bluuebunny/crossref_metadata_2025 huggingface dataset:
Nonequilibrium steady state transport via the reduced density matrix operator
Authors: Subotnik Joseph E. , Hansen Thorsten , Ratner Mark A. , Nitzan Abraham
Published: April 2009

We present a very simple model for numerically describing the steady state dynamics of a system interacting with continua of states representing a bath. Our model can be applied to equilibrium and nonequilibrium problems. For a one-state system coupled to two free electron reservoirs, our results match the Landauer formula for current traveling through a molecule. More significantly, we can also predict the nonequilibrium steady state population on a molecule between two out-of-equilibrium contacts. While the method presented here is for one-electron Hamiltonians, we outline how this model may be extended to include electron-electron interactions and correlations, an approach which suggests a connection between the conduction problem and the electronic structure problem.
Raman scattering in current-carrying molecular junctions
Authors: Galperin Michael , Ratner Mark A. , Nitzan Abraham
Published: April 2009

We present a theory for Raman scattering by current-carrying molecular junctions. The approach combines a nonequilibrium Green’s function (NEGF) description of the nonequilibrium junction with a generalized scattering theory formulation for evaluating the light scattering signal. This generalizes our previous study [M. Galperin and A. Nitzan, Phys. Rev. Lett. 95, 206802 (2005); J. Chem. Phys. 124, 234709 (2006)] of junction spectroscopy by including molecular vibrations and developing machinery for calculation of state-to-state (Raman scattering) fluxes within the NEGF formalism. For large enough voltage bias, we find that the light scattering signal contains, in addition to the normal signal associated with the molecular ground electronic state, also a contribution from the inverse process originated from the excited molecular state as well as an interference component. The effects of coupling to the electrodes and of the imposed bias on the total Raman scattering as well as its components are discussed. Our result reduces to the standard expression for Raman scattering in the isolated molecule case, i.e., in the absence of coupling to the electrodes. The theory is used to discuss the charge-transfer contribution to surface enhanced Raman scattering for molecules adsorbed on metal surfaces and its manifestation in the biased junction.
Diffusivity of wormlike particles in isotropic melts and the influence of local nematization
Authors: Cinacchi Giorgio , De Gaetani Luca
Published: April 2009

Systems of wormlike particles are studied by molecular dynamics computer simulations in the isotropic phase. The particles are modeled as a chain of nine soft repulsive, partially overlapping, spherical sites. These particles are characterized by a varying degree of internal flexibility: from very stiff and rodlike to very deformable and stringlike. Their self-diffusion coefficients have been evaluated at many thermodynamic conditions. Maintaining the temperature constant and sufficiently low, from the stiff rod case and letting the worms become more flexible, the self-diffusion coefficients first steeply increase, then reach a plateau. This behavior is rationalized in terms of local nematic domains. The presence of the latter significantly affects the equation of state of the wormlike particles as well, with the density of the stiffest rods being, respectively, the highest at lower temperatures and the lowest at higher temperatures. This fact might have significant implications for the theory of liquid-crystalline phase behavior in systems of flexible particles. If the density of all systems is fixed at the equilibrium value of the stiffest case, which is a way to single out the effects of flexibility, self-diffusion coefficients may exhibit a moderately nonmonotonic behavior: subsequently to the above-mentioned steep increase, they may reveal a shallow maximum for intermediate degrees of internal flexibility degrees, then gently decrease. This behavior is tentatively associated with the different effects that internal flexibility has on the average length and width of a wormlike particle.
Enhanced magnetization and polarization in chemically modified multiferroic (1−x)BiFeO3–xDyFeO3 solid solution
Authors: Zhu W.-M. , Su L. W. , Ye Z.-G. , Ren W.
Published: April 2009

In order to develop multiferroics with large magnetization and polarization, we have prepared the (1−x)BiFeO3–xDyFeO3 (BF-DF) solid solution and systematically studied its properties. A morphotropic phase transition from rhombohedral perovskite (R3c) to orthorhombic orthoferrite (Pbnm) was found at x around 0.1. The magnetic properties of BiFeO3 were improved by the introduction of Dy3+ on the perovskite A site. Chemically modified Bi0.9Dy0.1Fe1−xTixO3+x/2 ceramics by aliovalent ionic substitution of Ti4+ for Fe3+ with excess Bi2O3 exhibit weak ferromagnetism and a typical ferroelectric hysteresis loop with a large remnant polarization of 23 μC/cm2 at room temperature and a large saturated magnetization (Ms=0.5 μB/f.u.) at 2 K. These properties entitle the BF-DF solid solution one of few multiferroic materials that exhibit both decent magnetization and electric polarization.
High speed pulsed electrical spin injection in spin-light emitting diode
Authors: Truong V. G. , Binh P.-H. , Renucci P. , Tran M. , Lu Y. , Jaffrès H. , George J.-M. , Deranlot C. , Lemaître A. , Amand T. , Marie X.
Published: April 2009

We demonstrate high speed pulsed electrical spin injection from a CoFeB/MgO spin injector into a AlGaAs/GaAs semiconductor light emitting diode. Under pulsed electrical excitation, time-resolved electroluminescence on nanosecond time scale exhibits a plateau of circular polarization degree as high as 15% under a 0.8 T magnetic field. It follows an initial decay that could be due to electron spin-relaxation process in the quantum well embedded in the intrinsic region of the diode. The temporal buildup of the electronic spin polarization degree in the quantum well is much faster than the rise time of electroluminescence intensity.
A polarizer-free three step switch using distinct dye-doped liquid crystal gels
Authors: Lin Yi-Hsin , Yang Chih-Ming
Published: April 2009

A polarizer-free three step switch using distinct dye-doped liquid crystal (LC) gels is demonstrated in reflective mode. By controlling the spatial distribution of the density of polymer networks, the distinct dye-doped LC gels can produce multiple states: bright, dark, and information states without patterning indium-tin oxide. The multiple states are generated by adapting different polymer network density in different display regions. The dark state is due to the combination of scattering and absorption. It can be further extended for a four step switch. The potential applications are decorative displays, electrically tunable iris, and electrically tunable low pass or high pass filter.
Theoretical study on the dual fluorescence of 2-(4-cyanophenyl)-N,N-dimethylaminoethane and its deactivation pathway
Authors: Chen Xing , Zhao Yi , Cao Zexing
Published: April 2009

Low-lying singlet states and photophysical deactivation pathways of the electronically decoupled 2-(4-cyanophenyl)-N,N-dimethylaminoethane (PCN2NM) have been investigated by the density functional theory and CASSCF/CASPT2 approaches. PCN2NM in the ground state has two dominant configurations of the alkyl-twisted and alky-stretched structures with an interconversion barrier of 2.5 kcal/mol. The predicted vibrationally resolved weak absorption and fluorescence emission of (S1-Lb)1 exhibits clearly well-resolved vibronic features, whereas (S1-CT)1 state corresponding to the redshifted fluorescence has no fine structure. Due to the presence of low-energy (S1/S0)1CI, radiationless decay of the excited PCN2NM to the ground state is facile, once the excess energy beyond the barrier is available. Present results show reasonable agreement with experimental observations available and provide a basis for understanding of the dual fluorescence of the electronically decoupled species.
A digital control system for external magnetohydrodynamic modes in tokamak plasmas
Authors: Hanson J. M. , Klein A. J. , Mauel M. E. , Maurer D. A. , Navratil G. A. , Pedersen T. Sunn
Published: April 2009

A feedback system for controlling external, long-wavelength magnetohydrodynamic activity is described. The system is comprised of a network of localized magnetic pickup and control coils driven by four independent, low-latency field-programable gate array controllers. The control algorithm incorporates digital spatial filtering to resolve low mode number activity, temporal filtering to correct for frequency-dependent amplitude and phase transfer effects in the control hardware, and a Kalman filter to distinguish the unstable plasma mode from noise.
Direct ab initio dynamics calculations for rates and the kinetic isotope effects of multiproton transfer in ClONO2+HCl→HNO3+Cl2 reactions with water clusters: Breakdown of the rule of the geometric mean
Authors: Nam Kikyung , Kim Yongho
Published: April 2009

We performed high-level quantum mechanical calculations and direct ab initio reaction dynamics calculations for multiple proton transfers in ClONO2+HCl→HNO3+Cl2 with water clusters containing one to two water molecules, which can be used as a model of the reactions occurring on ice surface in stratospheric clouds. The energy barriers of these reactions depend on the number of water molecules involved. Two and three protons in these reactions with one and two water molecules, respectively, were transferred concertedly and asynchronously. The potential energy barrier at the MP2/6-311++(3df,3pd)//MP2/6-31G(d,p) level was 4.8 kcal/mol for the triple proton transfer involving two water molecules with a rate constant of 1.6×103 s−1 at 197 K. The potential energy curve near the saddle points was very flat and the tunneling effect on the proton transfer was negligible. The primary HH/DH kinetic isotope effect for the double proton transfer involving one water molecule was lower than unity due to the enhanced force constant at the transition state. The rule of the geometric mean for the concerted proton transfer does not hold in these reactions because the zero-point energy changes of each proton in flight at the transition state are not the same in the highly asynchronous processes.
Highly efficient and air-stable near infrared emission in erbium/bismuth codoped zeolites
Authors: Sun Hong-Tao , Hasegawa Takashi , Fujii Minoru , Shimaoka Fumiaki , Bai Zhenhua , Mizuhata Minoru , Hayashi Shinji , Deki Shigehito
Published: April 2009

We have shown that highly efficient and air-stable 1531 nm emission can be realized in erbium/bismuth codoped zeolites. The luminescence lifetime of Er3+ at 1531 nm can reach up to 4.2 ms. Bismuth compounds formed by high temperature annealing can act as blockages of selectively closing down the “in-out windows” of water molecules, i.e., Er3+ ions are sealed in a low-vibrational environment by bismuth agglomerates even when the samples contain a large amount of water. This finding may pave the way for the applications of active ions doped porous materials in infrared photonics.
Doping nanocrystals by in situ layer-by-layer overcoating
Authors: Chen Hsueh-Shih , Kumar Ramachandran Vasant , Hong Hsin-Yen
Published: April 2009

We demonstrate that internally doped nanocrystals can be obtained by an in situ overcoating process. In the case of ZnSe doped with iodine, ZnSe cores are overcoated by interlaced iodine layers and ZnSe layers to incorporate the iodine atoms into the ZnSe matrix. Photoluminescence from the ZnSe band edge is gradually depressed, while emission from the deep-level recombination caused by iodine is dramatically improved up to fourfolds with increasing number of iodine/ZnSe overcoats. This result suggests that the impurity atoms are incorporated into the host matrix.
Reconstruction of atomic force microscopy image by using nanofabricated tip characterizer toward the actual sample surface topography
Authors: Xu Mingsheng , Fujita Daisuke , Onishi Keiko
Published: April 2009

The atomic force microscopy (AFM) image is a dilation of the sample surface topography due to the finite-sized AFM tip. We accurately estimated the tip apex shape with a nanofabricated Si tip characterizer and applied the estimated tip shape function to a dilation-erosion algorithm for image reconstruction. The reconstructed images from the original AFM images attained with different AFM tips show consistent surface features and closely match the high-resolution field-emission scanning electron microscope image. The results demonstrate the reliability of our method and suggest the importance of AFM image reconstruction for a variety of technologies requiring new strategies of measuring, interpreting, manipulating, and positioning in the submicrometer and nanometer range.
Microwave phase detection at the level of 10−11 rad
Authors: Ivanov Eugene N. , Tobar Michael E.
Published: April 2009

We report on a noise measurement system with the highest spectral resolution ever achieved in the microwave domain. It is capable of detecting the phase fluctuations in rms amplitude of 2×10−11 rad/Hz at Fourier frequencies above a few kilohertz. Such precision allows the study of intrinsic fluctuations in various microwave components and materials, as well as precise tests of fundamental physics. Employing this system we discovered a previously unknown phenomenon of down-conversion of pump oscillator phase noise into the low-frequency voltage fluctuations.
Phase sensitive Brillouin scattering measurements with a novel magneto-optic modulator
Authors: Fohr F. , Serga A. A. , Schneider T. , Hamrle J. , Hillebrands B.
Published: April 2009

A recently reported phase sensitive Brillouin light scattering technique is improved by use of a magnetic modulator. This modulator is based on Brillouin light scattering in a thin ferrite film. Using this magnetic modulator in time and space Brillouin light scattering measurements, we have increased phase contrast and excluded influence of optical inhomogeneities in the sample. We also demonstrate that the quality of the resulting interference patterns can be improved by data postprocessing using the simultaneously recorded information about the reference light.
Effect of gas rarefaction on the performance of submicron fins
Authors: Ramanan Suresh , Yang Ronggui
Published: April 2009

High thermal conductivity and high surface to volume ratios of nanostructures such as carbon nanotubes and metallic nanowires make them great candidates as micro/nano-fins and thus a potential solution to the ever-increasing thermal management challenges in electronics and photonics. With sizes ranging in the order of a few hundred nanometers or less, the fluid flow through these structures fall in the transition, slip, and even molecular transport regimes. The effects of the velocity and temperature slips (gas rarefaction) could not be neglected. In this study, a simple analytical model has been developed to predict the effect of gas rarefaction on the heat transfer performance of submicron fins. It is shown that the effects of gas rarefaction should be taken into account when designing micro/nano-fins since such effects can significantly reduce the heat transfer enhancement postulated for micro/nano-fins.
Doping tuned rectifying properties in La2−xSrxCuO4/Nb:SrTiO3 heterojunctions
Authors: Guo Y. F. , Guo X. , Lei M. , Chen L. M. , Tang W. H. , Li P. G. , Fu X. L. , Li L. H.
Published: April 2009

Here, we carried out a study on strontium doping effect on the rectifying properties of La2−xSrxCuO4 (LSCO)/NSTO heterojunctions. The intimate relationship between the change in electronic structure of LSCO and the variation of diffusion potential (Vd) of the junction supports opportunities for detecting Fermi level shift and superconducting gap evolution of LSCO upon hole doping. The results agree well to generally perceived viewpoints obtained by other methods. Even the suppression of Fermi level shift in the underdoped regime and weak-coupling d-wave BCS superconductivity behavior in the overdoped regime of LSCO are clearly exhibited by the tuned rectifying behaviors. This work not only reveals rich properties of LSCO/NSTO but also opens an alternative route to monitor the Fermi level and superconducting gap of high-temperature superconductors.
Superconductivity in heavily compensated Mg-doped InN
Authors: Tiras E. , Gunes M. , Balkan N. , Airey R. , Schaff W. J.
Published: April 2009

We report superconductivity in Mg-doped InN grown by molecular beam epitaxy. Superconductivity phase transition temperature occurs Tc=3.97 K as determined by magnetoresistance and Hall resistance measurements. The two-dimensional (2D) carrier density of the measured sample is n2D=9×1014 cm−2 corresponding to a three-dimensional (3D) electron density of n3D=1.8×1019 cm−3 which is within the range of values between Mott transition and the superconductivity to metal transition. We propose a plausible mechanism to explain the existence of the superconductivity in terms of a uniform distribution of superconducting InN nanoparticles or nanosized indium dots forming microscopic Josephson junctions in the heavily compensated insulating bulk InN matrix.
Band offsets at the Ge/GeO2 interface through hybrid density functionals
Authors: Broqvist Peter , Binder Jan Felix , Pasquarello Alfredo
Published: April 2009

Band offsets of the Ge/GeO2 interface are calculated through a hybrid density functional scheme. We first generate a model of disordered GeO2 through ab initio molecular dynamics to describe the oxide component. For addressing the interface, we then consider an atomistic model in which amorphous GeO2 is connected to crystalline Ge through a suboxide transition region showing regular structural parameters. The band offsets are obtained through the application of an alignment scheme, which reproduces the experimental band gaps of the interface components. The calculated valence band offset of 3.7 eV favors the low-energy side of the range of measured offsets.
Efficiency improvement of blended poly(3-hexylthiophene) and 1-(3-methoxycarbonyl)-propyl-1-phenyl-(6,6)C61 solar cells by nanoimprinting
Authors: Shih C. F. , Hung K. T. , Wu J. W. , Hsiao C. Y. , Li W. M.
Published: April 2009

This work demonstrates the effects of nanoimprinting on poly(3-hexylthiophene) and 1-(3-methoxycarbonyl)-propyl-1-phenyl-(6,6)C61 (P3HT:PCBM)-blended organic solar cells at room temperature. Textured Si wafer was used as a stamp. Nanoimprinting significantly increased the open-circuit voltage, the short-circuit current, and the fill factor, increasing the power conversion efficiency by ∼50%. The fill factor contributed most to the cell efficiency. Upon nanoimprinting, not only the surface structure but also the applied pressure contributed to the performance of the device. The origin of the hydrostatic pressure-induced efficiency improvement was also investigated. The proposed approach has potential to be applied in the future to improve the efficiency of various organic solar cells.
Experimental and computational studies on structural transitions in the LiBH4–LiI pseudobinary system
Authors: Oguchi H. , Matsuo M. , Hummelshøj J. S. , Vegge T. , Nørskov J. K. , Sato T. , Miura Y. , Takamura H. , Maekawa H. , Orimo S.
Published: April 2009

Structural transition properties of the LiBH4+xLiI (x=0–1.00) pseudobinary system were examined by powder x-ray diffraction and differential scanning calorimetry combined with periodic density functional theory calculations. We experimentally and computationally confirmed the stabilization of the high-temperature [hexagonal, lithium super(fast-)ionic conduction] phase of LiBH4 with x=0.33 and 1.00, and the results also imply the existence of intermediate phases with x=0.07–0.20. The studies are of importance for further development of LiBH4 and the derived hydrides as solid-state electrolytes.
Transparent amorphous silicon channel waveguides with silicon nitride intercladding layer
Authors: Sun Rong , McComber Kevin , Cheng Jing , Sparacin Daniel K. , Beals Mark , Michel Jurgen , Kimerling Lionel C.
Published: April 2009

We have experimentally demonstrated single mode amorphous silicon channel waveguides with low optical transmission loss of 2.7±0.4 dB/cm for TE mode in the 1550 nm range. This result was achieved by using hydrogen passivation of a-Si dangling bonds and a thin, low loss silicon nitride intercladding layer prepared by plasma enhanced chemical vapor deposition between the waveguide core and the oxide cladding layer. The silicon nitride intercladding layer reduces waveguide sidewall roughness scattering and preserves the hydrogen passivation.
In-plane anisotropic vortex pinning and relaxation in a stripe-ordered La1.45Nd0.4Sr0.15CuO4 superconductor
Authors: Ding J. F. , Liu H. , Huang X. H. , Yin Y. W. , Yu Q. X. , Li X. G.
Published: April 2009

The angular dependence of the ac susceptibility for the magnetic field rotated in the CuO2 plane of a stripe-ordered La1.45Nd0.4Sr0.15CuO4 single crystal shows an unusual fourfold symmetry below the superconducting transition temperature (Tc). The real part of the ac susceptibility reaches its maximum for the magnetic field parallel to the stripes, and the in-plane anisotropy of the susceptibility is enhanced with increasing temperature, which indicates that the anisotropy can be ascribed to the vortex pinning of the fourfold symmetric static stripe phase. The in-plane dc magnetic relaxation rate also shows the fourfold symmetry and proves the existence of the anisotropic vortex pinning effect.
Single-crystal-like organic heterojunction with 40 nm thick charge accumulation layers
Authors: Zhu Feng , Yang Jianbing , Song De , Li Chunhong , Yan Donghang
Published: April 2009

Single-crystal-like organic heterojunction films of copper phthalocyanine (CuPc) and copper-hexadecafluoro-phthalocyanine (F16CuPc) were fabricated by weak-epitaxy-growth method. The intrinsic properties of organic heterojunction were revealed through threshold voltage shift of field-effect transistors and measurement of single-crystal-like diodes. At both sides of the heterojunction interface 40 nm thick charge accumulation layers formed, which showed that the long carriers’ diffusion length is due to the high crystallinity and low density of deep bulk traps of single-crystal-like films. This also indicated the electronic properties of organic heterojunction can be adjusted by controlling the growth condition.
Characteristics of 1.3 μm InAs/InGaAs/GaAs quantum dot electroabsorption modulator
Authors: Ngo C. Y. , Yoon S. F. , Loke W. K. , Cao Q. , Lim D. R. , Wong Vincent , Sim Y. K. , Chua S. J.
Published: April 2009

We report the characteristics of 1.3 μm electroabsorption modulators (EAMs) utilizing the InAs/InGaAs/GaAs quantum dot (QD) structures. While extinction ratio of ∼10 dB was obtained, suppression of absorption at low reverse bias was observed. Theoretical analysis using a strained-modified, single-band, constant-potential three-dimensional model shows that this is due to the presence of In0.15Ga0.85As acting as potential barrier for the heavy hole. From the device point-of-view, this suggests that InAs/InGaAs/GaAs QD-EAMs are potentially feasible for higher optical power handling capability, which is crucial for high link gain in analog fiber links. We believe that the findings are beneficial to those working on QD-EAMs.
High output power density from GaN-based two-dimensional nanorod light-emitting diode arrays
Authors: Lee Ya-Ju , Lin Shawn-Yu , Chiu Ching-Hua , Lu Tien-Chang , Kuo Hao-Chung , Wang Shing-Chung , Chhajed Sameer , Kim Jong Kyu , Schubert E. Fred
Published: April 2009

Here we propose and realize a scheme for making a direct contact to a two-dimensional nanorod light-emitting diode (LED) array using the oblique-angle deposition approach. And, more importantly, we demonstrate highly efficient electrical carrier injection into the nanorods. As a result, we show that at a 20 mA dc current injection, the light output power density of our nanorod LED array is 3700 mW cm−2. More general, this contact scheme will pave the ways for making direct contacts to other kinds of nanoscale optoelectronic devices.
Non-obese diabetic mice select a low-diversity repertoire of natural regulatory T cells
Authors: Ferreira Cristina , Singh Yogesh , Furmanski Anna L. , Wong F. Susan , Garden Oliver A. , Dyson Julian
Published: April 2009

Thymus-derived Foxp3
+
natural regulatory CD4 T cells (nTregs) prevent autoimmunity through control of pathogenic, autoreactive T cells and other immune effector cells. Using T cell receptor (TCR) transgenic models, diversity within this lineage has been found to be similar to that of conventional CD4 T cells. To determine whether balanced TCR diversity may be perturbed in autoimmunity, we have analyzed receptor composition in C57BL/6 and autoimmune non-obese diabetic (NOD) mice. The natural regulatory and conventional CD4 repertoires of C57BL/6 had similar diversities. Despite the apparently normal thymic development of the NOD nTreg lineage, TCR diversity within the selected repertoire was markedly restricted. Detailed analysis of TCRα and -β chain composition is consistent with positive selection into the natural regulatory lineage being under stringent audition for interaction with MHC class II/self-peptide. The NOD MHC region, including the unique H2-A
g7
class II molecule, partly accounts for the reduction in diversity, but additional NOD genetic contribution(s) are required for complete repertoire compaction. Mechanistic links between MHC, autoimmunity, and nTreg diversity identified in this study are discussed.
Induction of corticospinal regeneration by lentiviral trkB-induced Erk activation
Authors: Hollis Edmund R. , Jamshidi Pouya , Löw Karin , Blesch Armin , Tuszynski Mark H.
Published: April 2009

Several experimental manipulations of the CNS environment successfully elicit regeneration of sensory and bulbospinal motor axons but fail to elicit regeneration of corticospinal axons, suggesting that cell-intrinsic mechanisms limit the regeneration of this critical class of motor neurons. We hypothesized that enhancement of intrinsic neuronal growth mechanisms would enable adult corticospinal motor axon regeneration. Lentiviral vectors were used to overexpress the BDNF receptor trkB in layer V corticospinal motor neurons. After subcortical axotomy, trkB transduction induced corticospinal axon regeneration into subcortical lesion sites expressing BDNF. In the absence of trkB overexpression, no regeneration occurred. Selective deletion of canonical, trkB-mediated neurite outgrowth signaling by mutation of the Shc/FRS-2 activation domain prohibited Erk activation and eliminated regeneration. These findings support the hypothesis that the refractory regenerative state of adult corticospinal axons can be attributed at least in part to neuron-intrinsic mechanisms, and that activation of ERK signaling can elicit corticospinal tract regeneration.
Proliferation and cell fate establishment during
Arabidopsis
male gametogenesis depends on the Retinoblastoma protein
Authors: Chen Zhong , Hafidh Said , Poh Shi Hui , Twell David , Berger Frederic
Published: April 2009

The Retinoblastoma (Rb) protein is a conserved repressor of cell proliferation. In animals and plants, deregulation of Rb protein causes hyperproliferation and perturbs cell differentiation to various degrees. However, the primary developmental impact of the loss of Rb protein has remained unclear. In this study we investigated the direct consequences of Rb protein knockout in the
Arabidopsis
male germline using cytological and molecular markers. The
Arabidopsis
germ line derives from the unequal division of the microspore, producing a small germ cell and a large terminally differentiated vegetative cell. A single division of the germ cell produces the 2 sperm cells. We observed that the loss of Rb protein does not have a major impact on microspore division but causes limited hyperproliferation of the vegetative cell and, to a lesser degree, of the sperm cells. In addition, cell fate is perturbed in a fraction of Rb-defective vegetative cells. These defects are rescued by preventing cell proliferation arising from down-regulation of cyclin-dependent kinase A1. Our results indicate that hyperproliferation caused by the loss of Rb protein prevents or delays cell determination during plant male gametogenesis, providing further evidence for a direct link between fate determination and cell proliferation.
Gene encoding erythrocyte binding ligand linked to blood stage multiplication rate phenotype inPlasmodium yoelii yoelii
Authors: Pattaradilokrat Sittiporn , Culleton Richard L. , Cheesman Sandra J. , Carter Richard
Published: April 2009

Variation in the multiplication rate of blood stage malaria parasites is often positively correlated with the severity of the disease they cause. The rodent malaria parasitePlasmodium yoelii yoeliihas strains with marked differences in multiplication rate and pathogenicity in the blood. We have used genetic analysis by linkage group selection (LGS) to identify genes that determine differences in multiplication rate. Genetic crosses were generated between genetically unrelated, fast- (17XYM) and slowly multiplying (33XC) clones ofP. y. yoelii.The uncloned progenies of these crosses were placed under multiplication rate selection in blood infections in mice. The selected progenies were screened for reduction in intensity of quantitative genetic markers of the slowly multiplying parent. A small number of strongly selected markers formed a linkage group onP. y. yoeliichromosome 13. Of these, that most strongly selected marked the gene encoding theP. yoeliierythrocyte binding ligand (pyebl), which has been independently identified by Otsuki and colleagues [Otsuki H, et al. (2009)Proc Natl Acad Sci USA106:10.1073/pnas.0811313106] as a major determinant of virulence in these parasites. In an analysis of a previous genetic cross inP. y. yoelii,pyeblalleles of fast- and slowly multiplying parents segregated with the fast and slow multiplication rate phenotype in the cloned recombinant progeny, implying the involvement of thepyebllocus in determining the multiplication rate. Our genome-wide LGS analysis also indicated effects of at least 1 other locus on multiplication rate, as did the findings of Otsuki and colleagues on virulence inP. y. yoelii.
Cell–cell contact globally activates microRNA biogenesis
Authors: Hwang Hun-Way , Wentzel Erik A. , Mendell Joshua T.
Published: April 2009

MicroRNAs (miRNAs) are 18- to 24-nt RNA molecules that regulate messenger RNAs (mRNAs). Posttranscriptional mechanisms regulate miRNA abundance during development as well as in cancer cells where miRNAs frequently exhibit dysregulated expression. The molecular mechanisms that govern the global efficiency of miRNA biogenesis in these settings remain incompletely understood, and experimental systems for the biochemical dissection of these pathways are currently lacking. Here, we demonstrate that miRNAs are subject to dynamic posttranscriptional regulation in widely used cell culture systems. As diverse mammalian and
Drosophila
cell lines are grown to increasing density, miRNA biogenesis is globally activated, leading to elevated mature miRNA levels and stronger repression of target constructs. This broad increase in miRNA abundance is associated with enhanced processing of miRNAs by Drosha and more efficient formation of RNA-induced silencing complexes. These findings uncover a critical parameter necessary for accurate analysis of miRNAs in cell culture settings, establish a tractable system for the study of regulated miRNA biogenesis, and may provide insight into mechanisms that influence miRNA expression in physiologic and pathophysiologic states.
De novo design and in vivo activity of conformationally restrained antimicrobial arylamide foldamers
Authors: Choi Sungwook , Isaacs Andre , Clements Dylan , Liu Dahui , Kim Hyemin , Scott Richard W. , Winkler Jeffrey D. , DeGrado William F.
Published: April 2009

The emergence of drug-resistant bacteria has compromised the use of many conventional antibiotics, leading to heightened interest in a variety of antimicrobial peptides. Although these peptides have attractive potential as antibiotics, their size, stability, tissue distribution, and toxicity have hampered attempts to harness these capabilities. To address such issues, we have developed small (molecular mass <1,000 Da) arylamide foldamers that mimic antimicrobial peptides. Hydrogen-bonded restraints in the arylamide template rigidify the conformation via hydrogen bond formation and increase activity toward
Staphylococcus aureus
and
Escherichia coli
. The designed foldamers are highly active against
S. aureus
in an animal model. These results demonstrate the application of foldamer templates as therapeutics.
Small interfering RNA-induced TLR3 activation inhibits blood and lymphatic vessel growth
Authors: Cho Won Gil , Albuquerque Romulo J. C. , Kleinman Mark E. , Tarallo Valeria , Greco Adelaide , Nozaki Miho , Green Martha G. , Baffi Judit Z. , Ambati Balamurali K. , De Falco Massimo , Alexander Jonathan S. , Brunetti Arturo , De Falco Sandro , Ambati Jayakrishna
Published: April 2009

Neovascularization in response to tissue injury consists of the dual invasion of blood (hemangiogenesis) and lymphatic (lymphangiogenesis) vessels. We reported recently that 21-nt or longer small interfering RNAs (siRNAs) can suppress hemangiogenesis in mouse models of choroidal neovascularization and dermal wound healing independently of RNA interference by directly activating Toll-like receptor 3 (TLR3), a double-stranded RNA immune receptor, on the cell surface of blood endothelial cells. Here, we show that a 21-nt nontargeted siRNA suppresses both hemangiogenesis and lymphangiogenesis in mouse models of neovascularization induced by corneal sutures or hindlimb ischemia as efficiently as a 21-nt siRNA targeting vascular endothelial growth factor-A. In contrast, a 7-nt nontargeted siRNA, which is too short to activate TLR3, does not block hemangiogenesis or lymphangiogenesis in these models. Exposure to 21-nt siRNA, which we demonstrate is not internalized unless cell-permeating moieties are used, triggers phosphorylation of cell surface TLR3 on lymphatic endothelial cells and induces apoptosis. These findings introduce TLR3 activation as a method of jointly suppressing blood and lymphatic neovascularization and simultaneously raise new concerns about the undesirable effects of siRNAs on both circulatory systems.
Using photons to manipulate enzyme inhibition by an azobenzene-modified nucleic acid probe
Authors: Kim Youngmi , Phillips Joseph A. , Liu Haipeng , Kang Huaizhi , Tan Weihong
Published: April 2009

The ability to inhibit an enzyme in a specific tissue with high spatial resolution combined with a readily available antidote should find many biomedical applications. We have accomplished this by taking advantage of the
cis–trans
photoisomerization of azobenzene molecules. Specifically, we positioned azobenzene moieties within the DNA sequence complementary to a 15-base-long thrombin aptamer and then linked the azobenzene-modified cDNA to the aptamer by a polyethylene glycol (PEG) linker to make a unimolecular conjugate. During the photoisomerization of azobenzene by visible light, the inhibition of thrombin is disabled because the probe hybridizes with the cDNA in the
trans
-azobenzene conformation so that the aptamer cannot bind its target thrombin. However, when UV light is applied, melting of the hairpin structure (duplex) is induced via
trans-
to-
cis
conversion, thereby changing conformation of the aptamer and making the aptamer free to bind to and inhibit its target thrombin. By using standard clotting assays, we measured the IC
200
of various probe designs in both states and concluded the feasibility of using photon energy to temporally and spatially regulate these enzymatic reactions. Thus, we can report the development of DNA probes in the form of photon-controllable (thrombin) inhibitors, termed PCIs, and we expect that this approach will be highly beneficial in future biomedical and pharmaceutical applications.
p21-Activated kinase mediates rapid estradiol-negative feedback actions in the reproductive axis
Authors: Zhao Zhen , Park Cheryl , McDevitt Melissa A. , Glidewell-Kenney Christine , Chambon Pierre , Weiss Jeffrey , Jameson J. Larry , Levine Jon E.
Published: April 2009

Nonclassical estrogen receptor α (ERα) signaling can mediate E
2
negative feedback actions in the reproductive axis; however, downstream pathways conveying these effects remain unclear. These studies tested the hypothesis that p21-activated kinase 1 (PAK1), a serine/threonine kinase rapidly activated by E
2
in nonneural cells, functions as a downstream node for E
2
signaling pathways in cells of the preoptic area, and it may thereby mediate E
2
negative feedback effects. Treatment of ovariectomized (OVX) rats with estradiol benzoate (EB) caused rapid and transient induction of phosphorylated PAK1 immunoreactivity in the medial preoptic nucleus (MPN) but not the arcuate nucleus. To determine whether rapid induction of PAK phosphorylation by E
2
is mediated by nonclassical [estrogen response element (ERE)-independent] ERα signaling, we used female ERα null (ERα
−/−
) mice possessing an ER knock-in mutation (E207A/G208A; AA), in which the mutant ERα is incapable of binding DNA and can signal only through membrane-initiated or ERE-independent genotropic pathways (ERα
−/AA
mice). After 1-h EB treatment, the number of pPAK1-immunoreactive cells in the MPN was increased in both wild-type (ERα
+/+
) and ERα
−/AA
mice but was unchanged in ERα
−/−
mice. Serum luteinizing hormone (LH) was likewise suppressed within 1 h after EB treatment in ERα
+/+
and ERα
−/AA
but not ERα
−/ −
mice. In OVX rats, 5-min intracerebroventricular infusion of a PAK inhibitor peptide but not control peptide blocked rapid EB suppression of LH secretion. Taken together, our findings implicate PAK1 activation subsequent to nonclassical ERα signaling as an important component of the negative feedback actions of E
2
in the brain.
Fermi surface nesting induced strong pairing in iron-based superconductors
Authors: Terashima K. , Sekiba Y. , Bowen J. H. , Nakayama K. , Kawahara T. , Sato T. , Richard P. , Xu Y.-M. , Li L. J. , Cao G. H. , Xu Z.-A. , Ding H. , Takahashi T.
Published: April 2009

The discovery of high-temperature superconductivity in iron pnictides raised the possibility of an unconventional superconducting mechanism in multiband materials. The observation of Fermi-surface (FS)-dependent nodeless superconducting gaps suggested that inter-FS interactions may play a crucial role in superconducting pairing. In the optimally hole-doped Ba
0.6
K
0.4
Fe
2
As
2
, the pairing strength is enhanced simultaneously (2Δ/T
c
≈7) on the nearly nested FS pockets, i.e., the inner hole-like (α) FS and the 2 hybridized electron-like FSs, whereas the pairing remains weak (2Δ/T
c
≈3.6) in the poorly nested outer hole-like (β) FS. Here, we report that in the electron-doped BaFe
1.85
Co
0.15
As
2
, the FS nesting condition switches from the α to the β FS due to the opposite size changes for hole- and electron-like FSs upon electron doping. The strong pairing strength (2Δ/T
c
≈6) is also found to switch to the nested β FS, indicating an intimate connection between FS nesting and superconducting pairing, and strongly supporting the inter-FS pairing mechanism in the iron-based superconductors.
Mechanisms of chiral discrimination by topoisomerase IV
Authors: Neuman K. C. , Charvin G. , Bensimon D. , Croquette V.
Published: April 2009

Topoisomerase IV (Topo IV), an essential ATP-dependent bacterial type II topoisomerase, transports one segment of DNA through a transient double-strand break in a second segment of DNA. In vivo, Topo IV unlinks catenated chromosomes before cell division and relaxes positive supercoils generated during DNA replication. In vitro, Topo IV relaxes positive supercoils at least 20-fold faster than negative supercoils. The mechanisms underlying this chiral discrimination by Topo IV and other type II topoisomerases remain speculative. We used magnetic tweezers to measure the relaxation rates of single and multiple DNA crossings by Topo IV. These measurements allowed us to determine unambiguously the relative importance of DNA crossing geometry and enzymatic processivity in chiral discrimination by Topo IV. Our results indicate that Topo IV binds and passes DNA strands juxtaposed in a nearly perpendicular orientation and that relaxation of negative supercoiled DNA is perfectly distributive. Together, these results suggest that chiral discrimination arises primarily from dramatic differences in the processivity of relaxing positive and negative supercoiled DNA: Topo IV is highly processive on positively supercoiled DNA, whereas it is perfectly distributive on negatively supercoiled DNA. These results provide fresh insight into topoisomerase mechanisms and lead to a model that reconciles contradictory aspects of previous findings while providing a framework to interpret future results.
First-principles design of nanomachines
Authors: Banavar Jayanth R. , Cieplak Marek , Hoang Trinh Xuan , Maritan Amos
Published: April 2009

Learning from nature's amazing molecular machines, globular proteins, we present a framework for the predictive design of nanomachines. We show that the crucial ingredients for a chain molecule to behave as a machine are its inherent anisotropy and the coupling between the local Frenet coordinate reference frames of nearby monomers. We demonstrate that, even in the absence of heterogeneity, protein-like behavior is obtained for a simple chain molecule made up of just 30 hard spheres. This chain spontaneously switches between 2 distinct geometries, a single helix and a dual helix, merely because of thermal fluctuations.
Synthetic and structural studies on syringolin A and B reveal critical determinants of selectivity and potency of proteasome inhibition
Authors: Clerc Jérôme , Groll Michael , Illich Damir J. , Bachmann André S. , Huber Robert , Schellenberg Barbara , Dudler Robert , Kaiser Markus
Published: April 2009

Syrbactins, a family of natural products belonging either to the syringolin or glidobactin class, are highly potent proteasome inhibitors. Although sharing similar structural features, they differ in their macrocyclic lactam core structure and exocyclic side chain. These structural variations critically influence inhibitory potency and proteasome subsite selectivity. Here, we describe the total synthesis of syringolin A and B, which together with enzyme kinetic and structural studies, allowed us to elucidate the structural determinants underlying the proteasomal subsite selectivity and binding affinity of syrbactins. These findings were used successfully in the rational design and synthesis of a syringolin A-based lipophilic derivative, which proved to be the most potent syrbactin-based proteasome inhibitor described so far. With a
K
i
′ of 8.65 ± 1.13 nM for the chymotryptic activity, this syringolin A derivative displays a 100-fold higher potency than the parent compound syringolin A. In light of the medicinal relevance of proteasome inhibitors as anticancer compounds, the present findings may assist in the rational design and development of syrbactin-based chemotherapeutics.
Body branded
Authors: Caldas-Coulthard Carmen Rosa
Published: April 2009

Using a discursive/social semiotic perspective, tourism advertising is here investigated as a global discourse worth of critical investigation. Different identities are construed in texts for tourists and they are not purely reflections of personal identities. They are recontextualisations whose realisations and forms are conditioned by the social practices of the advertisers and by their stereotypical views of the countries being advertised. Gender representation is a key factor and the use of the human body, as a branding strategy, is an essential part in the construction of such identities. Exemplifying from tourism brochures and web pages, my aims are to discuss the different types of identities construed in the discourse, the way the representation of the human body is used as a semiotic resource and as a branding strategy, and the values which underlie the appeal to possible travellers and the implications of the branding strategies for gender representation.
Pure ovarian choriocarinoma mimicking ectopic pregnancy in true hermaphroditism
Authors: WANG DANQING , HU YAYI , HE YING , XIE CONG , YIN RUTIE
Published: April 2009

Ovarian choriocarinoma is a rare tumor and has not been described before in a true hermaphrodite condition. A 23‐year‐old karyotype 46XX parous female was admitted to hospital because of amenorrhea, irregular vaginal bleeding, an adnexal mass, and an increased β‐hCG serum level. Ectopic pregnancy was suspected three times and exploratory laparoscopy done each time removing the right ovarian mass and local pelvic and omental spread. Final pathology revealed a true hermaphrodite state with testicular tissue with distinct tubules, ovarian tissue with follicles, and ovarian choriocarinoma with necrosis and hemorrhage. She received chemotherapy followed by radical pelvic surgery.
Optimization of the chemical composition and manufacturing route for ODS RAF steels for fusion reactor application
Authors: Oksiuta Z. , Baluc N.
Published: April 2009

As the upper temperature for use of reduced activation ferritic/martensitic steels is presently limited by a drop in mechanical strength at about 550 °C, Europe, Japan and the US are actively researching steels with high strength at higher operating temperatures, mainly using stable oxide dispersion. In addition, the numerous interfaces between matrix and oxide particles are expected to act as sinks for the irradiation-induced defects. The main R&D activities aim at finding a compromise between good tensile and creep strength and sufficient ductility, especially in terms of fracture toughness. Oxide dispersion strengthened (ODS) reduced activation ferritic (RAF) steels appear as promising materials for application in fusion power reactors up to about 750 °C. Six different ODS RAF steels, with compositions of Fe–(12–14)Cr–2W–(0.1–0.3-0.5)Ti–0.3Y2O3 (in wt%), were produced by powder metallurgy techniques, including mechanical alloying, canning and degassing of the milled powders and compaction of the powders by hot isostatic pressing, using various devices and conditions. The materials have been characterized in terms of microstructure and mechanical properties. The results have been analysed in terms of optimal chemical composition and manufacturing conditions. In particular, it was found that the composition of the materials should lie in the range Fe–14Cr–2W–(0.3–0.4)Ti–(0.25–0.3)Y2O3, as 14Cr ODS RAF steels exhibit higher tensile strength and better Charpy impact properties and are more stable than 12Cr materials (no risk of martensitic transformation), while materials with 0.5% Ti or more should not be further investigated, due to potential embrittlement by large TiO2 particles.