bluuebunny/crossref_metadata_2025_split huggingface dataset:
A chemogenomic analysis of the transmembrane binding cavity of human G‐protein‐coupled receptors
Authors: Surgand Jean‐Sebastien , Rodrigo Jordi , Kellenberger Esther , Rognan Didier 
Published: November 2005

AbstractThe amino acid sequences of 369 human nonolfactory G‐protein‐coupled receptors (GPCRs) have been aligned at the seven transmembrane domain (TM) and used to extract the nature of 30 critical residues supposed—from the X‐ray structure of bovine rhodopsin bound to retinal—to line the TM binding cavity of ground‐state receptors. Interestingly, the clustering of human GPCRs from these 30 residues mirrors the recently described phylogenetic tree of full‐sequence human GPCRs (Fredriksson et al., Mol Pharmacol2003;63:1256–1272) with few exceptions. A TM cavity could be found for all investigated GPCRs with physicochemical properties matching that of their cognate ligands. The current approach allows a very fast comparison of most human GPCRs from the focused perspective of the predicted TM cavity and permits to easily detect key residues that drive ligand selectivity or promiscuity. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Nurturing a strong process safety culture
Authors: Kadri Shakeel H. , Jones David W. 
Published: November 2005

AbstractProcess safety management introduced a formal, structured, management systems approach to accident prevention that represented a “step change” improvement in identifying and reducing the potential for major process plant accidents. Although the process safety management elements have proven effective, the overall sustainability remains a challenge. This paper highlights the importance of a strong process safety culture that is needed to sustain a strong process safety performance. We use the Columbia Shuttle disaster incident as a backdrop to focus the attention on the significance of not having an optimal “Safety Culture.” Examples have been included from our industry to further exemplify its broad applicability. The paper proposes an approach that will help organizations to self‐assess the state of the process safety culture in their organizations, which can be an aid in their ongoing cultural improvement effort. Four important cultural themes are identified and described: (1) Create awareness and buy‐in about process safety culture themes, (2) adapt process safety culture themes to your company experience, (3) use suggested indicators to identify specific areas of improvement, and (4) develop a strategic improvement plan to strengthen and sustain process safety culture. © 2005 American Institute of Chemical Engineers Process Saf Prog, 2006
Strain relaxation by 〈100〉 misfit dislocations in dilute nitride InxGa1–xAs1–yNy/GaAs quantum wells
Authors: Young E. C. , Koveshnikov A. N. , Tixier S. , Kavanagh K. L. , Tiedje T. 
Published: November 2005

AbstractThe effect of dilute N alloying and Bi surfactant growth on strain relaxation in highly strained InGaAs single quantum well (QWs) was investigated by using high resolution X‐ray diffraction (HRXRD) and transmission electron microscopy (TEM). Dilute nitride InxGa1–xAs0.99N0.01 QWs of varying thickness, constant lattice mismatch 1.7%, were grown by molecular beam epitaxy on oriented GaAs (001) substrates. Some samples were exposed to a flux of Bi surfactant during the growth procedure, which acts to enhance the N incorporation, increase the optical emission, and create smoother interfaces. The QWs were observed to relax through the formation of pure edge‐type, misfit dislocations aligned with in‐plane 〈100〉 directions. These were found to be directly associated with degradation in the optical emission, however, 1% N addition, with or without Bi surfactant, did not have a detectable effect on the critical thickness nor the rate of this relaxation mechanism. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Morphology, interface polarity and branching of electrochemically etched pores in InP
Authors: Spiecker E. , Rudel M. , Jäger W. , Leisner M. , Föll H. 
Published: November 2005

AbstractThe 3‐dimensional morphology of individual pores grown in InP(001) by electrochemical etching, their interface polarities and their branching behavior have been investigated by transmission electron microscopy (TEM) in various crystal lattice projections and by convergent‐beam electron diffraction (CBED). Pores start to grow irregularly shaped with preferential orientation perpendicular to the surface. Following this nucleation layer long straight pores with triangular cross‐section grow deep into the crystal along inclined 〈111〉B directions. Along the pore axis the pore diameter oscillates. The morphology of the pore tips can be described approximately by a chain of interconnected tetrahedrons bounded by {111}A‐facets. Some pores show additional {001} facets at the transition regions between the tetrahedrons. With increasing distance from the pore tips the mean pore diameters increase and the pores approach the shape of open prismatic channels with channel walls that are bounded, on the average, by {112}‐planes. Self‐assembling pore branching in all four 〈111〉B crystal directions leads to 3‐dimensional pore arrangements which are of considerable interest for the fabrication of photonic crystals. – We discuss the observed pore morphologies within the framework of a model that describes the pore formation as an interplay of dissolution and surface passivation with the surface passivation being affected by the crystal polarity of the material. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Cathodoluminescence spectroscopy of single SnO2 nanowires and nanobelts
Authors: Salviati Giancarlo , Lazzarini Laura , Zha Ming Zheng , Grillo Vincenzo , Carlino Elvio 
Published: November 2005

Abstract1D semiconducting SnO2 nanoribbons in form of nanowires and nanobelts with a lateral size ranging from 50 to 700 nm and length of several hundreds of micrometers are studied by Cathodoluminescence in the Scanning Electron Microscope and Transmission Electron Microscopy.Experimental High Angle Annular Dark Field imaging suggests compositional modulations along the 〈100〉 direction in agreement with recent theoretical predictions. Single nanobelt and nanowire cathodoluminescence spectroscopy reveals the presence of a broad emission made of two sub‐bands centered at about 460 nm and 580 nm at room temperature. No near band edge emission is found. This result is assigned to a major role of surface effects with respect to bulk properties. CL spectroscopy carried out at different temperatures and Sn vapour pressure, before and after thermal treatments in Oxygen atmosphere and under electron beam irradiation show that the integrated intensity of the sole emission at 580 nm changes. A red and blue shift of about 20 nm are found respectively for the two bands by decreasing the temperature. A correlation between Oxygen vacancies and the cathodoluminescence emission peak at 580 nm is discussed. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Types and origin of dislocations in large GaAs and InP bulk crystals with very low dislocation densities
Authors: Müller G. , Schwesig P. , Birkmann B. , Härtwig J. , Eichler S. 
Published: November 2005

AbstractBulk GaAs and InP crystals with diameter of 4″ or more can now be grown with very low dislocation densities (EPD considerably below 1000 cm–2) using the Vertical Gradient Freeze (VGF) growth technique and rigorous process optimization by the aid of numerical simulation. It turns out that the usually dominating 60°‐dislocations are no longer the dominating type if the dislocation density is in the range of EPD = 100 cm–2 or below. The goal of growing large dislocation‐free GaAs and InP crystals like Si can only be reached if the types of these “residual dislocations” are identified and their origin is fully understood. This paper therefore reviews the present knowledge about these residual dislocations in GaAs and InP for various dopants. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Partial dislocations in wurtzite GaN
Authors: Komninou Ph. , Kioseoglou J. , Dimitrakopulos G. P. , Kehagias Th. , Karakostas Th. 
Published: November 2005

AbstractThe partial dislocations in wurtzite‐structured GaN are reviewed and new results are presented. A multiplicity of partials is possible depending on stacking fault (SF) type, orientation, and interactions. The partials that delimit the I1 intrinsic basal SFs have 5/7, 8, or 12‐atom cores as more probable configurations. The core structures of 90° partial dislocations with 1/6〈20$ \bar 2 $3〉 Burgers vector were studied from high resolution transmission electron microscopy observations in comparison with simulated models obtained from energetic calculations. Two cases were distinguished with one structure involving a 5/7 or 12‐atom ring core and the other an 8‐atom ring core. Another type of partials, in particular dislocations accommodating mirror variants of basal SFs were also studied experimentally. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Surface orientation as a control parameter for the growth of non‐stoichiometric gallium arsenide
Authors: Marek T. , Schür C. , Kunsági‐Máté S. 
Published: November 2005

AbstractIn order to study the effect of the substrate orientation on the incorporation of excess arsenic into low temperature grown gallium arsenide, we examine molecular beam epitaxial layers grown at constant low substrate temperatures and constant III/V flux ratio on exactly (001) oriented substrates and on vicinal substrates tilted up to 10° towards the 〈111〉A and 〈111〉B directions. Our experiments show that the substrate orientation has a significant influence on the excess arsenic content and thus needs to be considered as an additional parameter to control low temperature growth of gallium arsenide. Respective ab‐initio calculations offer first models for the incorporation of excess arsenic into As antisite and As interstitial positions on misoriented as well as exactly oriented substrates. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Room temperature photo‐CVD SiO2 layers on AlGaN and AlGaN/GaN MOS‐HFETs
Authors: Wang C. K. , Chang S. J. , Su Y. K. , Chiou Y. Z. , Lin T. K. , Wong C. C. , Liu H. L. , Chang S. P. , Tang J. J. 
Published: November 2005

AbstractHigh quality SiO2 layers were successfully deposited onto AlGaN by photo‐chemical vapor deposition (photo‐CVD) using D2 lamp as the excitation source at room temperature. The resulting interface state density was only 8.86 × 1011 cm–2 eV–1. With a 2 µm gate, it was found that maximum drain–source current, maximum transconductance (gm,max) and gate voltage swing (GVS) of the fabricated nitride‐based metal–oxide–semiconductor heterostructure field effect transistors (MOS‐HFETs) were 225 mA/mm, 33 mS/mm and 6.5 V, respectively. Compared with metal‐semiconductor HFETs (MES‐HFETs), it was found that noise power density of MOS‐HFETs was lower and presented pure 1/f noise with smaller trapping effects. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Self‐consistent calculations of phonon scattering rates in the GaAs transistor structure with one‐dimensional electron gas
Authors: Borzdov A. V. , Pozdnyakov D. V. , Galenchik V. O. , Borzdov V. M. , Komarov F. F. 
Published: November 2005

AbstractSelf‐consistent calculations of acoustic and polar optical phonon scattering rates in GaAs quantum wire transistor structures were carried out with account of collisional broadening. The influence of the gate bias on the scattering rates was examined, too. It was shown that in order to treat the scattering rates rigorously it is important to search for electron energy levels by means of the self‐consistent solution of Schrödinger and Poisson equations and to take into account the collisional broadening. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
An Electrophilicity Based Analysis of Toxicity of Aromatic Compounds Towards Tetrahymena Pyriformis
Authors: Roy D. R. , Parthasarathi R. , Subramanian V. , Chattaraj P. K. 
Published: November 2005

AbstractElectrophilicity index is one of the important quantum chemical descriptors in describing toxicity or biological activities of the diverse classes of chemicals to bio‐systems in the context of development of Quantitative Structure Activity Relationship (QSAR). In this study a large number of selected 174 aromatic compounds containing phenols, nitrobenzenes and benzonitriles are chosen as the training set to verify their toxic potency to Tetrahymena pyriformis in the light of electrophilicity. A systematic analysis has been made to find out the electron donation/acceptance nature of these model compounds by comparing their electronegativity values with those of the NA bases/DNA base pairs. The training sets are classified into two groups, viz., the electron donor group comprising 97 phenol derivatives and the electron acceptor group consisting of 77 nitrobenzenes and benzonitriles grouped together. Regression analysis in terms of correlation coefficient ($\rm{ R}$), variance adjusted to degrees of freedom ($\rm{ R_{adj}^2 }$) and variance of leave‐one‐out cross‐validation ($\rm{ R_{CV}^2 }$) has been made for both the electron donor and acceptor aromatic groups to predict the toxicity values of these model compounds to Tetrahymena pyriformis. It is heartening to note that the global and local electrophilicity indices along with the total Hartree‐Fock energy can explain more than 80% of cross‐validation variance of data of those aromatic molecules.
N‐band Hubbard models. III. Boson–fermion and interaction–boson models for high‐Tc superconductivity
Authors: Yamaguchi K. , Nakano M. , Nagao H. , Okumura M. , Yamanaka S. , Kawakami T. , Yamada S. , Yamaki D. , Kitagawa Y. , Takeda R. , Nitta H. 
Published: November 2005

AbstractIn this series of articles (I, II), N‐band Hubbard models have been considered for strongly correlated electron systems, which are realized in d–p, π–d, π–R, and σ–R conjugated systems. The magnetism and superconductivity of these systems have been elucidated in terms of effective exchange integrals (J), which are calculated by first‐principle methods. In part III of this series, the BCS–BEC crossover theory, has been introduced to elucidate the physical foundation of our J and JP model for the high‐Tc superconductivity (HTSC). The boson–fermion (BF) model for this theory is found useful for a reasonable explanation of the experimental phase diagrams of HTSC. The underlying physics of the BF model is different from that of the slave boson field‐theoretical model assuming spinon–holon condensations in the low dimension. The interaction boson model (IBM) for nuclear matter is also employed to describe the cooperative mechanisms of electron–phonon (EP), spin fluctuation (SF), charge fluctuation (CF), and many‐bands (MB) effects. This phenomenological model is useful for pictorial understanding and for the theoretical explanation of the cooperative mechanisms: (EP + SF), (SF + CF), (EP + SF + MB), etc. These are also investigated in analogy to BF model of fermionic gases, where the Feshbach resonance between boson and fermion is responsible for their coupling. The implications of these theoretical results are discussed in relation to recent ALPES and STM experiments for HTSC, which suggest the contributions of SF (J) and EP (P) interactions. The recently discovered superconductivity of boron‐doped diamond is examined as an example of two‐band sigma‐radical (σ–R) conjugated systems. Finally, the bipolaron model is briefly discussed in relation to boson–fermion model via EP interaction to superconductivity. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Electronic structure of BeH2
Authors: Penotti Fabio E. 
Published: November 2005

AbstractNonorthogonal single‐configuration and multiconfiguration ab initio calculations are carried out on the BeH2 molecule in its equilibrium (D∞h) geometry, using a highly optimized even‐tempered Slater‐type orbital (STO) basis set. The results are used as a basis for a discussion of the electronic structure of the molecule in modern‐VB terms. A value of Re = 1.329 Å is obtained. Values are also obtained for the symmetric‐stretch harmonic frequency (2053 cm−1), electric quadrupole moment (−5.60 Buckingham), and nuclear quadrupole coupling constants (−3.59 MHz for 9Be and 0.0915 MHz for 2H). © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Ab initio calculations and analysis of chemical bonding in SrTiO3 and SrZrO3 cubic crystals
Authors: Evarestov R. A. , Tupitsyn I. I. , Bandura A. V. , Alexandrov V. E. 
Published: November 2005

AbstractThe possibility of the different first‐principles methods to describe the chemical bonding in SrTiO3 and SrZrO3 cubic crystals is investigated. The local properties of the electronic structure (atomic charges, bond orders, atomic delocalization indexes, and polarization fractions) were calculated with different methods: traditional Mulliken population analysis in LCAO calculations, two projection techniques in plane‐wave (PW) calculations, population analysis based on Wannier‐type atomic orbitals, and chemical bonding analysis based on the localized Wannier functions for occupied (valence band) LCAO states. All the techniques considered except the traditional Mulliken analysis demonstrate that the ionicity of chemical bonding in SrZrO3 is larger than in SrTiO3, in agreement with the Zr and Ti electronegativities relation and the relative bandgaps observed. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Potential energy surface of thionylimide
Authors: Bharatam P. V. , Amita  , Kaur D. , Senthil Kumar P. 
Published: November 2005

AbstractThe potential energy surface (PES) of thionylimide has been searched using ab initio MO and density functional calculations. The electronic structures of the isomers of HNSO have been studied using the HF/6‐31+G*, MP2(full)/6‐31+G*, and B3LYP/6‐31+G* levels. Final energies of these molecules have been calculated at the high‐accuracy G2 and CBS‐Q levels. The probable pathways of isomerization of thionylimide to its isomers (e.g., thiocyanic acid, HONS, nitrosothiols) have been explored by studying the three‐ or four‐membered transition states. This study identified total eight possible isomers (1–8) of HNSO, of which four (1–4) have already been realized experimentally. Of the remaining four (5–8), at least two (5, 7) can be generated experimentally. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
An integrated strategy for identification and relative quantification of site‐specific protein phosphorylation using liquid chromatography coupled to MS2/MS3
Authors: Wolschin Florian , Lehmann Ute , Glinski Mirko , Weckwerth Wolfram 
Published: November 2005

AbstractReversible and differential multisite protein phosphorylation is an important mechanism controlling the activity of cellular proteins. Here we describe a robust and highly selective approach for the identification and relative quantification of site‐specific phosphorylation events. This integrated strategy has three major parts: visualisation of phosphorylated proteins using fluorescently stained polyacrylamide gels, determination of the phosphorylation site(s) using automatic MS3 triggered by the loss of phosphoric acid, and relative quantification of phosphorylation by integrating MS2‐ and MS3‐extracted ion traces using a fast‐scanning, linear ion trap mass spectrometer. As a test case, recombinant sucrose‐phosphate synthase (SPS) from Arabidopsis thaliana (At5g1110) was used for identification and quantification of site‐specific phosphorylation. The identified phosphorylation site of the actively expressed protein coincides with the major regulatory in vivo phosphorylation site in spinach SPS. Site‐specific differential in vitro phosphorylation of native protein was demonstrated after incubation of the recombinant protein with cold‐adapted plant leaf extracts from A. thaliana, suggesting regulatory phosphorylation events of this key enzyme under stress response. Copyright © 2005 John Wiley & Sons, Ltd.
Application of combined high‐performance thin‐layer chromatography immunostaining and nanoelectrospray ionization quadrupole time‐of‐flight tandem mass spectrometry to the structural characterization of high‐ and low‐affinity binding ligands of Shiga toxin 1
Authors: Meisen Iris , Friedrich Alexander W. , Karch Helge , Witting Ute , Peter‐Katalinić Jasna , Müthing Johannes 
Published: November 2005

AbstractShiga toxin 1 (Stx1) represents an AB5 toxin produced by enterohemorrhagic Escherichia coli, which cause gastrointestinal diseases in humans that are often followed by potentially fatal systemic complications, such as acute encephalopathy and hemolytic uremic syndrome. The expression of the preferential Stx1 receptor, Gb3Cer/CD77 (Galα1‐4Galβ1‐4Glcβ1‐1Cer), is one of the primary determinants of susceptibility to tissue injury. Due to the clinical importance of this life‐threatening toxin, a combined strategy of preparative high‐performance thin‐layer chromatography (HPTLC) overlay assay and mass spectrometry was developed for the detection and structural characterization of Stx1‐binding glycosphingolipids (GSLs). A preparation of neutral GSLs from human erythrocytes, comprising 21.4% and 59.1% of the high‐ and low‐affinity Stx1‐binding ligands Gb3Cer/CD77 and Gb4Cer, respectively, was separated on silica gel precoated HPTLC plates and probed for the presence of Stx1 receptors. Stx1 positive on the one hand and anti‐Gb3Cer/CD77 and anti‐Gb4Cer antibody positive bands from parallel reference runs on the other hand were extracted with chloroform/methanol/water (30/60/8, v/v/v). These crude extracts were used without any further purification for a detailed structural analysis by nanoelectrospray ionization quadrupole time‐of‐flight mass spectrometry (nanoESI‐QTOF‐MS) in the negative ion mode. In all extracts investigated, neutral GSLs were detected as singly charged deprotonated molecular ions, [M–H]−, and neither buffer‐derived salt adducts nor coextracted contaminants from the overlay assay procedure or the silica gel layer were observed. For the structural characterization of Stx1‐ and antibody‐binding GSLs low‐energy collision‐induced dissociation (CID) was applied to high and low abundant receptor species of the crude extracts. All MS/MS spectra obtained contained full series of Y‐type ions, B‐type ions and additional ions generated by ring cleavages of the sugar moiety. Only analytical quantities in the microgram scale of a single GSL species within the complex GSL mixture were required for the structural MS characterization of Stx1 ligands as Gb3Cer/CD77 and Gb4Cer. This effective combined HPTLC/MS procedure offers a broad range of applications, not only for toxins of bacterial origin, but also for any GSL‐binding agents such as plant‐derived lectins or human proteins with yet unknown binding specificities. Copyright © 2005 John Wiley & Sons, Ltd.
A technical challenge for robot‐assisted minimally invasive surgery: precision surgery on soft tissue
Authors: Stallkamp J , Schraft R D 
Published: November 2005

AbstractIn minimally invasive surgery, a higher degree of accuracy is required by surgeons both for current and for future applications. This could be achieved using either a manipulator or a robot which would undertake selected tasks during surgery. However, a manually‐controlled manipulator cannot fully exploit the maximum accuracy and feasibility of three‐dimensional motion sequences. Therefore, apart from being used to perform simple positioning tasks, manipulators will probably be replaced by robot systems more and more in the future. However, in order to use a robot, accurate, up‐to‐date and extensive data is required which cannot yet be acquired by typical sensors such as CT, MRI, US or common x‐ray machines. This paper deals with a new sensor and a concept for its application in robot‐assisted minimally invasive surgery on soft tissue which could be a solution for data acquisition in future. Copyright © 2005 Robotic Publications Ltd.