bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of DNA binding across protein superfamilies
Authors: Contreras‐Moreira Bruno , Sancho Javier , Angarica Vladimir Espinosa 
Published: July 2009

AbstractSpecific protein–DNA interactions are central to a wide group of processes in the cell and have been studied both experimentally and computationally over the years. Despite the increasing collection of protein–DNA complexes, so far only a few studies have aimed at dissecting the structural characteristics of DNA binding among evolutionarily related proteins. Some questions that remain to be answered are: (a) what is the contribution of the different readout mechanisms in members of a given structural superfamily, (b) what is the degree of interface similarity among superfamily members and how this affects binding specificity, (c) how DNA‐binding protein superfamilies distribute across taxa, and (d) is there a general or family‐specific code for the recognition of DNA. We have recently developed a straightforward method to dissect the interface of protein–DNA complexes at the atomic level and here we apply it to study 175 proteins belonging to nine representative superfamilies. Our results indicate that evolutionarily unrelated DNA‐binding domains broadly conserve specificity statistics, such as the ratio of indirect/direct readout and the frequency of atomic interactions, therefore supporting the existence of a set of recognition rules. It is also found that interface conservationfollows trends that are superfamily‐specific. Finally, this article identifies tendencies in the phylogenetic distribution of transcription factors, which might be related to the evolution of regulatory networks, and postulates that the modular nature of zinc finger proteins can explain its role in large genomes, as it allows for larger binding interfaces in a single protein molecule. Proteins 2010. © 2009 Wiley‐Liss, Inc.
PSM system upgrade in response to an Occupational Safety and Health Administration NEP inspection
Authors: Walter Robert , Foottit Richard , Nelson Brian 
Published: July 2009

AbstractThis article presents a brief analysis of the Occupational Safety and Health Administration (OSHA) Petroleum Refinery Process Safety Management National Emphasis Program (NEP) citation results as of early 2009. It includes trends distilled from the OSHA inspections performed to date. Recommendations for preparing for PSM NEP level inspections are provided.A proven approach to designing and implementing an upgrade project for OSHA process safety management systems and EPA risk management program is described. The model presented can be targeted to a facility's NEP specific citations or used for a general PSM system effectiveness upgrade.This article includes recommendations for improving PSM as a result of an NEP inspection. The recommendations are for the PSM elements that routinely have major OSHA citations; that is: Operating Procedures, Mechanical Integrity, Process Hazards Analysis, Process Safety Information, Management of Change, and Incident Investigations. © 2009 American Institute of Chemical Engineers Process Saf Prog 2009
Changes in phosphine sorption in wheat after storage at two temperatures
Authors: Daglish Gregory J , Pavic Hervoika 
Published: July 2009

AbstractBACKGROUND: Wheat can be stored for many months before being fumigated with phosphine to kill insects, so a study was undertaken to investigate whether the sorptive capacity of wheat changes as it ages. Wheat was stored at 15 or 25 °C and 55% RH for up to 5.5 months, and samples were fumigated at intervals to determine sorption. Sealed glass flasks (95% full) were injected with 1.5 mg L−1 of phosphine based on flask volume. Concentrations were monitored for 11 days beginning 2 h after injection. Some wheat samples were refumigated after a period of ventilation. Several fumigations of wheat were conducted to determine the pattern of sorption during the first 24 h.RESULTS: Phosphine concentration declined exponentially with time from 2 h after injection. Rate of sorption decreased with time spent in storage at either 15 or 25 °C and 55% RH. Rate of sorption tended to be lower when wheat was refumigated, but this could be explained by time in storage rather than by refumigation per se. The data from the 24 h fumigations did not fit a simple exponential decay equation. Instead, there was a rapid decline in the first hour, with phosphine concentration falling much more slowly thereafter.CONCLUSIONS: The results have implications for phosphine fumigation of insects in stored wheat. Both the time wheat has spent in storage and the temperature at which it has been stored are factors that must be considered when trying to understand the impact of sorption on phosphine concentrations in commercial fumigations. Copyright © The state of Queensland (through the Department of Employment, Economic Development and Innovation) 2009. Published by John Wiley and Sons, Ltd.
Influence of Al additions and thermobaric treatment on the UV emission from ceramic and polycrystalline Gd‐activated cubic boron nitride
Authors: Shishonok E. M. , Leonchik S. V. , Steeds J. W. 
Published: July 2009

AbstractThe effects of thermobaric treatments and aluminum additions on the spectral properties of Gd‐activated cBN have been investigated. Two types of sample have been studied: polycrystalline and ceramic forms. Spectra related to the Gd3+ ions were found to shift to higher energy as a result of secondary thermobaric treatment of the polycrystals and on sintering micropowders to form the ceramic samples. Additional fine structure appeared as a result of aluminum doping. These changes are described in detail and the results discussed in the light of available evidence.
One‐dimensional disordered magnetic Ising systems: A new approach
Authors: Gasparian Vladimir , Badalian David , Jódar Esther 
Published: July 2009

AbstractWe reconsider the problem of a one‐dimensional Ising model with an arbitrary nearest‐neighbor random exchange integral, temperature, and random magnetic field in each site. A convenient formalism is developed that reduces the partition function to a recurrence equation, which is convenient both for numerical as well as for analytical approaches. We have calculated asymptotic expressions for an ensemble averaged free energy and the averaged magnetization in the case of strong and weak couplings in external constant magnetic field. With a random magnetic field at each site in addition to nearest‐neighbor random exchange integrals we also evaluated the free energy. We show that the zeros of the partition function for the Ising model in the complex external magnetic field plane formally coincide with the singularities of the real part of electron's transmission amplitude through the chain of δ‐function potentials.
Current‐induced spin polarization for a general two‐dimensional electron system
Authors: Wang C. M. , Cui H. T. , Lin Q. 
Published: July 2009

AbstractIn this paper, current‐induced spin polarization (CISP) for a two‐dimensional electron gas with a general spin–orbit interaction is investigated. For an isotropic energy spectrum, the in‐plane CISP is found to be dependent on the electron density for a non‐linear spin–orbit interaction and increases with the increment of sheet density, in contrast to the case for the k‐linear spin–orbit coupling model. The numerical evaluation is performed for an InAs/InSb heterojunction with spin–orbit coupling of both linear and cubic spin–orbit coupling types. For δ‐type short‐range electron‐impurity scattering, it is found that the CISP increases with increasing density when cubic spin–orbit couplings are considered. However, for remote disorders, a rapid enhancement of CISP is always observed at high electron density, even in the case without cubic spin–orbit coupling. This result demonstrates the collision‐related feature of CISP. The effects of different high‐order spin–orbit couplings on spin polarization can be comparable.
Hysteresis loops and reversal modes of two‐phase nanoparticle
Authors: Liu Yan , Du An 
Published: July 2009

AbstractThe hysteresis loops of cubic two‐phase nanoparticles composed of a spherical nanocrystalline grain in the center and an amorphous matrix is simulated by the micromagnetic simulation method. The influence of the anisotropy axis direction of the nanocrystalline grain on the reversal mode and coercivity are studied. It is found that there are three kinds of reversal mode with different anisotropy axis directions, and the coercive force of the system is also dependent on the direction of the anisotropy axis of the inner grain and the configurational anisotropy axis of the cube.
Chalcogenide glassy photoresists: History of development, properties, and applications
Authors: Lyubin Victor 
Published: July 2009

AbstractThe history of the development of photoresists based on the photostructural transformations in chalcogenide glassy semiconductors is discussed in this paper. The properties of such photoresists including the possibility of an essential increase of their photosensitivity and also applications are examined. Together with the photoresists, the chalcogenide glassy roentgen‐, electron beam‐, and plasma‐resists are briefly considered.
The individual core/shell silicon nanowire structure probed by Raman spectroscopy
Authors: Marczak M. , Judek J. , Kozak A. , Gębicki W. , Jastrzębski C. , Adamowicz L. , Luxembourg D. , Hourlier D. , Mélin T. 
Published: July 2009

AbstractThe results of Raman scattering study of well‐separated core/shell silicon nanowires grown by CVD method and deposited on an Au surface are presented. The Raman spectra analysis indicates a presence of both crystalline (520 cm–1) and amorphous (470 cm–1) silicon phases, forming quite independent fractions. From the growth conditions, nanowires are expected to form such a core‐shell cone, with the amorphous silicon phase (aSi) outside, and the crystalline silicon phase (cSi) inside. The nanowires' diameter varies from 100 nm to 400 nm, what is seen in the SEM pictures. The Raman spectra have been acquired from the three points of the cone shaped nanowire: base, centre and tip. Based on the Stokes/anti‐Stokes (St/aSt) intensity ratios, the position and full width at half maximum of the Raman peaks temperatures of the amorphous shell and the cSi core in different nanowire's position have been determined. Against our expectations, the crystalline silicon (cSi) temperature was found lower than the amorphous silicon temperature (aSi). This suggests that the nanowire cSi core is in a good thermal contact with the metallic substrate, thus improving the heat evacuation of the SiNW core, for which the thermal conductivity is known to be low. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Influence of hydrogen on hydrogenated cadmium telluride optical spectra
Authors: Pociask M. , Polit J. , Sheregii E. , Cebulski J. , Kisiel A. , Mycielski A. , Morgiel J. , Piccinini M. , Marcelli A. , Robouch B. , Guidi M. Cestelli , Savchyn V. , Izhnin I. I. , Zajdel P. , Nucara A. 
Published: July 2009

AbstractThe presence of oxygen impurity in semiconducting materials affects the electrical properties of crystals and significantly limits their application. To remove oxygen impurity, ultra‐pure hydrogen is used while growing Te‐containing crystals such as CdTe, CdZnTe, and ZnTe. The hydrogenation of CdTe crystals is a technological process that purifies the basic material from oxygen, mainly cadmium and tellurium oxide compounds incorporated in CdTe crystalline lattice. In the present work we analyses the deformations induced by hydrogen and oxygen atoms in CdTe crystals looking at their influence on the near fundamental band (NFB), middle infrared (MIR) and far infrared (FIR) reflectivity spectra as well as on cathodoluminescence (CL) spectra. Comparison of the hydrogenated CdTe phonon structure profiles confirms the presence of hydrogen atoms bounded inside the lattice. The possible localization of hydrogen and oxygen ions within the tetrahedron coordinated lattice is discussed in the framework of a model that shows a good agreement with recent NFB, MIR and FIR experiments carried out on hydrogenated CdTe crystals. Measured reflection spectra in the wavelength range 190‐1400 nm (NFB) indicate the appearance in CdTe(HM) and CdTe(HL) of additional maxima at 966 nm related to the electron transitions from level about 0.2 eV above the valence band. The CL spectra confirmed existence of this electron level. We present a possible H2 alignment similar to the single H model i.e., over the face (at about 0.38 Å). For this model the angle from the central atom to the H atoms is equal to 64° which is also close to the bonding angle of CdH2 (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Influence of electron‐phonon coupling on transport through a quantum dot in the Kondo regime
Authors: Świrkowicz R. , Wilczyński M. 
Published: July 2009

AbstractTransport through a quantum dot attached to nonmagnetic electrodes subject to spin bias and charge bias is studied theoretically within the non‐equilibrium Green function formalism and effects of local vibrational modes are analysed. A presence of phonons strongly influences the spin and charge conductance characteristics leading to an appearance of phonon satellites apart from Kondo peaks.Superposition of the main Kondo resonances and their phonon satellites in the conductance curves corresponding to two individual spin channels can lead to a variety of peak patterns in dependence on the charge voltage applied to the system (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Phonons in InAs quantum dot structures
Authors: Milekhin Alexander , Toropov Alexander , Zahn Dietrich R. T. 
Published: July 2009

AbstractWe present a Raman study of the phonon spectra of periodical structures with (In,Ga)As QDs in (Al,Ga)As matrix as well as AlAs QDs embedded in InAs grown by molecular beam epitaxy. Raman scattering by optical, interface and acoustic phonons was observed in the QD structures. TO and LO phonons in the QDs are strongly affected by both strain and confinement. The Raman study reveals a two‐mode behavior of optical phonons in the whole composition range for both InGaAs QDs and the AlGaAs matrix. Raman scattering by InAs‐ and GaAs‐like LO phonons in InGaAs QDs shows a size‐selective resonant behaviour. Interface phonons were investigated in InGaAs QDs and the AlGaAs matrix. Their frequency positions were analyzed as a function of the alloy content within the dielectric continuum model. The positions of IF phonons in the QD structures observed in the experiment agree well with calculated ones assuming that the QDs have the shape of oblate ellipsoids. Multiple phonon Raman scattering involving both pure overtones of the first‐order InAs, GaAs and AlAs optical and interface phonons and combination of phonons from the materials is observed in the vicinity with E0 resonance in QDs. Possible mechanisms of these processes are discussed. Low frequency resonant Raman scattering by acoustic phonons was observed in the QD structures. The periodic oscillations seen in the Raman spectra are well described by the elastic continuum model. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electron–phonon interaction in double quantum wells
Authors: Płoch D. , Sheregii E. M. , Marchewka M. , Woźny M. , Tomaka G. 
Published: July 2009

AbstractThe experimental results for the magneto‐transport in the InGaAs/InAlAs double quantum wells (DQW) structures of two different shapes of wells and different value of the electron density obtained in pulse magnetic fields are reported. The Magnetophonon Resonance (MPR) was observed for both types of the structures at 77‐125 K temperatures. Four kinds of LO‐phonons are taken into account to interpret the MPR oscillations in DQW and a method of the Landau Level calculation in DQW is elaborated for this aim. The particularity of MPR in DQW is the great number of Landau levels caused by SAS‐splitting of electron states and great number of the phonon assistance electron transitions between Landau levels. The significant role of carriers statistics is shown too. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Water vapour variability induced by urban/rural surface heterogeneities during convective conditions
Authors: Champollion C. , Drobinski P. , Haeffelin M. , Bock O. , Tarniewicz J. , Bouin M. N. , Vautard R. 
Published: July 2009

AbstractScientific interest in urban meteorology has increased because highly populated areas experience high vulnerability to pollution or heavy rain. However, compared to urban air quality or urban heat island (UHI) processes, the urban water vapour cycle is poorly understood because it has been investigated less due to the lack of upper‐air measurements and the high sensitivity of surface measurements to local heterogeneities. In this paper, surface measurements of wind, temperature, pressure and humidity, as well as integrated water vapour (IWV) from GPS and MODIS and numerical simulations, have been used to investigate the urban cycle of water vapour in May and June 2004 during the VAPIC field experiment in the Paris area.The surface data show the typical characteristics of an urban area with the absence of water vapour sources and a UHI of about 6 °C at night. The urban IWV distribution differs completely, with an urban IWV excess on average between 1600 and 0600 UTC (with a maximum of about 1.5 kg m−2 at 0600 and 1700 UTC). No IWV difference between the urban and rural areas is found in the middle of the day. The numerical simulations reproduce accurately the urban IWV anomaly.Shallow surface wind convergence associated with the UHI during nighttime provides moisture from the rural areas. Urban areas are therefore under wind convergence for most of the time. The rural water vapour sources and the depth of the convergence control the amplitude of the urban IWV excess. At about 1200 UTC, entrainment at the top of the urban boundary layer is the key process that inhibits the urban IWV excess observed at night. Copyright © 2009 Royal Meteorological Society
The monomolecular mechanism of the gas‐phase thermal decomposition of primary N‐nitramines
Authors: Mazilov Elisey , Ogurtsova Evgeniya , Shamov Alexander , Khrapkovskii Grigorii 
Published: July 2009

AbstractUsing nonempirical methods and DFT‐methods the geometrical parameters formation enthalpies of molecules and radicals, energies dissociation of NNO2 bonds of primary and secondary N‐nitramines have been investigated. The basic tendencies in the changes of the geometrical and electronic structures, formation enthalpies, and dissociation energies have been analyzed in basic homologous series of nitramines. Various alternative mechanisms of the gas‐phase monomolecular thermal decomposition have been studied by of the example of N‐methylnitramine. The process of the aci‐form formation and its further multistage destruction is the most advantageous way of decomposition of the primary N‐nitramines. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Broken symmetry density functional study of a mixed‐valence unsymmetrical dinuclear iron complex
Authors: Ferreira Dalva E. C. , De Almeida Wagner B. , Neves Ademir , Rocha Willian R. 
Published: July 2009

AbstractDensity functional theory (DFT) calculations with different exchange‐correlation functionals were performed for a mixed valence Fe(II)/Fe(III) binuclear complex with μ‐methoxo and two μ‐carboxylate bridging ligands, (1) with geometry optimizations being performed for all possible spin multiplicities (MS = 2, 4, 6, 8, and 10). Within the exchange‐correlation functionals studied, only the hybrid GGA functionals B3P and B3LYP and also the pure GGA functional RPBE, predicts the geometry with high spin (S = 9/2) to be more stable than the geometry with low spin state (S = 1/2) by 20 kcal/mol, in agreement with the experimental findings. These functionals also predict the same stability order for the different spin states, being MS = 10>8>6>2>4. The meta‐GGA functionals TPSS and TPSSh and also the pure GGA functionals BLYP and BP86 predict different stability orders. The computed average EPR g‐tensor, gav, of 2.03, at the B3LYP level, is in good agreement with the experimental findings. Heisenberg exchange coupling constants, J, were calculated within the broken‐symmetry formalism, at the B3LYP level, showing that the two iron centers are antiferromagnetic coupling, with a very weak coupling constant of about −7 cm−1, in good agreement with the experimental value. Additionally, the effect of using different multiplicities of the reference geometries on the computed J value is discussed. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Microscopic self‐organization and self‐referential systems: A progress report
Authors: Brändas Erkki J. 
Published: July 2009

AbstractIt is contended that (the classical canonical form of) Jordan blocks, play a role analogous to those of paradoxes and self‐referential contradictions in philosophy and mathematical logic. As examples we will briefly discuss the occurrence of such triangular units in appropriately generalized quantum theory of microscopic as well as open dissipative systems with structures appearing on both the fundamental as well as in higher order levels of organization. The mathematical structure centers on specific transformations within coherent‐dissipative ensembles that exhibit certain factorization properties allowing prime number algorithms, cf. the Gödel encoding system used to derive the celebrated incompleteness theorem. This prompts the suggestion that an additional meta‐code, cf. the genetic code, might be a‐scripted for the mapping between the genotype and phenotype spaces. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Flow and water temperature simulation for habitat restoration in the Shasta River, California
Authors: Null Sarah E. , Deas Michael L. , Lund Jay R. 
Published: July 2009

AbstractLow instream flows and high water temperatures are two factors limiting survival of native salmon in California's Shasta River. This study examines the potential to improve fish habitat conditions by better managing water quantity and quality using flow and water temperature simulation to evaluate potential restoration alternatives. This analysis provides a reasonable estimate of current and potential flows and temperatures for a representative dry year (2001) in the Shasta River, California. Results suggest restoring and protecting cool spring‐fed sources provides the most benefit for native salmon species from a broad range of restoration alternatives. Implementing a combination of restoration alternatives further improves instream habitat. Results also indicate that substituting higher quality water can sometimes benefit native species without increasing environmental water allocations. This study shows the importance of focusing on the limitations of specific river systems, rather than systematically increasing instream flow as a one size fits all restoration approach. Copyright © 2009 John Wiley & Sons, Ltd.