bluuebunny/crossref_metadata_2025 huggingface dataset:
Homodimerization and isoform-specific heterodimerization of neuroligins
Authors: Poulopoulos Alexandros , Soykan Tolga , Tuffy Liam P. , Hammer Matthieu , Varoqueaux Frédérique , Brose Nils
Published: June 2012

Neuroligins are postsynaptic adhesion proteins involved in the establishment of functional synapses in the central nervous system. In rodents, four genes give rise to neuroligins that function at distinct synapses, with corresponding neurotransmitter and subtype specificities. In the present study, we examined the interactions between the different neuroligins by isolating endogenous oligomeric complexes using in situ cross-linking on primary neurons. Examining hippocampal, striatal, cerebellar and spinal cord cultures, we found that neuroligins form constitutive dimers, including homomers and, most notably, neuroligin 1/3 heteromers. Additionally, we found that neuroligin monomers are specifically retained in the secretory pathway through a cellular quality control mechanism that involves the neuroligin transmembrane domain, ensuring that dimerization occurs prior to cell surface trafficking. Lastly, we identified differences in the dimerization capacity of autism-associated neuroligin mutants, and found that neuroligin 3 R471C mutants can form heterodimers with neuroligin 1. The pervasive nature of neuroligin dimerization indicates that the unit of neuroligin function is the dimer, and raises intriguing possibilities of distinct heterodimer functions, and of interactions between native and mutant neuroligins contributing to disease phenotypes.
Chronic kidney disease and vascular remodelling: molecular mechanisms and clinical implications
Authors: Briet Marie , Burns Kevin D.
Published: June 2012

CKD (chronic kidney disease) is a severe and complex disease with a very high prevalence of CV (cardiovascular) complications. CKD patients are exposed to haemodynamic disturbances in addition to severe metabolic abnormalities that lead to a specific form of arterial remodelling, which contributes to the development of CV disease. Arterial calcification is a major event in the arterial remodelling process and is strongly linked to mineral metabolism abnormalities associated with CKD. Arterial remodelling is not limited to arterial calcification and modifications in arterial wall composition are also observed. Activation of the RAS (renin–angiotensin system), ET-1 (endothelin-1), endothelial dysfunction, oxidative stress and ADMA (asymmetric ω-NG,NG-dimethylarginine), as well as the anti-aging molecule Klotho, are implicated in this process. The present review details the mechanisms involved in arterial calcification and arterial remodelling associated with CKD, and provides the clinical consequences of large and small artery stiffness and remodelling in CKD patients.
Magnesium and its transporters in cancer: a novel paradigm in tumour development
Authors: Wolf Federica I. , Trapani Valentina
Published: June 2012

The relationship between magnesium and cancer is not as simple as could be assumed from the well-established requirement of magnesium for cell proliferation. Basic and pre-clinical studies indicate that magnesium deficiency can have both anti- and pro-tumour effects. In the present review, we briefly outline the new findings on the role of magnesium in angiogenesis and metastatization, and focus on the relationship between tumour cell proliferation and metabolic reprogramming, discussing how magnesium and its transporters are involved in these processes. The role of magnesium in cancer is also critically examined with regard to mitochondrial function, apoptosis and resistance to treatment. Finally, we bring together the latest experimental evidence indicating that alteration in the expression and/or activity of magnesium channels is a frequent finding in cancer cells and human tumour tissues examined to date, and we discuss the potential implications for developing novel diagnostic and therapeutic strategies.
Ferromagnetism and its stability in n-type Gd-doped GaN: First-principles calculation
Authors: Liu Zhiqiang , Yi Xiaoyan , Wang Jianwei , Kang Jun , Melton Andrew G. , Shi Yi , Lu Na , Wang Junxi , Li Jinmin , Ferguson Ian
Published: June 2012

In this work, effects of interstitial oxygen on the ferromagnetism in Gd-doped GaN system were investigated via first principles, including both total energy and band structure calculation. The results of these calculations indicate that splitting interstitial sites oxygen is a plausible candidate for defect-induced magnetism in n-type GaN:Gd due to the p-d hybridization. The total energy difference was found to be more than 100 meV in a wide electron concentration range. Furthermore, the formation energies of various interstitial oxygen atomic configurations are also discussed.
All-optical tuning of a quantum dot in a coupled cavity system
Authors: Bose Ranojoy , Cai Tao , Solomon Glenn S. , Waks Edo
Published: June 2012

We demonstrate a method for tuning a semiconductor quantum dot (QD) onto resonance with a cavity mode all-optically using a system comprised of two evanescently coupled cavities containing a single QD. One resonance of the coupled cavity system is utilized to generate a cavity enhanced optical Stark shift, enabling the QD to be resonantly tuned to the other cavity mode. A twenty-seven fold increase in photon emission from the QD is measured when the off-resonant QD is Stark shifted onto the cavity mode resonance, which is attributed to radiative enhancement of the QD. A maximum tuning of 0.06 nm is achieved for the QD at an incident power of 88 μW.
Causally simple inextendible spacetimes are hole-free
Authors: Minguzzi E.
Published: June 2012

It is shown that causally simple inextendible spacetimes are hole-free, thus confirming the expectation that causal simplicity removes holes from spacetime. This result is optimal in the sense that causal simplicity cannot be weakened to causal continuity. Physically, it means that if there is some partial Cauchy hypersurface which, for some reason, does not fully develop its influence, then there is some discontinuity in the causal relation.
Amorphous/crystalline silicon heterojunction solar cells via remote inductively coupled plasma processing
Authors: Xiao S. Q. , Xu S. , Zhou H. P. , Wei D. Y. , Huang S. Y. , Xu L. X. , Sern C. C. , Guo Y. N. , Khan S.
Published: June 2012

Low-frequency inductively coupled plasma (ICP) has been widely used to deposit amorphous or microcrystalline Si thin films, but the intrinsic drawback namely ion bombardment effect limits its application in Si heterojunction solar cells. In this letter, we redesigned typical ICP and realized a remote plasma deposition with suppressed ion bombardment effect. This remote ICP system enables the synthesis of high quality amorphous Si layers with a compact network and a high hydrogen content (10.5%). By using this remote ICP system, we achieved amorphous/crystalline silicon heterojunction solar cells with an efficiency of 14.1% without any back surface field or textures.
Neutron diffusion in a randomly inhomogeneous multiplying medium with random phase approximation
Authors: Imre Kaya , Akcasu A. Ziya
Published: June 2012

Neutron diffusion in a randomly inhomogeneous multiplying medium is studied. By making use of a random phase assumption we show that the average neutron density approximately satisfies an integral equation in Fourier space, which is solved using Kummer functions. We used multi-dimensional formulation. In the case of one dimension, we obtain the result of Rosenbluth and Tao for the mean total density for large t. In the three-dimensional case, a closed form of solution is derived for the mean total neutron density. Its asymptotic behavior is also investigated for large t.
The effect of topology on the structure and free energy landscape of DNA kissing complexes
Authors: Romano Flavio , Hudson Alexander , Doye Jonathan P. K. , Ouldridge Thomas E. , Louis Ard A.
Published: June 2012

We use a recently developed coarse-grained model for DNA to study kissing complexes formed by hybridization of complementary hairpin loops. The binding of the loops is topologically constrained because their linking number must remain constant. By studying systems with linking numbers −1, 0, or 1 we show that the average number of interstrand base pairs is larger when the topology is more favourable for the right-handed wrapping of strands around each other. The thermodynamic stability of the kissing complex also decreases when the linking number changes from −1 to 0 to 1. The structures of the kissing complexes typically involve two intermolecular helices that coaxially stack with the hairpin stems at a parallel four-way junction.
Multi-dimensional wavepacket and potential reconstruction by resonant coherent anti-Stokes Raman scattering: Application to H2O and HOD
Authors: Avisar David , Tannor David J.
Published: June 2012

We have recently proposed a methodology for reconstructing excited-state (ExS) molecular wavepackets, and the corresponding potential energy surface, from three-pulse resonant coherent anti-Stokes Raman scattering and knowledge of the ground-state potential [Avisar and Tannor, Phys. Rev. Lett. 106, 170405 (2011)10.1103/PhysRevLett.106.170405]. The methodology is general for polyatomics and applies to any form of ExS potential – bound or dissociative. In our previous work we demonstrated the method on diatomics. Here, we demonstrate the method on the triatomics H2O and HOD, reconstructing the ExS wavepacket and potential in the two bond-stretching coordinates.
Charge transfer effects in electrocatalytic Ni-C revealed by x-ray photoelectron spectroscopy
Authors: Haslam G. E. , Sato K. , Mizokawa T. , Chin X.-Y. , Burstein G. T.
Published: June 2012

Binary Ni-C thin-film alloys, which have been shown to be passive against corrosion in hot sulphuric acid solution whilst also being electrocatalytically active, were investigated by XPS to determine the oxidation state of the metal and carbon components. The Ni component produces a Ni 2p spectrum similar to that of metallic nickel (i.e., no oxidation occurs) but with a 0.3 eV shift to higher binding energy (BE) due to electron donation to the carbon matrix. The C 1s peak shows a shift to lower BE by accepting electrons from the Ni nanocrystals. A cluster-model analysis of the observed Ni 2p spectrum is consistent with the electron transfer from the nickel to the carbon.
Origin of the oscillations in the self-diffracted signal in degenerate-two wave mixing experiment in azo-polymer
Authors: Sobolewska Anna , Bartkiewicz Stanislaw
Published: June 2012

The authors report on temporal oscillation in the first-order self-diffracted signal observed during the holographic grating recording in the azobenezne-functionalized polymer in the degenerate two-wave mixing experiment. Explanation of the oscillating character of the diffracted signal is given based on the assumption of appearance of symmetrical phase shift between the light intensity pattern and the diffraction grating. Simulations of the experimental results were performed based on simple theoretical considerations and they have shown a good agreement with the experimental data.
Transport of indirect excitons in a potential energy gradient
Authors: Leonard J. R. , Remeika M. , Chu M. K. , Kuznetsova Y. Y. , High A. A. , Butov L. V. , Wilkes J. , Hanson M. , Gossard A. C.
Published: June 2012

We realized a potential energy gradient—a ramp—for indirect excitons using a shaped electrode at constant voltage. We studied transport of indirect excitons along the ramp and observed that the exciton transport distance increases with increasing density and temperature.
Nanoscale thermal radiation between two gold surfaces
Authors: Shen Sheng , Mavrokefalos Anastassios , Sambegoro Poetro , Chen Gang
Published: June 2012

In this letter, we measured the nanoscale thermal radiation between a microsphere and a substrate which were both coated with thick gold films. Although gold is highly reflective for thermal radiation, the radiative heat transfer between two gold surfaces was demonstrated to be significantly enhanced at nanoscale gaps beyond the blackbody radiation limit due to the tunneling of non-resonant evanescent waves. The measured heat transfer coefficient between two gold surfaces agreed well with theoretical prediction. At a gap d = 30 nm ± 5 nm, the heat transfer coefficient between two gold surfaces was observed to be as large as ∼400 W/m2·K, much greater than the blackbody radiation limit (∼5 W/m2·K).
The np Rydberg series of boron monohydride: l-uncoupling and Rydberg electron interactions with the rovibrational motion of the ion core
Authors: Viteri C. Ricardo , Gilkison Andrew T. , Grant Edward R.
Published: June 2012

A simple two-channel quantum defect theory approach accounts for resonance positions in the np Rydberg series of 11BH. The transition from Hund's case (b) to (d) in the interacting levels of this np series represents a fundamental example of electron orbital ⇔ cation core rotational coupling, and frame transformation theory offers a means to connect close-coupled electronically excited-state potentials and l-uncoupled Rydberg positions. This evolving interaction of the np Rydberg electron with the rotational and the vibrational motion of the 11BH+ core is formulated in terms of quantum defects, μλ(v+).
Hierarchical ZnO nanostructures: Growth mechanisms and surface correlated photoluminescence
Authors: Grinblat G. , Capeluto M. G. , Tirado M. , Bragas A. V. , Comedi D.
Published: June 2012

ZnO nanowires were grown by vapor-transport and deposition on Au nanocluster covered fused and thermal silica and c-Si. The nanowire size and density depended strongly on the substrate type. By decreasing the O2 to local Zn partial pressure ratio, the growth pattern changed to nanocombs and nanosheets. ZnO nanohedgehogs were found on bare c-Si. We observe a remarkable correlation between the defect to exciton photoluminescence intensity ratio and the nanostructures specific surface areas. These results indicate that changes in strain and O deficiency defects at surfaces are behind the observed morphology changes, one to two-dimensional growth transition, and corresponding luminescence.
Sensitivity of 2-D turbulent flow past a D-shaped cylinder using global stability
Authors: Meliga Philippe , Pujals Gregory , Serre Éric
Published: June 2012

We use adjoint-based gradients to analyze the sensitivity of turbulent wake past a D-shaped cylinder at Re = 13000. We assess the ability of a much smaller control cylinder in altering the shedding frequency, as predicted by the eigenfrequency of the most unstable global mode to the mean flow. This allows performing beforehand identification of the sensitive regions, i.e., without computing the actually controlled states. Our results obtained in the frame of 2-D, unsteady Reynolds-averaged Navier–Stokes compare favorably with experimental data reported by Parezanović and Cadot [J. Fluid Mech. 693, 115 (2012)] and suggest that the control cylinder acts primarily through a local modification of the mean flow profiles.
Enhanced light extraction in organic light-emitting devices: Using conductive low-index layers and micropatterned indium tin oxide electrodes with optimal taper angle
Authors: Choi Jungmin , Koh Tae-Wook , Lee Soohyun , Yoo Seunghyup
Published: June 2012

We present our study on organic light-emitting diodes (OLEDs) in which outcoupling is enhanced based on a bilayer electrode consisting of a conductive low-index layer and micro-patterned indium tin oxide (ITO) layers. Optical simulation reveals that the taper angle of an ITO pattern is among the most critical parameters influencing the outcoupling efficiency in the proposed structure. A fabrication method based on a lift-off process is then employed to control the taper angle of the ITO pattern to be in the optimal range. OLEDs with the proposed electrode structure exhibit 50%–70% enhancement in external quantum efficiency over reference devices.
The effects of diameter and chirality on the thermal transport in free-standing and supported carbon-nanotubes
Authors: Qiu Bo , Wang Yan , Zhao Qing , Ruan Xiulin
Published: June 2012

We use molecular dynamics simulations to explore the lattice thermal transport in free-standing and supported single-wall carbon-nanotube (SWCNT) in comparison to that in graphene nanoribbon and graphene sheet. For free-standing SWCNT, the lattice thermal conductivity increases with diameter and approaches that of graphene, partly due to the curvature. Supported SWCNT thermal conductivity is reduced by 34%-41% compared to the free-standing case, which is less than that in supported graphene. Also, it shows an evident chirality dependence by varying about 10%, which we attribute to chirality-dependent interfacial phonon scattering.
Novel temperature dependent tensile test of freestanding copper thin film structures
Authors: Smolka M. , Motz C. , Detzel T. , Robl W. , Griesser T. , Wimmer A. , Dehm G.
Published: June 2012

The temperature dependent mechanical properties of the metallization of electronic power devices are studied in tensile tests on micron-sized freestanding copper beams at temperatures up to 400 °C. The experiments are performed in situ in a scanning electron microscope. This allows studying the micromechanical processes during the deformation and failure of the sample at different temperatures.
Multiple Fano resonances in monolayer hexagonal non-close-packed metallic shells
Authors: Chen Jing , Shen Qi , Chen Zhuo , Wang Qiugu , Tang Chaojun , Wang Zhenlin
Published: June 2012

In this study, we first numerically investigate the appearance and properties of multiple Fano resonances in two-dimensional hexagonal non-close-packed arrays of symmetric metallic shells. The coexistence of broad sphere-like plasmon modes formed from the near-field interaction between the individual sphere plasmons and substantially narrower void plasmon modes supported by the inner surface of the individual shell resonant over the same range of energies can produce such Fano resonances. In particular, void and sphere-like plasmon modes of different angular momentum could directly interact without the need of symmetry breaking in the structure. A cost-effective colloidal crystal templating method is utilized to prepare the arrays of the metallic shells with small openings. The effect of the symmetry breaking on the Fano resonances in metallic cup arrays is experimentally and numerically investigated. Further tunability on the Fano resonances is gained by changing the size of the inner dielectric core, hence changing the moment of the void plasmon modes and consequently the resonance frequency. By adopting the polymer dielectric core with gain materials, our study may offer realizable experimental opportunities towards subwavelength low threshold plasmonic lasing.
Laser-sintered thin films of doped SiGe nanoparticles
Authors: Stoib B. , Langmann T. , Matich S. , Antesberger T. , Stein N. , Angst S. , Petermann N. , Schmechel R. , Schierning G. , Wolf D. E. , Wiggers H. , Stutzmann M. , Brandt M. S.
Published: June 2012

We present a study of the morphology and the thermoelectric properties of short-pulse laser-sintered (LS) nanoparticle (NP) thin films, consisting of SiGe alloy NPs or composites of Si and Ge NPs. Laser-sintering of spin-coated NP films in vacuum results in a macroporous percolating network with a typical thickness of 300 nm. The Seebeck coefficient for LS samples is the same as for bulk samples prepared by current-assisted sintering and is typical for degenerate doping. The electrical conductivity of LS films is influenced by two-dimensional percolation effects and rises with increasing temperature, approximately following a power-law.
Admittance spectroscopy of Cu2ZnSnS4 based thin film solar cells
Authors: Fernandes P. A. , Sartori A. F. , Salomé P. M. P. , Malaquias J. , da Cunha A. F. , Graça M. P. F. , González J. C.
Published: June 2012

In this report, we propose an AC response equivalent circuit model to describe the admittance measurements of Cu2ZnSnS4 thin film solar cell grown by sulphurization of stacked metallic precursors. This circuit describes the contact resistances, the back contact, and the heterojunction with two trap levels. The study of the back contact resistance allowed the estimation of a back contact barrier of 246 meV. The analysis of the trap series with varying temperature revealed defect activation energies of 45 meV and 113 meV. The solar cell’s electrical parameters were obtained from the J-V curve: conversion efficiency, 1.21%; fill factor, 50%; open circuit voltage, 360 mV; and short circuit current density, 6.8 mA/cm2.
Ion irradiation tolerance of graphene as studied by atomistic simulations
Authors: Åhlgren E. H. , Kotakoski J. , Lehtinen O. , Krasheninnikov A. V.
Published: June 2012

As impermeable to gas molecules and at the same time transparent to high-energy ions, graphene has been suggested as a window material for separating a high-vacuum ion beam system from targets kept at ambient conditions. However, accumulation of irradiation-induced damage in the graphene membrane may give rise to its mechanical failure. Using atomistic simulations, we demonstrate that irradiated graphene even with a high vacancy concentration does not show signs of such instability, indicating a considerable robustness of graphene windows. We further show that upper and lower estimates for the irradiation damage in graphene can be set using a simple model.
Coulomb-damped resonant generators using piezoelectric transduction
Authors: Miller L. M. , Mitcheson P. D. , Halvorsen E. , Wright P. K.
Published: June 2012

Switching interface circuits employed with piezoelectric energy harvesters can increase the electrical damping considerably over that achievable with passive rectifiers. We show that a piezoelectric harvester coupled to certain types of switching circuits becomes a Coulomb-damped resonant generator. This allows analysis of such harvester systems within a well-known framework and, subject to practical constraints, allows the optimal electrical damping to be achieved. In the piezoelectric pre-biasing technique, the Coulomb damping is set by a pre-bias voltage whose optimal value is derived as a function of piezoelectric harvester parameters.
Experimental isolation of degradation mechanisms in capacitive microelectromechanical switches
Authors: Olszewski Z. , Houlihan R. , Ryan C. , O’Mahony C. , Duane R.
Published: June 2012

DC and bipolar voltage stresses are used to isolate mechanical degradation of the movable electrode from charging mechanism in microelectromechanical capacitive switches. Switches with different metals as the movable electrode were investigated. In titanium switches, a shift in the pull-in voltages is observed after dc stressing whereas no shift occurs after the bipolar stressing, which is to be expected from charging theory. On switches with similar dielectric but made of aluminium, the narrowing effect occurs regardless if dc or bipolar stressing is used, which indicates the mechanical degradation as the mechanism responsible.
Probing characteristics of collagen molecules on various surfaces via atomic force microscopy
Authors: Su Hao-Wei , Ho Mon-Shu , Cheng Chao-Min
Published: June 2012

We examine, herein, specific dynamic responses of collagen molecules (i.e., observations of self-assembly and nanometric adhesion force measurements of type-I collagen molecules) as they interact with either a hydrophobic or a hydrophilic surface at two distinct temperatures, using a liquid-type atomic force microscope. We conclude that, regardless of surface hydrophobicity/hydrophilicity, assembled microfibrils eventually distribute homogeneously in accordance with changes in surface-related mechanical properties of collagen molecules at different self-assembly stages.
Tunnel electroresistance in junctions with ultrathin ferroelectric Pb(Zr0.2Ti0.8)O3 barriers
Authors: Pantel Daniel , Lu Haidong , Goetze Silvana , Werner Peter , Jik Kim Dong , Gruverman Alexei , Hesse Dietrich , Alexe Marin
Published: June 2012

In ferroelectric tunnel junctions, the ferroelectric polarization state of the barrier influences the quantum-mechanical tunneling through the junction, resulting in tunnel electroresistance (TER). Here, we investigate tunnel electroresistance in Co/PbZr0.2Ti0.8O3/La0.7Sr0.3MnO3 tunnel junctions. The ferroelectric polarization in tunnel junctions with 1.2-1.6 nm (three to four unit cells) PbZr0.2Ti0.8O3 thickness and an area of 0.04 μm2 can be switched by about 1 V yielding a resistive ON/OFF-ratio of about 300 at 0.4 V. Combined piezoresponse force microscopy and electronic transport investigations of these junctions reveal that the transport mechanism is quantum tunneling and the resistive switching in these junctions is due only to ferroelectric switching.
An optofluidics biosensor consisted of high-finesse Fabry-Pérot resonator and micro-fluidic channel
Authors: Liu Pengbo , Huang Hui , Cao Tun , Tang Zhenan , Liu Xueyu , Qi Zhenbin , Ren Mingkun , Wu Haibo
Published: June 2012

A high quality factor Fabry–Pérot cavity (FPC) biosensor with smooth and flat micro-channel surface is realized by using a silicon on insulator substrate, in which the oxide layer functions as an etch-stop layer. The measured quality factor and sensitivity of the FPC biosensor are 861 and 1100 nm/RIU (refractive index units), respectively, and the corresponding detection limit (DL) reaches 1.1 × 10−5 RIU. Moreover, due to the smooth and flat channel surface, higher quality factor and better DL can be obtained with increasing reflectivity of the Bragg reflector of the FPC biosensor.
Non-resonant optical excitation of mode-locked electron spin coherence in (In,Ga)As/GaAs quantum dot ensemble
Authors: Schwan A. , Varwig S. , Greilich A. , Yakovlev D. R. , Reuter D. , Wieck A. D. , Bayer M.
Published: June 2012

Two-color pump probe experiments reveal the possibility to use non-resonant pulsed laser excitation to create mode-locking of the ground state electron spin precessions in an ensemble of singly charged (In,Ga)As/GaAs quantum dots. The mode-locking shows a resonance for excitation into the first excited shell while for excitation into higher shells or barriers it disappears; however, spin coherence can still be induced. We conclude that the optically excited carriers relax spin-conserved from the p-shell into their ground states on a picosecond time scale, much shorter than the spin revolution period about the magnetic field.
Work function tuning and improved gate dielectric reliability with multilayer graphene as a gate electrode for metal oxide semiconductor field effect device applications
Authors: Misra Abhishek , Waikar Mayur , Gour Amit , Kalita Hemen , Khare Manali , Aslam Mohammed , Kottantharayil Anil
Published: June 2012

Graphene with varying number of layers is explored as metal gate electrode in metal oxide semiconductor structure by inserting it between the dielectric (SiO2) and contact metal (TiN) and results are compared with TiN gate electrode. We demonstrate an effective work function tuning of gate electrode upto 0.5 eV by varying the number of graphene layers. Inclusion of even 1-3 layers of graphene results in significantly improved dielectric reliability as measured by breakdown characteristics, charge to breakdown, and interface state density. These improvements are attributed to the impermeability of graphene for TiN and hence reduced metallic contamination in the dielectric.
Plasma plume effects on the conductivity of amorphous-LaAlO3/SrTiO3 interfaces grown by pulsed laser deposition in O2 and Ar
Authors: Sambri A. , Cristensen D. V. , Trier F. , Chen Y. Z. , Amoruso S. , Pryds N. , Bruzzese R. , Wang X.
Published: June 2012

Amorphous-LaAlO3/SrTiO3 interfaces exhibit metallic conductivity similar to those found for the extensively studied crystalline-LaAlO3/SrTiO3 interfaces. Here, we investigate the conductivity of the amorphous-LaAlO3/SrTiO3 interfaces grown in different pressures of O2 and Ar background gases. During the deposition, the LaAlO3 ablation plume is also studied, in situ, by fast photography and space-resolved optical emission spectroscopy. An interesting correlation between interfacial conductivity and kinetic energy of the Al atoms in the plume is observed: to assure conducting interfaces of amorphous-LaAlO3/SrTiO3, the kinetic energy of Al should be higher than 1 eV. Our findings add further insights on mechanisms leading to interfacial conductivity in SrTiO3-based oxide heterostructures.
The nature of nutrition: a unifying framework
Authors: Simpson Stephen J. , Raubenheimer David
Published: June 2012

We present a graphical approach, which we believe can help to integrate nutrition into the broader biological sciences, and introduce generality into the applied nutritional sciences. This ‘Geometric Framework’ takes account of the fact that animals need multiple nutrients in changing amounts and balance, and that nutrients come packaged in foods that are often hard to find, dangerous to subdue and costly to process. We then show how the Geometric Framework has been used to understand the links between nutrition and relevant aspects of the biology of individual animals. These aspects include the physiological mechanisms that direct the nutritional interactions of the animal with its environment, and the fitness consequences of these interactions. Having considered the implications of diet for individuals, we show that these effects can translate into the collective behaviour of groups and societies, and in turn ramify throughout food webs to influence the structure of ecosystems.
Reversible voltammograms and a Pourbaix diagram for a protein tyrosine radical
Authors: Berry Bruce W. , Martínez-Rivera Melissa C. , Tommos Cecilia
Published: June 2012

Reversible voltammograms and a voltammetry half-wave potential versus solution pH diagram are described for a protein tyrosine radical. This work required a de novo designed tyrosine-radical protein displaying a unique combination of structural and electrochemical properties. The
α
3
Y protein is structurally stable across a broad pH range. The redox-active tyrosine Y32 resides in a desolvated and well-structured environment. Y32 gives rise to reversible square-wave and differential pulse voltammograms at alkaline pH. The formal potential of the Y32-O
•
/Y32-OH redox couple is determined to 918 ± 2 mV versus the normal hydrogen electrode at pH 8.40 ± 0.01. The observation that Y32 gives rise to fully reversible voltammograms translates into an estimated lifetime of ≥30 ms for the Y32-O
•
state. This illustrates the range of tyrosine-radical stabilization that a structured protein can offer. Y32 gives rise to quasireversible square-wave and differential pulse voltammograms at acidic pH. These voltammograms represent the Y32 species at the upper edge of the quasirevesible range. The square-wave net potential closely approximates the formal potential of the Y32-O
•
/Y32-OH redox couple to 1,070 ± 1 mV versus the normal hydrogen electrode at pH 5.52 ± 0.01. The differential pulse voltammetry half-wave potential of the Y32-O
•
/Y32-OH redox pair is measured between pH 4.7 and 9.0. These results are described and analyzed.
Attachment ofChlamydia trachomatisL2 to host cells requires sulfation
Authors: Rosmarin David M. , Carette Jan E. , Olive Andrew J. , Starnbach Michael N. , Brummelkamp Thijn R. , Ploegh Hidde L.
Published: June 2012

Chlamydia trachomatisis a pathogen responsible for a prevalent sexually transmitted disease. It is also the most common cause of infectious blindness in the developing world. We performed a loss-of-function genetic screen in human haploid cells to identify host factors important inC. trachomatisL2 infection. We identified and confirmedB3GAT3,B4GALT7, andSLC35B2, which encode glucuronosyltransferase I, galactosyltransferase I, and the 3′-phosphoadenosine 5′-phosphosulfate transporter 1, respectively, as important in facilitatingChlamydiainfection. Knockout of any of these three genes inhibitsChlamydiaattachment. In complementation studies, we found that the introduction of functional copies of these three genes into the null clones restored full susceptibility toChlamydiainfection. The degree of attachment ofChlamydiastrongly correlates with the level of sulfation of the host cell, not simply with the amount of heparan sulfate. Thus, other, as-yet unidentified sulfated macromolecules must contribute to infection. These results demonstrate the utility of screens in haploid cells to study interactions of human cells with bacteria. Furthermore, the human null clones generated can be used to investigate the role of heparan sulfate and sulfation in other settings not limited to infectious disease.
Asymmetrical roles of zinc fingers in dynamic DNA-scanning process by the inducible transcription factor Egr-1
Authors: Zandarashvili Levani , Vuzman Dana , Esadze Alexandre , Takayama Yuki , Sahu Debashish , Levy Yaakov , Iwahara Junji
Published: June 2012

Egr-1 is an inducible transcription factor that recognizes 9-bp target DNA sites via three zinc finger domains and activates genes in response to cellular stimuli such as synaptic signals and vascular stresses. Using spectroscopic and computational approaches, we have studied structural, dynamic, and kinetic aspects of the DNA-scanning process in which Egr-1 is nonspecifically bound to DNA and perpetually changes its location on DNA. Our NMR data indicate that Egr-1 undergoes highly dynamic domain motions when scanning DNA. In particular, the zinc finger 1 (ZF1) of Egr-1 in the nonspecific complex is mainly dissociated from DNA and undergoes collective motions on a nanosecond timescale, whereas zinc fingers 2 and 3 (ZF2 and ZF3, respectively) are bound to DNA. This was totally unexpected because the previous crystallographic studies of the specific complex indicated that all of Egr-1’s three zinc fingers are equally involved in binding to a target DNA site. Mutations that are expected to enhance ZF1’s interactions with DNA and with ZF2 were found to reduce ZF1’s domain motions in the nonspecific complex suggesting that these interactions dictate the dynamic behavior of ZF1. By experiment and computation, we have also investigated kinetics of Egr-1’s translocation between two nonspecific DNA duplexes. Our data on the wild type and mutant proteins suggest that the domain dynamics facilitate Egr-1’s intersegment transfer that involves transient bridging of two DNA sites. These results shed light on asymmetrical roles of the zinc finger domains for Egr-1 to scan DNA efficiently in the nucleus.
Dual disease resistance mediated by the immune receptor Cf-2 in tomato requires a common virulence target of a fungus and a nematode
Authors: Lozano-Torres Jose L. , Wilbers Ruud H. P. , Gawronski Piotr , Boshoven Jordi C. , Finkers-Tomczak Anna , Cordewener Jan H. G. , America Antoine H. P. , Overmars Hein A. , Van ‘t Klooster John W. , Baranowski Lukasz , Sobczak Miroslaw , Ilyas Muhammad , van der Hoorn Renier A. L. , Schots Arjen , de Wit Pierre J. G. M. , Bakker Jaap , Goverse Aska , Smant Geert
Published: June 2012

Plants lack the seemingly unlimited receptor diversity of a somatic adaptive immune system as found in vertebrates and rely on only a relatively small set of innate immune receptors to resist a myriad of pathogens. Here, we show that disease-resistant tomato plants use an efficient mechanism to leverage the limited nonself recognition capacity of their innate immune system. We found that the extracellular plant immune receptor protein Cf-2 of the red currant tomato (
Solanum pimpinellifolium
) has acquired dual resistance specificity by sensing perturbations in a common virulence target of two independently evolved effectors of a fungus and a nematode. The Cf-2 protein, originally identified as a monospecific immune receptor for the leaf mold fungus
Cladosporium fulvum
, also mediates disease resistance to the root parasitic nematode
Globodera rostochiensis
pathotype Ro1-Mierenbos. The Cf-2–mediated dual resistance is triggered by effector-induced perturbations of the apoplastic Rcr3
pim
protein of
S. pimpinellifolium
. Binding of the venom allergen-like effector protein Gr-VAP1 of
G. rostochiensis
to Rcr3
pim
perturbs the active site of this papain-like cysteine protease. In the absence of the Cf-2 receptor, Rcr3
pim
increases the susceptibility of tomato plants to
G. rostochiensis
, thus showing its role as a virulence target of these nematodes. Furthermore, both nematode infection and transient expression of
Gr-VAP1
in tomato plants harboring
Cf-2
and

Rcr3
pim

trigger a defense-related programmed cell death in plant cells. Our data demonstrate that monitoring host proteins targeted by multiple pathogens broadens the spectrum of disease resistances mediated by single plant immune receptors.
Conflict adaptation: It is not what you expect
Authors: Duthoo Wout , Notebaert Wim
Published: June 2012

In two studies, a vocal Stroop task with eight different colours was employed in order to put two core assumptions of the original interpretation of the Gratton effect to the test. We verified whether top-down control processes can elicit conflict adaptation when episodic memory effects are controlled for and to what extent proactive adjustments driven by the subjects' expectancy for congruency level repetition contribute to this effect. Therefore, we presented Stroop stimuli without feature repetitions and investigated whether the induced expectancy manipulation of raising the amount of either congruency level repetitions or alternations in a training phase transferred to an unmanipulated test phase. Over the two experiments, a sequential modulation of the Stroop effect was found in the absence of stimulus feature repetitions, strongly confirming a share for top-down control processes in bringing about the Gratton effect. In the condition where congruency level repetitions were raised, a strong Gratton effect was found. When congruency level alternations outnumbered repetitions, the Gratton effect disappeared completely. However, this difference seemed mainly due to cumulative effects of local, dynamic, trial-to-trial control adjustments rather than expectancy-induced attentional shifting. Once the transition probability changed back to 50% in the test phase of each experiment, a similar Gratton effect was found in both conditions. Taken together, these results are best explained in terms of dynamic reactive control.
Calorimetric investigation of the magnetocaloric effect in Ni45Co5Mn37.5In12.5
Authors: Guillou F , Courtois P , Porcar L , Plaindoux P , Bourgault D , Hardy V
Published: June 2012

A calorimetric investigation of a Ni45Co5Mn37.5In12.5 single crystal has been carried out by combining differential scanning calorimetry (DSC) and heat capacity (C) measurements. The martensitic transition showing a first-order character spread over a wide temperature range, a specific measuring technique of C(T) has been developed. This method—based on a time-resolved analysis of successive heating pulses—was found to yield an entropy change at the transition (ΔS
tr) that is very close to that derived from DSC. To investigate the magnetocaloric effect, both the isothermal entropy change ΔS

T
and the adiabatic temperature change ΔT
ad were derived from heat capacity curves recorded in a series of magnetic fields up to 7 T. The maximum values of ΔS

T
(T, B) were observed to be in accordance with those determined from the Maxwell equation. Furthermore, maximum values of ΔT
ad(T, B) resulting from the application of 2 T, 5 T and 7 T were found to be equal to −2.3 K, −6.1 K and −9.4 K, respectively.
A double-ring Mach–Zehnder interferometer sensor with high sensitivity
Authors: Zhang Jing , Zhang Yundong , Song Qinghai , Tian He , Zhang Xuenan , Wu Hao , Wang Jinfang , Yu Changqiu , Li Geng , Fan Daikun , Yuan Ping
Published: June 2012

We theoretically proposed a cost-effective refractometer sensor, which includes an unbalanced two-ring Mach–Zehnder interferometer and can exhibit sharp asymmetric Fano lineshape. Our calculated results show this device has high sensitivity and can measure refractive index change in one of the resonators down to 10−9 refractive index units, which is two orders of magnitude higher than previous Fano lineshape based sensors.
Heat-driven size manipulation of Fe catalytic nanoparticles for precise control of single-walled carbon nanotube diameter
Authors: Kim Soo Youn , Song Wooseok , Jung Min Wook , Kim Minkook , Jeon Cheolho , Choi Won Chel , Park Chong-Yun
Published: June 2012

Size-tailored Fe catalytic nanoparticles (NPs) were formed by a heat-driven evaporation process, and precise control of single-walled carbon nanotube (SWCNT) diameter was achieved. The size and surface concentration of Fe NPs significantly decreased with increasing evaporation temperature, which was investigated by transmission electron microscopy (TEM) and x-ray photoelectron spectroscopy. TEM and Raman spectroscopy revealed that the synthesis of SWCNTs with an extremely narrow diameter distribution was achieved and their diameter can be manipulated by evaporation temperature. This diameter-controlled growth of SWCNTs is a step towards SWCNT-based applications.
Surface effects on the electroelastic responses of a thin piezoelectric plate with nanoscale thickness
Authors: Yan Zhi , Jiang Liying
Published: June 2012

This work aims to investigate the electroelastic responses of a thin piezoelectric plate under mechanical and electrical loads with the consideration of surface effects. Surface effects, including surface elasticity, residual surface stress and surface piezoelectricity, are incorporated into the conventional Kirchhoff plate theory for a piezoelectric plate via the surface piezoelectricity model and the generalized Young–Laplace equations. Different from the results predicted by the conventional plate theory ignoring the surface effects, the proposed model predicts size-dependent behaviours of the piezoelectric thin plate with nanoscale thickness. It is found that surface effects have significant influence on the electroelastic responses of the piezoelectric nanoplate. This work is expected to provide more accurate predictions on characterizing nanofilm or nanoribbon based piezoelectric devices in nanoelectromechanical systems.
Discrete flat surfaces and linear Weingarten surfaces in hyperbolic 3-space
Authors: Hoffmann T. , Rossman W. , Sasaki T. , Yoshida M.
Published: June 2012

We define discrete flat surfaces in hyperbolic

3
3

-space

H

3

\mathbb {H}^3

from the perspective of discrete integrable systems and prove properties that justify the definition. We show how these surfaces correspond to previously defined discrete constant mean curvature

1
1

surfaces in

H

3

\mathbb {H}^3

, and we also describe discrete focal surfaces (discrete caustics) that can be used to define singularities on discrete flat surfaces. Along the way, we also examine discrete linear Weingarten surfaces of Bryant type in

H

3

\mathbb {H}^3

, and consider an example of a discrete flat surface related to the Airy equation that exhibits swallowtail singularities and a Stokes phenomenon.
Cyclic AMP regulates formation of mammary epithelial acini in vitro
Authors: Nedvetsky Pavel I. , Kwon Sang-Ho , Debnath Jayanta , Mostov Keith E.
Published: June 2012

Epithelial cells form tubular and acinar structures notable for a hollow lumen. In three-dimensional culture utilizing MCF10A mammary epithelial cells, acini form due to integrin-dependent polarization and survival of cells contacting extracellular matrix (ECM), and the apoptosis of inner cells of acini lacking contact with the ECM. In this paper, we report that cyclic AMP (cAMP)-dependent protein kinase A (PKA) promotes acinus formation via two mechanisms. First, cAMP accelerates redistribution of α6-integrin to the periphery of the acinus and thus facilitates the polarization of outer acinar cells. Blocking of α6-integrin function by inhibitory antibody prevents cAMP-dependent polarization. Second, cAMP promotes the death of inner cells occupying the lumen. In the absence of cAMP, apoptosis is delayed, resulting in perturbed luminal clearance. cAMP-dependent apoptosis is accompanied by a posttranscriptional PKA-dependent increase in the proapoptotic protein Bcl-2 interacting mediator of cell death. These data demonstrate that cAMP regulates lumen formation in mammary epithelial cells in vitro, both through acceleration of polarization of outer cells and apoptosis of inner cells of the acinus.
Insights into structural and regulatory roles of Sec16 in COPII vesicle formation at ER exit sites
Authors: Yorimitsu Tomohiro , Sato Ken
Published: June 2012

COPII-coated buds are formed at endoplasmic reticulum exit sites (ERES) to mediate ER-to-Golgi transport. Sec16 is an essential factor in ERES formation, as well as in COPII-mediated traffic in vivo. Sec16 interacts with multiple COPII proteins, although the functional significance of these interactions remains unknown. Here we present evidence that full-length Sec16 plays an important role in regulating Sar1 GTPase activity at the late steps of COPII vesicle formation. We show that Sec16 interacts with Sec23 and Sar1 through its C-terminal conserved region and hinders the ability of Sec31 to stimulate Sec23 GAP activity toward Sar1. We also find that purified Sec16 alone can self-assemble into homo-oligomeric complexes on a planar lipid membrane. These features ensure prolonged COPII coat association within a preformed Sec16 cluster, which may lead to the formation of ERES. Our results indicate a mechanistic relationship between COPII coat assembly and ERES formation.
Major role of positive selection in the evolution of conservative segments ofDrosophilaproteins
Authors: Bazykin Georgii A. , Kondrashov Alexey S.
Published: June 2012

Slow evolution of conservative segments of coding and non-coding DNA is caused by the action of negative selection, which removes new mutations. However, the mode of selection that affects the few substitutions that do occur within such segments remains unclear. Here, we show that the fraction of allele replacements that were driven by positive selection, and the strength of this selection, is the highest within the conservative segments ofDrosophilaprotein-coding genes. The McDonald–Kreitman test, applied to the data on variation inDrosophila melanogasterand inDrosophila simulans, indicates that within the most conservative protein segments, approximately 72 per cent (approx. 80%) of allele replacements were driven by positive selection, as opposed to only approximately 44 per cent (approx. 53%) at rapidly evolving segments. Data on multiple non-synonymous substitutions at a codon lead to the same conclusion and additionally indicate that positive selection driving allele replacements at conservative sites is the strongest, as it accelerates evolution by a factor of approximately 40, as opposed to a factor of approximately 5 at rapidly evolving sites. Thus, random drift plays only a minor role in the evolution of conservative DNA segments, and those relatively rare allele replacements that occur within such segments are mostly driven by substantial positive selection.