bluuebunny/crossref_metadata_2025 huggingface dataset:
Direct simulation of proton-coupled electron transfer across multiple regimes
Authors: Kretchmer Joshua S. , Miller Thomas F.
Published: April 2013

The coupled transfer of electrons and protons is a central feature of biological and molecular catalysis, yet fundamental aspects of these reactions remain poorly understood. In this study, we extend the ring polymer molecular dynamics (RPMD) method to enable direct simulation of proton-coupled electron transfer (PCET) reactions across a wide range of physically relevant regimes. In a system-bath model for symmetric, co-linear PCET in the condensed phase, RPMD trajectories reveal distinct kinetic pathways associated with sequential and concerted PCET reaction mechanisms, and it is demonstrated that concerted PCET proceeds by a solvent-gating mechanism in which the reorganization energy is mitigated by charge cancellation among the transferring particles. We further employ RPMD to study the kinetics and mechanistic features of concerted PCET reactions across multiple coupling regimes, including the fully non-adiabatic (both electronically and vibrationally non-adiabatic), partially adiabatic (electronically adiabatic, but vibrationally non-adiabatic), and fully adiabatic (both electronically and vibrationally adiabatic) limits. Comparison of RPMD with the results of PCET rate theories demonstrates the applicability of the direct simulation method over a broad range of conditions; it is particularly notable that RPMD accurately predicts the crossover in the thermal reaction rates between different coupling regimes while avoiding a priori assumptions about the PCET reaction mechanism. Finally, by utilizing the connections between RPMD rate theory and semiclassical instanton theory, we show that analysis of ring-polymer configurations in the RPMD transition path ensemble enables the a posteriori determination of the coupling regime for the PCET reaction. This analysis reveals an intriguing and distinct “transient-proton-bridge” mechanism for concerted PCET that emerges in the transition between the proton-mediated electron superexchange mechanism for fully non-adiabatic PCET and the hydrogen atom transfer mechanism for partially adiabatic PCET. Taken together, these results provide a unifying picture of the mechanisms and physical driving forces that govern PCET across a wide range of physical regimes, and they raise the possibility for PCET mechanisms that have not been previously reported.
Similarity solutions of Fokker-Planck equation with moving boundaries
Authors: Ho C.-L.
Published: April 2013

In this work we present new exact similarity solutions with moving boundaries of the Fokker-Planck equation having both time-dependent drift and diffusion coefficients.
Magnetocaloric effect in the rare earth intermetallic compounds RCoNi (R = Gd, Tb, Dy, and Ho)
Authors: Mondal Rajib , Nirmala R. , Arout Chelvane J. , Nigam A. K.
Published: April 2013

Magnetic and magnetocaloric properties of cubic Laves phase RCoNi (R = Gd, Tb, Dy, and Ho) compounds have been studied. The RCoNi (R = Gd, Tb, Dy, and Ho) compounds order ferromagnetically at ∼200 K, ∼113 K, ∼68 K, and ∼42 K (TC), respectively. Field dependent magnetization data of RCoNi at 5 K in fields up to 7 T reveal saturation behaviour with minimal hysteresis. Magnetocaloric effect in terms of isothermal magnetic entropy change has been calculated. Maximum isothermal magnetic entropy change values of ∼−7.2 J/kg/K, ∼−10.1 J/kg/K, ∼−15.5 J/kg/K, and ∼−19.6 J/kg/K are obtained for RCoNi (R = Gd, Tb, Dy, and Ho) compounds for 7 T field change close to TC. Substitution of 50 at. % Ni in Co-site of RCo2 has led to the reduction of TC of the parent compounds by nearly one-half, but broadened the magnetic entropy change vs T curve and hence improved the relative cooling power. The large magnetocaloric effect associated with RCoNi compounds makes them potential candidates for low temperature magnetic refrigeration applications.
Thermally activated leakage current in high-performance short-wavelength quantum cascade lasers
Authors: Flores Y. V. , Semtsiv M. P. , Elagin M. , Monastyrskyi G. , Kurlov S. , Aleksandrova A. , Kischkat J. , Masselink W. T.
Published: April 2013

The threshold condition for a 4-level quantum cascade laser (QCL)-active region is formulated to include thermally activated leakage of charge carriers from active region confined states into states with higher energy. A method is described and demonstrated to extract the associated thermal escape current density from measurements at laser threshold. This current is modeled by including both the temperature dependent subband-distribution of charge carriers and longitudinal optical-phonon probability. The method is used to analyze the thermally activated leakage of charge carriers in two short-wavelength strain-compensated InGaAs/InAlAs QCL-structures. The energies of the higher-lying states extracted from the model are in good agreement with the values calculated numerically within the effective-mass approximation. The estimated scattering time for the thermal activation process agrees with the expected value as well. Our approach offers a straightforward and accurate method to analyze and troubleshoot thermally activated leakage in new QCL-active region designs.
Lattice dependent motion of voids during electromigration
Authors: Sindermann S. P. , Latz A. , Dumpich G. , Wolf D. E. , Meyer zu Heringdorf F.-J.
Published: April 2013

The influence of the crystal lattice configuration to electromigration processes, e.g., void formation and propagation, is investigated in suitable test structures. They are fabricated out of self-assembled, bi-crystalline Ag islands, grown epitaxially on a clean Si(111) surface. The μm-wide and approximately 100 nm thick Ag islands are a composition of a Ag(001) and a Ag(111) part. By focused ion beam milling, they are structured into wires with a single grain boundary, the orientation of which can be chosen arbitrarily. In-situ scanning electron microscopy (SEM) allows to capture an image sequence during electrical stressing and monitors the development of voids and hillocks in time. To visualize the position and motion of voids, we calculate void maps using a threshold algorithm. Most of the information from the SEM image sequence is compressed into one single image. Our present electromigration studies are based on in-situ SEM investigations for three different lattice configurations: Ag(001) (with electron current flow in [1¯1¯0] direction), Ag(111) (with electron current flow in [112¯] direction), and additionally 90∘ rotated Ag(111) (with electron current flow in [1¯10] direction). Our experimental results show that not only the formation and shape but also the motion direction of voids strongly depends on the crystal orientation.
Valence excitation energies of alkenes, carbonyl compounds, and azabenzenes by time-dependent density functional theory: Linear response of the ground state compared to collinear and noncollinear spin-flip TDDFT with the Tamm-Dancoff approximation
Authors: Isegawa Miho , Truhlar Donald G.
Published: April 2013

Time-dependent density functional theory (TDDFT) holds great promise for studying photochemistry because of its affordable cost for large systems and for repeated calculations as required for direct dynamics. The chief obstacle is uncertain accuracy. There have been many validation studies, but there are also many formulations, and there have been few studies where several formulations were applied systematically to the same problems. Another issue, when TDDFT is applied with only a single exchange-correlation functional, is that errors in the functional may mask successes or failures of the formulation. Here, to try to sort out some of the issues, we apply eight formulations of adiabatic TDDFT to the first valence excitations of ten molecules with 18 density functionals of diverse types. The formulations examined are linear response from the ground state (LR-TDDFT), linear response from the ground state with the Tamm-Dancoff approximation (TDDFT-TDA), the original collinear spin-flip approximation with the Tamm-Dancoff (TD) approximation (SF1-TDDFT-TDA), the original noncollinear spin-flip approximation with the TDA approximation (SF1-NC-TDDFT-TDA), combined self-consistent-field (SCF) and collinear spin-flip calculations in the original spin-projected form (SF2-TDDFT-TDA) or non-spin-projected (NSF2-TDDFT-TDA), and combined SCF and noncollinear spin-flip calculations (SF2-NC-TDDFT-TDA and NSF2-NC-TDDFT-TDA). Comparing LR-TDDFT to TDDFT-TDA, we observed that the excitation energy is raised by the TDA; this brings the excitation energies underestimated by full linear response closer to experiment, but sometimes it makes the results worse. For ethylene and butadiene, the excitation energies are underestimated by LR-TDDFT, and the error becomes smaller making the TDA. Neither SF1-TDDFT-TDA nor SF2-TDDFT-TDA provides a lower mean unsigned error than LR-TDDFT or TDDFT-TDA. The comparison between collinear and noncollinear kernels shows that the noncollinear kernel drastically reduces the spin contamination in the systems considered here, and it makes the results more accurate than collinear spin-flip TDDFT for functionals with a low percentage of Hartree-Fock exchange and sometimes for functionals with a higher percentage of Hartree-Fock exchange, but it yields less accurate results than ground-state TDDFT.
Controlling reactivity of nanoporous catalyst materials by tuning reaction product-pore interior interactions: Statistical mechanical modeling
Authors: Wang Jing , Ackerman David M. , Lin Victor S.-Y. , Pruski Marek , Evans James W.
Published: April 2013

Statistical mechanical modeling is performed of a catalytic conversion reaction within a functionalized nanoporous material to assess the effect of varying the reaction product-pore interior interaction from attractive to repulsive. A strong enhancement in reactivity is observed not just due to the shift in reaction equilibrium towards completion but also due to enhanced transport within the pore resulting from reduced loading. The latter effect is strongest for highly restricted transport (single-file diffusion), and applies even for irreversible reactions. The analysis is performed utilizing a generalized hydrodynamic formulation of the reaction-diffusion equations which can reliably capture the complex interplay between reaction and restricted transport.
A spectrometer on chemical vapour deposition-diamond basis for the measurement of the charge-state distribution of heavy ions in a laser-generated plasma
Authors: Cayzac Witold , Frank Alexander , Schumacher Dennis , Roth Markus , Blažević Abel , Wamers Felix , Träger Michael , Berdermann Elèni , Voss Bernd , Hessling Thomas
Published: April 2013

This article reports on the development and the first applications of a new spectrometer which enables the precise and time-resolved measurement of both the energy loss and the charge-state distribution of ion beams with 10 < Z < 30 at energies of 4–8 MeV/u after their interaction with a laser-generated plasma. The spectrometer is based on five 20 × 7 mm2 large and 20 μm thick polycrystalline diamond samples produced via the Chemical Vapour Deposition (CVD) process and was designed with the help of ion-optical simulations. First experiments with the spectrometer were successfully carried out at GSI using 48Ca ions at an energy of 4.8 MeV/u interacting with a carbon plasma generated by the laser irradiation of a thin foil target. Owing to the high rate capability and the short response time of the spectrometer, pulsed ion beams with 103–104 ions per bunch at a bunch frequency of 108 MHz could be detected. The temporal evolution of the five main charge states of the calcium ion beams as well as the corresponding energy loss values could be measured simultaneously. Due to the outstanding properties of diamond as a particle detector, a beam energy resolution \documentclass[12pt]{minimal}\begin{document}$\frac{\Delta E}{E}$\end{document}ΔEE ≈ 0.1% could be reached using the presented experimental method, while a precision of 10% in the energy loss and charge-state distribution data was obtained.
A new highly automated sputter equipment for in situ investigation of deposition processes with synchrotron radiation
Authors: Döhrmann Ralph , Botta Stephan , Buffet Adeline , Santoro Gonzalo , Schlage Kai , Schwartzkopf Matthias , Bommel Sebastian , Risch Johannes F. H. , Mannweiler Roman , Brunner Simon , Metwalli Ezzeldin , Müller-Buschbaum Peter , Roth Stephan V.
Published: April 2013

HASE (Highly Automated Sputter Equipment) is a new mobile setup developed to investigate deposition processes with synchrotron radiation. HASE is based on an ultra-high vacuum sputter deposition chamber equipped with an in-vacuum sample pick-and-place robot. This enables a fast and reliable sample change without breaking the vacuum conditions and helps to save valuable measurement time, which is required for experiments at synchrotron sources like PETRA III at DESY. An advantageous arrangement of several sputter guns, mounted on a rotative flange, gives the possibility to sputter under different deposition angles or to sputter different materials on the same substrate. The chamber is also equipped with a modular sample stage, which allows for the integration of different sample environments, such as a sample heating and cooling device. The design of HASE is unique in the flexibility. The combination of several different sputtering methods like standard deposition, glancing angle deposition, and high pressure sputter deposition combined with heating and cooling possibil-ities of the sample, the large exit windows, and the degree of automation facilitate many different grazing incidence X-ray scattering experiments, such as grazing incidence small and wide angle X-ray scattering, in one setup. In this paper we describe in detail the design and the performance of the new equipment and present the installation of the HASE apparatus at the Micro and Nano focus X-ray Scattering beamline (MiNaXS) at PETRA III. Furthermore, we describe the measurement options and present some selected results. The HASE setup has been successfully commissioned and is now available for users.
Suppressed 3D conductivity in Mn doped Cu0.5Tl0.5Ba2Ca2−yMnyCu3O10−δ superconductors
Authors: Qurat-ul-Ain  , Khan Nawazish A.
Published: April 2013

We have synthesised Mn-doped Cu0.5Tl0.5Ba2(Ca2−yMny)Cu3O10−δ superconducting samples and studied their Fluctuation Induced Conductivity (FIC) analysis. The Tc(R = 0) and magnitude of diamagnetism are suppressed with increased Mn-doping in the final compound. FIC analyses have shown a suppression of 3D Lawrence and Doniach (LD) regime and a significant enhancement of 2D LD regime of Mn-doping of y = 0.35. In the sample with Mn-doping of y = 0.5, the 3D LD regime vanishes altogether and only 2D LD regime is observed, showing the confinement of superconductivity in the two dimensional planes. The coherence length along the c-axis and the Fermi velocity of the carriers are suppressed with increased Mn doping. Using the Ginzburg-Landau (GL) number [NG] and GL equations, the thermodynamic critical magnetic field Bc(0), the lower critical field Bc1(0), the upper critical field Bc2(0), the critical current density Jc(0), and penetration depth λp.d are determined. The values of critical fields Bc(0) and Bc1(0) increases, despite suppression in the Tc(R = 0) with increased Mn-doping. The values of Jc(0), the penetration depth Λp.d, and inter-layer coupling are suppressed with enhanced Mn-doping. These observations suggested that Mn ions act as sub-nano-scale pinning centers between the CuO2 planes and their presence at the Ca-sites promote the de-coupling of CuO2 planes.
Optical spectroscopy and spectroscopic ellipsometry as a monitor for thin film growth by dc magnetron sputtering
Authors: Abundiz-Cisneros N. , Perez-Garcia A. , Gomez-Muñoz M. , Machorro R.
Published: April 2013

Measurements of line intensity ratios have been used in astronomy to determine physical properties of plasmas such as density and temperature. Herein, this procedure was applied to monitor thin film growth during plasma-assisted deposition and useful information about the plasma was obtained. The aim of this study was to monitor plasma variations during deposition, using wide field optical spectroscopy, and to establish a relationship with thin film stoichiometry using spectroscopic ellipsometry. With this purpose, inhomogeneous SiOxNy thin films were grown by dc magnetron sputtering.
Fuzzy logic control of wind energy conversion system
Authors: Farh Hassan M. , Eltamaly Ali M.
Published: April 2013

This paper proposes a variable speed control scheme of grid-connected wind energy conversion system, WECS, using permanent magnet synchronous generator. The control algorithm tracking the maximum power for wind speeds below rated speed of wind turbines (WTs) and ensure the power will not exceed the rated power for wind speeds higher than the rated speed of wind turbine. The control algorithm employed fuzzy logic controller (FLC) to effectively do this job. The WT is connected to the grid via back-to-back pulse width modulation-voltage source converter (PWM-VSC). Two effective computer simulation software packages (PSIM and SIMULINK) have been used to carry out the simulation effectively where psim contains the power circuit of the WECS and MATLAB/SIMULINK contains the control circuit of the system. The control system has two controllers for generator side and grid side converters. The main function of the generator side controller is to track the maximum power from wind through controlling the rotational speed of the turbine using FLC. In the grid side converter, active and reactive power control has been achieved by controlling d-axis and q-axis current components, respectively.
A kinetic model of radiating electrons
Authors: Noble A. , Burton D. A. , Gratus J. , Jaroszynski D. A.
Published: April 2013

A kinetic theory is developed to describe radiating electrons whose motion is governed by the Lorentz-Dirac equation. This gives rise to a generalized Vlasov equation coupled to an equation for the evolution of the physical submanifold of phase space. The pathological solutions of the 1-particle theory may be removed by expanding the latter equation in powers of τ ≔ q2/6πm. The radiation-induced change in entropy is explored and its physical origin is discussed. As a simple demonstration of the theory, the radiative damping rate of longitudinal plasma waves is calculated.
Infrared magneto-optical composite materials based on manganite powders
Authors: Telegin A. , Mostovshchikova E. , Bessonov V. , Telegin S. , Gizhevskii B.
Published: April 2013

First results on the study of the magneto-optical properties of powder composites based on doped manganites are presented. A giant change of the intensity of unpolarized infrared light transmitted through the composites under the external magnetic field applied (magnetotransmission effect) has been revealed. The optical properties of manganite composites and the magnitude of magnetotransmission effect were similar to those for the epitaxial films. The powder composites based on doped manganites seem to be prospective for the creation of any alternative infrared magnetooptical elements driven by the magnetic field.
First-principles study of Cl diffusion in cubic SiC
Authors: Alfieri G. , Kimoto T.
Published: April 2013

Chlorine-based precursors allow the fast growth of thick SiC epilayers for fabricating high-voltage devices. Since it was demonstrated that epitaxial growth with a Cl-based chemistry can affect p-type doping, the issue of Cl diffusion SiC is technologically relevant therefore we present a first principles study of the migration mechanisms of Cl in cubic SiC. We first discuss the equilibrium structure of different Cl-related defect configurations (isolated interstitials and complex defects) which have either been reported in the literature or calculated in the present study. Following this analysis, we focus on two migration mechanisms: The interstitialcy and the vacancy-mediated mechanism. We found that Cl diffuses in SiC via a vacancy-mediated mechanism and the value of the diffusivity is estimated.
Tilted epitaxy on (211)-oriented substrates
Authors: Woo S. Y. , Devenyi G. A. , Ghanad-Tavakoli S. , Kleiman R. N. , Preston J. S. , Botton G. A.
Published: April 2013

Spontaneous tilting of lattice mismatched epilayers grown on (211)-oriented substrates has been observed in numerous systems in literature. Here, we have examined a model system, GaSb/Si(211), with two dimensional X-ray diffraction and conventional transmission electron microscopy, and developed a universal model which explains the origin of the tilt phenomenon as the minimization of projected lattice mismatch for low-index planes across the film/substrate interface. The model developed predicts the tilt for lattice mismatches in the range of 0%–20% covering most semiconductor heteroepitaxial systems.
X-ray probe of GaN thin films grown on InGaN compliant substrates
Authors: Xu Xiaoqing , Li Yang , Liu Jianming , Wei Hongyuan , Liu Xianglin , Yang Shaoyan , Wang Zhanguo , Wang Huanhua
Published: April 2013

GaN thin films grown on InGaN compliant substrates were characterized by several X-ray technologies: X-ray reciprocal space mapping (RSM), grazing incidence X-ray diffraction (GIXRD), and X-ray photoemission spectrum (XPS). Narrow Lorentz broadening and stress free state were observed for GaN grown on InGaN compliant substrate, while mosaic structure and large tensile stress were observed at the presence of residual indium atoms. RSM disclosed the mosaicity, and the GIXRD was conducted to investigate the depth dependences of crystal quality and strain states. XPS depth profile of indium contents indicated that residual indium atoms deteriorated the crystal quality of GaN not only by producing lattice mismatch at the interface of InGaN and GaN but also by diffusing into GaN overlayers. Accordingly, two solutions were proposed to improve the efficiency of self-patterned lateral epitaxial overgrowth method. This research goes a further step in resolving the urgent substrate problem in GaN fabrication.
Converse piezoelectric effect induced misfit dislocation scattering in metal/AlGaN/GaN heterostructures
Authors: Ji Dong , Lu Yanwu , Liu Bing , Liu Jinlong
Published: April 2013

The converse piezoelectric effect on misfit dislocation (MD) generation and scattering in metal/AlGaN/GaN structures was quantitatively studied. The critical thickness of the structure decreased with increasing electric field in the growth direction and reached the maximum value at the zero field. The predicted MD density was in the order of 105 cm−1, which can be tuned by the gate voltage. The calculation result shows that MD scattering is a dominant limitation for electron mobility.
Optical evidence for donor behavior of Sb in ZnO nanowires
Authors: Senthil Kumar E. , Mohammadbeigi F. , Alagha S. , Deng Z. W. , Anderson I. P. , Wintschel T. , Watkins S. P.
Published: April 2013

High-resolution photoluminescence (PL) experiments show that Sb doped ZnO nanowires exhibit shallow donor bound exciton (D0X) transitions at 3364.3 meV, which is shallower than the well-known In, Ga, Al, and H D0X transitions. The relative intensity of the Sb D0X transition scales with dopant concentration. Temperature dependent PL measurements show that the Sb D0X behaves like other D0X transitions with a thermal activation energy close to the spectroscopic binding energy. No evidence of an ionized donor bound exciton (D+X) is observed, consistent with the expectation from Haynes' rule that such a state would have a higher energy than the free exciton.
Graphene: Why buckling occurs?
Authors: Shen Hui-Shen , Xu Yu-Mou , Zhang Chen-Li
Published: April 2013

We report here the buckling phenomenon of a monolayer graphene with four free edges subjected to uniaxial tension by molecular dynamics simulations. We find that the buckling occurs when tension force is applied and is sufficiently large for both armchair and zigzag single layer graphene sheets. The maximum amplitude is increased and the maximum wavelength is decreased with increase in temperature.
Nonvolatile bipolar resistive switching in amorphous Sr-doped LaMnO3 thin films deposited by radio frequency magnetron sputtering
Authors: Liu Dongqing , Wang Nannan , Wang Guang , Shao Zhengzheng , Zhu Xuan , Zhang Chaoyang , Cheng Haifeng
Published: April 2013

Amorphous Sr-doped LaMnO3 (a-LSMO) thin films were deposited on Pt/Ti/SiO2/Si substrate by radio frequency magnetron sputtering. The Ag/a-LSMO/Pt device exhibited reversible bipolar resistive switching over 100 cycles with a resistance ratio (high resistance state to low resistance state) of over 4 orders of magnitude and stable retention for over 104 s at room temperature. Analysis indicates that the resistive switching originates from the formation/rupture of Ag nanofilaments in the a-LSMO thin films acting as solid electrolytes. The device showed potential for multibit storage as well as low power consumption applications.
Effects of conjugated polymer on the magnetotransport properties in La0.7Sr0.3MnO3 ferromagnetic electrodes
Authors: Pesonen M. , Majumdar S. , Huhtinen H. , Paturi P. , Majumdar H. S. , Österbacka R.
Published: April 2013

Magnetotransport of La0.7Sr0.3MnO3 (LSMO)/regioregular poly3-hexylthiophene (rr-P3HT) interfaces were studied at 5–300 K to gain insight of spin transport in polymer coated LSMO. LSMO films on SrTiO3 (STO), MgO, and quartz substrates were characterized in pristine state, after depositing rr-P3HT and after removing rr-P3HT. Application and removal of rr-P3HT caused the disappearance of colossal magneto resistance and the emerging of low-field magnetoresistance (LFMR) in STO/LSMO, while the same treatment on MgO and quartz showed only a large LMFR signal with no significant changes during application and removal of rr-P3HT. This result signifies that epitaxial thin films of LSMO do not maintain their transport characteristics when coated with organic semiconductors, posing a limitation for efficient spin polarized injection at such interfaces.
Water-Assisted Organocatalysis: An Enantioselective Green Protocol for the Henry Reaction
Authors: Thorat Prashant B. , Goswami Santosh V. , Jadhav Wamanrao N. , Bhusare Sudhakar R.
Published: April 2013

We report an enantioselective Henry (nitroaldol) reaction catalysed by an organocatalyst using water as solvent. The enantioselective synthesis of β-nitroalcohols was achieved by using a neutral chiral organocatalyst, through strong hydrogen bonding, which results in the formation of corresponding products in excellent yield and enantioselectivity at room temperature. Other attractive features of the method are the eco-friendly, non-hazardous, and mild reaction conditions, inexpensive catalyst, and simple work up conditions.
Chemoselective Activation Strategies of Amidic Carbonyls towards Nucleophilic Reagents
Authors: Pace Vittorio , Holzer Wolfgang
Published: April 2013

Important advancements have been made in recent years in the development of chemoselective additions of nucleophiles to well known inert amide carbonyls in the presence of multi-electrophilic substrates. Herein, we present the most relevant results showing how carbonyl amides can be chemoselectively functionalised in the presence of electrophilic functionalities such as Weinreb amides.
Expanded GGGGCC repeat RNA associated with amyotrophic lateral sclerosis and frontotemporal dementia causes neurodegeneration
Authors: Xu Zihui , Poidevin Mickael , Li Xuekun , Li Yujing , Shu Liqi , Nelson David L. , Li He , Hales Chadwick M. , Gearing Marla , Wingo Thomas S. , Jin Peng
Published: April 2013

Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) share phenotypic and pathologic overlap. Recently, an expansion of GGGGCC repeats in the first intron of
C9orf72
was found to be a common cause of both illnesses; however, the molecular pathogenesis of this expanded repeat is unknown. Here we developed both
Drosophila
and mammalian models of this expanded hexanucleotide repeat and showed that expression of the expanded GGGGCC repeat RNA (rGGGGCC) is sufficient to cause neurodegeneration. We further identified Pur α as the RNA-binding protein of rGGGGCC repeats and discovered that Pur α and rGGGGCC repeats interact in vitro and in vivo in a sequence-specific fashion that is conserved between mammals and
Drosophila
. Furthermore, overexpression of Pur α in mouse neuronal cells and
Drosophila
mitigates rGGGGCC repeat-mediated neurodegeneration, and Pur α forms inclusions in the fly eye expressing expanded rGGGGCC repeats, as well as in cerebellum of human carriers of expanded GGGGCC repeats. These data suggest that expanded rGGGGCC repeats could sequester specific RNA-binding protein from their normal functions, ultimately leading to cell death. Taken together, these findings suggest that the expanded rGGGGCC repeats could cause neurodegeneration, and that Pur α may play a role in the pathogenesis of amyotrophic lateral sclerosis and frontotemporal dementia.
Epoxy metabolites of docosahexaenoic acid (DHA) inhibit angiogenesis, tumor growth, and metastasis
Authors: Zhang Guodong , Panigrahy Dipak , Mahakian Lisa M. , Yang Jun , Liu Jun-Yan , Stephen Lee Kin Sing , Wettersten Hiromi I. , Ulu Arzu , Hu Xiaowen , Tam Sarah , Hwang Sung Hee , Ingham Elizabeth S. , Kieran Mark W. , Weiss Robert H. , Ferrara Katherine W. , Hammock Bruce D.
Published: April 2013

Epidemiological and preclinical evidence supports that omega-3 dietary fatty acids (fish oil) reduce the risks of macular degeneration and cancers, but the mechanisms by which these omega-3 lipids inhibit angiogenesis and tumorigenesis are poorly understood. Here we show that epoxydocosapentaenoic acids (EDPs), which are lipid mediators produced by cytochrome P450 epoxygenases from omega-3 fatty acid docosahexaenoic acid, inhibit VEGF- and fibroblast growth factor 2-induced angiogenesis in vivo, and suppress endothelial cell migration and protease production in vitro via a VEGF receptor 2-dependent mechanism. When EDPs (0.05 mg⋅kg
−1
⋅d
−1
) are coadministered with a low-dose soluble epoxide hydrolase inhibitor, EDPs are stabilized in circulation, causing ∼70% inhibition of primary tumor growth and metastasis. Contrary to the effects of EDPs, the corresponding metabolites derived from omega-6 arachidonic acid, epoxyeicosatrienoic acids, increase angiogenesis and tumor progression. These results designate epoxyeicosatrienoic acids and EDPs as unique endogenous mediators of an angiogenic switch to regulate tumorigenesis and implicate a unique mechanistic linkage between omega-3 and omega-6 fatty acids and cancers.
Sumoylation of AMPKβ2 subunit enhances AMP-activated protein kinase activity
Authors: Rubio Teresa , Vernia Santiago , Sanz Pascual
Published: April 2013

AMP-activated protein kinase (AMPK) is a sensor of cellular energy status. It is a heterotrimer composed of a catalytic α and two regulatory subunits (β and γ). AMPK activity is regulated allosterically by AMP and by the phosphorylation of residue Thr-172 within the catalytic domain of the AMPKα subunit by upstream kinases. We present evidence that the AMPKβ2 subunit may be posttranslationally modified by sumoylation. This process is carried out by the E3-small ubiquitin-like modifier (SUMO) ligase protein inhibitor of activated STAT PIASy, which modifies the AMPKβ2 subunit by the attachment of SUMO2 but not SUMO1 moieties. Of interest, AMPKβ1 is not a substrate for this modification. We also demonstrate that sumoylation of AMPKβ2 enhances the activity of the trimeric α2β2γ1 AMPK complex. In addition, our results indicate that sumoylation is antagonist and competes with the ubiquitination of the AMPKβ2 subunit. This adds a new layer of complexity to the regulation of the activity of the AMPK complex, since conditions that promote ubiquitination result in inactivation, whereas those that promote sumoylation result in the activation of the AMPK complex.
Tumor suppressor miR-375 regulates MYC expression via repression of CIP2A coding sequence through multiple miRNA–mRNA interactions
Authors: Jung Hyun Min , Patel Rushi S. , Phillips Brittany L. , Wang Hai , Cohen Donald M. , Reinhold William C. , Chang Lung-Ji , Yang Li-Jun , Chan Edward K. L.
Published: April 2013

MicroRNAs (miRNAs) are small, noncoding RNAs involved in posttranscriptional regulation of protein-coding genes in various biological processes. In our preliminary miRNA microarray analysis, miR-375 was identified as the most underexpressed in human oral tumor versus controls. The purpose of the present study is to examine the function of miR-375 as a candidate tumor suppressor miRNA in oral cancer. Cancerous inhibitor of PP2A (CIP2A), a guardian of oncoprotein MYC, is identified as a candidate miR-375 target based on bioinformatics. Luciferase assay accompanied by target sequence mutagenesis elucidates five functional miR-375–binding sites clustered in the CIP2A coding sequence close to the C-terminal domain. Overexpression of CIP2A is clearly demonstrated in oral cancers, and inverse correlation between miR-375 and CIP2A is observed in the tumors, as well as in NCI-60 cell lines, indicating the potential generalized involvement of the miR-375–CIP2A relationship in many other cancers. Transient transfection of miR-375 in oral cancer cells reduces the expression of CIP2A, resulting in decrease of MYC protein levels and leading to reduced proliferation, colony formation, migration, and invasion. Therefore this study shows that underexpression of tumor suppressor miR-375 could lead to uncontrolled CIP2A expression and extended stability of MYC, which contributes to promoting cancerous phenotypes.
What Is Being Learned About Starch Properties from Multiple‐Level Characterization
Authors: Gilbert Robert G. , Witt Torsten , Hasjim Jovin
Published: April 2013

A survey is given of methods to characterize the lowest three levels of starch structural features: individual chains, branched molecules, and the arrangement of branched molecules in a sample (e.g., crystalline and amorphous lamellae of starch granules in grain). The survey also covers ways of treating the results so as to understand starch structure–property correlations: for example, the structural characteristics that control the rate of digestion of a starch‐containing food. A number of studies are then examined not only to show how these techniques have been used to discover correlations between these structural characteristics and properties of importance but also to deduce reasonable causal explanations for the correlations. An overview of problems that have not yet been solved in each of these starch structural levels is also given. The applications of these characterization methods have considerable potential as tools to choose and process native starches with improved functional properties for human food, animal feed, and industrial uses, including biomaterials.
The biodiscovery potential of marine bacteria: an investigation of phylogeny and function
Authors: Mühling Martin , Joint Ian , Willetts Andrew J.
Published: April 2013

A collection of marine bacteria isolated from a temperate coastal zone has been screened in a programme of biodiscovery. A total of 34 enzymes with biotechnological potential were screened in 374 isolates of marine bacteria. Only two enzymes were found in all isolates while the majority of enzyme activities were present in a smaller proportion of the isolates. A cluster analysis demonstrated no significant correlation between taxonomy and enzyme function. However, there was evidence of co‐occurrence of some enzyme activity in the same isolate. In this study marine Proteobacteria had a higher complement of enzymes with biodiscovery potential than Actinobacteria; this contrasts with the terrestrial environment where the Actinobacteria phylum is a proven source of enzymes with important industrial applications. In addition, a number of novel enzyme functions were more abundant in this marine culture collection than would be expected on the basis of knowledge from terrestrial bacteria. There is a strong case for future investigation of marine bacteria as a source for biodiscovery.
Arterial Tissue Regeneration for Pediatric Applications: Inspiration From Up‐to‐Date Tissue‐Engineered Vascular Bypass Grafts
Authors: Cittadella Giorgio , de Mel Achala , Dee Ryan , De Coppi Paolo , Seifalian Alexander M.
Published: April 2013

The need for a valid replacement for autologous tissues in vascular surgery has led to the development of tissue‐engineered vascular grafts (TEVGs). Currently, only three kinds of TEVG have been used in clinical trials: synthetic scaffold‐based TEVGs, self‐assembled grafts, and decellularized exogenous tissues. This review presents the current options in the construction of TEVG and the changes that have occurred in the design following the clinical experience while focusing on the potential for pediatric applications. The emerging trend in the field, which is also pertinent for pediatric applications, is a shift from the development of vascular analogues to implants composed of scaffolds with autologous cellular components. Designs of such implants are currently being fine‐tuned so that a natural, functional tissue can gradually take over the role of scaffolds to stimulate the host's regenerative capacity and maintain the physiological homeostasis.
From ‘wannabe’ Silicon Valley to global back office? Examining the socio‐spatial consequences of technopole planning practices in Malaysia
Authors: Brooker Daniel
Published: April 2013

Cyberjaya is one of a long line of aspiring science and technology parks in the Asia‐Pacific region that have attempted to create a successful technopole, and in doing so become the ‘Silicon Valley of Asia’. The paper attends to the place‐making strategies through which Cyberjaya was positioned as a new ‘global hub’ for information communication technology and multimedia industries, framed as an extremely ‘sticky place’ (Markusen, 1996). That is, a place within a global economic system where local skills, infrastructure and capital attracts and makes research and development and corporate headquarters reluctant to leave. The paper considers that despite considerable infrastructural investment and state‐led urban boosterism to ‘sell’ Cyberjaya to prospective investors, more than 10 years after its completion in 1999 the development has become little more than a zone of disconnected business process outsourcing industries comprising low value‐added outsourcing activities.
Urokinase‐type plasminogen activator receptor (uPAR) as a promising new imaging target: potential clinical applications
Authors: Persson Morten , Kjaer Andreas
Published: April 2013

Urokinase‐type plasminogen activator receptor (uPAR) has been shown to be of special importance during cancer invasion and metastasis. However, currently, tissue samples are needed for measurement of uPAR expression limiting the potential as a clinical routine. Therefore, non‐invasive methods are needed. In line with this, uPAR has recently been identified as a very promising imaging target candidate. uPAR consists of three domains attached to the cell membrane via a glycosylphosphatidylinositol (GPI) anchor and binds it natural ligand uPA with high affinity to localize plasminogen activation at the cell surface. Due to the importance of uPAR in cancer invasion and metastasis, a number of high‐affinity ligands have been identified during the last decades. These ligands have recently been used as starting point for the development of a number of ligands for imaging of uPAR using various imaging modalities such as optical imaging, magnetic resonance imaging, single photon emission computer tomography (SPECT) and positron emission topography (PET). In this review, we will discuss recent advances in the development of uPAR‐targeted imaging ligands according to imaging modality. In addition, we will discuss the potential future clinical application for uPAR imaging as a new imaging biomarker.
New species of Lonchaeidae (Diptera: Schizophora) from Japan and a re‐evaluation of genus Setisquamalonchaea Morge
Authors: MacGowan Iain , Okamoto Tomoko
Published: April 2013

Three new species of Lonchaeidae are described from material reared from fig syconia in Japan: Silba inubiwa sp. nov., S. ishigaki sp. nov. and S. japonica sp. nov. Based on the taxonomy of these and similar species the boundaries of the genus Silba are re‐evaluated, and, as a result, it is considered that Setisquamalonchaea Morge is synonymous with Silba Macquart. A revised key and generic notes on the tribe Lonchaeini are provided.
The Impact of Home Country Institutions on Corporate Technological Entrepreneurship via R&D Investments and Virtual World Presence
Authors: Judge William Q. , Liu–Thompkins Yuping , Brown J. Lee , Pongpatipat Chatdanai
Published: April 2013

In this study, we seek to understand how four dimensions of national business systems surrounding the corporate headquarters of multinational firms influence corporate technological entrepreneurship (CTE). After controlling for fairly well–established antecedents of corporate technological entrepreneurship at the firm and industry levels, we find that national–level predictors explain considerable variance above and beyond our control variables. Furthermore, we find that various national–level dimensions influence different measures of CTE. Overall, our study points to the remarkably strong role of home institutional context for understanding two types of technological entrepreneurship pursued by relatively large, multinational firms based in 24 different economies.
The Influence of Changes in Social Capital on Firm–Founding Activities
Authors: Kreiser Patrick M. , Patel Pankaj C. , Fiet James O.
Published: April 2013

This study examines how founders can manage changes in their network ties during firm founding. We find that an increase in tie strength is negatively associated with founding activities, whereas an increase in the number of ties is positively associated with founding activities. Furthermore, entrepreneurial intensity mitigates the negative relationship between an increase in tie strength and founding activities; and social competence reinforces the positive relationship between an increase in the number of ties and founding activities. Our study contributes to the social capital literature by theorizing and testing how changes in a founder's network structure can be beneficial to founding activities.
Altered expression of hyaluronan synthase and hyaluronidase mRNA may affect hyaluronic acid distribution in keloid disease compared with normal skin
Authors: Sidgwick Gary P. , Iqbal Syed A. , Bayat Ardeshir
Published: April 2013

Keloid disease (KD) is a fibroproliferative disorder characterised partly by an altered extracellular matrix (ECM) profile. In fetal scarring, hyaluronic acid (HA) expression is increased, but is reduced in KD tissue compared with normal skin (NS). The expression of Hyaluronan Synthase (HAS) and hyaluronidase (HYAL) in KD and NS tissue were investigated for the first time using a range of techniques. Hyaluronan synthase and HYAL mRNA expression were significantly increased in NS tissue compared with KD tissue (P < 0.05). Immunohistological analysis of tissue indicated an accumulation of HAS and HYAL protein expression in KD compared with NS due to the thicker epidermis. No differences were observed in mRNA or protein expression in KD and NS fibroblasts. Reduced expression of HAS and HYAL may alter HA synthesis, degradation and accumulation in KD. Better understanding of the role of HA in KD may lead to novel therapeutic approaches to address the resulting ECM imbalance.
Initial nitrous oxide, carbon dioxide, and methane costs of converting conservation reserve program grassland to row crops under no‐till vs. conventional tillage
Authors: Ruan Leilei , Philip Robertson G.
Published: April 2013

Around 4.4 million ha of land in USDA Conservation Reserve Program (CRP) contracts will expire between 2013 and 2018 and some will likely return to crop production. No‐till (NT) management offers the potential to reduce the global warming costs of CO2, CH4, and N2O emissions during CRP conversion, but to date there have been no CRP conversion tillage comparisons. In 2009, we converted portions of three 9–21 ha CRP fields in Michigan to conventional tillage (CT) or NT soybean production and reserved a fourth field for reference. Both CO2 and N2O fluxes increased following herbicide application in all converted fields, but in the CT treatment substantial and immediate N2O and CO2 fluxes occurred after tillage. For the initial 201‐day conversion period, average daily N2O fluxes (g N2O‐N ha−1 d−1) were significantly different in the order: CT (47.5 ± 6.31, n = 6) ≫ NT (16.7 ± 2.45, n = 6) ≫ reference (2.51 ± 0.73, n = 4). Similarly, soil CO2 fluxes in CT were 1.2 times those in NT and 3.1 times those in the unconverted CRP reference field. All treatments were minor sinks for CH4 (−0.69 ± 0.42 to −1.86 ± 0.37 g CH4–C ha−1 d−1) with no significant differences among treatments. The positive global warming impact (GWI) of converted soybean fields under both CT (11.5 Mg CO2e ha−1) and NT (2.87 Mg CO2e ha−1) was in contrast to the negative GWI of the unconverted reference field (−3.5 Mg CO2e ha−1) with on‐going greenhouse gas (GHG) mitigation. N2O contributed 39.3% and 55.0% of the GWI under CT and NT systems with the remainder contributed by CO2 (60.7% and 45.0%, respectively). Including foregone mitigation, we conclude that NT management can reduce GHG costs by ~60% compared to CT during initial CRP conversion.
Intention to adhere to HIV treatment: a patient‐centred predictor of antiretroviral adherence
Authors: Nelsen A , Gupta S , Trautner BW , Petersen NJ , Garza A , Giordano TP , Naik AD , Rodriguez‐Barradas MC
Published: April 2013

Objectives

Despite the effectiveness of highly active antiretroviral therapy (HAART), HIV remains a major cause of mortality in the USA, largely as a result of poor HIV treatment adherence. In this study we assessed the association between five patient‐centred factors and adherence to HIV treatment.

Methods

We surveyed 244 adults at two HIV clinics in Houston, Texas between October 2009 and April 2010. Participants were given a questionnaire and their charts were reviewed for clinical data. Survey items assessed the following factors: self‐assessed HIV knowledge, awareness of disease biomarkers, intention to adhere to HIV treatment, health literacy and decision‐making style. The primary outcome measure was HAART adherence during the previous month. Logistic regressions were performed to calculate the effect of each factor on adherence.

Results

All participants had HIV/AIDS and were on HAART at enrolment. Eight per cent of participants were female, 57% were African‐American and 16% were Hispanic. Mean age was 58.1 years. Sixty‐eight per cent were adherent to HAART during the last month. On univariate analysis, a preference for wanting choices, correct knowledge of recent HIV viral load level, and intention to adhere to HIV treatment were significantly associated with adherence. On multivariate analysis, only intention to adhere to HIV treatment remained statistically significant after adjusting for other factors (odds ratio 2.2; 95% confidence interval 1.1 to 4.3).

Conclusions

Intention to adhere to HIV treatment was significantly associated with self‐reported adherence to HAART. Interventions that bolster patients' intentions to adhere to HIV treatment during clinical encounters may improve adherence to HAART and HIV control.