bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of human liver proteome using replicate shotgun strategy
Authors: Chen Ming , Ying Wantao , Song Yanping , Liu Xin , Yang Bing , Wu Songfeng , Jiang Ying , Cai Yun , He Fuchu , Qian Xiaohong 
Published: July 2007

AbstractIn this study, a liquid‐based shotgun strategy was used to comprehensively identify the expression of human liver proteome. Proteins were extracted from human liver tissue and digested in‐solution. The tryptic digest mixture was desalted and separated by off‐line strong cation exchange (SCX) chromatography with a 60‐min elution. The MS/MS spectra were acquired in data‐dependent mode after an RP chromatographic separation combined with linear IT MS analysis. To obtain the most comprehensive human liver proteome, each SCX fraction was run six times in RPLC MS/MS manner. Finally, more than 6 000 000 MS/MS spectra were collected. Using a relatively strict filter criteria, 24 311 proteins (48.42% of the predicted human proteome from human International Protein Index (IPI) protein database 3.07) corresponding to 13 150 nonredundant proteins were successfully identified, in which 7001 proteins (53.24%) were identified by two or more peptides, which could be considered as a high‐confident dataset. Among the 6149 proteins (46.76%) identified by single peptide, 3812 proteins (61.99%) were detected more than twice in six repeated runs. Comparative analysis between different runs shows that the overlap of identified proteins between any two runs ranged from 25 to 44%. Of the nonredundant proteins identified, 8919 proteins (67.83%) were detected more than twice and 4231 proteins (32.17%) were detected only once in six RPLC MS/MS runs. The Gene Ontology annotation shows that the identified proteins come from various subcellular components. In addition, a large number of low abundant proteins were identified. The dynamic range of the approach reached at least nine orders of magnitude by estimating the concentration of proteins.
Interpretation support for multistage MS: A mathematical method for theoretical generation of glycan fragments and calculation of their masses
Authors: Meitei Ningombam Sanjib , Banerjee Snigdha 
Published: July 2007

AbstractGlycan fragmentation forms an integral part of the current research in glycomics. Creation of a database of glycan fragments and their masses for known glycan structures is an important step in the interpretation of mass spectra for the identification of unknown glycan structures. This paper introduces the concept of positional nomenclature, gives a systematic representation of glycan structure of any size, and hence develops a method for theoretically generating all possible first and second generation fragments resulting from glycosidic and cross ring cleavages. Matrix equations are developed for the calculation of theoretical masses. Algorithm is presented for iterative generation of all fragments and calculation of their masses. This method is applicable to glycan analytical techniques using MS, MS/MS, and multistage MS (MSn) with different ionization methods, derivatives, or ions used. The method is adaptable to computer program and has been verified for theoretical masses reported in literature. Rules for the theoretical validation of the fragments are presented.
Primary Care Mental Health & Education
Authors: Priebe Stefan , Worthing‐Davies Sally 
Published: July 2007

AbstractMore institutionalised mental health care –who is behind it?Despite a lack of formal evidence for benefit, the number of people with psychiatric illness cared for in institutional settings has risen significantly. The cost of this type of care is not insignificant and Professor Priebe discusses whether this trend is a good or bad thing.EMDR –effective in primary care counsellingEye movement desensitisation and reprocessing (EMDR) has proved to be a very effective treatment for post‐traumatic stress disorder (PTSD). Sally Worthing‐Davies explains this method of therapy and the advantages of its use in primary care. Copyright © 2007 Wiley Interface Ltd
Measurement of Slug Length and Slug Velocity in Pneumatic Conveying Using Capacitive Sensing
Authors: Fuchs Anton , Zangl Hubert 
Published: July 2007

AbstractThis paper describes a capacitive flow sensor and the development of a suitable algorithm for the determination of the slug length and the slug velocity in pneumatic dense phase conveying. The flow meter makes use of novel electrode topology. The algorithm is based on a two‐step approach using Fourier transformation. It allows for robust operation and features sub‐sample resolution for the flow parameters obtained. A process model for dense phase conveying is used to validate the proposed algorithm. Practical experiments are conducted to demonstrate the applicability of both the capacitive flow sensor and the algorithm in pneumatic dense phase conveying.
High‐resolution proteome/peptidome analysis of peptides and low‐molecular‐weight proteins in urine
Authors: Mischak Harald , Julian Bruce A. , Novak Jan 
Published: July 2007

AbstractAll organisms contain thousands of proteins and peptides in their body fluids. A deeper insight into the functional relevance of these polypeptides under different physiological and pathophysiological conditions and the discovery of specific peptide biomarkers would greatly enhance diagnosis and therapy of specific diseases. The low‐molecular‐weight proteome, also termed peptidome, provides a rich source of information. Due to its unique features, the technical challenges differ somewhat from those in “common” proteomics. In this paper, we focus on the low‐molecular‐weight urinary proteome. We review the methodological aspects of sample collection, preparation, analysis, and subsequent data evaluation. In the second part of this review, we summarize the recent progress in the definition and identification of clinically relevant polypeptide markers.
Functional and structural characterization of the catalytic domain of the starch synthase III from Arabidopsis thaliana
Authors: Busi Maria V. , Palopoli Nicolas , Valdez Hugo A. , Fornasari Maria S. , Wayllace Nahuel Z. , Gomez‐Casati Diego F. , Parisi Gustavo , Ugalde Rodolfo A. 
Published: July 2007

AbstractGlycogen and starch are the major energy storage compounds in most living organisms. The metabolic pathways leading to their synthesis involve the action of several enzymes, among which glycogen synthase (GS) or starch synthase (SS) catalyze the elongation of the α‐1,4‐glucan backbone. At least five SS isoforms were described in Arabidopsis thaliana; it has been reported that the isoform III (SSIII) has a regulatory function on the synthesis of transient plant starch. The catalytic C‐terminal domain of A. thaliana SSIII (SSIII‐CD) was cloned and expressed. SSIII‐CD fully complements the production of glycogen by an Agrobacterium tumefaciens glycogen synthase null mutant, suggesting that this truncated isoform restores in vivo the novo synthesis of bacterial glycogen. In vitro studies revealed that recombinant SSIII‐CD uses with more efficiency rabbit muscle glycogen than amylopectin as primer and display a high apparent affinity for ADP‐Glc. Fold class assignment methods followed by homology modeling predict a high global similarity to A. tumefaciens GS showing a fully conservation of the ADP‐binding residues. On the other hand, this comparison revealed important divergences of the polysaccharide binding domain between AtGS and SSIII‐CD. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Integrating statistical pair potentials into protein complex prediction
Authors: Mintseris Julian , Pierce Brian , Wiehe Kevin , Anderson Robert , Chen Rong , Weng Zhiping 
Published: July 2007

AbstractThe biophysical study of protein–protein interactions and docking has important implications in our understanding of most complex cellular signaling processes. Most computational approaches to protein docking involve a tradeoff between the level of detail incorporated into the model and computational power required to properly handle that level of detail. In this work, we seek to optimize that balance by showing that we can reduce the complexity of model representation and thus make the computation tractable with minimal loss of predictive performance. We also introduce a pair‐wise statistical potential suitable for docking that builds on previous work and show that this potential can be incorporated into our fast fourier transform‐based docking algorithm ZDOCK. We use the Protein Docking Benchmark to illustrate the improved performance of this potential compared with less detailed other scoring functions. Furthermore, we show that the new potential performs well on antibody‐antigen complexes, with most predictions clustering around the Complementarity Determining Regions of antibodies without any manual intervention. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Exciton Attenuation of Hypersound in a Strong Magnetic Field
Authors: Ruvinskii M. A. , Glauberman A. E. 
Published: July 2007

AbstractAn investigation is made of the attenuation of hypersound by Wannier‐Mott excitons in a strong magnetic field when the distance between the Landau zones exceeds the characteristic Coulomb energy and the hypersonic wave propagates perpendicularly to the magnetic field direction in semiconductors with piezoelectric and deformational electron‐phonon interactions. It is also compared with the attenuation of hypersound by the free electrons and holes in the strong magnetic field.
Stacking Fault Energies of α‐CuAl Alloys
Authors: Pande C. S. 
Published: July 2007

AbstractStacking fault energy of Cu‐2at% Al has been estimated to be 83 erg/cm2 (± 30%) by faulted dipole method and by extended nodes measurements. Using this value, and those obtained by Howie and Swann, the stacking fault energy of copper is estimated to be 94 erg/cm2. It is shown that the variation of stacking fault energy of Cu‐Al alloys with concentration is given approximately as γCuAl = γCu exp {K [C/(1+C)]2}, where C = X/X0, X being the alloying concentration in at% and X0 the solubility limit in at% at high temperature, and K is a constant ≈ ‐ 10.2.
The Relation between Cottrell‐Stokes Ratios and Stacking Fault Energies in Pure F.C.C. Metals
Authors: McKcousland S. 
Published: July 2007

AbstractIt is shown that the temperature dependence of the flow stress, expressed as a Cottrell‐Stokes ratio, correlates with stacking fault energy for aluminium, nickel, copper, silver, lead, and gold. Since the variation of dislocation configuration with stacking fault energy is not great enough to explain the observed correlation, the variations in width of dissociated dislocations and of energy needed for constriction are considered to be responsible.
Nachweis von durch Druck‐ oder Mahlbehandlung verursachten bleibenden Fehlordnungen in Eisenoxiden mittels Mößbauereffekt
Authors: Krauth A. , Tomandl G. 
Published: July 2007

AbstractDurch hohen Druck und Langzeitmahlung können in Festkörpergitter bleibende Fehlordnungen eingebracht werden, die sich röntgenorgraphisch als Spannungen nachweisen lassen. Im Falle des Fe3O4 erzeugen diese Fehlordnungen (z.B. eindimensionale Versetzungslinien) bleibende Veränderungen der nächsten Umgebung der Fe2+‐Ionen, die sich in einer Linienverbreiterung des zugehörigen Mößbauer‐Liniensextetts bemerkbar machen. Analoge, aber wesentlich geringere Effekte konnten an α‐ und γ‐Fe2O3 festgestellt werden.
Two‐Dimensional Comparison of Electron Micrographs with Computer Calculations
Authors: Spring M. S. , Steeds J. W. 
Published: July 2007

AbstractTwo methods of displaying two‐dimensional intensity data are developed and used to compare many‐beam dynamical theory calculations with electron micrographs. The effect of different published values of the real lattice potential is investigated and for Cu‐10 at% Al the following values of the imaginary lattice potential V′g were obtained, expressed in terms of U′g = 2 me V′g/h2: U′111/U111 = 0.0275 ± 0.0025, U′0/U111 = 0.0358 ± 0.0026, U′0 = 0.007 ± 0.0005 Å−2. The many‐beam effects at high microscope accelerating voltages are considered.
Excitons and Photoconductivity in Transition‐Metal Dichalcogenides
Authors: Wieting T. J. , Yoffe A. D. 
Published: July 2007

AbstractThe photoelectrical properties of several transition‐metal dichalcogenides, principally MoS2, MoSe2, and MoTe2 have been measured and compared with the optical absorption spectra. Both hexagonal and rhombohedral polytypes of MoS2 were investigated. The regular structure near the absorption edge in photoconductivity has been interpreted by means of an exciton‐phonon ionization model, which accounts for the displacement and temperature dependence of the peak positions in MoS2.
Quenched‐in Photoluminescent Color Centers in NaI
Authors: Fontana M. P. , van Sciver W. J. 
Published: July 2007

AbstractCrystals of NaI, KI, and KCl have been quenched from temperatures as high as 450 °C by rapid immersion in liquid nitrogen. In the case of NaI, very strong absorption bands at 255 nm (Q1) and 226 nm (Q2) may be produced by quenching the crystal from about 360 °C. The excitation spectrum for a characteristic luminescence at 375 nm, is identical, within the limits of experimental accuracy, with bands produced by stoichiometric excess iodine. Similar results were obtained for quenched KI, although the luminescent quantum efficiency was smaller. Negative results were obtained for quenched KCl. Analysis of the observed properties leads to the conclusion that the defect responsible for the 375 nm luminescence is, or is related to, the single cation vacancy.
Plastic Deformation of Lead in the Normal and Superconducting States
Authors: Pustovalov V. V. , Startsev V. I. , Fomenko V. S. 
Published: July 2007

AbstractThe results are given of a systematic investigation of the differences between the macroscopic characteristics of plasticity of lead single and polycrystals of 99.9992 and 99.9995% purity in the superconducting state and in the normal state at the same temperature. In the superconducting state the critical resolved shear stress of single crystals, the yield point of polycrystals, and the flow stress for different stages of deformation are lower than in the normal state. Near the fracture and at the tensile strength no difference between the flow stress in the normal and superconducting state was observed. A temperature dependence of macroscopic property changes was not found in the temperature range of 1.8 to 4.2 °K. The results obtained reveal an essential contribution from the drag due to conduction electrons to the resistance to dislocation motion. The essential interaction with conduction electrons implies that in pure metals the dislocations move with rather large velocities (102 to 105 cm/s) at low temperatures.
ESR Spectra of MoO3 Single Crystals Doped with Vanadium and Niobium
Authors: Ioffe V. A. , Patrina I. B. , Zelenetskaya E. V. 
Published: July 2007

AbstractIn MoO3:V single crystals ESR spectra of V4+ ions and electron hole centres interacting with V51 (I = 7/2) are observed. The relative intensities of the V4+ ions and hole signals change with the atmosphere of crystal growth. In MoO3:Nb single crystals electron hole centres interacting with Nb93 (I = 9/2) nuclei are present; the electrons are partly localized in the molybdenum sublattice. Nb4+ ions are absent. Symmetry of the electron hole spectra shows that the V51 nuclei are in substitutional positions and the Nb93 nuclei are in interstitial ones.
Model‐Potential Theory of Ultrasonic Attenuation in Metals
Authors: Mertsching J. , Rösler M. 
Published: July 2007

AbstractThe matrix element of the electron—phonon interaction, the deformation potential and the longitudinal ultrasonic attenuation of metals in the high‐frequency range are calculated in terms of model potentials. In order to obtain the correct anisotropy of these quantities, the ion model potentials are properly screened with a solid‐state dielectric function rather than with the Hartree dielectric function for free electrons. In zero order in the model‐potential form factors, the free‐electron results are obtained without essential effectivemass corrections, whereas in second order our result differs from Pippard's quasiclassical theory of ultrasonic attenuation. In potassium the deviations from the free‐electron theory are found to be small.
Mössbauer Effect in (Mn1−x−yFexZny)4[BeSiO4]3S Solid Solutions
Authors: Romanov V. P. , Valter A. A. , Zverev N. D. , Eremenko G. K. 
Published: July 2007

AbstractFeII ion spectra of a nuclear gamma resonance on Fe57 nuclei have been investigated in (Mn1−x−yFexZny)4[BeSiO4]3S solid solutions. The characteristic feature of the spectra is that at 85 °K the electric quadrupole splitting is observed, but at 294 °K the spectra are single, considerably broadened lines. This broadening is assumed to be caused by a unresolved electrical fine structure. According to this assumption, ΔEQ values calculated from the spectra appear to be unusually low and characteristic rather of Fe3+ ions than of Fe2+. The isomer shift values obtained are not characteristic for Fe2+ ions as well. The experimental data on ΔEQ and the isomer shift are explained by the ligand unequivalences and the mechanism of d2p‐hybridization of FeII ion electronic shells.
Infrared Absorption in Crystals with Line Defect
Authors: Celý J. 
Published: July 2007

AbstractA theoretical study is made of the one‐phonon infrared absorption in harmonic crystals lattices with a line defect. The absorption spectrum has been found in an analytic form for a simple model‐one atomic row of charged isotopes in the direction [001] of the simple cubic lattice consisting of uncharged atoms interacting with nearest neighbours, only.
Amplification of Magnetization Waves in Ferromagnetic Conductors
Authors: Kornyushin Yu. V. 
Published: July 2007

AbstractA general linear theory of spin wave amplification similar to the theory of amplification of acoustic waves in crystals is presented which takes into account the space charge arising in the course of spin wave propagation in the crystal. The treatment is given for the case of an arbitrary orientation of the wave propagation vector and an external electric field with respect to the vector of crystal magnetic moment. It is found that in an approximation linear in the deviation from the unperturbed spin value the spin—spin interaction does not contribute to spin wave amplification. It is the spin—orbit interaction that contributes to the amplification in a linear approximation. The spin wave amplification factor proves to be proportional to the value of the direct current through the sample and attains appreciable values (about 25 cm−1) at rather weak currents (about 3.5 A/cm2) and wave vectors about 103 cm−1. With increasing wave vector the amplification factor diminishes inversely proportional to the first power of the wave vector in the case of time amplification, and inversely proportional to the second power of the wave vector in the case of space amplification.
Electron Microscopic Study of the Structure Defects and Their Interactions in Niobiumditelluride
Authors: van Landuyt J. , Remaut G. , Amelinckx S. 
Published: July 2007

AbstractThe structure of niobiumditelluride is analysed in terms of its deviations from the cadmiumiodide structure. From this structure model several types of defects are predicted: three types of domain boundaries, two types of antiphase boundaries, and dislocations having a particular fine structure. Direct evidence for the existence of these defects is provided by a series of observations with the electron microscope. The domain configurations as well as the dislocation fine structure are analysed in detail and an excellent agreement is found between the theoretical predictions and the experimental results. Also the interaction between the dislocation multiribbons and the domain boundaries is studied. The behaviour of the dislocations fully supports the structural model.
Dispersion Relations and Selection Rules for Magnons in Antiferromagnetic NiF2
Authors: Joshua S. J. 
Published: July 2007

AbstractThe dispersion relations for magnons in NiF2 are calculated using the recently available values of the exchange constants [1] and the selection rules for two magnon electric and magnetic dipole absorption are deduced. The dispersion curves are found to exhibit the symmetry predicted by Joshua and Cracknell [2].
Line Shape of Mössbauer Hyperfine Spectra
Authors: Schwegler H. 
Published: July 2007

AbstractA general theory of the line shape of Mössbauer hyperfine spectra is developed within the framework of a new operator space formulation. In the present paper, this theory is applied to hyperfine spectra in the paramagnetic region. The phenomenological Wickman equations are derived from a microscopic quantum mechanical starting point. Explicit expressions for the relaxation terms are obtained, which make possible their discussion and evaluation and a comparison of Mössbauer results with the results of other measurements, especially those of the longitudinal susceptibility χ‖. It is suggested that the discrepancies so far reported between Mössbauer and paramagnetic relaxation experiments are caused by the use of concentrated samples in the latter case.
Electron Spin Resonance on AlCl3:Fe3+
Authors: Bang G. , Sperlich G. , Becker W.‐J. 
Published: July 2007

AbstractThe ESR spectrum of Fe3+ ions, substituting Al3+ ions on lattice sites in AlCl3 single crystals, can be described by the following spin Hamiltonian:

with gx = 2.0112; gy = 2.0118; gz = 1.9947; D = −0.189 cm−1; E = 1.61 ×10−3 cm−3; a = −0.22 × 10−3 cm−1, a + (2/3) F = − 1.6 × 10−3 cm−1; c ≈ 0 cm−1.
Nucleation in Solid Solution Stimulated by Non‐Equilibrium Electrons. II. Electronic Model
Authors: Stoyanov S. , Kashchiev D. , Geoegiev M. 
Published: July 2007

AbstractA model of the processes of electron trapping and recombination in a supersaturated solid solution of metal atoms in a non‐metallic crystal is considered. The electrons are assumed to occur as a result of exposure to light or other irradiation. Expressions for the steady state nucleation rate as well as for the total number of nuclei formed within a certain time are obtained. An equation is also derived relating the amount of absorbed radiative energy, leading to the formation of a given number of nuclei, to the time of exposure. The results obtained can be applied to nucleation phenomena in solids induced by external irradiation, e.g. the photographic process.
The Separability of the Diffusion Equation with Drift Term
Authors: Seeger A. 
Published: July 2007

AbstractThe paper investigates the diffusion equation with drift term, ∂C/∂t = div (D grad C + + μ C grad U), in particular the question of its separability in three dimensions. (D is the diffusion coefficient, μ the mobility, both assumed to be constant scalar quantities; U denotes the potential giving rise to the drift.) The transformation to a new dependent variable f = C exp (μ U/2 D) transforms the equation into a Schrödinger equation. Using this it is shown that, for appropriate choices of the potentials U, the diffusion‐drift equation is separable with modulation factor in the ellipsoidal coordinates (and its degenerate special cases) but in no other coordinate systems. The conditions to which U has to be subjected in order to lead to separability are stated and shown to have a close relationship to the factorization of the solutions of the original equation.
Magnetic Properties of As2Sx Glasses
Authors: Cimpl Z. , Kosek F. , Matyáš M. 
Published: July 2007

AbstractThe diamagnetic component of the magnetic susceptibility of As2Sx glasses is interpreted under the assumption that this material consists of As2Sx molecules having no magnetic moment in the ground state. The van Vleck formula [6] is applied and the Langevin diamagnetic and van Vleck paramagnetic terms are discussed in details.