bluuebunny/crossref_metadata_2025_split huggingface dataset:
Taking advantage of local structure descriptors to analyze interresidue contacts in protein structures and protein complexes
Authors: Martin Juliette , Regad Leslie , Etchebest Catherine , Camproux Anne‐Claude 
Published: May 2008

AbstractInterresidue protein contacts in proteins structures and at protein–protein interface are classically described by the amino acid types of interacting residues and the local structural context of the contact, if any, is described using secondary structures. In this study, we present an alternate analysis of interresidue contact using local structures defined by the structural alphabet introduced by Camproux et al. This structural alphabet allows to describe a 3D structure as a sequence of prototype fragments called structural letters, of 27 different types. Each residue can then be assigned to a particular local structure, even in loop regions. The analysis of interresidue contacts within protein structures defined using Voronoï tessellations reveals that pairwise contact specificity is greater in terms of structural letters than amino acids. Using a simple heuristic based on specificity score comparison, we find that 74% of the long‐range contacts within protein structures are better described using structural letters than amino acid types. The investigation is extended to a set of protein–protein complexes, showing that the similar global rules apply as for intraprotein contacts, with 64% of the interprotein contacts best described by local structures. We then present an evaluation of pairing functions integrating structural letters to decoy scoring and show that some complexes could benefit from the use of structural letter‐based pairing functions. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Constitutive and dynamic phosphorylation and acetylation sites on NUCKS, a hypermodified nuclear protein, studied by quantitative proteomics
Authors: Wiśniewski Jacek R. , Zougman Alexandre , Krüger Sonja , Ziółkowski Piotr , Pudełko Marek , Bębenek Marek , Mann Matthias 
Published: May 2008

AbstractNuclear ubiquitous casein and cyclin‐dependent kinases substrate (NUCKS) is a 27 kDa chromosomal protein of unknown function. Its amino acid composition as well as the structure of its DNA binding domain resembles that of high mobility group A (HMGA) proteins, chromosomal proteins known as modulators of chromatin conformation and regulators of transcription. Conformation and function of the HMGA proteins are regulated by phosphorylation and acetylation. So far 19 phosphorylation sites had been reported in NUCKS. In this study, we have identified all known and six additional phosphorylation sites, and also mapped multiple sites of acetylation, methylation and formylation. We measured cell cycle dependent changes of phosphorylation and acetylation of NUCKS in HeLa cells through stable isotope labeling by amino acids in cell culture (SILAC), using the dephosphorylated protein for normalization. We identified sites that were highly phosphorylated or dephosphorylated in mitotically arrested cells as well as sites that were constitutively phosphorylated. The extent of acetylation is reduced in mitotically and G1 arrested cells. Analysis of human cancer specimens revealed that in tissues the extent of acetylation, formylation and methylation is higher than in cultured cells. In breast cancer samples, seven acetylation, three methylation, and three formylation sites were mapped in NUCKS. Of the 243 amino acids, at least 36 can be modified with a total of 57 posttranslational modifications. Thus, NUCKS appears to have the highest ratio of modified to unmodified residues of any protein so far described. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Cookbook versus performance SIS practices
Authors: Gentile Michela , Summers Angela E. 
Published: May 2008

AbstractA safety instrumented system (SIS) is designed to achieve or maintain a safe state of the process when unacceptable process conditions are detected. An SIS is an independent protection layer that is covered by the performance‐based standard ANSI/ISA 84.00.01‐2004. The risk reduction allocated to the SIS determines its target safety integrity level (SIL). ANSI/ISA 84.00.01‐2004 allows a combination of factors to be considered in the verification of the SIL of the SIS. Performance‐based practices provide flexibility to users, yet add complexity to the design process, encouraging project teams to reinvent the wheel for even widely used process equipment.For many engineering applications, prescriptive approaches are favored due to simplicity. These so‐called cookbook practices were very common in the process industry when ANSI/ISA 84.01‐1996 was issued. They are also the backbone of many application standards and recommended practices. The cookbook typically specifies the SIS and maximum proof test interval based on analysis and accepted practice. The user must ensure that the cookbook assumptions are met by the existing equipment and mechanical integrity program. Otherwise, the installed risk reduction may not achieve the expected performance. This article provides an example of a “cookbook” approach for a simple SIS and illustrates the effect of extending the proof test interval from 1 year to 5 years on its probability of failure on demand. © 2008 American Institute of Chemical Engineers Process Saf Prog 2008
Reflection anisotropy spectroscopy of biological molecules with the 4GLS source
Authors: Weightman P. , Bowler M. , Clarke J. A. , Farrell T. , Flavell W. , Harrison P. , Martin D. S. , Papiz M. Z. , Poole M. A. , Quinn F. , Seddon E. A. , Smith C. I. , Smith S. , Surman M. 
Published: May 2008

AbstractThe main characteristics of the UK Fourth Generation Light Source (4GLS) are described. It is explained how the output of 4GLS could be used in studies of biological systems using Reflection Anisotropy Spectroscopy (RAS). (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Reflection anisotropy spectroscopy of decanethiol adsorbed at Au(110)/liquid interfaces
Authors: Bowfield A. , Smith C. I. , Cuquerella M. C. , Farrell T. , Fernig D. G. , Edwards C. , Weightman P. 
Published: May 2008

AbstractReflection Anisotropy Spectroscopy (RAS) has been used to monitor the adsorption of decanethiol as a function of coverage on the Au(110)/ethanol interface. The coverage saturates after 60 minutes for a solution of 0.5 µM. It is found that the RAS observed after 30 minutes can be represented as a linear sum of the RAS observed after 15 minutes and after saturation coverage. This implies that the molecule does not change its orientation as function of coverage. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Surface strain contributions to the lineshapes of reflectance difference spectra for one‐electron and discrete‐exciton transitions
Authors: Lastras‐Martínez L. F. , Ortega‐Gallegos J. , Balderas‐Navarro R. E. , Flores‐Camacho J. M. , Chavira‐Rodríguez M. E. , Lastras‐Martínez A. , Cardona M. 
Published: May 2008

AbstractReflectance difference spectroscopy (RDS/RAS) constitutes a very sensitive tool for the study of the optical properties of semiconductors. RDS spectra comprise several components of different physical origins. One of these components is the strain induced by the surface. In the present work, we report RD spectra measured on GaAs at room temperature at around E1 and the E1+Δ1 transitions. Two cases were studied, the surface strains induced by the c (4× 4) reconstruction and by the vacancies generated by the annealing of semi insulating GaAs crystal. Fits to the line shape of the c (4× 4) reconstructed and annealed spectra were performed by using a surface strain component for one‐electron and discrete‐exciton lineshapes respectively. The character of the fits were interpreted by estimating the piezoelectric field induced by surface strain. For the c (4× 4) surface the strength of the field partially quenches the exciton while for the annealing surface this field is fifty times lower, and an excitonic lineshape is expected.We also inferred that the RD spectra include a component related to surface roughness. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Reflectance‐anisotropy study of the dynamics of molecular beam epitaxy growth of GaAs and InGaAs on GaAs (001)
Authors: Ortega‐Gallegos J. , Lastras‐Martínez A. , Lastras‐Martínez L. F. , Balderas‐Navarro R. E. 
Published: May 2008

AbstractReflectance‐Anisotropy (RA) observations during the Molecular Beam Epitaxy (MBE) growth of zincblende semiconductors films were carried out using the E1 optical transition as a probe. We follow the kinetics of the deposition of GaAs and In0.3Ga0.7As on GaAs (001) at growth rates of 0.2 and 0.25 ML/s, respectively. During growth we used a constant As4 or As2 flux pressure of 5× 10–6 Torr. Clear RA‐oscillations were observed during growth with a period that nearly coincides with the growth period for a Ga‐As bilayer. RHEED was used as an auxiliary technique in order to obtain a correlation between RHEED and RA oscillations. On the basis of our results, we argue that RAS oscillations are mainly associated to periodic changes in surface atomic structure. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Optical anisotropy induced by mechanical strain around the fundamental gap of GaAs
Authors: Ortega‐Gallegos J. , Lastras‐Martínez A. , Lastras‐Martínez L. F. , Balderas‐Navarro R. E. 
Published: May 2008

AbstractWe report on a theoretical‐experimental study of reflectance anisotropy spectroscopy (RAS) of GaAs (001) crystals under uniaxial stress. The study was carried out in the energy region around the fundamental transition. RAS spectra in the energy range from 1.2‐1.7 eV were measured with a photoelastic‐modulator‐based spectrometer. To induce an optical anisotropy, the GaAs crystals were thinned down to 400 mm and an calibrated uniaxial stress was applied by deflection. RAS showed a line shape consisting of an oscillation at around E0. On the basis of a perturbative approach employing the Pikus‐Bir Hamiltonian, we calculated the RAS line shape and found a close agreement with the experimental spectra. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Reflectance‐difference spectroscopy as an optical probe for in situ determination of doping levels in GaAs
Authors: Lastras‐Martínez A. , Lara‐Velázquez I. , Balderas‐Navarro R. E. , Ortega‐Gallegos J. , Guel‐Sandoval S. , Lastras‐Martínez L. F. 
Published: May 2008

AbstractWe report on in situ Reflectance Difference Spectroscopy measurements carried out on GaAs (001). Measurements were performed at temperatures of 580 °C and 430 °C, in both n and p‐type doped films and for both (2×4) and c(4×4) reconstructions. Samples employed were grown by Molecular Beam Epitaxy with doping levels in the range from 1016 – 1019 cm–3. We demonstrate the potential of Reflectance Difference Spectroscopy for impurity level determinations under growth conditions. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
AMPA receptor imaging by infrared scanning near‐field optical microscopy
Authors: Generosi J. , Kropf M. , Margaritondo G. , Hirling H. , Catsicas S. , Johnsson K. , Tolk N. H. , Piston D. W. , Cricenti A. 
Published: May 2008

AbstractInfrared scanning near‐field optical microscopy is used to detect AMPA‐type glutamate receptor clusters in hippocampal neuron cells. AMPA's GluR2‐subunits were marked with the fluorophore Alexa488 and high‐resolution micrographs were taken at 6.25 µm wavelength, corresponding to the maker's strong infrared absorption. The use of infrared light avoids photobleaching and makes this approach suitable for long‐term observations; this technique can be used in general to localize different IR‐absorbing molecules over the complex background of other cell components. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Pump‐probe studies of travelling coherent longitudinal acoustic phonon oscillations in GaAs
Authors: Xu Y. , Qi J. , Miller J. , Cho Y.‐J. , Liu X. , Furdyna J. K. , Shahbazyan T. V. , Tolk Norman 
Published: May 2008

AbstractWe report comprehensive studies of long‐lived oscillations in femtosecond optical pump‐probe measurements on GaAs based systems. The oscillations arise from a photo‐generated coherent longitudinal acoustic phonon wave at the sample surface, which subsequently travels from the surface into the GaAs substrate, thus providing information on the optical properties of the material as a function of time/depth. Wavelength‐dependent studies of the oscillations near the bandgap of GaAs indicate strong correlations to the optical properties of GaAs. We also use the coherent longitudinal acoustic phonon waves to probe a thin buried Ga0.1In0.9As layers non‐invasively. The observed phonon oscillations experience a reduction in amplitude and a phase change at wavelengths near the bandgap of the GaAs, when it passes through the thin GaxIn1‐xAs layer. The layer depth and thicknesses can be extracted from the oscillation responses. A model has been developed that satisfactorily characterizes the experimental results. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Photoluminescence of InP: an in situ probe for characterizing nanostructured PbSe electrodeposited on InP
Authors: Gérard I. , Froment M. , Cachet H. , Etcheberry A. 
Published: May 2008

AbstractPbSe electrodeposition was performed at fixed potential onto n‐InP in an EDTA electrolyte. Conditions are chosen to favour polycrystalline growth. The process was followed in situ by recording the photoluminescence (PL) of the substrate. Characteristic PL decays are observed which depend on the wavelengths of the excitations and are totally related to the PbSe growth. Estimation of the absorption coefficient at 930 nm, 850 nm and 633 nm points out a blue shift towards higher energies after comparison with data on PbSe single crystal. This suggests a quantum sizes effect which agrees to crystallite size evaluated to be in the range 10 to 20 nm by TEM observations. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A novel diagnostics for polymer degradation based on near‐field two‐photon photoluminescence
Authors: Biagioni P. , Celebrano M. , Labardi M. , Polli D. , Zavelani‐Rossi M. , Cerullo G. , Lanzani G. , Finazzi M. , Duò L. 
Published: May 2008

AbstractBy coupling femtosecond pulses to a hollow‐pyramid aperture SNOM, we demonstrate nonlinear near‐field two‐photon photoluminescence imaging of organic semiconductors. We discover that two‐photon excitation of the blue‐emitting poly(9,9‐dioctylfluorene) (PFO) selectively addresses the keto‐defect units which are responsible for a shifted green‐orange emission. We exploit this effect to map oxidized sites in the PFO film with high contrast and spatial resolution, introducing a novel tool for characterizing oxygen‐induced degradation in electroluminescent materials. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Near‐field second‐harmonic generation from gold nanoellipsoids
Authors: Celebrano M. , Biagioni P. , Finazzi M. , Duò L. , Zavelani‐Rossi M. , Polli D. , Labardi M. , Allegrini M. , Grand J. , Adam P.‐M. , Royer P. , Cerullo G. 
Published: May 2008

AbstractSecond‐harmonic generation from single gold nanofabricated particles is experimentally investigated by a nonlinear scanning near‐field optical microscope (SNOM). High peak power femtosecond polarized light pulses at the output of a hollow pyramid aperture allow for efficient second‐harmonic imaging, with sub‐100‐nm spatial resolution and high contrast. The near‐field nonlinear response is found to be directly related to both local surface plasmon resonances and particle morphology. The combined analysis of linear and second‐harmonic SNOM images allows one to discriminate among near‐field scattering, absorption and re‐emission processes, which would not be possible with linear techniques alone. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Second‐harmonic generation from ZnO nanowires
Authors: Pedersen K. , Fisker C. , Pedersen T. G. 
Published: May 2008

AbstractOptical second‐harmonic generation (SHG) from ZnO nanowires is investigated in the region around the band gap. Strong multiphoton excited luminescence and SHG appearing together in the spectra from wires are separated and the SHG part is compared to that of a bulk crystal. The spectrum of the effective second‐order nonlinear susceptibility of the nanowires is extracted from measured SHG intensity by taking into account linear optical propagation governed by effective refractive indices reflecting the volume fraction of ZnO in the nanowire film. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Optical second‐harmonic generation study of charge trapping dynamics in HfO2/SiO2 films on Si(100)
Authors: Price J. , An Y. Q. , Downer M. C. 
Published: May 2008

AbstractElectrostatic‐Field‐Induced Second Harmonic (EFISH) generation is used to characterize laser‐induced charge trapping dynamics in thin HfO2 films deposited on chemically oxidized P‐type Si(100) substrates. We monitor EFISH generation as a function of time, HfO2 thickness and post‐deposition annealing (PDA). In as‐deposited films, the results show that electrons and holes are injected and trapped in comparable amounts, but on different time scales. In annealed films, electron dynamics dominate at all times. Quantitative details depend on film thickness. These results show that time‐dependent EFISH generation can provide an in situ, non‐destructive diagnostic of charge trapping in thin high‐k gate dielectric films. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Optical second‐harmonic and reflectance‐anisotropy spectroscopy of molecular adsorption at Si(001) step‐edges
Authors: Ehlert Robert , Kwon Jinhee , Downer Michael C. 
Published: May 2008

AbstractReflectance‐anisotropy spectroscopy (RAS) and spectroscopic second harmonic generation (SHG) are used to probe a single‐domain reconstructed stepped Si(001) surface offcut 6° toward [110] before and after dissociative adsorption of H2 at the DB step edges. Preliminary analysis with a simplified bond hyperpolarizability model supports the mutual consistency of RA and SHG spectra and suggests that hydrogen termination redistributes oscillator strength from the chemically active step dangling bond into the step back bonds. The data provide a benchmark for first‐principles calculations of the optical response of stepped Si surfaces to step edge molecular adsorption. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Second‐harmonic spectroscopy of Si nanocrystals embedded in silica
Authors: Wirth A. , Wei J. , Gielis J. J. H. , Figliozzi P. , Rafaelsen J. , An Y. Q. , Downer M. C. 
Published: May 2008

AbstractExtending previous second‐harmonic generation (SHG) single‐wavelength studies [1] of Si nanocrystals (NCs) embedded in fused silica, we implement spectroscopic cross‐polarized two‐beam SHG (XP2‐SHG) by employing an optical parametric amplifier as a source of widely tunable (1.6 ≤ Eph ≤ 2.4 eV) femtosecond pulses.Subsequent isolation of the SH signal produced by the NCs yields the oscillator strength and phase of their nonlinear response. We obtain a broad resonance between bulk Si E1 and E2 critical points. Possible explanations for the spectroscopic result are discussed. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Dipole model for the linear response of adsorbed overlayers
Authors: Vázquez‐Nava R. A. , Arzate N. , Mejía J. E. , Mochán W. L. 
Published: May 2008

AbstractThis paper present theoretical calculations of reflectance anisotropy spectra (RAS) for overlayers of alkali atoms adsorbed on a crystalline metallic surface. We assume that the overlayer is formed by an ordered twodimensional (2D) array of adatoms that respond to the local electric field like point‐like harmonic oscillators. We consider overlayers with several rational coverages, assuming that the adsorbates occupy high symmetry sites which form a Bravais lattice that is commensurate with the substrate [1,2]. RAS spectra are obtained for the five 2D Bravais lattices. We found that RAS can be used to observe ordered phases when the ordered phase has a rectangular, centered‐rectangular or oblique symmetry. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Linear optical response of (6,0) boron nitride nanotubes adsorbed with molecular hydrogen
Authors: Arzate N. , Vázquez‐Nava R. A. , Mejía J. E. 
Published: May 2008

AbstractWe performed a study of the molecular adsorption of hydrogen on BN nanotubes. We present ab initio calculations for the linear optical response of single wall zigzag BN(6,0) nanotubes as a function of the hydrogen adsorption on the exterior surface of the nanotube. The calculation of the linear optical response is performed by using density functional theorywith the use of plane waves and pseudopotentials. We consider four different nanotube‐structures adsorbed with different coverage of molecular hydrogen.We find optimized atomic coordinates for such structures and calculate binding energies for the molecule of hydrogen on the nanotube.After having the linear response of the considered structures, we have calculated their energy loss function spectra. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Microsynthesis and mass spectral study of Chemical Weapons Convention related 2‐alkyl‐1,3,6,2‐dioxathiaphosphocane‐2‐oxides
Authors: Palit Meehir , Mallard W. Gary , Yang Imsuk 
Published: May 2008

AbstractChemical Weapons Convention (CWC)‐related compounds where the phosphorus atom is part of a ring have very limited representation in mass spectral libraries and the open literature. Here we report electron ionization (EI), chemical ionization (CI) and electrospray ionization tandem mass spectrometry (ESI‐MSn) spectra and retention indices for 2‐alkyl‐1,3,6,2‐dioxathiaphosphocane‐2‐oxides (alkyl C1 to C3) which are new cyclic chemicals covered under the CWC. The EI mass spectra show a pattern of ion fragmentation that is similar to that of other cyclic phosphonates in that loss of the alkylphosphonic acid as a neutral loss is more important than the presence of the protonated alkylphosphonic acid. In contrast to other cyclic phosphonates, the 2‐alkyl‐1,3,6,2‐dioxathiaphosphocane‐2‐oxides show almost no protonated alkylphosphonic acid and as a result the spectra do not carry the same distinctive signature of the phosphorus–carbon bond that is required for the chemical to be covered under the CWC. Copyright © 2008 John Wiley & Sons, Ltd.