bluuebunny/crossref_metadata_2025 huggingface dataset:
First-principles study for stability and binding mechanism of graphene/Ni(111) interface: Role of vdW interaction
Authors: Zhang Wei-Bing , Chen Chuan , Tang Ping-Ying
Published: July 2014

The interaction between graphene and Ni(111) surface has been investigated systematically by density functional theory calculations, in which two different functionals PBE and optB88-vdW are used. PBE calculation indicates no binding between graphene and Ni(111) surface, while optB88-vdW, which is evidenced to consider van der Waals interaction reasonably, predicts the correct binding picture. The accurate potential energy surfaces suggest that top-fcc, bridge-top, and top-hcp are possible stable structures of graphene on Ni(111) surface, which are also found to have very close energies, in agreement with coexistence of different phases found experimentally. Different from PBE, the optB88-vdW functional predicts that top-fcc is the most stable configuration, following by bridge-top and then top-hcp, which is consistent with the surface distribution given by a statistical analysis of high-resolution scanning tunneling microscopy (STM) images. The Dirac points are destroyed in chemisorbed phases of all stable structures. Further analysis indicates that strong hybridization between Ni-3d and C-2p orbitals and asymmetry induced by substrate are responsible for the gap opening at K point. The detailed binding mechanisms have been analysed using differential charge density and the STM images.
First-principles investigation on Rydberg and resonance excitations: A case study of the firefly luciferin anion
Authors: Noguchi Yoshifumi , Hiyama Miyabi , Akiyama Hidefumi , Koga Nobuaki
Published: July 2014

The optical properties of an isolated firefly luciferin anion are investigated by using first-principles calculations, employing the many-body perturbation theory to take into account the excitonic effect. The calculated photoabsorption spectra are compared with the results obtained using the time-dependent density functional theory (TDDFT) employing the localized atomic orbital (AO) basis sets and a recent experiment in vacuum. The present method well reproduces the line shape at the photon energy corresponding to the Rydberg and resonance excitations but overestimates the peak positions by about 0.5 eV. However, the TDDFT-calculated positions of some peaks are closer to those of the experiment. We also investigate the basis set dependency in describing the free electron states above vacuum level and the excitons involving the transitions to the free electron states and conclude that AO-only basis sets are inaccurate for free electron states and the use of a plane wave basis set is required.
Linear optical response of finite systems using multishift linear system solvers
Authors: Hübener Hannes , Giustino Feliciano
Published: July 2014

We discuss the application of multishift linear system solvers to linear-response time-dependent density functional theory. Using this technique the complete frequency-dependent electronic density response of finite systems to an external perturbation can be calculated at the cost of a single solution of a linear system via conjugate gradients. We show that multishift time-dependent density functional theory yields excitation energies and oscillator strengths in perfect agreement with the standard diagonalization of the response matrix (Casida's method), while being computationally advantageous. We present test calculations for benzene, porphin, and chlorophyll molecules. We argue that multishift solvers may find broad applicability in the context of excited-state calculations within density-functional theory and beyond.
Assessing corrections to the Fick–Jacobs equation
Authors: Dorfman Kevin D. , Yariv Ehud
Published: July 2014

We utilize macrotransport theory to compute the effective diffusion coefficient of a point-sized particle in a periodic channel of slowly varying cross-section to the second order in the long-wavelength limit. This asymptotic result serves as a benchmark test for the respective modifications of the Fick–Jacobs equation proposed by Zwanzig [J. Phys. Chem. 96, 3926 (1992)], Reguera and Rubi [Phys. Rev. E 64, 061106 (2001)], and Kalinay and Percus [Phys. Rev. E 74, 041203 (2006)]. While all three modifications result in an identical effective diffusivity at first order, only the model proposed by Kalinay and Percus agrees at second order with our asymptotic result.
The scaling of weak field phase-only control in Markovian dynamics
Authors: Am-Shallem Morag , Kosloff Ronnie
Published: July 2014

We consider population transfer in open quantum systems, which are described by quantum dynamical semigroups (QDS). Using second order perturbation theory of the Lindblad equation, we show that it depends on a weak external field only through the field's autocorrelation function, which is phase independent. Therefore, for leading order in perturbation, QDS cannot support dependence of the population transfer on the phase properties of weak fields. We examine an example of weak-field phase-dependent population transfer, and show that the phase-dependence comes from the next order in the perturbation.
Voltage-controllable generator of pure spin current: A three-terminal model
Authors: Ma Zheng , Wu Reng-Lai , Yu Ya-Bin , Wang Miao
Published: July 2014

Three-terminal devices have been frequently proposed to generate the pure spin current. However, the controllability and stability of pure spin current still needs to be improved. In this paper, a three-terminal device, composed of a ferromagnetic metallic lead and two nonmagnetic semiconductor leads coupled with a quantum dot, is employed to study the properties of electron spin transport. The results show that when the external voltage on one of nonmagnetic semiconductor leads is adjusted to a proper range, a pure spin current plateau or a fully spin-polarized current plateau appears in another nonmagnetic semiconductor lead. In a wide range of external voltage, the pure spin current or the spin-polarized current is kept unchanged. Since the change of temperature may considerably influence the spin-polarization of current and is inevitable actually, we studied the corresponding compensation to keep the pure spin current unchanged. Furthermore, the effect of device parameters on the pure spin current is also investigated.
High Bi content GaSbBi alloys
Authors: Rajpalke M. K. , Linhart W. M. , Birkett M. , Yu K. M. , Alaria J. , Kopaczek J. , Kudrawiec R. , Jones T. S. , Ashwin M. J. , Veal T. D.
Published: July 2014

The epitaxial growth, structural, and optical properties of GaSb1–xBix alloys have been investigated. The Bi incorporation into GaSb is varied in the range 0 < x ≤ 9.6% by varying the growth rate (0.31–1.33 μm h−1) at two growth temperatures (250 and 275 °C). The Bi content is inversely proportional to the growth rate, but with higher Bi contents achieved at 250 than at 275 °C. A maximum Bi content of x = 9.6% is achieved with the Bi greater than 99% substitutional. Extrapolating the linear variation of lattice parameter with Bi content in the GaSbBi films enabled a zinc blende GaBi lattice parameter to be estimated of 6.272 Å. The band gap at 300 K of the GaSbBi epitaxial layers decreases linearly with increasing Bi content down to 410 ± 40 meV (3 μm) for x = 9.6%, corresponding to a reduction of ∼35 meV/%Bi. Photoluminescence indicates a band gap of 490 ± 5 meV at 15 K for x = 9.6%.
Two-photon interference and coherent control of single InAs quantum dot emissions in an Ag-embedded structure
Authors: Liu X. , Kumano H. , Nakajima H. , Odashima S. , Asano T. , Kuroda T. , Suemune I.
Published: July 2014

We have recently reported the successful fabrication of bright single-photon sources based on Ag-embedded nanocone structures that incorporate InAs quantum dots. The source had a photon collection efficiency as high as 24.6%. Here, we show the results of various types of photonic characterizations of the Ag-embedded nanocone structures that confirm their versatility as regards a broad range of quantum optical applications. We measure the first-order autocorrelation function to evaluate the coherence time of emitted photons, and the second-order correlation function, which reveals the strong suppression of multiple photon generation. The high indistinguishability of emitted photons is shown by the Hong-Ou-Mandel-type two-photon interference. With quasi-resonant excitation, coherent population flopping is demonstrated through Rabi oscillations. Extremely high single-photon purity with a g(2)(0) value of 0.008 is achieved with π-pulse quasi-resonant excitation.
Functional form for plasma velocity in a rapidly rotating tokamak discharge
Authors: Burrell K. H. , Chrystal C.
Published: July 2014

A recently developed technique using charge exchange spectroscopy determines the ion poloidal rotation in tokamak plasmas from the poloidal variation in the toroidal angular rotation speed. The basis for this technique is the functional form for the plasma velocity calculated from the equilibrium equations. The initial development of this technique utilized the functional form determined for conditions where the ion toroidal rotation speed is much smaller than the ion thermal speed. There are cases, however, where the toroidal rotation can be comparable to the ion thermal speed, especially for high atomic number impurities. The present paper extends the previous analysis to this high rotation speed case and demonstrates how to extract the poloidal rotation speed from measurements of the toroidal angular rotation speed at two points on a flux surface.
Toward phonon-boundary engineering in nanoporous materials
Authors: Romano Giuseppe , Grossman Jeffrey C.
Published: July 2014

Tuning thermal transport in nanostructured materials is a powerful approach to develop high-efficiency thermoelectric materials. Using a recently developed approach based on the phonon mean free path dependent Boltzmann transport equation, we compute the effective thermal conductivity of nanoporous materials with pores of various shapes and arrangements. We assess the importance of pore-pore distance in suppressing thermal transport, and identify the pore arrangement that minimizes the thermal conductivity, composed of a periodic arrangement of two misaligned rows of triangular pores. Such a configuration yields a reduction in the thermal conductivity of more than 60% with respect the simple circular aligned case with the same porosity.
Improvement of graphene field-effect transistors by hexamethyldisilazane surface treatment
Authors: Chowdhury Sk. Fahad , Sonde Sushant , Rahimi Somayyeh , Tao Li , Banerjee Sanjay , Akinwande Deji
Published: July 2014

We report the improvement of the electrical characteristics of graphene field-effect transistors (FETs) by hexamethyldisilazane (HMDS) treatment. Both electron and hole field-effect mobilities are increased by 1.5 × –2×, accompanied by effective residual carrier concentration reduction. Dirac point also moves closer to zero Volt. Time evolution of mobility data shows that mobility improvement saturates after a few hours of HMDS treatment. Temperature-dependent transport measurements show small mobility variation between 77 K and room temperature (295 K) before HMDS application. But mobility at 77 K is almost 2 times higher than mobility at 295 K after HMDS application, indicating reduced carrier scattering. Performance improvement is also observed for FETs made on hydrophobic substrate—an HMDS-graphene-HMDS sandwich structure. Raman spectroscopic analysis shows that G peak width is increased, G peak position is down shifted, and intensity ratio between 2D and G peaks is increased after HMDS application. We attribute the improvements in electronic transport mainly to enhanced screening and mitigation of adsorbed impurities from graphene surface upon HMDS treatment.
Nitride passivation reduces interfacial traps in atomic-layer-deposited Al2O3/GaAs (001) metal-oxide-semiconductor capacitors using atmospheric metal-organic chemical vapor deposition
Authors: Aoki T. , Fukuhara N. , Osada T. , Sazawa H. , Hata M. , Inoue T.
Published: July 2014

Using an atmospheric metal-organic chemical vapor deposition system, we passivated GaAs with AlN prior to atomic layer deposition of Al2O3. This AlN passivation incorporated nitrogen at the Al2O3/GaAs interface, improving the capacitance-voltage (C–V) characteristics of the resultant metal-oxide-semiconductor capacitors (MOSCAPs). The C–V curves of these devices showed a remarkable reduction in the frequency dispersion of the accumulation capacitance. Using the conductance method at various temperatures, we extracted the interfacial density of states (Dit). The Dit was reduced over the entire GaAs band gap. In particular, these devices exhibited Dit around the midgap of less than 4 × 1012 cm−2eV−1, showing that AlN passivation effectively reduced interfacial traps in the MOS structure.
Renormalization screening and collision-induced quantum interference in dense plasmas
Authors: Jung Young-Dae , Rasheed A. , Jamil M.
Published: July 2014

The influence of renormalization screening and collision-induced quantum interference in electron-electron collisions is investigated in partially ionized dense hydrogen plasmas. The effective interaction potential with the total spin-states of the collision system is considered to obtain the differential electron-electron scattering cross section. The results show that the renormalization plasma screening effect suppresses the electron-electron scattering cross section, including the quantum interference effect, especially, except for the forward and backward scattering directions. It is also shown that the renormalization plasma screening effect on the scattering cross section decreases with increasing collision energy. However, the renormalization screening effect is found to be important for the forward directions in the scattering cross section neglecting the quantum interference effect. The variations of the renormalization screening and collision-induced quantum interference effects are also discussed.
Anisotropic transport for parabolic, non-parabolic, and linear bands of different dimensions
Authors: Tang Shuang , Dresselhaus Mildred S.
Published: July 2014

We have developed a robust analytical methodology for modeling the anisotropic transport distribution function, which can be then used to describe various transport properties of anisotropic systems, including the electrical conductivity, carrier mobility, Seebeck coefficient, and thermal conductivity. Our methodology has considered the general cases for 3-, 2-, and 1-dimensional systems with parabolic, non-parabolic, and linear dispersion relations. Calculations are made using both the relaxation time approximation and the mean free path approximation. We have found that the Onsager relation can be violated under certain conditions. Furthermore, the methodology developed in the present work is compared with the traditionally used numerical methodology.
Enhancing optical gains in Si nanocrystals via hydrogenation and cerium ion doping
Authors: Wang Dong-Chen , Chen Jia-Rong , Li Yan-Li , Song Sheng-Chi , Guo Wen-Ping , Lu Ming
Published: July 2014

We report optical gain enhancements in Si nanocrystals (Si-NCs) via hydrogenation and Ce3+ ion doping. Variable stripe length technique was used to obtain gains. At 0.3 W/cm2 pumping power density of pulsed laser, net gains were observed together with gain enhancements after hydrogenation and/or Ce3+ ion doping; gains after loss corrections were between 89.52 and 341.95 cm−1; and the photoluminescence (PL) lifetime was found to decrease with the increasing gain enhancement. At 0.04 W/cm2 power density, however, no net gain was found and the PL lifetime increased with the increasing PL enhancement. The results were discussed according to stimulated and spontaneous excitation and de-excitation mechanisms of Si-NCs.
Reduction of off-state drain leakage in InGaAs-based metal-oxide-semiconductor field-effect transistors
Authors: Mo Jiongjiong , Lind Erik , Roll Guntrade , Wernersson Lars-Erik
Published: July 2014

Off-state drain leakage current has been investigated for InGaAs-based metal-oxide-semiconductor field-effect transistors with different drain configurations, InGaAs, and InP, respectively. The introduction of an InP drain presents a lower leakage current compared to InGaAs drain devices. From temperature dependent measurements, the leakage current mechanisms have been differentiated, and the role of drain direct band-to-band tunneling, as well as gate-induced drain leakage, has been identified.
Hydrogen passivation of titanium impurities in silicon: Effect of doping conditions
Authors: Santos P. , Coutinho J. , Torres V. J. B. , Rayson M. J. , Briddon P. R.
Published: July 2014

While the contamination of solar silicon by fast diffusing transition metals can be now limited through gettering, much attention has been drawn to the slow diffusing species, especially the early 3d and 4d elements. To some extent, hydrogen passivation has been successful in healing many deep centers, including transition metals in Si. Recent deep-level transient spectroscopy (DLTS) measurements concerning hydrogen passivation of Ti revealed the existence of at least four electrical levels related to TiiHn in the upper-half of the gap. These findings challenge the existing models regarding both the current level assignment as well as the structure/species involved in the defects. We revisit this problem by means of density functional calculations and find that progressive hydrogenation of interstitial Ti is thermodynamically stable in intrinsic and n-doped Si. Full passivation may not be possible to attain in p-type Si as TiiH3 and TiiH4 are metastable against dissociation and release of bond-centered protons. All DLTS electron traps are assigned, namely, E40′ to TiiH(-/0), E170′ to TiiH3(0/+), E(270) to TiiH2(0/+), and E170 to TiiH(0/+) transitions. TiiH4 is confirmed to be electrically inert.
Enhancement of Curie temperature of barium hexaferrite by dense electronic excitations
Authors: Sharma Manju , Kashyap Subhash C. , Gupta Hem C. , Dimri Mukesh C. , Asokan K.
Published: July 2014

Curie temperature of polycrystalline barium hexaferrite (BaFe12O19), prepared by conventional solid state technique, is anomalously and significantly enhanced (by nearly 15%) by energetic heavy ion irradiation (150 MeV, Ag12+) at ambient temperature due to dense electronic excitations Moderate fluence (1 × 1012 ions/cm2) induces structural defects giving rise to above enhancement. As established by X-ray diffraction, scanning electron microscopy and Raman studies, higher fluence (1 × 1013 ions/cm2) has structurally transformed the sample to amorphous phase with marginal change in magnetization and Curie temperature.
Temperature driven nano-domain evolution in lead-free Ba(Zr0.2Ti0.8)O3-50(Ba0.7Ca0.3)TiO3 piezoceramics
Authors: Lu Shengbo , Xu Zhengkui , Su Shi , Zuo Ruzhong
Published: July 2014

Hierarchical micro- and nanoscale domain structures in Pb-free Ba(Zr0.2Ti0.8)O3-50(Ba0.7Ca0.3)TiO3 piezoceramics were investigated by transmission electron microscopy. In situ heating and cooling studies of domain structure evolution reveal an irreversible domain transformation from a wedge-shaped rhombohedral nanodomain structure to a lamellar tetragonal domain structure, which could be associated with strong piezoelectricity in Ba(Zr0.2Ti0.8)O3-50(Ba0.7Ca0.3)TiO3 piezoceramics.
A Simple Paper-Based Lab-on-a-Chip for the Detection of a Highly Pathogenic Strain of Porcine Reproductive and Respiratory Syndrome Virus
Authors: Chaumpluk Piyasak , Suriyasomboon Annop
Published: July 2014

A paper-based laboratory-on-a-chip assay for the rapid detection of a highly pathogenic strain of porcine reproductive and respiratory syndrome virus (HP-PRRSV) was developed for the first time. The single-unit chip was simply fabricated using Whatman filter paper and plastic lamination. The chip measured 2.5 × 3.0 cm2 and was divided into two parts, one for nucleic acid amplification and the other for signal detection. The HP-PRRSV assay was performed by specific ORF I Nsp 2 gene amplification via an isothermal reverse transcription loop-mediated DNA amplification platform, whereas the cDNA signal detection was performed by visual observation of colorimetric changes in blue silver nanoplates (AgNPls). Positive results caused non-aggregation of the blue AgNPls on the detection pad, whereas negative results induced colorimetric changes in the AgNPls from blue to colourless on the pad. The assay had a limit of detection of 100 copies of the target Nsp 2 gene and high specificity for other types of infectious viruses. The assay required only one hour to complete. This work demonstrates a simple and rapid assay for viruses using a simple, low-cost, paper-based chip.
Brachypodium distachyon: a model species for aluminium tolerance in Poaceae
Authors: Contreras Roberto , Figueiras Ana M. , Gallego Francisco J. , Benito Cesar
Published: July 2014

Aluminium (Al) toxicity is the main abiotic stress limiting plant productivity in acidic soils. Studies on Al tolerance have been conducted in Poaceae but their genomes are very complex. Fifty-nine diploid lines (2n = 10) of Brachypodium distachyon (L.) P. Beauv. and 37 allotetraploid samples (2n = 30) of Brachypodium hybridum Catalán, Joch. Müll., Hasterok & Jenkins sp. nov. were used to evaluate their tolerance to different Al concentrations. B. distachyon is Al-sensitive compared with oat, rice and rye. The diploid lines (except ABR8) were sensitive like barley and Arabidopsis; however, 10 allotetraploid samples were Al-tolerant. Four different root-staining methods were used to detect Al accumulation, cell death, lipid peroxidation and H2O2 production in diploid and allotetraploid plants. The roots treated with Al showed more intense staining in sensitive than tolerant lines. Also, without any staining, the Al treated roots of sensitive plants appear darker than roots from tolerant ones. The study concerning to the organic acids exudation shows that the exudation of citrate and malate was induced only in the roots from tolerant diploid line (ABR8) and tolerant allotetraploid samples. In contrast, the mRNA expression changes of several candidate genes for Al-activated transporters belonging to the ALMT and MATE families were analysed by quantitative PCR (qRT–PCR). The data obtained indicate that the transcripts from BdALMT1, BdMATE1 and BdMATE2 were present mainly in roots and, moreover, that the BdALMT1 transcript is present in higher amounts in the tolerant ABR8 than in the sensitive ABR1 plants indicating that this gene may be involved in Al tolerance. Finally, an insertion was detected in the promoter region of the BdALMT1 of tolerant diploid and allotetraploid plants.
Structure of β-galactosidase at 3.2-Å resolution obtained by cryo-electron microscopy
Authors: Bartesaghi Alberto , Matthies Doreen , Banerjee Soojay , Merk Alan , Subramaniam Sriram
Published: July 2014

Significance

Atomic resolution models for proteins and protein complexes are usually obtained using X-ray crystallography or NMR spectroscopy, and in selected instances, by cryo-electron microscopy (cryo-EM) of ordered protein assemblies. The vast majority of high-resolution structures obtained using cryo-EM have been typically restricted to large, well-ordered entities such as helical or icosahedral assemblies or two-dimensional crystals. We show here that emerging methods in single-particle cryo-EM now allow structure determination at near-atomic resolution, even for much smaller protein complexes with low symmetry, by determining the structure of the 465-kDa enzyme β-galactosidase. In addition, by quantitative comparison of density maps obtained at different electron dosages, we demonstrate preferential sensitivity of residues such as Asp and Glu to damage upon irradiation with electrons.
Efficient UV-induced charge separation and recombination in an 8-oxoguanine-containing dinucleotide
Authors: Zhang Yuyuan , Dood Jordan , Beckstead Ashley A. , Li Xi-Bo , Nguyen Khiem V. , Burrows Cynthia J. , Improta Roberto , Kohler Bern
Published: July 2014

Significance

UV photons are absorbed strongly by DNA, but rarely cause permanent photodamage. Single nucleobases are protected by ultrafast nonradiative decay, but excited states in single- and double-stranded DNA decay very differently. An intensely debated question is whether a UV photon can move an electron from one nucleobase to another along a single strand. This study demonstrates that UV absorption efficiently transfers an electron from an oxidatively damaged guanine (8-oxo-G) to adenine in a dinucleotide mimic of the flavin cofactor FADH
2
, yielding radicals that decay in 60 ps. It is proposed that the photoredox activity of 8-oxo-G, which may have repaired cyclobutane pyrimidine dimers in the RNA world, reflects the importance of ultrafast charge separation between stacked nucleobases by UV radiation.
Single-molecule FRET reveals a corkscrew RNA structure for the polymerase-bound influenza virus promoter
Authors: Tomescu Alexandra I. , Robb Nicole C. , Hengrung Narin , Fodor Ervin , Kapanidis Achillefs N.
Published: July 2014

Significance

The genome of the influenza virus consists of eight single-stranded segments of RNA with highly conserved 5′ and 3′ termini. These termini associate to form double-stranded structures that act as promoters for viral transcription and replication. Structural information on the polymerase-bound promoter currently does not exist, so to address this we developed a sensitive single-molecule FRET assay that allowed us to measure distances between fluorescent dyes located on the promoter and map its structure. The distances obtained are consistent with the polymerase-bound RNA promoter being in a “corkscrew” conformation, in which the 5′ and 3′ termini form short hairpins. This work has implications for the development of inhibitors that target polymerase–promoter interactions in this important group of pathogens.
Calorie restriction does not elicit a robust extension of replicative lifespan inSaccharomyces cerevisiae
Authors: Huberts Daphne H. E. W. , González Javier , Lee Sung Sik , Litsios Athanasios , Hubmann Georg , Wit Ernst C. , Heinemann Matthias
Published: July 2014

Significance

Calorie restriction (CR) has been shown to extend the lifespans of various organisms. Consequently, a considerable amount of research has been performed to elucidate its mechanisms, especially in the yeastSaccharomyces cerevisiae. Here, we show that due to small sample sizes, large variation exists between measurements. In addition, the effect of CR on lifespan has been routinely overestimated in yeast due to the use of short-lived experimental controls, which together may explain why contradictory mechanisms were found to mediate CR-induced lifespan extension. Moreover, we did not observe any lifespan-enhancing effect of CR using an alternative measurement technique. The inability of CR to robustly extend lifespan suggests that calories alone do not modulate the lifespan of this important model organism.
KCNJ10 determines the expression of the apical Na-Cl cotransporter (NCC) in the early distal convoluted tubule (DCT1)
Authors: Zhang Chengbiao , Wang Lijun , Zhang Junhui , Su Xiao-Tong , Lin Dao-Hong , Scholl Ute I. , Giebisch Gerhard , Lifton Richard P. , Wang Wen-Hui
Published: July 2014

Significance

Loss of function mutations in the potassium channel KCNJ10 causes a salt-wasting syndrome. The phenotype resembles Gitelman syndrome, which results from loss of sodium chloride transport along the distal convoluted tubule (DCT), but the mechanisms involved are not clear. Here, we perform experiments in the kidney from Kcnj10 knockout mice and demonstrate that Kcnj10 is a main contributor to the basolateral potassium conductance in the DCT and that the potassium channel activity regulates the expression of ste20-related proline–alanine-rich kinase (SPAK) and determines Na-Cl cotransporter (NCC) expression. Our study suggests the possibility that the regulation of basolateral Kcnj10 activity in the DCT may be the first step in response to a variety of physiological stimuli for initiating SPAK-WNK-dependent modulation of NCC expression in the kidney.
Progression of coronary artery calcification seems to be inevitable, but predictable - results of the Heinz Nixdorf Recall (HNR) study
Authors: Erbel Raimund , Lehmann Nils , Churzidse Sofia , Rauwolf Michael , Mahabadi Amir A. , Möhlenkamp Stefan , Moebus Susanne , Bauer Marcus , Kälsch Hagen , Budde Thomas , Montag Michael , Schmermund Axel , Stang Andreas , Führer-Sakel Dagmar , Weimar Christian , Roggenbuck Ulla , Dragano Nico , Jöckel Karl-Heinz
Published: July 2014

Aim

Coronary artery calcification (CAC), as a sign of atherosclerosis, can be detected and progression quantified using computed tomography (CT). We develop a tool for predicting CAC progression.

Methods and results

In 3481 participants (45–74 years, 53.1% women) CAC percentiles at baseline (CACb) and after five years (CAC5y) were evaluated, demonstrating progression along gender-specific percentiles, which showed exponentially shaped age-dependence. Using quantile regression on the log-scale (log(CACb+1)) we developed a tool to individually predict CAC5y, and compared to observed CAC5y. The difference between observed and predicted CAC5y (log-scale, mean±SD) was 0.08±1.11 and 0.06±1.29 in men and women. Agreement reached a kappa-value of 0.746 (95% confidence interval: 0.732–0.760) and concordance correlation (log-scale) of 0.886 (0.879–0.893). Explained variance of observed by predicted log(CAC5y+1) was 80.1% and 72.0% in men and women, and 81.0 and 73.6% including baseline risk factors. Evaluating the tool in 1940 individuals with CACb>0 and CACb<400 at baseline, of whom 242 (12.5%) developed CAC5y>400, yielded a sensitivity of 59.5%, specificity 96.1%, (+) and (−) predictive values of 68.3% and 94.3%. A pre-defined acceptance range around predicted CAC5y contained 68.1% of observed CAC5y; only 20% were expected by chance. Age, blood pressure, lipid-lowering medication, diabetes, and smoking contributed to progression above the acceptance range in men and, excepting age, in women.

Conclusion

CAC nearly inevitably progresses with limited influence of cardiovascular risk factors. This allowed the development of a mathematical tool for prediction of individual CAC progression, enabling anticipation of the age when CAC thresholds of high risk are reached.
Quantifying sequence and structural features of protein–RNA interactions
Authors: Li Songling , Yamashita Kazuo , Amada Karlou Mar , Standley Daron M.
Published: July 2014

Increasing awareness of the importance of protein–RNA interactions has motivated many approaches to predict residue-level RNA binding sites in proteins based on sequence or structural characteristics. Sequence-based predictors are usually high in sensitivity but low in specificity; conversely structure-based predictors tend to have high specificity, but lower sensitivity. Here we quantified the contribution of both sequence- and structure-based features as indicators of RNA-binding propensity using a machine-learning approach. In order to capture structural information for proteins without a known structure, we used homology modeling to extract the relevant structural features. Several novel and modified features enhanced the accuracy of residue-level RNA-binding propensity beyond what has been reported previously, including by meta-prediction servers. These features include: hidden Markov model-based evolutionary conservation, surface deformations based on the Laplacian norm formalism, and relative solvent accessibility partitioned into backbone and side chain contributions. We constructed a web server called aaRNA that implements the proposed method and demonstrate its use in identifying putative RNA binding sites.
Crucial role of the Rcl1p–Bms1p interaction for yeast pre-ribosomal RNA processing
Authors: Delprato Anna , Kadri Yasmine Al , Pérébaskine Natacha , Monfoulet Cécile , Henry Yves , Henras Anthony K. , Fribourg Sébastien
Published: July 2014

The essential Rcl1p and Bms1p proteins form a complex required for 40S ribosomal subunit maturation. Bms1p is a GTPase and Rcl1p has been proposed to catalyse the endonucleolytic cleavage at site A2 separating the pre-40S and pre-60S maturation pathways. We determined the 2.0 Å crystal structure of Bms1p associated with Rcl1p. We demonstrate that Rcl1p nuclear import depends on Bms1p and that the two proteins are loaded into pre-ribosomes at a similar stage of the maturation pathway and remain present within pre-ribosomes after cleavage at A2. Importantly, GTP binding to Bms1p is not required for the import in the nucleus nor for the incorporation of Rcl1p into pre-ribosomes, but is essential for early pre-rRNA processing. We propose that GTP binding to Bms1p and/or GTP hydrolysis may induce conformational rearrangements within the Bms1p-Rcl1p complex allowing the interaction of Rcl1p with its RNA substrate.
An archaeal family-B DNA polymerase variant able to replicate past DNA damage: occurrence of replicative and translesion synthesis polymerases within the B family
Authors: Jozwiakowski Stanislaw K. , Keith Brian J. , Gilroy Louise , Doherty Aidan J. , Connolly Bernard A.
Published: July 2014

A mutant of the high fidelity family-B DNA polymerase from the archaeon Thermococcus gorgonarius (Tgo-Pol), able to replicate past DNA lesions, is described. Gain of function requires replacement of the three amino acid loop region in the fingers domain of Tgo-Pol with a longer version, found naturally in eukaryotic Pol ζ (a family-B translesion synthesis polymerase). Inactivation of the 3′–5′ proof-reading exonuclease activity is also necessary. The resulting Tgo-Pol Z1 variant is proficient at initiating replication from base mismatches and can read through damaged bases, such as abasic sites and thymine photo-dimers. Tgo-Pol Z1 is also proficient at extending from primers that terminate opposite aberrant bases. The fidelity of Tgo-Pol Z1 is reduced, with a marked tendency to make changes at G:C base pairs. Together, these results suggest that the loop region of the fingers domain may play a critical role in determining whether a family-B enzyme falls into the accurate genome-replicating category or is an error-prone translesion synthesis polymerase. Tgo-Pol Z1 may also be useful for amplification of damaged DNA.
Characteristics and Prognostic Analysis of 69 Patients With Pulmonary Sarcomatoid Carcinoma
Authors: Lin Yongbin , Yang Han , Cai Qingqing , Wang Daofeng , Rao Huilan , Lin Suxia , Long Hao , Fu Jianhua , Zhang Lanjun , Lin Peng , Xu Guangchuan , Rong Tiehua , Xiong Xiaoxing , Ma Guowei , Liang Ying
Published: July 2014

Background:

Pulmonary sarcomatoid carcinoma (PSC) is a rare malignancy.

Methods:

A total of 69 patients with PSC treated at a single institution in southern China with long-term follow-up were evaluated in this study. We analyzed the clinical characteristics, immunohistochemical profiles, epidermal growth factor receptor mutation status, K-RAS mutation status, treatments, and prognosis.

Results:

PSC mainly occurred in young male patients with a history of smoking. Most patients received multimodality treatments and the majority had early-stage disease. The median survival time was 19.1 months, and the 5-year survival rate was 17.4%. The patients without distant metastasis, with normal or higher body mass index (≥18.5), with normal hemoglobin, with smaller tumor size (≤4 cm), and those who received complete resection had significantly better overall survival (P<0.05). The patients with pleomorphic carcinoma had much worse prognosis. In a Cox regression model, M stage, pathology, and having received a complete resection were independent prognostic factors (P<0.05).

Conclusions:

PSC is a unique lung malignancy with poor prognosis. Patients receiving complete resection had better prognosis, likely a reflection of early-stage disease. Neither neoadjuvant nor adjuvant chemotherapy improved patient survival for those with early-stage disease. The retrospective design and small sample size limited the generalizability. Future multicenter collaborations may be necessary to determine the optimal treatment.
Use of Hematopoietic Growth Factors in Elderly Lung Cancer Patients Receiving Chemotherapy
Authors: Rajan Suja S. , Cai Yi , Yi Min , Tsai Chu-Lin , Du Xianglin L.
Published: July 2014

Objectives:

Hematopoietic growth factors (HGFs) are essential for successful completion of chemotherapy in lung cancer patients. However, because of their adverse effects, clinical guidelines recommend their use in only selective clinical scenarios. This study, for the first time, explores patient characteristics and temporal trends associated with HGF utilization among elderly lung cancer patients receiving chemotherapy.

Methods:

This is a retrospective analysis of the Surveillance, Epidemiology, and End Results (SEER)-Medicare linked data containing 80,940 patients, aged 65 years and older, diagnosed with stage I to IV lung cancer between 1992 and 2009, and who received chemotherapy. Descriptive statistics and logistic regressions were used to examine the characteristics associated with 2 types of HGFs—colony stimulating factors (CSFs) and erythropoiesis-stimulating agents (ESAs).

Results:

Twenty-five percent of the patients received CSFs and 42% received ESAs. Temporal variations were most predictive of HGF utilization, with an increase from 2.6% in 1992 to 47.3% in 2009 for CSFs and 1.3% to 30.5% for ESAs. Higher chemotherapy-based risk profiles increased the odds of HGF receipt 2 to 3 times (P<0.0001). Even after controlling for relevant clinical characteristics, unexplained sociodemographic associations persisted, suggesting lack of compliance with HGF guidelines.

Conclusions:

There has been a significant increase in the use of HGFs over time. Although chemotherapy-based risk profiles were significant predictors of HGF receipt, the study results suggest possible lack of compliance with treatment guidelines, which should be investigated. Given the high cost of HGFs, future studies are also needed to determine cost-effectiveness of these drugs among lung cancer patients.
Propagation of short stress pulses in discrete strongly nonlinear tunable metamaterials
Authors: Xu Yichao , Nesterenko Vitali F.
Published: July 2014

The propagation of short pulses with wavelength comparable to the size of a unit cell has been studied in a one-dimensional discrete metamaterial composed of steel discs alternating with toroidal nitrile O-rings under different levels of precompression using experiments, numerical simulations and theoretical analysis. This strongly nonlinear metamaterial is more tunable than granular chains composed of linear elastic spherical particles and has better potential for attenuation of dynamic loads. A double power-law relationship for compressed O-rings was found to describe adequately their quasi-static and dynamic behaviour with significantly different elastic moduli. It is demonstrated that the double power-law metamaterial investigated allows a dramatic increase in sound speed and acoustic impedance of three to four times using a moderate force.
Burrow architectural types of the Atlantic ghost crab,Ocypode quadrata(Fabricius, 1787) (Brachyura: Ocypodidae), in Brazil
Authors: Silva Willian T. A. F. , Calado Tereza C. S.
Published: July 2014

A broad range of aspects from paleontology to physiology of the ghost crabsOcypode quadratahave been studied worldwide. These crabs have been used as ecological indicators of the levels of anthropogenic impacts on sandy beaches. Our aim is to report the variety of burrow architecture types constructed by ghost crabsOcypode quadrataon beaches of Maceió, Brazil. We found 20 types of burrows that differ in shape (number of axes, number of openings, orientation of blind end, number of branches). The slash-shaped burrows (type C) were the most frequent shape, followed by types K (spiral) and E (Y-shaped). Type C also showed the largest opening diameter and length ranges. Burrow types F, J, P, S and T were the least frequent. The G-test for goodness of fit to a time-independent uniform frequency distribution (G = 417.61; d.f. = 18; p < 0.005) reject the hypothesis that burrow types are constructed randomly (uniform distribution). The dominance of type C burrows and other simple-type burrows over more elaborate types indicates preference for simplicity.
Near–optimal decoding of transient stimuli from coupled neuronal subpopulations
Authors: Trousdale James , Carroll Sam , Gabbiani Fabrizio , Josić Krěsimir
Published: July 2014

Coupling between sensory neurons impacts their tuning properties and correlations in their responses. How such coupling affects sensory representations and ultimately behavior remains unclear. We investigated the role of neuronal coupling during visual processing using a realistic biophysical model of the vertical system (VS) cell network in the blow fly. These neurons are thought to encode the horizontal rotation axis during rapid free flight manoeuvres. Experimental findings suggest neurons of the vertical system are strongly electrically coupled, and that several downstream neurons driving motor responses to ego-rotation receive inputs primarily from a small subset of VS cells. These downstream neurons must decode information about the axis of rotation from a partial readout of the VS population response. To investigate the role of coupling, we simulated the VS response to a variety of rotating visual scenes and computed optimal Bayesian estimates from the relevant subset of VS cells. Our analysis shows that coupling leads to near–optimal estimates from a subpopulation readout. In contrast, coupling between VS cells has no impact on the quality of encoding in the response of the full population. We conclude that coupling at one level of the fly visual system allows for near–optimal decoding from partial information at the subsequent, pre-motor level. Thus, electrical coupling may provide a general mechanism to achieve near–optimal information transfer from neuronal subpopulations across organisms and modalities.
Data mining of Gene expression profiles of Saccharomyces cerevisiae in response to mild heat stress response
Authors: Ji Kaiyuan , Ma Wenli , Zheng Wenling
Published: July 2014

We chose yeast as a model organism to explore how eukaryotic cells respond to heat stress. This study provides details on the way yeast responds to temperature changes and is therefore an empirical reference for basic cell research and industrial fermentation of yeast. We use the Qlucore Omics Explorer (QOE) bioinformatics software to analyze the gene expression profiles of the heat stress from Gene Expression Omnibus (GEO). Genes and their expression are listed in heat maps, and the gene function is analyzed against the biological processes and pathways. We can find that the expression of genes changed over time after heat stress. Gene expression changed rapidly from 0 min to 60 min after heat shock, and gene expression stabilized between 60 min to 360 min. The yeast cells begin to adjust themselves to the high temperatures in terms of the level of gene expression at about 60 min. In all of the involved pathways and biological processes, those related to ribosome and nucleic acid metabolism declined in about 15–30 min and those related to starch and sucrose increased in the same time frame. Temperature can be a simple way to control the biological processes and pathways of cell.
The theory-practice gap: epistemology, identity, and education
Authors: Roth Wolff-Michael , Mavin Tim , Dekker Sidney
Published: July 2014

Purpose

– The purpose of this paper is to theorize the theory-practice gap and to provide examples of how it currently expresses itself and how it might be addressed to better integrate between the worlds of thought and praxis.

Design/methodology/approach

– Two empirical examples exemplify how the theory-practice gap is an institutionally embodied social reality. Cultural-historical activity theory is described as a means for theorizing the inevitable gap. An example from the airline industry shows how the gap may be dealt with in, and integrated into, practice.

Findings

– Cultural-historical activity theory suggests different forms of consciousness to exist in different activity systems because of the different object/motives in the world in which we think and the practical world in which we live. A brief case study of the efforts of one airline to integrate reflection on practice (i.e. theory) into their on-the-job training shows how the world in which pilots think about what they do is made part of the world in which pilots live.

Practical implications

– First, in some cases, such as teacher education, institutional arrangements can be made to situate education/training in the workplace. Second, even in the training systems with high fidelity, high validity (transferability) cannot be guaranteed.

Originality/value

– The approach proposed provides a theory not only for understanding the theory-practice gap but also the gap that exists even between very high-fidelity (“photo-realistic”) training situations and the real-world praxis full of surprises.
Using grey relational analysis to evaluate resource configuration and service ability for hospital on public private partnership model in China
Authors: Li Xiaoning , Liao Xinbo , Tan Xuerui , Wang Haijing
Published: July 2014

Purpose

– The purpose of this paper is to evaluate resource configuration and service ability in hospital on public private partnership (PPP) model (Chaonan Minsheng Hospital of Guangdong Province), supplying decision-making reference for participants of hospital on PPP model.

Design/methodology/approach

– Four model of grey relational analysis (GRA) (Deng's correlation degree, grey absolute correlation degree, grey relative correlation degree and grey comprehensive correlation degree) are applied to evaluate resource configuration and service ability, a total of 11 indicators of hospital on PPP model public hospital and private hospital from 2007 to 2011.

Findings

– The paper finds that different GRA models have different results when the paper applied them to evaluate resource configuration and service ability in hospital on PPP model. More than 60 per cent indicators of resource configuration (total six indicators) and service ability (total six indicators) are assessed as “hospital on PPP model ≻ public hospital” or “hospital on PPP model≻ private hospital” from three models of Deng's correlation degree, grey absolute correlation degree and grey comprehensive correlation degree.

Practical implications

– Evaluation of resource configuration and service ability for hospital on PPP model with GRA makes results quantified objective and provides reference for decision making and management. GRA makes the comparison of resource configuration and service ability between hospital on PPP model and other model hospitals becoming possible.

Originality/value

– The shortcoming for data analysis method of “large sample” is overcome and data analysis method of “small sample” is realized by using GRA, which broaden the method of evaluating hospital on PPP model.