bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dissection of the conformational cycle of the multidrug/lipidA ABC exporter MsbA
Authors: Doshi Rupak , Woebking Barbara , van Veen Hendrik W. 
Published: July 2010

AbstractRecent crystal structures of the multidrug ATP‐binding cassette (ABC) exporters Sav1866 from Staphylococcus aureus, MsbA from Escherichia coli, Vibrio cholera, and Salmonella typhimurium, and mouse ABCB1a suggest a common alternating access mechanism for export. However, the molecular framework underlying this mechanism is critically dependent on assumed conformational relationships between nonidentical crystal structures and therefore requires biochemical verification. The structures of homodimeric MsbA reveal a pair of glutamate residues (E208 and E208′) in the intracellular domains of its two half‐transporters, close to the nucleotide‐binding domains (NBDs), which are in close proximity of each other in the outward‐facing state but not in the inward‐facing state. Using intermolecular cysteine crosslinking between E208C and E208C′ in E. coli MsbA, we demonstrate that the NBDs dissociate in nucleotide‐free conditions and come close on ATP binding and ADP·vanadate trapping. Interestingly, ADP alone separates the half‐transporters like a nucleotide‐free state, presumably for the following catalytic cycle. Our data fill persistent gaps in current studies on the conformational dynamics of a variety of ABC exporters. Based on a single biochemical method, the findings describe a conformational cycle for a single ABC exporter at major checkpoints of the ATPase reaction under experimental conditions, where the exporter is transport active. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Solution conformation of a tetradecapeptide stabilized by two di‐n‐propyl glycine residues
Authors: Sarojini Vijayalekshmi , Balaji Rao R. , Ragothama S. , Balaram Padmanabhan 
Published: July 2010

AbstractThe solution conformation of a designed tetradecapeptide Boc‐Val‐Ala‐Leu‐Dpg‐Val‐Ala‐Leu‐Val‐Ala‐Leu‐Dpg‐Val‐Ala‐Leu‐OMe (Dpg‐14) containing two di‐n‐propyl glycine (Dpg) residues has been investigated by 1H NMR and circular dichroism in organic solvents. The peptide aggregates formed at a concentration of 3 mM in the apolar solvent CDCl3 were broken by the addition of 12% v/v of the more polar solvent DMSO‐d6. Successive NiH $\leftrightarrow$ Ni+1H NOEs observed over the entire length of the sequence in this solvent mixture together with the observation of several characteristic medium‐range NOEs support a major population of continuous helical conformations for Dpg‐14. Majority of the observed coupling constants ($^{3}_{\rm {JNHC}}{^{\alpha}}_{\rm {H}}$) also support ϕ values in the helical conformation. Circular dichroism spectra recorded in methanol and propan‐2‐ol give further support in favor of helical conformation for Dpg‐14 and the stability of the helix at higher temperature. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd.
Epimerization‐free synthesis of cyclic peptide by use of the O‐acyl isopeptide method
Authors: Yoshiya Taku , Kawashima Hiroyuki , Hasegawa Yuka , Okamoto Kazuhiro , Kimura Tooru , Sohma Youhei , Kiso Yoshiaki 
Published: July 2010

AbstractA head‐to‐tail cyclization of a protected linear hexapeptide with a C‐terminal O‐acyl isopeptide proceeded to give a cyclic O‐acyl isopeptide without epimerization. The cyclic O‐acyl isopeptide possessed different secondary structures compared with the native cyclic peptide. The isopeptide was then efficiently converted to the desired cyclic peptide via an O‐to‐N acyl migration reaction using a silica gel‐anchored base. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd.
Growth and structural characterization of pyramidal site‐controlled quantum dots with high uniformity and spectral purity
Authors: Dimastrodonato Valeria , Mereni Lorenzo O. , Young Robert J. , Pelucchi Emanuele 
Published: July 2010

AbstractThis work presents some fundamental features of pyramidal site‐controlled InGaAs Quantum Dots (QDs) grown by metal–organic vapour phase epitaxy on patterned GaAs (111)B substrate. The dots self‐form inside pyramidal recesses patterned on the wafer via pre‐growth processing. The major advantage of this growth technique is the control it provides over the dot nucleation position and the dimensions of the confined structures onto the substrate. The fundamental steps of substrate patterning and the QD formation mechanism are described together with a discussion of the structural particulars. The post‐growth processes, including surface etching and substrate removal, which are required to facilitate optical characterization, are discussed. With this approach extremely high uniformity and record spectral purity are both achieved.
Fast construction of the Kohn–Sham response function for molecules
Authors: Koval Peter , Foerster Dietrich , Coulaud Olivier 
Published: July 2010

AbstractThe use of the linear combination of atomic orbitals method for excited states involves products of orbitals that are known to be linearly dependent. We identify a basis in the space of orbital products that is local for orbitals of finite support and with a residual error that vanishes exponentially with its dimension. As an application of our previously reported technique we compute the Kohn–Sham density response function $\chi _{0} $ for a molecule consisting of N atoms in $N^{2} N_{\omega } $ operations, with $N_{\omega } $ the number of frequency points. We test our construction of $\chi _{0} $ by computing molecular spectra directly from the equations of Petersilka–Gossmann–Gross in $N^{2} N_{\omega } $ operations rather than from Casida's equations which takes $N^{3} $ operations. We consider the good agreement with previously calculated molecular spectra as a validation of our construction of $\chi _{0} $. Ongoing work indicates that our method is well suited for the computation of the GW self‐energy $\Sigma = {\rm i}GW$ and we expect it to be useful in the analysis of exitonic effects in molecules.
Magnetic properties of a cylindrical Ising nanowire (or nanotube)
Authors: Kaneyoshi T. 
Published: July 2010

AbstractMagnetic properties (phase diagram and magnetization) of a cylindrical Ising nanowire or nanotube are investigated by the use of the effective‐field theory with correlations. Particular emphasis is given to the effects of the surface and its dilution on them. Much attention is paid to the thermal variation of the magnetization when the spins at the surface are coupled antiferromagnetically to the ferromagnetic core spins by the negative shell coupling. The effects of dilution at the surface, the surface exchange interaction, and the shell coupling on the magnetization profiles are investigated. We find a number of characteristic phenomena for them.
Elastic properties of superconducting MAX phases from first‐principles calculations
Authors: Shein Igor R. , Ivanovskii Alexander L. 
Published: July 2010

AbstractUsing first‐principles density functional calculations, a systematic study of the elastic properties for all known superconducting MAX phases (Nb2SC, Nb2SnC, Nb2AsC, Nb2InC, Mo2GaC, and Ti2InC) was performed. As a result, the optimized lattice parameters, independent elastic constants, indicators of elastic anisotropy, and brittle/ductile behavior as well as the so‐called machinability indexes were calculated. We also derived bulk and shear moduli, Young's moduli, and Poisson's ratios for ideal polycrystalline MAX aggregates. The results obtained are discussed in comparison with available theoretical and experimental data and elastic parameters for other layered superconductors.
First principles theoretical study of complex magnetic order in transition‐metal nanowires
Authors: Saubanère M. , Tanveer M. , Ruiz‐Díaz P. , Pastor G. M. 
Published: July 2010

AbstractThe electronic and magnetic properties of one‐dimensional (1D) transition‐metal (TM) systems are investigated from a first principles theoretical perspective. The development of local magnetic moments and the stability of various collinear and non‐collinear spin arrangements are determined in the framework of a generalized gradient approximation to density‐functional theory (DFT). Two specific complementary problems are considered. The first one concerns the local moment formation in Cu wires doped with Co and Ni impurities. Recent results as a function of wire length, interatomic distances, impurity position within the wire, and total spin polarization$S_{z} $are reviewed. It is shown that both Co and Ni impurities preserve their magnetic degree of freedom in monoatomic Cu wires by developing almost saturated local moments in all low‐lying total spin configurations ($S_{z} \leq 5/2$). The impurity moments are largely dominated by the d‐electron contributions. In the ground state they couple ferromagnetically with the moments induced at the Cu host atoms. The changes in the spin‐density distribution and in the local densities of electronic states are quantified as a function of the position of the impurity position within the wire. In addition, recent results on the ground‐state magnetic order in V nanowires are reviewed. The stability of ferromagnetic (FM), antiferromagnetic (AF), and spiral non‐collinear (NC) orders is analyzed in terms of the frozen‐magnon spectrum. A remarkable transition from FM to NC order is observed as a function of the nearest‐neighbor (NN) distancea. The dependence of the single‐particle electronic structure of the wire on the wave‐vector of the spin‐density wave (SDW) is demonstrated. Finally, the role of magnetic anisotropy on the stability of NC order is discussed in the framework of a simple classical spin model.
Effects of strain‐control layers on piezoelectric field and indium incorporation in InGaN/GaN blue quantum wells
Authors: Song Jae‐Ho , Dong Yanqun , Kim Ho‐Jong , Ahn Byung‐Jun , Kim Tae‐Soo , Hong Soon‐Ku , Yuh Hwan‐Kuk , Choi Sung‐Chul , Moon Youngboo , Shee Sangkee , Lee Jae‐Hak , Song Jung‐Hoon 
Published: July 2010

AbstractWe investigated the effects of a strain‐control layer on piezoelectric fields and indium incorporation in blue‐emitting InGaN/GaN quantum wells (QWs) using reverse‐biased electroreflectance spectroscopy. With this technique, we could determine the change in both indium incorporation and the piezoelectric field by the inserted buffer layer. We compared two test samples, which have identical structures except for the insertion of an additional InGaN layer at the bottom of the blue‐QW. The magnitude of the piezoelectric fields in the QWs with the added layer was significantly smaller even with a slightly higher indium composition. The result shows that the strain in the QW is partially released and can be controlled quantitatively by the strain‐control layer underneath. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Ge/Si(100) quantum dots grown via a thin Sb layer
Authors: Tonkikh Alexander , Zakharov Nikolay , Talalaev Vadim , Werner Peter 
Published: July 2010

AbstractWe report on a way to grow very small Ge islands (basis about 15 nm, height about 1 nm, density 2 × 1011 cm–2) on a Si substrate by molecular beam epitaxy. By the deposition of lowest amounts of antimony prior to the Ge deposition we could influence the formation kinetics of Ge islands. After the covering of the islands by a Si layer the samples show pronounced photoluminescence at room temperature in the range of 1.5 μm. The results of the optical spectroscopy experiments are interpreted in this way that these Ge nanoislands show a quantum confinement, and therefore, they can be regarded as quantum dots.magnified imageAFM and TEM micrographs, and room temperature PL spectrum of Sb assisted Ge/Si(100) QDs.(© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Highly confined surface plasmon polariton resonances in rectangular nanopore cavities
Authors: Chen Chang , Lagae Liesbet , Maes Guido , Borghs Gustaaf , Van Dorpe Pol 
Published: July 2010

AbstractThe excitation of surface plasmons in nanoslits in metal films is known to result in large electromagnetic field enhancements. The enhancement factor strongly depends on the exact geometrical parameters, such as widths and lengths. In this work, we numerically study field enhancement and transmission resonances inside short nanoslits (nanopores) with varying lengths using three‐dimensional finite difference time domain (FDTD) simulations. The results indicate that the excitation of highly confined lateral Fabry–Pérot surface plasmon resonances results in enhancement factors greatly exceeding the two‐dimensional case. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Theoretical study of the structural and electronic properties of aggregates, wires, and bulk phases formed from M@Si16 superatoms (M = Sc−, Ti, V+)
Authors: Torres M. B. , Fernández E. M. , Balbás L. C. 
Published: July 2010

AbstractStarting with the nearly spherical endohedral M@Si16 cage‐like clusters (M = Sc−, Ti, V+) in their fullerene‐like isomerical form with D4d symmetry, we study the trends in the formation of [Ti@Si16]n, [Sc@Si16K]n, and [V@Si16F]n aggregates as their size increase (n ≤ 9). We identify specially stable linear, planar, and three‐dimensional patterns, which can serve to grow low‐dimensional infinite systems. The structure and cohesive energy of a few infinite chains of that type are optimized. We also present calculations of fcc, bcc, and single cubic crystal meta stable phases having the Ti@Si16 superatom as basic unit, as well as cubic NaCl and CsCl bulk structures of Sc@Si16K and V@Si16F supermolecules. The orientation and isomerization of the superatom or supermolecule in the cubic cell plays an important role. The projected density of states of V@Si16F crystal with NaCl structure shows a meta stable ferromagnetic phase due to polarization of d electrons of vanadium. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
A new perspective on implementation by voting trees
Authors: Fischer Felix , Procaccia Ariel D. , Samorodnitsky Alex 
Published: July 2010

AbstractVoting trees describe an iterative procedure for selecting a single vertex from a tournament. They provide a very general abstract model of decision‐making among a group of individuals, and it has therefore been studied which voting rules have a tree that implements them, i.e., chooses according to the rule for every tournament. While partial results concerning implementable rules and necessary conditions for implementability have been obtained over the past 40 years, a complete characterization of voting rules implementable by trees has proven surprisingly hard to find. A prominent rule that cannot be implemented by trees is the Copeland rule, which singles out vertices with maximum degree.In this paper, we suggest a new angle of attack and re‐examine the implementability of the Copeland solution using paradigms and techniques that are at the core of theoretical computer science. We study the extent to which voting trees can approximate the maximum degree in a tournament, and give upper and lower bounds on the worst‐case ratio between the degree of the vertex chosen by a tree and the maximum degree, both for the deterministic model concerned with a single fixed tree, and for randomizations over arbitrary sets of trees. Our main positive result is a randomization over surjective trees of polynomial size that provides an approximation ratio of at least 1/2. The proof is based on a connection between a randomization over caterpillar trees and a rapidly mixing Markov chain. © 2010 Wiley Periodicals, Inc. Random Struct. Alg., 39, 59–82, 2011
Lecturing to 200 students and its effects on cytokine concentration and salivary markers of adrenal activation
Authors: Filaire Edith , Larue Jacques , Portier Hugues , Abed Aicha , Graziella Pavon‐Djavid , Teixeira Anna , Anne Pelle 
Published: July 2010

AbstractStress not only activates the SAM system and the hypothalamic–pituitary–adrenal axes, but also the immune system. The aims of this study are to assess the physiological variations in saliva (cytokines, cortisol and alpha‐amylase) and perceived stress in professors when they had to lecture to 200 students. A total of eight unstimulated saliva samples were collected from nine professors: four on a working day that included the lecture and four controls on a working day without a lecture. The professors also rated subjective stress on a seven‐point scale 5 min before the lecture, immediately after the lecture and at the same times on the control day. The lecture elicited substantial increases in subjective stress ratings, with the values on the lecture day significantly higher than those on the control day. Lecturing resulted in significant increases in Tumor Necrosis Factor (TNF)‐α, Interleukin (IL)‐2 and IL‐4 concentrations, but did not affect the IL‐10 values. These changes appeared to be concomitant with changes in the concentrations of the stress markers, alpha‐amylase and cortisol. The mechanisms by which psychosocial stress can induce cytokine changes and modify the activity of salivary alpha‐amylase are not entirely understood, and further research is thus warranted. Copyright © 2010 John Wiley & Sons, Ltd.
Patient and nurse perceptions of stressors in the intensive care unit
Authors: Yava Ayla , Tosun Nuran , Ünver Vesile , Çiçek Hatice 
Published: July 2010

AbstractThe objective of the study was to determine the perceptions of a group of patients on intensive care units' (ICUs) stressors and the perceptions of nurses on ICU patients' stressors in Turkey, and compare the differences in patients' and nurses' perception of the stressors in ICUs. In this descriptive study, 155 patients who were admitted to medical or surgical ICUs and 152 nurses who are employed in the same units of two training and research hospitals in Turkey were enrolled in this study. The ICU Environmental Stressor Scale (ICUESS) was used to determine intensive care stressors. According to total ICUESS mean scores, patients (91.41 ± 34.91) perceived significantly less stress than the ICU nurses (133.23 ± 32.20) perceived them to have. Both patients and nurses ranked ‘fear of death’ as the greatest stressor. Physiological stressors were identified as the most important stressors by both patients and nurses. Patients and nurses in medical ICUs were more affected by stressors than their counterparts in surgical ICUs. Patients with unplanned or emergency admissions perceived higher stress than that of patients with planned admissions. Several factors could help reduce these stressors, such as having familiar arrangements, humane ICU environment, individual patient assessments and appropriate nursing interventions. Copyright © 2010 John Wiley & Sons, Ltd.
Writing, Self‐Healing, and Self‐Erasing on Conductive Pressure‐Sensitive Adhesives
Authors: Alessandri Ivano 
Published: July 2010

AbstractA simple strategy for enabling conductive pressure sensitive adhesives (PSAs) to work as light‐responsive materials is reported. Direct laser‐writing of PSA substrates was achieved by means of a continuous‐wave He‐Ne laser focused through the objectives of an optical microscope. This approach takes advantage of cooperative interplay between viscoelastic properties of PSAs and enhanced thermal conductivity provided by an extra overlayer of gold. In particular, the thickness of the gold layer is a crucial parameter for tuning the substrate responsiveness. Self‐healing and self‐degradation processes can be exploited for controlling the lifetime of the written information, whereas additional protective coatings can be introduced to achieve permanent storage.
A theory of knowledge construction systems
Authors: Nakamori Yoshiteru , Wierzbicki Andrzej P. , Zhu Zhichang 
Published: July 2010

AbstractThis paper considers the problem of knowledge integration, and proposes a theory of knowledge construction systems, which consists of three fundamental parts: a knowledge construction system, a structure–agency–action paradigm, and evolutionary‐constructive objectivism. The first part is a model of collecting and synthesizing knowledge, the second relates to necessary abilities of actors when collecting knowledge in individual domains, and the third comprises a set of principles to justify collected and synthesized knowledge. The paper starts with a brief introduction of our basic systems approach, called ‘informed systems thinking’, followed by a summary of our proposal: a theory of knowledge construction systems. The paper then explains its three fundamental parts, with a special emphasis on the types of knowledge integration, and finally gives a detailed explanation of the theory with an example. Copyright © 2010 John Wiley & Sons, Ltd.
The molecular structures of starch components and their contribution to the architecture of starch granules: A comprehensive review
Authors: Pérez Serge , Bertoft Eric 
Published: July 2010

AbstractRecent developments in methods and instrumentation have contributed to major advances in our understanding of the fine structure of amylose and amylopectin. The structure of the starch granule slowly unravels with new insight into key structural features. Following a brief presentation of the structural features common to all starches, the most recent findings for the structure of amylose and amylopectin are reported. The organization of different types of chains in amylopectin is discussed with a critical review of the ‘cluster’ model leading to the presentation of alternative models. The locations of molecular components in the starch granule are described according to a progress structural order. The description of the crystalline components is followed by a presentation of their supramolecular arrangements. The crystalline components comprise platelet nanocrystals which have already been identified and characterized, and other less well characterized ‘blocklet components’. The location and state of amylose within the granule is also presented. This comprehensive review aims at distinguishing between those structural features that have received widespread acceptance and those that are still under debate, with the ambition of being educational and to provide stimulation for further fundamental investigation into the starch granule as a macromolecular assembly.
Oxidative stress induced by 2,4‐phenoxyacetic acid in liver of female rats and their progeny: Biochemical and histopathological studies
Authors: Troudi Afef , Ben Amara Ibtissem , Samet Amira Mahjoubi , Zeghal Najiba 
Published: July 2010

AbstractThe 2,4‐Dichlorophenoxyacetic acid (2,4‐D) was used in agriculture as an herbicide in many countries including Tunisia. The aim of this study was to evaluate the effects of 2,4‐D on liver function of adult rats and their progeny. Female Wistar rats were divided into two groups: the controls and the treated rats which received 600 ppm of 2,4‐D in their drinking water from the 14th day of pregnancy until day 14 after delivery. In 2,4‐D group, a significant decrease in body weight of pups was noted, when compared to controls. Liver antioxidant enzyme activities, superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPx) decreased, while malondialdehyde (MDA) levels increased in dams and pups. Moreover, plasma aminotransferases (ALT, AST), gamma glutamil transpeptidase (GGT), lactate dehydrogenase (LDH), bilirubin and albumin levels were increased significantly. The biochemical modifications were correlated with histopathological studies. We concluded that 2,4‐D induced hepatotoxicity in adult and suckling rats. © 2010 Wiley Periodicals, Inc. Environ Toxicol, 2012.