacle Tetraclita rufotincta.

    Science.gov (United States)

    Astachov, Liliana; Nevo, Zvi; Brosh, Tamar; Vago, Razi

    2011-09-01

    The microstructure and chemical composition of the calcite shell of the sea barnacle Tetraclita rufotincta (Pilsbry, 1916) were investigated using microscopic and analytical methods. The barnacle shell was separated mechanically into its three substructural units: outer, interior, and inner layers. The organic matrices of these structural parts were further separated into soluble and insoluble constituents and their characteristic functional groups were studied by FTIR. Investigation of the mechanical properties of the interior mass of the shell reveals remarkable viscoelastic behavior. In general, the mechanical behavior of the shell is a function of its geometry as well as of the material, of which it is constructed. In the case of T. rufotincta, as calcite is a brittle material, the elastic behavior of the shell is apparently related to its micro- and macroarchitecture. The latter enables the shell to fulfill its primary function which is to protect the organism from a hostile environment and enables its survival. Our detailed identification of the similarities and differences between the various structural components of the shell in regard to the composition and properties of the organic component will hopefully throw light on the role of organic matrices in biomineralization processes.

  11. Anti-MrkA Monoclonal Antibodies Reveal Distinct Structural and Antigenic Features of MrkA

    Science.gov (United States)

    Wang, Qun; Chen, Yan; Cvitkovic, Romana; Pennini, Meghan E.; Chang, Chew shun; Pelletier, Mark; Bonnell, Jessica; Wu, Herren; Dall’Acqua, William F.; Stover, C. Kendall; Xiao, Xiaodong

    2017-01-01

    Antibody therapy against antibiotics resistant Klebsiella pneumoniae infections represents a promising strategy, the success of which depends critically on the ability to identify appropriate antibody targets. Using a target-agnostic strategy, we recently discovered MrkA as a potential antibody target and vaccine antigen. Interestingly, the anti-MrkA monoclonal antibodies isolated through phage display and hybridoma platforms all recognize an overlapping epitope, which opens up important questions including whether monoclonal antibodies targeting different MrkA epitopes can be generated and if they possess different protective profiles. In this study we generated four anti-MrkA antibodies targeting different epitopes through phage library panning against recombinant MrkA protein. These anti-MrkA antibodies elicited strong in vitro and in vivo protections against a multi-drug resistant Klebsiella pneumoniae strain. Furthermore, mutational and epitope analysis suggest that the two cysteine residues may play essential roles in maintaining a MrkA structure that is highly compacted and exposes limited antibody binding/neutralizing epitopes. These results suggest the need for further in-depth understandings of the structure of MrkA, the role of MrkA in the pathogenesis of Klebsiella pneumoniae and the protective mechanism adopted by anti-MrkA antibodies to fully explore the potential of MrkA as an efficient therapeutic target and vaccine antigen. PMID:28107434

  12. Distinct structural features of TFAM drive mitochondrial DNA packaging versus transcriptional activation.

    Science.gov (United States)

    Ngo, Huu B; Lovely, Geoffrey A; Phillips, Rob; Chan, David C

    2014-01-01

    TFAM (transcription factor A, mitochondrial) is a DNA-binding protein that activates transcription at the two major promoters of mitochondrial DNA (mtDNA)--the light strand promoter (LSP) and the heavy strand promoter 1 (HSP1). Equally important, it coats and packages the mitochondrial genome. TFAM has been shown to impose a U-turn on LSP DNA; however, whether this distortion is relevant at other sites is unknown. Here we present crystal structures of TFAM bound to HSP1 and to nonspecific DNA. In both, TFAM similarly distorts the DNA into a U-turn. Yet, TFAM binds to HSP1 in the opposite orientation from LSP explaining why transcription from LSP requires DNA bending, whereas transcription at HSP1 does not. Moreover, the crystal structures reveal dimerization of DNA-bound TFAM. This dimerization is dispensable for DNA bending and transcriptional activation but is important in DNA compaction. We propose that TFAM dimerization enhances mitochondrial DNA compaction by promoting looping of the DNA.

  13. Active vibration control of hybrid smart structures featuring piezoelectric films and electrorheological fluids

    Science.gov (United States)

    Choi, Seung-Bok; Park, Yong-Kun; Cheong, ChaeCheon

    1996-05-01

    This paper presents a proof-of-concept investigation on an active vibration control of a hybrid smart structure (HSS) consisting of a piezoelectric film actuator (PFA) and an electro- rheological fluid actuator (ERFA). Firstly, an HSS beam is constructed by inserting a starch- based electro-rheological fluid into a hollow composite beam and perfectly bonding two piezoelectric films on the upper and lower surfaces of the structure as an actuator and as a sensor, respectively. As for the PFA, a neuro-sliding mode controller (NSC) incorporating neural networks with the concept of sliding mode control is formulated. On the other hand, the control scheme for the ERFA is developed as a function of excitation frequencies on the basis of field-dependent frequency responses. An experimental implementation for the PFA and ERFA is then established to perform an active vibration control of the HSS in the transient and forced vibrations. Both the increment of damping ratios and the suppression of tip deflections are evaluated in order to demonstrate control effectiveness of the PFA, the ERFA, and the hybrid actuation. The experimental results exhibit a superior ability of the hybrid actuation system to tailor elastodynamic responses of the HSS rather than a single class of actuation system alone.

  14. Correlation spectroscopy and molecular dynamics simulations to study the structural features of proteins.

    Directory of Open Access Journals (Sweden)

    Antonio Varriale

    Full Text Available In this work, we used a combination of fluorescence correlation spectroscopy (FCS and molecular dynamics (MD simulation methodologies to acquire structural information on pH-induced unfolding of the maltotriose-binding protein from Thermus thermophilus (MalE2. FCS has emerged as a powerful technique for characterizing the dynamics of molecules and it is, in fact, used to study molecular diffusion on timescale of microsecond and longer. Our results showed that keeping temperature constant, the protein diffusion coefficient decreased from 84±4 µm(2/s to 44±3 µm(2/s when pH was changed from 7.0 to 4.0. An even more marked decrease of the MalE2 diffusion coefficient (31±3 µm(2/s was registered when pH was raised from 7.0 to 10.0. According to the size of MalE2 (a monomeric protein with a molecular weight of 43 kDa as well as of its globular native shape, the values of 44 µm(2/s and 31 µm(2/s could be ascribed to deformations of the protein structure, which enhances its propensity to form aggregates at extreme pH values. The obtained fluorescence correlation data, corroborated by circular dichroism, fluorescence emission and light-scattering experiments, are discussed together with the MD simulations results.

  15. Homochiral Cu(II) and Ni(II) malates with tunable structural features

    Science.gov (United States)

    Zavakhina, Marina S.; Samsonenko, Denis G.; Virovets, Alexander V.; Dybtsev, Danil N.; Fedin, Vladimir P.

    2014-02-01

    Four new homochiral metal-organic frameworks (MOFs) based on S-malate anions and N-donor linkers of different length have been prepared under solvothermal conditions. [Cu(mal)(bpy)]·H2O (1), [Cu(mal)(bpe)]·2H2O (2), [Ni(mal)(bpy)]·1.3CH3OH (3) and [Ni(mal)(bpe)]·4H2O (4) (mal=S-malate, bpy=4,4‧-bipyridil, bpe=trans-1,2-bis(4-pyridyl)ethylene) were characterized by a number of analytical methods including powder X-ray diffraction, elemental, thermogravimetric analyses, IR spectroscopy. Compounds 1-3 were structurally characterized by X-ray crystallography. The absence of the chiral ligand racemization under synthetic conditions was unambiguously confirmed by polarimetry experiments. Compounds 1 and 2 contain metal-malate layered motives, connected by N-donor linkers and contribute to the family of isoreticular Cu(II) malates and tartrates [Cu(mal)L] and [Cu(tart)L], (tart=tartrate; L=ditopic rigid organic ligand). The Ni-based compounds 3 and 4 share 1D chiral {Ni(mal)} motives and possess novel type of the chiral framework, previously unknown for chiral carboxylates. The linear N-donor linkers connect these chiral chains, thus controlling the channel diameter and guest accessible volume of the homochiral structure, which exceeds 60 %.

  16. Nano-structured morphological features of pulsed direct current magnetron sputtered Mo films for photovoltaic applications

    Energy Technology Data Exchange (ETDEWEB)

    Karthikeyan, Sreejith, E-mail: s.karthikeyan@edu.salford.ac.uk; Hill, Arthur E.; Pilkington, Richard D.

    2011-10-31

    Historically, molybdenum thin films have been used as the back contact for Cu(In,Ga)Se{sub 2} based solar cells and as such the properties of these layers play an important role in the overall cell structure. This paper describes the production of molybdenum films using pulsed d.c. magnetron sputtering from compressed molybdenum powder targets. The films were deposited at different substrate temperatures under constant power and constant current modes, and analysed using X-ray diffraction, scanning electron microscopy, atomic force microscopy and four point resistance probe. Mechanical strain and resistivity were found to decrease with substrate temperature together with a shift in the (110) crystallographic plane towards higher diffraction angles. All films were well adhered to the glass substrates irrespective of their high tensile strain. Surface morphology analysis revealed the presence of nano-structured stress relief patterns which can enhance the nucleation sites for subsequent CuInSe{sub 2} deposition. A high-resolution cross sectional image showed the columnar growth of the films. Surface roughness analysis revealed that roughness increased with increase in substrate temperature.

  17. Mutagenicity in a Molecule: Identification of Core Structural Features of Mutagenicity Using a Scaffold Analysis.

    Directory of Open Access Journals (Sweden)

    Kuo-Hsiang Hsu

    Full Text Available With advances in the development and application of Ames mutagenicity in silico prediction tools, the International Conference on Harmonisation (ICH has amended its M7 guideline to reflect the use of such prediction models for the detection of mutagenic activity in early drug safety evaluation processes. Since current Ames mutagenicity prediction tools only focus on functional group alerts or side chain modifications of an analog series, these tools are unable to identify mutagenicity derived from core structures or specific scaffolds of a compound. In this study, a large collection of 6512 compounds are used to perform scaffold tree analysis. By relating different scaffolds on constructed scaffold trees with Ames mutagenicity, four major and one minor novel mutagenic groups of scaffold are identified. The recognized mutagenic groups of scaffold can serve as a guide for medicinal chemists to prevent the development of potentially mutagenic therapeutic agents in early drug design or development phases, by modifying the core structures of mutagenic compounds to form non-mutagenic compounds. In addition, five series of substructures are provided as recommendations, for direct modification of potentially mutagenic scaffolds to decrease associated mutagenic activities.

  18. The structural features of Trask that mediate its anti-adhesive functions.

    Directory of Open Access Journals (Sweden)

    Danislav S Spassov

    Full Text Available Trask/CDCP1 is a transmembrane protein with a large extracellular and small intracellular domains. The intracellular domain (ICD undergoes tyrosine phosphorylation by Src kinases during anchorage loss and, when phosphorylated, Trask functions to inhibit cell adhesion. The extracellular domain (ECD undergoes proteolytic cleavage by serine proteases, although the functional significance of this remains unknown. There is conflicting evidence regarding whether it functions to signal the phosphorylation of the ICD. To better define the structural determinants that mediate the anti-adhesive functions of Trask, we generated a series of deletion mutants of Trask and expressed them in tet-inducible cell models to define the structural elements involved in cell adhesion signaling. We find that the ECD is dispensable for the phosphorylation of the ICD or for the inhibition of cell adhesion. The anti-adhesive functions of Trask are entirely embodied within its ICD and are specifically due to tyrosine phosphorylation of the ICD as this function is completely lost in a phosphorylation-defective tyrosine-phenylalanine mutant. Both full length and cleaved ECDs are fully capable of phosphorylation and undergo phosphorylation during anchorage loss and cleavage is not an upstream signal for ICD phosphorylation. These data establish that the anti-adhesive functions of Trask are mediated entirely through its tyrosine phosphorylation. It remains to be defined what role, if any, the Trask ECD plays in its adhesion functions.

  19. X-Ray Crystal Structure of the Full Length Human Chitotriosidase (CHIT1) Reveals Features of Its Chitin Binding Domain

    Science.gov (United States)

    Fadel, Firas; Zhao, Yuguang; Cousido-Siah, Alexandra; Ruiz, Francesc X.; Mitschler, André; Podjarny, Alberto

    2016-01-01

    Chitinases are enzymes that catalyze the hydrolysis of chitin. Human chitotriosidase (CHIT1) is one of the two active human chitinases, involved in the innate immune response and highly expressed in a variety of diseases. CHIT1 is composed of a catalytic domain linked by a hinge to its chitin binding domain (ChBD). This latter domain belongs to the carbohydrate-binding module family 14 (CBM14 family) and facilitates binding to chitin. So far, the available crystal structures of the human chitinase CHIT1 and the Acidic Mammalian Chitinase (AMCase) comprise only their catalytic domain. Here, we report a crystallization strategy combining cross-seeding and micro-seeding cycles which allowed us to obtain the first crystal structure of the full length CHIT1 (CHIT1-FL) at 1.95 Å resolution. The CHIT1 chitin binding domain (ChBDCHIT1) structure shows a distorted β-sandwich 3D fold, typical of CBM14 family members. Accordingly, ChBDCHIT1 presents six conserved cysteine residues forming three disulfide bridges and several exposed aromatic residues that probably are involved in chitin binding, including the highly conserved Trp465 in a surface- exposed conformation. Furthermore, ChBDCHIT1 presents a positively charged surface which may be involved in electrostatic interactions. Our data highlight the strong structural conservation of CBM14 family members and uncover the structural similarity between the human ChBDCHIT1, tachycitin and house mite dust allergens. Overall, our new CHIT1-FL structure, determined with an adapted crystallization approach, is one of the few complete bi-modular chitinase structures available and reveals the structural features of a human CBM14 domain. PMID:27111557

  20. X-Ray Crystal Structure of the Full Length Human Chitotriosidase (CHIT1 Reveals Features of Its Chitin Binding Domain.

    Directory of Open Access Journals (Sweden)

    Firas Fadel

    Full Text Available Chitinases are enzymes that catalyze the hydrolysis of chitin. Human chitotriosidase (CHIT1 is one of the two active human chitinases, involved in the innate immune response and highly expressed in a variety of diseases. CHIT1 is composed of a catalytic domain linked by a hinge to its chitin binding domain (ChBD. This latter domain belongs to the carbohydrate-binding module family 14 (CBM14 family and facilitates binding to chitin. So far, the available crystal structures of the human chitinase CHIT1 and the Acidic Mammalian Chitinase (AMCase comprise only their catalytic domain. Here, we report a crystallization strategy combining cross-seeding and micro-seeding cycles which allowed us to obtain the first crystal structure of the full length CHIT1 (CHIT1-FL at 1.95 Å resolution. The CHIT1 chitin binding domain (ChBDCHIT1 structure shows a distorted β-sandwich 3D fold, typical of CBM14 family members. Accordingly, ChBDCHIT1 presents six conserved cysteine residues forming three disulfide bridges and several exposed aromatic residues that probably are involved in chitin binding, including the highly conserved Trp465 in a surface- exposed conformation. Furthermore, ChBDCHIT1 presents a positively charged surface which may be involved in electrostatic interactions. Our data highlight the strong structural conservation of CBM14 family members and uncover the structural similarity between the human ChBDCHIT1, tachycitin and house mite dust allergens. Overall, our new CHIT1-FL structure, determined with an adapted crystallization approach, is one of the few complete bi-modular chitinase structures available and reveals the structural features of a human CBM14 domain.

  1. Temperature and Magnetic Field Driven Modifications in the I-V Features of Gold-DNA-Gold Structure

    Directory of Open Access Journals (Sweden)

    Nadia Mahmoudi Khatir

    2014-10-01

    Full Text Available The fabrication of Metal-DNA-Metal (MDM structure-based high sensitivity sensors from DNA micro-and nanoarray strands is a key issue in their development. The tunable semiconducting response of DNA in the presence of external electromagnetic and thermal fields is a gift for molecular electronics. The impact of temperatures (25–55 °C and magnetic fields (0–1200 mT on the current-voltage (I-V features of Au-DNA-Au (GDG structures with an optimum gap of 10 μm is reported. The I-V characteristics acquired in the presence and absence of magnetic fields demonstrated the semiconducting diode nature of DNA in GDG structures with high temperature sensitivity. The saturation current in the absence of magnetic field was found to increase sharply with the increase of temperature up to 45 °C and decrease rapidly thereafter. This increase was attributed to the temperature-assisted conversion of double bonds into single bond in DNA structures. Furthermore, the potential barrier height and Richardson constant for all the structures increased steadily with the increase of external magnetic field irrespective of temperature variations. Our observation on magnetic field and temperature sensitivity of I-V response in GDG sandwiches may contribute towards the development of DNA-based magnetic sensors.

  2. Structural and Morphological Features of Acid-Bearing Polymers for PEM Fuel Cells

    DEFF Research Database (Denmark)

    Yang, Yunsong; Siu, Ana; Peckham, Timothy J.;

    2008-01-01

    significantly enhance the transport of water and protons. For membranes that contain a high content of water, phase separation is less influential. Continuity of ionic aggregates is influential on the diffusion of water and electroosmotic drag within a membrane. A balance of these properties must be considered......Chemical structure, polymer microstructure, sequence distribution, and morphology of acid-bearing polymers are important factors in the design of polymer electrolyte membranes (PEMs) for fuel cells. The roles of ion aggregation and phase separation in vinylic- and aromatic-based polymers in proton...... conductivity and water transport are described. The formation, dimensions, and connectivity of ionic pathways are consistently found to play an important role in determining the physicochemical properties of PEMs. For polymers that possess low water content, phase separation and ionic channel formation...

  3. Comparison of Algorithms for Prediction of Protein Structural Features from Evolutionary Data.

    Science.gov (United States)

    Bywater, Robert P

    2016-01-01

    Proteins have many functions and predicting these is still one of the major challenges in theoretical biophysics and bioinformatics. Foremost amongst these functions is the need to fold correctly thereby allowing the other genetically dictated tasks that the protein has to carry out to proceed efficiently. In this work, some earlier algorithms for predicting protein domain folds are revisited and they are compared with more recently developed methods. In dealing with intractable problems such as fold prediction, when different algorithms show convergence onto the same result there is every reason to take all algorithms into account such that a consensus result can be arrived at. In this work it is shown that the application of different algorithms in protein structure prediction leads to results that do not converge as such but rather they collude in a striking and useful way that has never been considered before.

  4. Effect of several structural features in coal on its tendency to reduce

    Energy Technology Data Exchange (ETDEWEB)

    Grigor' eva, E.A.; Bakirova, E.V.; Lesnikova, E.B.; Larina, N.K.; Zharova, M.N.; Dzhalyabova, L.V.

    1981-07-01

    Relationship between the tendency of coal to be reduced and the nature and quantity of the ether and organo-mineral bonds in the structure of coals is studied. The purpose of the study was to determine the intensity of the reaction during coal hydrogenation. Sodium borhydrate was used as a reducing agent because of its selective action on carbonyl groups and because of the possibility of describing the nature of hydrolyzed bonds in coal which form carbonyl groups. By hydrolysis of hard and brown coals and subsequent selective reduction, the effect of various carbonyl groups and organo-mineral bonds formed as a result of the destruction of ether groupings and carbon to carbon cross linkages were demonstrated. (17 refs.) (In Russian)

  5. Structural feature and electronic property of an (8, 0)carbon-silicon carbide nanotube heterojunction

    Institute of Scientific and Technical Information of China (English)

    Liu Hong-Xia; Zhang He-Ming; Hu Hui-Yong; Song Jiu-Xu

    2009-01-01

    A supercell of a nanotube heterojunction formed by an (8, 0) carbon nanotube (CNT) and an (8, 0) silicon carbide nanotube (SiCNT) is established, in which 96 C atoms and 32 Si atoms are included. The geometry optimization and the electronic property of the heterojunction are implemented through the first-principles calculation based on the density functional theory (DFT). The results indicate that the structural rearrangement takes place mainly on the interface and the energy gap of the heterojunetion is 0.31 eV, which is narrower than those of the isolated CNT and the isolated SiCNT. By using the average bond energy method, the valence band offset and the conduction band offset axe obtained as 0.71 and -0.03eV, respectively.

  6. The bats (Chiroptera; Mammalia of Mordovia: specific structure and features of distribution

    Directory of Open Access Journals (Sweden)

    Oleg N. Artaev

    2016-05-01

    Full Text Available This article presents the specific structure and distribution of the bats made in the territory of the Republic of Mordovia (Central Russia from the first half of the 20th century to the present. Occurence, relative abundance and patterns of distribution are briefly assessed for rare species. On this base, recommendations for inclusion these bats in the regional Red Data Book are presented. .In Mordovia twelve species of bats have been observed. There are widespread and numerous species: Pipistrellus nathusii, Myotis daubentonii, M. dasycneme, Nyctalus noctula and Vespertilio murinus. Widespread but less numerous species are: Myotis brandtii and Plecotus auritus. Finally, rare species are: Myotis nattereri, Nyctalus lasiopterus, N. leisleri, Pipistrellus pygmaeus and P. kuhlii.

  7. Characterization of structural features controlling the receptiveness of empty class II MHC molecules

    DEFF Research Database (Denmark)

    Rupp, Bernd; Günther, Sebastian; Makhmoor, Talat;

    2011-01-01

    MHC class II molecules (MHC II) play a pivotal role in the cell-surface presentation of antigens for surveillance by T cells. Antigen loading takes place inside the cell in endosomal compartments and loss of the peptide ligand rapidly leads to the formation of a non-receptive state of the MHC...... known MHC molecules. This shift causes a narrowing of the two helices flanking the binding site and results in a closure, which is further stabilized by the formation of a critical hydrogen bond between residues aQ9 and ßN82. Mutagenesis experiments confirmed that replacement of either one of the two......-receptiveness. Manipulation of peptide loading efficiency for improved peptide vaccination strategies could be one of the applications profiting from the structural knowledge provided by this study....

  8. Polarization dependent formation of femtosecond laser-induced periodic surface structures near stepped features

    Science.gov (United States)

    Murphy, Ryan D.; Torralva, Ben; Adams, David P.; Yalisove, Steven M.

    2014-06-01

    Laser-induced periodic surface structures (LIPSS) are formed near 110 nm-tall Au microstructured edges on Si substrates after single-pulse femtosecond irradiation with a 150 fs pulse centered near a 780 nm wavelength. We investigate the contributions of Fresnel diffraction from step-edges and surface plasmon polariton (SPP) excitation to LIPSS formation on Au and Si surfaces. For certain laser polarization vector orientations, LIPSS formation is dominated by SPP excitation; however, when SPP excitation is minimized, Fresnel diffraction dominates. The LIPSS orientation and period distributions are shown to depend on which mechanism is activated. These results support previous observations of the laser polarization vector influencing LIPSS formation on bulk surfaces.

  9. Polarization dependent formation of femtosecond laser-induced periodic surface structures near stepped features

    Energy Technology Data Exchange (ETDEWEB)

    Murphy, Ryan D. [Applied Physics Program, University of Michigan, Ann Arbor, Michigan 48109 (United States); Torralva, Ben [Department of Atmospheric, Oceanic and Space Sciences, University of Michigan, Ann Arbor, Michigan 48109 (United States); Adams, David P. [Sandia National Laboratories, Albuquerque, New Mexico 87123 (United States); Yalisove, Steven M. [Department of Materials Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109 (United States)

    2014-06-09

    Laser-induced periodic surface structures (LIPSS) are formed near 110 nm-tall Au microstructured edges on Si substrates after single-pulse femtosecond irradiation with a 150 fs pulse centered near a 780 nm wavelength. We investigate the contributions of Fresnel diffraction from step-edges and surface plasmon polariton (SPP) excitation to LIPSS formation on Au and Si surfaces. For certain laser polarization vector orientations, LIPSS formation is dominated by SPP excitation; however, when SPP excitation is minimized, Fresnel diffraction dominates. The LIPSS orientation and period distributions are shown to depend on which mechanism is activated. These results support previous observations of the laser polarization vector influencing LIPSS formation on bulk surfaces.

  10. Structural Feature and Solute Trapping of Rapidly Grown Ni3Sn Intermetallic Compound

    Institute of Scientific and Technical Information of China (English)

    QIN Hai-Yan; WANG Wei-Li; WEI Bing-Bo

    2009-01-01

    The rapid dendritic growth of primary Ni3Sn phase in undercooled Nio30.9%Sn-5%Ge alloy is investigated by using the glass fluxing technique. The dendritic growth velocity of Ni3Sn compound is measured as a function of undercooling, and a velocity of 2.47m/s is achieved at the maximum undercooling of 251 K (0.17TL). The addition of the Ge element reduces its growth velocity as compared with the binary Ni75Sn25 alloy. During rapid solidification, the Ni3Sn compound behaves like a normal sofid solution and it displays a morphological transition of "coarse dendrite-equiaxed grain-vermicular structure" with the increase of undercooling. Significant solute trapping of Ge atoms occurs in the whole undercooling range.

  11. Monomeric Chiral and Achiral Basket-Handle Porphyrins: Synthesis, Structural Features, and Arrested Tautomerism.

    Science.gov (United States)

    Gehrold, Andreas C; Bruhn, Torsten; Schneider, Heidi; Radius, Udo; Bringmann, Gerhard

    2015-12-18

    Chiral and achiral basket-handle porphyrins (BHPs) with different p-xylene straps and peripheral solubilizing groups were synthesized using a previously established synthetic approach. Subsequent modification, functionalization, and metalation of the tetrapyrrolic macrocycle yielded more than 80 BHPs. The chiral representatives were resolved into their enantiomers, whose absolute configurations were determined by comparison of their ECD spectra with other experimental or quantum chemically calculated spectra. NMR studies and coupled-cluster calculations proved that the free base BHPs, although highly symmetric, exhibited the phenomenon of "arrested tautomerism". Comparison of the solid-state structures of three metalated BHPs offered detailed insight into their three-dimensional shape. Finally, directly linked dimeric porphyrins with a BHP subunit were synthesized from functionalized BHPs to prove their value as synthetic building blocks.

  12. Synthesis, characterisation and crystal structures of two bi-oxadiazole derivatives featuring the trifluoromethyl group.

    Science.gov (United States)

    Kettner, Marcos A; Klapötke, Thomas M; Witkowski, Tomasz G; von Hundling, Felix

    2015-03-01

    The synthesis, characterisation, and crystal structure determination of the closely related compounds 3,3'-bi-(5-trifluoromethyl-1,2,4-oxadiazole) and 5,5'-bi-(2-trifluoromethyl-1,3,4-oxadiazole) are reported. These two compounds are known for their bioactivity; however, in this study they serve as model compounds to evaluate the suitability of the heterocyclic oxadiazole ring system for energetic materials when the fluorine atoms in the exocyclic CF3 groups are substituted successively by nitro groups. Quantum chemical calculations for the bi-1,3,4-oxadiazole derivatives with difluoronitromethyl, fluorodinitromethyl, and trinitromethyl groups have been carried out and predict promising energetic performances for both explosive and propulsive applications.

  13. Sub-volume averaging of repetitive structural features in angularly filtered electron tomographic reconstructions.

    Science.gov (United States)

    Kováčik, L; Kereïche, S; Matula, P; Raška, I

    2014-01-01

    Electron tomographic reconstructions suffer from a number of artefacts arising from effects accompanying the processes of acquisition of a set of tilted projections of the specimen in a transmission electron microscope and from its subsequent computational handling. The most pronounced artefacts usually come from imprecise projection alignment, distortion of specimens during tomogram acquisition and from the presence of a region of missing data in the Fourier space, the "missing wedge". The ray artefacts caused by the presence of the missing wedge can be attenuated by the angular image filter, which attenuates the transition between the data and the missing wedge regions. In this work, we present an analysis of the influence of angular filtering on the resolution of averaged repetitive structural motives extracted from three-dimensional reconstructions of tomograms acquired in the single-axis tilting geometry.

  14. Structural features of silver-doped phosphate glasses in zone of femtosecond laser-induced modification

    Energy Technology Data Exchange (ETDEWEB)

    Vasileva, A.A., E-mail: anvsilv@gmail.com [Saint-Petersburg State University, Institute of Chemistry, Saint-Petersburg (Russian Federation); Nazarov, I.A. [Saint-Petersburg State University, Department of Physics, Saint-Petersburg (Russian Federation); Olshin, P.K.; Povolotskiy, A.V. [Saint-Petersburg State University, Institute of Chemistry, Saint-Petersburg (Russian Federation); Sokolov, I.A. [St.Petersburg State Polytechnical University, St.Petersburg (Russian Federation); LTD “AtomTjazhMash”, St.Petersburg (Russian Federation); Manshina, A.A. [Saint-Petersburg State University, Institute of Chemistry, Saint-Petersburg (Russian Federation)

    2015-10-15

    Femtosecond (fs) laser writing of two-dimensional microstructures (waveguides) is demonstrated in bulk phosphate glasses doped with silver ions. Silver-content phosphate and silver-content niobium–phosphate glasses with high concentration of silver oxide 55 mol% were used as samples for fs laser writing. The chemical network structure of the synthesized samples is analyzed through Raman spectroscopy and was found to be strongly sensitive to Nb incorporation. It was found that the direct laser writing process enables not only reorganization of glass network, but also formation of color centers and silver nanoparticles that are revealed in appearance of luminescence signal and plasmon absorption. The process of NPs' formation is more efficient for Nb-phosphate glass, while color centers are preferably formed in phosphate glass. - Graphical abstract: Formation of silver NPs on the surface of 0.5Ag{sub 2}O–0.4P{sub 2}O{sub 5}–0,1Nb{sub 2}O{sub 5} glass induced by CW laser irradiation. - Highlights: • The structure of 0.5Ag{sub 2}O–0.1Nb{sub 2}O{sub 5}–0.4P{sub 2}O{sub 5} and 0.55Ag{sub 2}O–0.45P{sub 2}O{sub 5} glasses was investigated by Raman spectroscopy. • Fs laser writing induces formation of silver NPs in investigated glasses. • Surface plasmon resonance in the absorption spectra confirms the formation of NP. • The possibility of CW laser induced formation of silver NPs on the surface of sample with niobium is shown.

  15. Features of highly structured equatorial plasma irregularities deduced from CHAMP observations

    Science.gov (United States)

    Xiong, C.; Lühr, H.; Ma, S. Y.; Stolle, C.; Fejer, B. G.

    2012-08-01

    In this study five years of CHAMP (Challenging Mini-satellite Payload) fluxgate magnetometer (FGM) data is used to investigate the characteristics of Equatorial Plasma Bubbles (EPBs). We filtered the FGM data by using band-passes with four different cut-off periods to get the EPBs with different maximum spatial scale sizes in the meridional plane ranging from 76-608 km. Associated with the EPB observations at about 400 km, the typical altitude of CHAMP during the year 2000-2005, we also investigate the post-sunset equatorial vertical plasma drift data from ROCSAT-1 (Republic of China Satellite 1). Since the height of the F-layer is highly correlated with the vertical plasma drift and solar flux, we sorted the ROCSAT-1 data into different groups by F10.7. From the integrated vertical drift we have estimated the post-sunset uplift of the ionosphere. By comparing the properties of EPB occurrence for different scale sizes with the global distribution of plasma vertical uplift, we have found that EPBs reaching higher altitudes are more structured than those which are sampled by CHAMP near the top side of the depleted fluxtube. Such a result is in accord with 3-D model simulations (Aveiro and Hysell, 2010). Small-scale EPB structures are observed by CHAMP when the irregularities reach apex heights of 800 km and more. Such events are encountered primarily in the Brazilian sector during the months around November, when the post-sunset vertical plasma drift is high.

  16. Features of highly structured equatorial plasma irregularities deduced from CHAMP observations

    Directory of Open Access Journals (Sweden)

    C. Xiong

    2012-08-01

    Full Text Available In this study five years of CHAMP (Challenging Mini-satellite Payload fluxgate magnetometer (FGM data is used to investigate the characteristics of Equatorial Plasma Bubbles (EPBs. We filtered the FGM data by using band-passes with four different cut-off periods to get the EPBs with different maximum spatial scale sizes in the meridional plane ranging from 76–608 km. Associated with the EPB observations at about 400 km, the typical altitude of CHAMP during the year 2000–2005, we also investigate the post-sunset equatorial vertical plasma drift data from ROCSAT-1 (Republic of China Satellite 1. Since the height of the F-layer is highly correlated with the vertical plasma drift and solar flux, we sorted the ROCSAT-1 data into different groups by F10.7. From the integrated vertical drift we have estimated the post-sunset uplift of the ionosphere. By comparing the properties of EPB occurrence for different scale sizes with the global distribution of plasma vertical uplift, we have found that EPBs reaching higher altitudes are more structured than those which are sampled by CHAMP near the top side of the depleted fluxtube. Such a result is in accord with 3-D model simulations (Aveiro and Hysell, 2010. Small-scale EPB structures are observed by CHAMP when the irregularities reach apex heights of 800 km and more. Such events are encountered primarily in the Brazilian sector during the months around November, when the post-sunset vertical plasma drift is high.

  17. Structural, thermal and optical absorption features of heavy metal oxides doped tellurite rich glasses

    Science.gov (United States)

    Kaky, Kawa M.; Lakshminarayana, G.; Baki, S. O.; Kityk, I. V.; Taufiq-Yap, Y. H.; Mahdi, M. A.

    In order to improve tellurite glass stability to be applicable for optical fiber amplifier applications, glasses with the composition of (70 - x)TeO2. (10)ZnO. (10)WO3. (5)Na2O. (5)TiO2. (x)Bi2O3 (x = 1, 2, 3, 4, and 5 mol%) have been produced and characterized using the related methods. Structural properties were investigated using X-ray diffraction (XRD) which confirms the non-crystalline structure and scanning electron microscopy (SEM) micrographs also confirm the XRD results. The energy dispersive X-ray (EDX) analysis profiles show that all the mentioned elements are present in the prepared glasses. Following the IR spectra, all the tellurium bonds such as stretching vibrations of TeO4 tbp and TeO3/TeO3+1 unit are revealed. Raman spectra confirm the presence of different functional groups, actually, it shows bands mainly in four spectral regions: R1 (65-150) cm-1, R2 (280-550) cm-1, R3 (880-950) cm-1 and R4 (916-926) cm-1 and the identified bands are assigned to respective molecular groups. The thermal study was carried out using Differential scanning calorimetry (DSC) which indicates good thermal stability of the synthesized glasses with increasing Bi concentration. From the optical absorption spectra, we evaluated cut-off edge wavelengths and found increasing cutoff wavelength with an increase in Bi2O3 concentration. In the UV-Visible region, optical band gap energy and allowed transitions were investigated using three methods; direct, indirect, and absorption spectrum fitting (ASF), and band gaps from indirect and ASF were matched.

  18. Nitrogen fertilization strategies, morphogenetic and structural features in Brachiaria decumbens deferred for 95 days

    Directory of Open Access Journals (Sweden)

    Fábio Andrade Teixeira

    2014-02-01

    Full Text Available The aim this work was to evaluate the morphogenic and structural characteristics of Brachiaria decumbens pastures to determine the most suitable nitrogen fertilization strategies, for pastures deferred for a period of 95 days. Four strategies of fertilization at the beginning and end of the summer (0-0, 100- 0, 50-50, 0-100 kg ha-1 N were studied, respectively, with four replications. The strategy of 100 kg ha-1 N applied at the end of the summer (0-100, followed the parceling strategy at the beginning and end of the summer (50-50 favored higher rates of leaf appearance and lower values of phyllochron. Greater rate of leaf elongation was observed for 0-100 strategy, resulting in 40% increase compared to pastures that were not fertilized. However, there was no effect of fertilization strategies on stem elongation rate, registering an average of 0.28 cm.dia-1. There was a higher blade:stem ratio for the stratum A (40 cm above the soil in all treatments, observing higher blade:stem ratio for strategies 0-100 and 50-50, at this stratum. There was no effect for the total number of leaves and final leaf length. However, greater stem lengths were observed in pastures with 0-100 fertilizer strategy, followed by the 50-50 strategy. The strategy of applying 100 kg ha-1 at the end of summer, followed by the strategy of 50 kg ha-1 nitrogen divided at the beginning and end of summer, promote greater influence on the morphogenic and structural traits, in pastures deferred for 95 days.

  19. How neighborhood structural and institutional features can shape neighborhood social connectedness: a multilevel study of adolescent perceptions.

    Science.gov (United States)

    Lenzi, Michela; Vieno, Alessio; Santinello, Massimo; Perkins, Douglas D

    2013-06-01

    According to the norms and collective efficacy model, the levels of social connectedness within a local community are a function of neighborhood structural characteristics, such as socioeconomic status and ethnic composition. The current work aims to determine whether neighborhood structural and institutional features (neighborhood wealth, percentage of immigrants, population density, opportunities for activities and meeting places) have an impact on different components of neighborhood social connectedness (intergenerational closure, trust and reciprocity, neighborhood-based friendship and personal relationships with neighbors). The study involved a representative sample of 389 early and middle adolescents aged 11-15 years old, coming from 31 Italian neighborhoods. Using hierarchical linear modeling, our findings showed that high population density, ethnic diversity, and physical and social disorder might represent obstacles for the creation of social ties within the neighborhood. On the contrary, the presence of opportunities for activities and meeting places in the neighborhood was associated with higher levels of social connectedness among residents.

  20. Observation of the Zero Hall Plateau in a Quantum Anomalous Hall Insulator

    Energy Technology Data Exchange (ETDEWEB)

    Feng, Yang; Feng, Xiao; Ou, Yunbo; Wang, Jing; Liu, Chang; Zhang, Liguo; Zhao, Dongyang; Jiang, Gaoyuan; Zhang, Shou-Cheng; He, Ke; Ma, Xucun; Xue, Qi-Kun; Wang, Yayu

    2015-09-16

    We report experimental investigations on the quantum phase transition between the two opposite Hall plateaus of a quantum anomalous Hall insulator. We observe a well-defined plateau with zero Hall conductivity over a range of magnetic field around coercivity when the magnetization reverses. The features of the zero Hall plateau are shown to be closely related to that of the quantum anomalous Hall effect, but its temperature evolution exhibits a significant difference from the network model for a conventional quantum Hall plateau transition. We propose that the chiral edge states residing at the magnetic domain boundaries, which are unique to a quantum anomalous Hall insulator, are responsible for the novel features of the zero Hall plateau.

  1. Anomalous absorption in CO2-laser-target interactions

    Science.gov (United States)

    Offenberger, A. A.; Ng, A.

    1980-10-01

    Efficient absorption of long-pulse CO2-laser radiation is observed to follow a transient phase of stimulated Brillouin backscatter in critical density, laminar oxygen gas target irradiation experiments. Nearly complete energy absorption occurs for not more than 10 nsec following stimulated Brillouin backscatter after which target burnthrough and refraction dominate. Inverse bremsstrahlung and resonance absorption cannot account for the general features observed. Anomalous collisions due to strong ion turbulence produced by the incident laser radiation are postulated to account for the efficient absorption.

  2. Study of supported platinum catalysts by anomalous scattering

    Energy Technology Data Exchange (ETDEWEB)

    Georgopoulos, P.; Cohen, J.B.

    1985-01-01

    Platinum metal catalysts supported on silica gel and alumina were examined by wide-angle anomalous x-ray scattering at the Cornell High Energy Synchrotron Source. Complete removal of the support background features is achieved by this method, eliminating errors due to inaccurate background estimation. Platinum diffraction patterns from very-high-percentage metal-exposed catalysts were obtained for the first time, as well as from platinum supported on alumina. This technique is suitable for examining catalysts under working conditions and is superior to EXAFS for determinations of particle morphology and size distribution. 10 references, 8 figures.

  3. Anomalous Hall effect in Fe/Gd bilayers

    KAUST Repository

    Xu, W. J.

    2010-04-01

    Non-monotonic dependence of anomalous Hall resistivity on temperature and magnetization, including a sign change, was observed in Fe/Gd bilayers. To understand the intriguing observations, we fabricated the Fe/Gd bilayers and single layers of Fe and Gd simultaneously. The temperature and field dependences of longitudinal resistivity, Hall resistivity and magnetization in these films have also been carefully measured. The analysis of these data reveals that these intriguing features are due to the opposite signs of Hall resistivity/or spin polarization and different Curie temperatures of Fe and Gd single-layer films. Copyright (C) EPLA, 2010

  4. Prediction of viral microRNA precursors based on human microRNA precursor sequence and structural features.

    Science.gov (United States)

    Kumar, Shiva; Ansari, Faraz A; Scaria, Vinod

    2009-08-20

    MicroRNAs (small approximately 22 nucleotide long non-coding endogenous RNAs) have recently attracted immense attention as critical regulators of gene expression in multi-cellular eukaryotes, especially in humans. Recent studies have proved that viruses also express microRNAs, which are thought to contribute to the intricate mechanisms of host-pathogen interactions. Computational predictions have greatly accelerated the discovery of microRNAs. However, most of these widely used tools are dependent on structural features and sequence conservation which limits their use in discovering novel virus expressed microRNAs and non-conserved eukaryotic microRNAs. In this work an efficient prediction method is developed based on the hypothesis that sequence and structure features which discriminate between host microRNA precursor hairpins and pseudo microRNAs are shared by viral microRNA as they depend on host machinery for the processing of microRNA precursors. The proposed method has been found to be more efficient than recently reported ab-initio methods for predicting viral microRNAs and microRNAs expressed by mammals.

  5. Individual features of the physical development and the onset of biological maturity of morphological and functional structures of the body

    Directory of Open Access Journals (Sweden)

    Oleksandr Aghyppo

    2015-12-01

    Full Text Available Purpose: to justify the observed features of physical development of the individual and the nature of the flow pattern of biological maturity of morphological and functional structures of the body other than the population norm of behavior trends of these processes. Materials and Methods: analysis of scientific literature on the research, the use of survey data contingent of children of preschool and primary school age, the use of attributive semantic spaces, method of similarity and dimensions, the method of analogy, the method of slowly varying amplitudes. Results: the nature of occurrence of the individual characteristics of the physical development and the onset of biological maturity of morphological and functional structures of the whole organism. Substantiates the nature of occurrence of the individual variation of these processes. Conclusions: the existing differences in the individual development of physical and somatotype shaping involve a violation of the synchronization of interdependent relations system. This reduces the potential viability and is expressed in the constitution somatotype features that can be used for preclinical diagnosis

  6. Anomalous refraction of guided waves via embedded acoustic metasurfaces

    Science.gov (United States)

    Zhu, Hongfei; Semperlotti, Fabio

    2016-04-01

    We illustrate the design of acoustic metasurfaces based on geometric tapers and embedded in thin-plate structures. The metasurface is an engineered discontinuity that enables anomalous refraction of guided wave modes according to the Generalized Snell's Law. Locally-resonant geometric torus-like tapers are designed in order to achieve metasurfaces having discrete phase-shift profiles that enable a high level of control of refraction of the wavefronts. Results of numerical simulations show that anomalous refraction can be achieved on transmitted anti-symmetric modes (A0) either when using a symmetric (S0) or anti-symmetric (A0) incident wave, where the former case clearly involves mode conversion mechanisms.

  7. Porous and Fluffy Grains in the Regions of Anomalous Extinction

    Indian Academy of Sciences (India)

    D. B. Vaidya; B. G. Anandarao; J. N. Desai; R. Gupta

    2000-06-01

    It has long been established that the ratio of total to selective extinction is anomalously large (≥ 5) in certain regions of the interstellar medium. In these regions of anomalous extinction the dust grains are likely to be irregular in shape and fluffy in structure. Using discrete dipole approximation (DDA) we calculate the extinction for porous and fluffy grains. We apply DDA first to solid spheroidal particles assumed to be made of a certain (large) number of dipoles. Then we systematically reduce the number of dipoles to model the porous grains. The aggregates of these particles are suggested to form the fluffy grains. We study the extinction for these particles as a function of grain size, porosity and wavelength. We apply these calculations to interpret the observed extinction data in the regions of star formation (e.g. the Orion complex).

  8. In Silico Analysis of the Structural and Biochemical Features of the NMD Factor UPF1 in Ustilago maydis.

    Directory of Open Access Journals (Sweden)

    Nancy Martínez-Montiel

    Full Text Available The molecular mechanisms regulating the accuracy of gene expression are still not fully understood. Among these mechanisms, Nonsense-mediated Decay (NMD is a quality control process that detects post-transcriptionally abnormal transcripts and leads them to degradation. The UPF1 protein lays at the heart of NMD as shown by several structural and functional features reported for this factor mainly for Homo sapiens and Saccharomyces cerevisiae. This process is highly conserved in eukaryotes but functional diversity can be observed in various species. Ustilago maydis is a basidiomycete and the best-known smut, which has become a model to study molecular and cellular eukaryotic mechanisms. In this study, we performed in silico analysis to investigate the structural and biochemical properties of the putative UPF1 homolog in Ustilago maydis. The putative homolog for UPF1 was recognized in the annotated genome for the basidiomycete, exhibiting 66% identity with its human counterpart at the protein level. The known structural and functional domains characteristic of UPF1 homologs were also found. Based on the crystal structures available for UPF1, we constructed different three-dimensional models for umUPF1 in order to analyze the secondary and tertiary structural features of this factor. Using these models, we studied the spatial arrangement of umUPF1 and its capability to interact with UPF2. Moreover, we identified the critical amino acids that mediate the interaction of umUPF1 with UPF2, ATP, RNA and with UPF1 itself. Mutating these amino acids in silico showed an important effect over the native structure. Finally, we performed molecular dynamic simulations for UPF1 proteins from H. sapiens and U. maydis and the results obtained show a similar behavior and physicochemical properties for the protein in both organisms. Overall, our results indicate that the putative UPF1 identified in U. maydis shows a very similar sequence, structural organization

  9. In Silico Analysis of the Structural and Biochemical Features of the NMD Factor UPF1 in Ustilago maydis.

    Science.gov (United States)

    Martínez-Montiel, Nancy; Morales-Lara, Laura; Hernández-Pérez, Julio M; Martínez-Contreras, Rebeca D

    2016-01-01

    The molecular mechanisms regulating the accuracy of gene expression are still not fully understood. Among these mechanisms, Nonsense-mediated Decay (NMD) is a quality control process that detects post-transcriptionally abnormal transcripts and leads them to degradation. The UPF1 protein lays at the heart of NMD as shown by several structural and functional features reported for this factor mainly for Homo sapiens and Saccharomyces cerevisiae. This process is highly conserved in eukaryotes but functional diversity can be observed in various species. Ustilago maydis is a basidiomycete and the best-known smut, which has become a model to study molecular and cellular eukaryotic mechanisms. In this study, we performed in silico analysis to investigate the structural and biochemical properties of the putative UPF1 homolog in Ustilago maydis. The putative homolog for UPF1 was recognized in the annotated genome for the basidiomycete, exhibiting 66% identity with its human counterpart at the protein level. The known structural and functional domains characteristic of UPF1 homologs were also found. Based on the crystal structures available for UPF1, we constructed different three-dimensional models for umUPF1 in order to analyze the secondary and tertiary structural features of this factor. Using these models, we studied the spatial arrangement of umUPF1 and its capability to interact with UPF2. Moreover, we identified the critical amino acids that mediate the interaction of umUPF1 with UPF2, ATP, RNA and with UPF1 itself. Mutating these amino acids in silico showed an important effect over the native structure. Finally, we performed molecular dynamic simulations for UPF1 proteins from H. sapiens and U. maydis and the results obtained show a similar behavior and physicochemical properties for the protein in both organisms. Overall, our results indicate that the putative UPF1 identified in U. maydis shows a very similar sequence, structural organization, mechanical stability

  10. Immunological Features of the Non-Structural Proteins of Porcine Reproductive and Respiratory Syndrome Virus

    Directory of Open Access Journals (Sweden)

    Edgar Rascón-Castelo

    2015-02-01

    Full Text Available Porcine reproductive and respiratory syndrome virus (PRRSV is currently one of the most important viruses affecting the swine industry worldwide. Despite the large number of papers published each year, the participation of non-structural proteins (nsps in the immune response is not completely clear. nsps have been involved in the host innate immune response, specifically, nsp1α/β, nsp2, nsp4 and nsp11 have been associated with the immunomodulation capability of the virus. To date, only participation by nsp1, nsp2, nsp4 and nsp7 in the humoral immune response has been reported, with the role of other nsps being overlooked. Furthermore, nsp1, nsp2, nsp5, nsp7 nsp9, nsp10, nsp11 have been implicated in the induction of IFN-γ and probably in the development of the cell-mediated immune response. This review discusses recent reports involving the participation of nsps in the modulation of the innate immune response and their role in the induction of both the humoral and cellular immune responses.

  11. Plume and surface feature structure and compositional effects on Europa's global exosphere: Preliminary Europa mission predictions

    Science.gov (United States)

    Teolis, B. D.; Wyrick, D. Y.; Bouquet, A.; Magee, B. A.; Waite, J. H.

    2017-03-01

    A Europa plume source, if present, may produce a global exosphere with complex spatial structure and temporal variability in its density and composition. To investigate this interaction we have integrated a water plume source containing multiple organic and nitrile species into a Europan Monte Carlo exosphere model, considering the effect of Europa's gravity in returning plume ejecta to the surface, and the subsequent spreading of adsorbed and exospheric material by thermal desorption and re-sputtering across the entire body. We consider sputtered, radiolytic and potential plume sources, together with surface adsorption, regolith diffusion, polar cold trapping, and re-sputtering of adsorbed materials, and examine the spatial distribution and temporal evolution of the exospheric density and composition. These models provide a predictive basis for telescopic observations (e.g. HST, JWST) and planned missions to the Jovian system by NASA and ESA. We apply spacecraft trajectories to our model to explore possible exospheric compositions which may be encountered along proposed flybys of Europa to inform the spatial and temporal relationship of spacecraft measurements to surface and plume source compositions. For the present preliminary study, we have considered four cases: Case A: an equatorial flyby through a sputtered only exosphere (no plumes), Case B: a flyby over a localized sputtered 'macula' terrain enriched in non-ice species, Case C: a south polar plume with an Enceladus-like composition, equatorial flyby, and Case D: a south polar plume, flyby directly through the plume.

  12. Structural features of antiviral APOBEC3 proteins are linked to their functional activities

    Directory of Open Access Journals (Sweden)

    Shingo eKitamura

    2011-12-01

    Full Text Available APOBEC3 (A3 proteins are cellular cytidine deaminases that potently restrict the replication of retroviruses by hypermutating viral cDNA and/or inhibiting reverse transcription. There are seven members of this family including A3A, B, C, DE, F, G, and H, all encoded in a tandem array on human chromosome 22. A3F and A3G are the most potent inhibitors of HIV-1, but only in the absence of the virus-encoded protein, Vif. HIV-1 utilizes Vif to abrogate A3 functions in the producer cells. More specifically, Vif, serving as a substrate receptor, facilitates ubiquitination of A3 proteins by forming a Cullin5 (Cul5-based E3 ubiquitin ligase complex, which targets A3 proteins for rapid proteasomal degradation. The specificity of A3 degradation is determined by the ability of Vif to bind to the target. Several lines of evidence have suggested that three distinct regions of A3 proteins are involved in the interaction with Vif. Here, we review the biological functions of A3 family members with special focus on A3G and base our analysis on the available structural information.

  13. Structural feature and tectonic evolution of Awati——Bachu area in Tarim Basin

    Institute of Scientific and Technical Information of China (English)

    Zhihong LIU; Defeng ZHU; Junyi GAO; Xiangmei WU; Dongcheng LIN; Liguo ZHANG

    2008-01-01

    The research area is situated in the western part of Tarim basin,which includes Awati depression and Bachu uplifted block. It underwent three times processes of compression in a large scale and a near term extension since Cambrian. The first compression occurred during Middle Cambrian to Devonian, which formed fault band folds in NW axial direction. They were "under-water uplift"and distributed all over the research area. The second compression occurred in Late Permian and formed fault band folds and a few fault propagation folds in NS axial direction. They are developed near Tumuxiuke fault belt and the northern research area. The western anticline is bigger than the eastern one in extent and size. The third compression occurred during Palaeogene to Quaternary and formed tumuxiuke fault belt and fault propagation folds in NW direction. They are distributed over the south part of the research area. Tumuxiuke fault belt is a big scale dextral reversed strike-slip fault belt; it transformed or destroyed the fold structure of the research area. A short-term extension occurred during Early Permian. Tarim Basin is in the rift forming stage of craton, and there exist widespread basic volcanic rocks, basic intrusive bodies and dikes.

  14. Inherent structure features of beryllium and their influence on the performance polycrystalline metal under different conditions

    Energy Technology Data Exchange (ETDEWEB)

    Khomutov, A.M.; Mikhailov, V.S.; Pronin, V.N.; Pakhomov, Ya.D. [State Scientific Center of Russian Federation `A.A. Bochvar All-Russia Research Inst. of Inorganic Materials (VNIINM)`, Moscow (Russian Federation)

    1998-01-01

    The anisotropy of physical properties of beryllium single crystals resulting from covalent bonds in crystal lattice leads to significant residual thermal microstresses (RTM) in the polycrystalline metal. It is demonstrated experimentally that there is a simple linear dependence between the magnitude of RTM and the ultimate tensile strength. The factors controlling RTM are analysed and in the framework of powder metallurgy process the technological methods of producing beryllium with the needed properties are recommended. Primarily it is necessary to control the quantity and extent of dispersity of intergranular oxide inclusions and mean grain size in combination with the high degree of macro- and microhomogenity of the structure. The requirements to beryllium microstructure for different operating conditions including neutron fluxes and transient temperature fields are formulated. In the framework of the concept under development one can explain formerly not fully understandable effects, which are characteristic of polycrystalline beryllium such as unexpected Petch-Stro curve, the role of twinning etc., and predict new ones. In particular, it can be possible to expect the growth of ductility of high strength beryllium grades as neutron irradiated. (author)

  15. Fast characterization of gold nanorods ensemble by correlating its structure with optical extinction spectral features

    Directory of Open Access Journals (Sweden)

    Z. J. Hu

    2014-11-01

    Full Text Available Owing to unique size- and shape- dependent localized surface plasmon resonance (LSPR of noble metal nanoparticles (NPs, the optical extinction spectroscopy method (OES has received much attention to characterize the geometry of metal NPs by fitting experimental UV-vis-NIR spectra. In this work, we aimed to develop a more convenient and accurate OES method to characterize the structural parameters and concentration of the gold nanorods (GNRs ensemble. The main difference between our approach and previous OES methods is that we solve this inverse spectra problem by establishing the LSPR relation equations of GNRs ensemble so that there is no need of UV-vis-NIR spectra fitting process. The aspect ratio (AR and AR distribution can be directly retrieved from two of UV-vis-NIR spectral parameters (peak position and full width at half maximum using the obtained relation equations. Furthermore, the relation equations are modified for applying to the more general GNRs samples by considering the plasmon shift due to the near distance dielectric sensitivity. Finally, instead of inductively coupled plasma mass spectrometry (ICP-MS measurement, we provide a more facile measure of the mass-volume concentration which can be determined from the extinction value at 400 nm. By comparing with the experimental results, it shows that the retrieved results by the relation equations are reliable.

  16. The Rhetorical Structure & Discursive Features of Call for Papers as a Genre

    Directory of Open Access Journals (Sweden)

    Mohammad Javad Mohammadi

    2013-07-01

    Full Text Available This paper, at the first stage, presents a genre analysis of 50 calls for papers of conferences held in Iran at both national and international levels from 2000 to 2012 (Swales, 1990. The study also targets the politeness strategies employed in such texts adopting Arundale's (2006 face model. The results obtained from the first phase of the study revealed four moves and a number of constituting steps including opening, salutation, informing (interested areas, necessary dates and formats, and complementary close and signature. Interestingly, findings of the second phase of the study, based on Arundale’s theory, demonstrated that all sentences and phrases used in this genre in Iranian academic contexts function as connection face as all were apparent as unity, interdependence, solidarity, association, congruence, and more, between the conference chair/s and other academicians as the members of a same discourse community. It can also further justified by different request strategies employed by the conference chair/s. Keywords: call for paper; genre; generic structure; politeness; face

  17. Experimental impact features in Stardust aerogel: How track morphology reflects particle structure, composition, and density

    Science.gov (United States)

    Kearsley, Anton T.; Burchell, Mark J.; Price, Mark C.; Cole, Michael J.; Wozniakiewicz, Penelope J.; Ishii, Hope A.; Bradley, John P.; Fries, Marc; Foster, Nicholas J.

    2012-04-01

    The Stardust collector shows diverse aerogel track shapes created by impacts of cometary dust. Tracks have been classified into three broad types (A, B, and C), based on relative dimensions of the elongate "stylus" (in Type A "carrots") and broad "bulb" regions (Types B and C), with occurrence of smaller "styli" in Type B. From our experiments, using a diverse suite of projectile particles shot under Stardust cometary encounter conditions onto similar aerogel targets, we describe differences in impactor behavior and aerogel response resulting in the observed range of Stardust track shapes. We compare tracks made by mineral grains, natural and artificial aggregates of differing subgrain sizes, and diverse organic materials. Impacts of glasses and robust mineral grains generate elongate, narrow Type A tracks (as expected), but with differing levels of abrasion and lateral branch creation. Aggregate particles, both natural and artificial, of a wide range of compositions and volatile contents produce diverse Type B or C shapes. Creation of bulbous tracks is dependent upon impactor internal structure, grain size distribution, and strength, rather than overall grain density or content of volatile components. Nevertheless, pure organic particles do create Type C, or squat Type A* tracks, with length to width ratios dependent upon both specific organic composition and impactor grain size. From comparison with the published shape data for Stardust aerogel tracks, we conclude that the abundant larger Type B tracks on the Stardust collector represent impacts by particles similar to our carbonaceous chondrite meteorite powders.

  18. Understanding the structural features of high-amylose maize starch through hydrothermal treatment.

    Science.gov (United States)

    Yang, Jianing; Xie, Fengwei; Wen, Wenqiang; Chen, Ling; Shang, Xiaoqin; Liu, Peng

    2016-03-01

    In this study, high-amylose starches were hydrothermally-treated and the structural changes were monitored with time (up to 12h) using scanning electron microscopy (SEM), confocal laser scanning microscopy (CLSM), small-angle X-ray scattering (SAXS), X-ray diffraction (XRD), and differential scanning calorimetry (DSC). When high-amylose starches were treated in boiling water, half-shell-like granules were observed by SEM, which could be due to the first hydrolysis of the granule inner region (CLSM). This initial hydrolysis could also immediately (0.5h) disrupt the semi-crystalline lamellar regularity (SAXS) and dramatically reduce the crystallinity (XRD); but with prolonged time of hydrothermal treatment (≥2 h), might allow the perfection or formation of amylose single helices, resulting in slightly increased crystallinity (XRD and DSC). These results show that the inner region of granules is composed of mainly loosely-packed amylopectin growth rings with semi-crystalline lamellae, which are vulnerable under gelatinization or hydrolysis. In contrast, the periphery is demonstrated to be more compact, possibly composed of amylose and amylopectin helices intertwined with amylose molecules, which require greater energy input (higher temperature) for disintegration.

  19. Cordilleran front range structural features in northwest Montana interpreted from vintage seismic reflection data

    Science.gov (United States)

    Porter, Mason C.; Rutherford, Bradley S.; Speece, Marvin A.; Mosolf, Jesse G.

    2016-04-01

    Industry seismic reflection data spanning the Rocky Mountain Cordillera front ranges of northwest Montana were reprocessed and interpreted in this study. Five seismic profiles represent 160 km of deep reflection data collected in 1983 that span the eastern Purcell anticlinorium, Rocky Mountain Trench (RMT), Rocky Mountain Basal Décollement (RMBD), and Lewis thrust. The data were reprocessed using modern techniques including refraction statics, pre-stack time migration (PSTM), and pre- and post-stack depth migration. Results indicate the RMBD is 8-13 km below the Earth's surface and dip 3-10° west. Evidence for the autochthonous Mesoproterozoic Belt and basal Cambrian rocks beneath the RMBD is present in all of the profiles and appears to extend east of the RMT. The Lewis thrust was identified in the seismic profiles and appears to sole into the RMBD east of the RMT. The RMT fault system has a dip displacement of 3-4 km and forms a half graben filled with 1 km of unconsolidated Tertiary sedimentary deposits. The RMT and adjacent Flathead fault systems are interpreted to be structurally linked and may represent a synthetic, en echelon fault system.

  20. Structural features and antitumor activity of a novel polysaccharide from alkaline extract of Phellinus linteus mycelia.

    Science.gov (United States)

    Pei, Juan-Juan; Wang, Zhen-Bin; Ma, Hai-Le; Yan, Jing-Kun

    2015-01-22

    A novel high molecular weight polysaccharide (PL-N1) was isolated from alkaline extract of the cultured Phellinus linteus mycelia. The weight average molecular weight (Mw) of PL-N1 was estimated at 343,000kDa. PL-N1 comprised arabinose, xylose, glucose, and galactose in the molar ratio of 4.0:6.7:1.3:1.0. The chemical structure of PL-N1 was investigated by FTIR and NMR spectroscopies and methylation analysis. The results showed that the backbone of PL-N1 comprised (1→4)-linked β-D-xylopyranosyl residues, (1→2)-linked α-D-xylopyranosyl residues, (1→4)-linked α-D-glucopyranosyl residues, (1→5)-linked β-D-arabinofuranosyl residues, (1→4)-linked β-D-xylopyranosyl residues which branched at O-2, and (1→4)-linked β-D-galactopyranosyl residues which branched at O-6. The branches consisted of (1→)-linked α-D-arabinofuranosyl residues. Antitumor activity assay in vitro showed that PL-N1 could inhibit the growth of HepG2 cells to a certain extent in a dose-dependent manner. Thus, PL-N1 may be developed as a potential, natural antitumor agent and functional food.