bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new size‐independent score for pairwise protein structure alignment and its application to structure classification and nucleic‐acid binding prediction
Authors: Yang Yuedong , Zhan Jian , Zhao Huiying , Zhou Yaoqi 
Published: April 2012

AbstractA structure alignment program aligns two structures by optimizing a scoring function that measures structural similarity. It is highly desirable that such scoring function is independent of the sizes of proteins in comparison so that the significance of alignment across different sizes of the protein regions aligned is comparable. Here, we developed a new score called SP‐score that fixes the cutoff distance at 4 Å and removed the size dependence using a normalization prefactor. We further built a program called SPalign that optimizes SP‐score for structure alignment. SPalign was applied to recognize proteins within the same structure fold and having the same function of DNA or RNA binding. For fold discrimination, SPalign improves sensitivity over TMalign for the chain‐level comparison by 12% and over DALI for the domain‐level comparison by 13% at the same specificity of 99.6%. The difference between TMalign and SPalign at the chain level is due to the inability of TMalign to detect single domain similarity between multidomain proteins. For recognizing nucleic acid binding proteins, SPalign consistently improves over TMalign by 12% and DALI by 31% in average value of Mathews correlation coefficients for four datasets. SPalign with default setting is 14% faster than TMalign. SPalign is expected to be useful for function prediction and comparing structures with or without domains defined. The source code for SPalign and the server are available at http://sparks.informatics.iupui.edu. Proteins 2012;. © 2012 Wiley Periodicals, Inc.
Biaxially textured copper–iron alloys for coated conductors
Authors: Gallistl Bernhard , Kirchschlager Raimund , Hassel Achim Walter 
Published: April 2012

AbstractTwo copper based biaxially textured alloys containing 0.37 and 0.91 wt.%‐Fe have been investigated for the use as substrate material for coated conductors. Average full width at half maximum (FWHM) values of 7.3° (CuFe0.37) and 6.8° (CuFe0.91) for in‐plane alignment and 7.2° (CuFe0.37, CuFe0.91) for out‐of‐plane are achieved. Ultimate tensile strength for the two alloys is found to be much higher compared to the values for Cu and CuFe2.35. Hysteresis losses are dramatically reduced compared to other available substrate materials. Magnetisation data for both alloys obtained at 5 K show an anticipated saturation magnetisation (Ms) <0.35 µWb m kg−1, which is less than 1% of pure Ni. magnified image
Selective dissolution in AlFeNb alloys
Authors: Drensler Stefanie , Mardare Cezarina Cela , Milenkovic Srdjan , Hassel Achim Walter 
Published: April 2012

AbstractThree different AlFeNb alloys of various compositions were prepared by arc melting. X‐ray diffraction (XRD) investigation of the melted samples proved the presence of two phases identified as a bcc α(Fe,Al) solid solution and a hexagonal C14 (Fe,Al)2Nb Laves phase. Subsequent electrochemical treatment allowed for a selective dealloying of the α(Fe,Al) or respective FeAl phase and resulted in releasing differently microstructured surfaces. These structures ranged from regular lamellar structures towards branched, fibrous structures. Scanning electron microscope (SEM) characterisation along with a local energy dispersive X‐ray spectroscopic (EDX) analysis of the samples and atomic absorption spectrometry (AAS) analysis of the electrolyte revealed a preferential Fe dissolution and the passive nature of the Nb. The results demonstrate that the phases present in the alloys strongly depend on the production and heat treatment history of the sample.magnified imageSEM micrograph of (A) Fe‐15Al‐10Nb and (B) Fe‐26Al‐4Nb after anodisation in 0.4 M borate buffer.
Structural and magnetic properties of Co2MnSi thin films
Authors: Belmeguenai M. , Zighem F. , Faurie D. , Tuzcuoglu H. , Chérif S.‐M. , Moch P. , Westerholt K. , Seiler W. 
Published: April 2012

AbstractCo2MnSi (CMS) films of different thicknesses (20, 50, and 100 nm) were grown by radio frequency (RF) sputtering on a‐plane sapphire substrates. Our X‐rays diffraction (XRD) study shows that, in all the samples, the cubic 〈110〉 CMS axis is normal to the substrate and that six well defined preferential in‐plane orientations are present. Static and dynamic magnetic properties were investigated using vibrating sample magnetometry (VSM) and microstrip line ferromagnetic resonance (MS‐FMR), respectively. From the resonance measurements versus the direction and the amplitude of an applied magnetic field, most of the magnetic parameters are derived, i.e.: the magnetization, the gyromagnetic factor, the exchange stiffness coefficient, and the magnetic anisotropy terms. The in‐plane anisotropy results from the superposition of two terms showing a twofold and a fourfold symmetry, respectively. The observed behavior of the hysteresis loops is in agreement with this complex form of the in‐plane anisotropy.
Secondary electron emission yield (SEY) in amorphous and graphitic carbon films prepared by PLD
Authors: Alberti M. , Ayouchi R. , Bhattacharyya S. R. , Bundaleski N. , Moutinho A. , Teodoro O. , Aguilera L. , Taborelli M. , Schwarz R. 
Published: April 2012

AbstractHigh secondary emission yield (SEY), and the subsequent build‐up of a secondary electron cloud, may severely limit the stability of high‐intensity particle beams inside particle accelerators. One of the best candidates of beam pipe coating for reduced SEY has been amorphous carbon (a‐C) produced by direct current (D.C.) magnetron sputtering. Here we used pulsed laser deposition (PLD), to prepare a‐C films from a pure carbon target at substrate temperatures ranging from 300 K to 773 K. The ablating laser was a Nd:YAG system operating at 1064 nm wavelength. With increasing temperature the optical band gap dropped from about 2.1 eV to 1.0 eV. This trend indicates transition from predominantly a‐C films to films with more graphitic content, which was also confirmed by Raman measurements. SEY spectra were taken upto 1732 eV of primary electron energy. The maximum SEY value decreased from 1.9 in a‐C films down to 1.4 in highly graphitic films deposited at higher temperatures (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Fabrication and properties of nanocrystalline Zn‐Ir‐O thin films
Authors: Grochowski Jakub , Kamińska Eliana , Piotrowska Anna , Dynowska Elżbieta , Dłużewski Piotr , Dyczewski Jan , Szczepańska Alicja , Kaźmierczak Piotr 
Published: April 2012

AbstractNew p‐type semiconducting ZnIrSiO thin films were fabricated using reactive magnetron RF sputtering from ZnIrSi target. Their transport properties were: resistivity ρ=0.6 Ωcm, hole concentration p=5x1018 cm‐3 and mobility μ=2 cm2/Vs. Optical transmission in the visible wavelength region is 70% and band gap width Eg=3.17 eV. Films are XRD amorphous. HRTEM analysis revealed that ZnIrSiO films were composed of 1‐3 nm in diameter nanograins of Ir3Si and ZnIr2O4 embedded in an amorphous SiO2 matrix. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The February 2010 Arctic Oscillation Index and its stratospheric connection
Authors: Ripesi P. , Ciciulla F. , Maimone F. , Pelino V. 
Published: April 2012

AbstractThe atmospheric dynamics during the occurrence of the extreme negative value of the Arctic Oscillation Index in February 2010 are investigated using meteorological fields from ERA‐Interim and ERA‐40 reanalysis data. The study focuses on the possible causes of this anomalous value, finding that it was forced by a geopotential anomaly that propagated downward from the stratosphere to the troposphere in association with a major sudden stratospheric warming event which occurred at the end of January. An analysis of the dynamics of this warming is also developed, together with a comparison with past similar events. Synoptic and spectral properties of the geopotential fields are analyzed, and the time series of the ‘Baroclinic Activity Index’ are computed, finding an abrupt increase of the middle latitude baroclinic activity immediately after the central date of the warming event. A possible interpretation of this feature is proposed. Copyright © 2012 Royal Meteorological Society
Nonorthogonal orbitals; the Hartree–Fock–Heitler–London method and preliminary applications
Authors: Clementi Enrico , Corongiu Giorgina 
Published: April 2012

AbstractSince the early days of quantum chemical computations, the determinantal wave function can be constructed either with orthogonal or nonorthogonal one electron functions (the orbitals). The two classical quantum mechanical methods, the Hartree–Fock (HF), and the Heitler–London (HL) are examples of the use of orthogonal, and nonorthogonal orbitals, respectively. Both models are approximations yielding approximately half of the experimental binding energy, due to the correlation error. Very extended expansions (with many thousand determinants) recover the error. The two methods have been recently merged into the Hartree–Fock–Heitler–London method (HF–HL), which systematically ensures correct molecular dissociation and a binding energy generally more correct than that obtained with the two parent models. Relatively short expansions of HL configurations yield correct binding energies, at the expense, however, of a high computational time in the optimization of the orbital expansion coefficients. In the HF–HL model, the inner shell electronic correlation is computed with a Coulomb hole functional. We compare computations at the HF, HL, and HF–HL levels, and for the latter, we consider relatively short expansions leading to reasonable binding energies. The computations compare the ground‐state potential energies of the hydrides and homopolar diatomic molecules of the first and second period of the atomic table, a few excited states, and small polyatomic molecules like H2O, C2H2, and HCN. © 2012 Wiley Periodicals, Inc.
Electrostatic potentials and polarization effects in proton‐molecule interactions by means of multipoles from the quantum theory of atoms in molecules
Authors: Terrabuio Luiz Alberto , Haiduke Roberto L. A. 
Published: April 2012

AbstractSome atomic multipoles (charges, dipoles and quadrupoles) from the Quantum Theory of Atoms in Molecules (QTAIM) and CHELPG charges are used to investigate interactions between a proton and a molecule (F2, Cl2, BF, AlF, BeO, MgO, LiH, H2CO, NH3, PH3, BF3, and CO2). Calculations were done at the B3LYP/6‐311G(3d,3p) level. The main aspect of this work is the investigation of polarization effects over electrostatic potentials and atomic multipoles along a medium to long range of interaction distances. Large electronic charge fluxes and polarization changes are induced by a proton mainly when this positive particle approaches the least electronegative atom of diatomic heteronuclear molecules. The search for simple equations to describe polarization on electrostatic potentials from QTAIM quantities resulted in linear relations withr(ris the interaction distance) for many cases. Moreover, the contribution from atomic dipoles to these potentials is usually the most affected contribution by polarization what reinforces the need for these dipoles to a minimal description of purely electrostatic interactions. Finally, CHELPG charges provide a description of polarization effects on electrostatic potentials that is in disagreement with physical arguments for certain of these molecules. © 2012 Wiley Periodicals, Inc.
ID‐CUBE direct analysis in real time high‐resolution mass spectrometry and its capabilities in the identification of phenolic components from the green leaves of Bergenia crassifolia L.
Authors: Chernetsova Elena S. , Crawford Elizabeth A. , Shikov Alexander N. , Pozharitskaya Olga N. , Makarov Valery G. , Morlock Gertrud E. 
Published: April 2012

RATIONALEBergenia crassifolia is a plant widely used in herbal medicine. Its chemical composition has been little studied, and no studies using high‐resolution mass spectrometry (HRMS) have been performed. Its phenolic components are of particular interest, due to the interest in such compounds in medicine and cosmetics. The ID‐CUBE, a simplified Direct Analysis in Real Time (DART) ion source, suitable for the fast MS analysis of liquids without complex sample preparation, offers a new method of studying extracts of such plant. Coupling the ID‐CUBE with a high‐resolution mass spectrometer can provide identification of extract components.METHODSMass spectral conditions were optimized for model solutions of the flavonoid naringenin and used for the identification of phenolic compounds in green leaves extracts of Bergenia crassifolia. OpenSpot sample cards with a metal grid surface were used for sample introduction into the ID‐CUBE ion source on an Obitrap mass spectrometer. The samples were applied as 5‐μL aliquots of the extract onto the metal grid of the card. Sample ionization was stimulated in the ion source within 20 s by applying an electric current to the metal grid to thermally desorb the analytes into the gas flow of metastable helium atoms from the ID‐CUBE.RESULTSElemental compositions were assigned to abundant ions in the mass spectra of the extracts. The major phenolic components were confirmed by their [M–H]– ions. Thirty‐six other marker ions were found, and elemental compositions were suggested for 30% of them, based on a search for compounds found in herbal extracts.CONCLUSIONSThe ID‐CUBE–Orbitrap MS coupling allowed the rapid accurate mass determination of the phenolic components (and other compounds) in herbal extracts. Higher confidence in component identification could be provided by using additional structural elucidation methods, including tandem mass spectrometry (MS/MS), and this will be the focus of future studies. Copyright © 2012 John Wiley & Sons, Ltd.
How Shape Influences Uptake: Interactions of Anisotropic Polymer Nanoparticles and Human Mesenchymal Stem Cells
Authors: Florez Laura , Herrmann Christine , Cramer Jens M. , Hauser Christoph P. , Koynov Kaloian , Landfester Katharina , Crespy Daniel , Mailänder Volker 
Published: April 2012

AbstractAmong several nanoparticle properties, shape is important for their interaction with cells and, therefore, relevant for uptake studies and applications. In order to further investigate such characteristics, fluorescently labeled spherical polymer nanoparticles are synthesized by free‐radical polymerization via the miniemulsion process. The spherical nanoparticles are subsequently submitted to controlled mechanical deformation to yield quasi‐ellipsoidal polymeric nanoparticles with different aspect ratios. The uptake behaviors of spherical and non‐spherical particles with equal volume are investigated qualitatively and quantitatively by electron microscopy, confocal laser scanning microscopy, and flow cytometry measurements. Non‐spherical particles show fewer uptake by cells than their spherical counterparts with a negative correlation between aspect ratio and uptake rate. This is attributed to the larger average curvature radius of adsorbed non‐spherical particles experienced by the cells.
STT and DTT Diagrams of Austenitic Cr–Mn–Ni As‐Cast Steels and Crucial Thermodynamic Aspects of γ → α′ Transformation
Authors: Kovalev Alexander , Jahn Andreas , Weiß Andreas , Wolf Steffen , Scheller Piotr R. 
Published: April 2012

AbstractThe mechanical behavior and microstructure evolution during deformation of novel austenitic Cr–Mn–Ni as‐cast steels with varied Ni content were investigated at various temperatures using static tensile tests, optical microscopy, and the magnetic scale for the detection of ferromagnetic phase fraction. To summarize all knowledge about the deformation‐induced processes, the STT and DTT diagrams were developed for Cr–Mn–Ni steels. The diagrams illustrate the different deformation mechanisms depending on temperature and tension load, and quantify the elongation of the deformation mechanisms. The deformation‐induced ε‐ and α' martensite formation and twinning – the TRIP and TWIP effects – occur in the Cr–Mn–Ni steels depending on the chemical composition and temperature. The differences of deformation‐induced processes depend on thermodynamics and are confirmed by thermodynamic calculations. The nucleation threshold of γ → α′ transformation was determined for the investigated Cr–Mn–Ni steels.
SEM Investigation of High‐Alloyed Austenitic Stainless Cast Steels With Varying Austenite Stability at Room Temperature and 100°C
Authors: Biermann Horst , Solarek Johannes , Weidner Anja 
Published: April 2012

AbstractThe deformation mechanisms of high‐alloyed cast austenitic steels with 16% of chromium, 6% of manganese, and a nickel content of 3–9% were investigated by in situ and ex situ scanning electron microscopy. The austenite stability and the stacking fault energy were influenced by variation of the chemical composition as well as by changing deformation temperature (room temperature; RT and 100°C). The study shows that both an increase in austenite stability and stacking fault energy yield a significant change in the deformation mechanisms. Both increase of nickel content and increase in deformation temperature reduce the intensity of the martensitic phase transformation. Thus, the steel with low nickel content shows at RT pronounced formation of α′‐martensite. The steel with the highest nickel content, however, shows pronounced twinning.
Suppression of Fusarium graminearium growth by differently structured starch types
Authors: Svensson Jan T. , Olas Justyna J. , Skibior Renate , Giese Henriette , Blennow Andreas 
Published: April 2012

AbstractWe investigated the growth behavior and amylolytic enzymes of Fusarium graminearum cultivated on different types of native starch granules including barley (A‐type crystalline polymorph), potato and Curcuma zedoaria (B‐type crystalline polymorph), cassava (C‐type crystalline polymorph), and high AM maize (A + Vh‐type crystalline polymorphs). F. graminearum grew poorly on B‐type starches and the accumulation of biomass was similar to that obtained for fungi cultivated under carbohydrate starvation conditions. In comparison, three‐ to fivefold higher accumulation of fungal biomass was observed for growth on the A‐, C‐ and A + Vh‐type starches. Fungal glucoamylase and α‐amylase activity increased over time in the presence of native starch granules. Interestingly, resistant B‐type starches induced the highest amylolytic activity indicating that F. graminearum interacts with B‐type granules although only limited degradation occur. Starch degradation products maltose and malto‐oligosacharides was found to increase glucoamylase and α‐amylase activity, whereas glucose acted as a catabolite repressor.
Study on properties of Cyperus esculentus starch grown in Xinjiang, China
Authors: Jing Siqun , Yan Xiaoxin , Ouyang Weiqi , Xiang Hengxu , Ren Zhiyan 
Published: April 2012

AbstractThe chemical composition, morphological characteristics, and pasting properties of Cyperus esculentus starch (CES) grown in Xinjiang, China, were investigated and compared with those of potato starch (PS). The amylopectin (AP) content in CES was measured as of 83.82%. Most of the starch granules of Cyperus esculentus (CE) were round or elliptical while the granule diameter ranged from 3.41 to 12.12 µm with an average value of 8.60 µm, and had a typical polarization cross. The X‐ray diffraction (XRD) data showed that CES was of A‐type crystals. The peak viscosity value of CES paste was much lower than that of PS, and the freeze–thaw stability of CES paste was slightly higher than that of PS, but its light transmittance was lower.
Synthesis and characterization of hydrophobically modified starch by ring opening polymerization using imidazole as catalyst
Authors: Zerroukhi Amar , Jeanmaire Thomas , Raveyre Claude , Ainser Auder 
Published: April 2012

AbstractThis paper reports on the synthesis of polyester‐grafted starch (starch‐g‐PCL) by in situ ring‐opening polymerization (ROP) of ε‐caprolactone (ε‐CL) catalyzed by a metal free organic catalyst (imidazole). This reaction has been carried out in bulk, without solvent. The structure of starch‐g‐PCL was characterized by IR, NMR, DSC, and SEM. A moisture sorption isotherm of modified starch revealed a more hydrophobic material. A water contact angle measurement also confirmed the hydrophobic character of starch‐g‐PCL. As expected, this chemical modification reduced the diffusion coefficient of water. The use of an organic catalyst instead of the traditional organometallic catalyst offers an interesting alternative for producing moisture tolerant thermoplastic starch‐based materials.
Evidence for the improvement of thermostability of the maltogenic α‐amylase of Aspergillus niger by negative pressure
Authors: Herale Rajalakshmi , Sukumaran Umesh‐Kumar , Kadeppagari Ravi‐Kumar 
Published: April 2012

AbstractThermostability of the enzymes is influenced by the different parameters and pressure also influences the biological activity of the enzymes. Recently reported maltogenic α‐amylase from Aspergillus niger acts optimally on starch at 40°C and it was unstable above 40°C at atmospheric pressure. Calcium could stabilize the maltogenic α‐amylase activity up to 50°C at atmospheric pressure. But, at negative pressure (−200 mbar) enzyme was stable at temperatures higher than 50°C either in the presence or absence of the substrate, starch making it adoptable for starch processing. Enzyme showed higher affinity to the starch at negative pressure compared to the atmospheric pressure and change in the surface roughness of the enzyme is almost similar to the native state at 70°C and negative pressure. These results suggest that thermolabile enzymes can be used at negative pressures for industrial applications.
Facile preparation of sago starch esters using full factorial design of experiment
Authors: Soetaredjo Felycia Edi , Ismadji Suryadi , Huynh Lien Huong , Kasim Novy S. , Tran‐Thi Ngoc Yen , Ayucitra Aning , Ju Yi‐Hsu 
Published: April 2012

AbstractA facile solvent‐free method to acetylate sago starch (Metroxylon sagu) is reported. Microwave (100 W) was used as the heating source and the heating time was varied from 2 to 10 min with the temperature of acetylation maintained at 100°C under continuous stirring. Using a 24 full factorial design of experiment, it was found that the degree of substitution (DS) of acetylated sago starch was strongly affected by the ratio of starch to acylating reagents, the ratio of acetic anhydride to acetic acid as the acylating reagents, the concentration of iodine as catalyst and reaction time. The physicochemical characteristics of the acetylated sago starch were assessed based on the FTIR spectra, the XRD spectra, the water absorption index (WAI), and the water solubility index (WSI). SEM was used to study the surface morphology of the acetylated sago starch at different DS.