bluuebunny/crossref_metadata_2025 huggingface dataset:
Expression of human tissue plasminogen activator in the trypanosomatid protozoan Leishmania tarentolae
Authors: Soleimani Mohammad , Mahboudi Fereidoun , Davoudi Noushin , Amanzadeh Amir , Azizi Mohammad , Adeli Ahmad , Rastegar Hossein , Barkhordari Farzaneh , Mohajer‐Maghari Behrokh
Published: August 2007

A variety of recombinant protein expression systems have been developed for heterologous genes in both prokaryotic and eukaryotic systems such as bacteria, yeast, mammals, insects, transgenic animals and transgenic plants. Also, it has been reported that Leishmania tarentolae, a trypanosomatid protozoan parasite of the white‐spotted wall gecko (Tarentola annularis), has the capability of expressing heterologous genes. Trypanosomatidae are rich in glycoproteins, which can account for more than 10% of total protein. The oligosaccharide structures of their glycoproteins are similar to those of mammals with N‐linked galactose, and sialic acid residues. For a variety of reasons, including the glycosylation patterns and the secondary structures of some of these proteins, synthesis in eukaryotic system is highly preferable. In addition, formation of native disulfide bonds in complex eukaryotic proteins is tremendously important. In the present study, we tried to express the tPA (tissue plasminogen activator) gene in L. tarentolae. This protein is a thrombolytic agent with 527 amino acid residues. tPA possesses serine‐protease activity, with 35 cysteine residues that participate in the formation of 17 disulfide bonds. We have used an expression cassette, including the α intergenic regions of Leishmania major and two sites at the 3′‐ and 5′‐ends, for homologous recombination in L. tarentolae, in addition to antibiotic‐resistant genes. Southern‐blot analysis showed that the human tPA gene had been inserted into the genome of the parasite. The expression of the tPA at the mRNA and protein levels was confirmed. It was shown that the expressed tPA in this system was 70 i.u. (international units)/ml of culture media, which is much higher than levels reported previously in other systems.
A highly efficient method for the generation of a recombinant Bombyx mori nuclear‐polyhedrosis‐virus Bacmid and large‐scale expression of foreign proteins in silkworm (B. mori) larvae
Authors: Yao Lun Guang , Liu Zong Cai , Zhang Xiang Man , Kan Yun Chao , Zhou Jing‐Jiang
Published: August 2007

In the post‐genomic era, one of the challenges and a source of competition is the development of high‐throughput, large‐scale and low‐cost eukaryotic cDNA cloning and expression systems. The baculovirus expression system is the most popular one and plays an important role in the high‐level expression of eukaryotic proteins. In the present study, a convenient, rapid and highly efficient method for the construction of recombinant BmNPV (Bombyx mori nuclear polyhedrosis virus)‐Bacmid vector (BmBacmid) for low‐cost protein expression in silkworm (B. mori) larvae was established by using the MAGIC (mating‐assisted genetically integrated cloning) strategy. By simply mixing the donor bacteria strain containing the constructed donor vector pCTdual harbouring foreign genes and the recipient strain containing modified BmBacmid, 99.8% positive recombinant BmNPV‐Bacmids were obtained. Reporter genes egfp (enhanced green fluorescent protein gene) and DsRed (Discosoma sp. red fluorescent protein gene) and target gene man (β‐mannanase gene) encoding β‐mannanase were expressed in the silkworm larvae of B. mori at high level by injection of recombinant BmBacmid DNA directly with the standard calcium phosphate transfection procedure. The possibility of constructing a high‐quality baculovirus cDNA library by transferring an ordinal plasmid cDNA library into the recipient BmBacmid in Escherichia coli was explored.
Reaction pathways and excited states in H2O2+OH→HO2+H2O: A new ab initio investigation
Authors: Ginovska Bojana , Camaioni Donald M. , Dupuis Michel
Published: August 2007

The mechanism of the hydrogen abstraction reaction H2O2+OH→HO2+H2O in gas phase was revisited using density functional theory and other highly correlated wave function theories. We located two pathways for the reaction, both going through the same intermediate complex OH–H2O2, but via two distinct transition state structures that differ by the orientation of the hydroxyl hydrogen relative to the incipient hydroperoxy hydrogen. The first two excited states were calculated for selected points on the pathways. An avoided crossing between the two excited states was found on the product side of the barrier to H transfer on the ground state surface, near the transition states. We report on the calculation of the rate of the reaction in the gas phase for temperatures in the range of 250–500K. The findings suggest that the strong temperature dependence of the rate at high temperatures is due to reaction on the low-lying excited state surface over a barrier that is much larger than on the ground state surface.
Local heat fluxes in turbulent Rayleigh-Bénard convection
Authors: Shishkina Olga , Wagner Claus
Published: August 2007

The vertical turbulent heat flux Ω in Rayleigh-Bénard convection, its spatial distribution, and some mean characteristics are investigated by means of direct numerical simulations for the Rayleigh numbers Ra=106 and 107 and well resolved large-eddy simulations for Ra=108. All simulations were performed for Prandtl number Pr=0.7 and aspect ratio of a cylindrical container Γ=5. Analyzing the spatial distribution of Ω, it is shown that the fluid volume with negative Ω values increases with Ra and reaches one-third of the total volume for Ra=108. The spread in the local heat flux values expands with increasing distance from the top or the bottom plates. For example, for Ra=107, about 31% and 19% of the center horizontal cross section reflects, respectively, negative and large positive (⩾2Nu) values of Ω, while at the plates the local heat flux values vary basically between 0 and 2Nu. Further, it is shown that with growing Rayleigh numbers, the zones of higher values of the time-averaged local heat flux move toward the corners, where horizontal and vertical walls intersect. Analytical relations between the components of Ω and the thermal dissipation rates, proven in the paper, show that the square root of the thermal dissipation rate describes well the spatial distribution of the local heat transport close to the top or the bottom plates.
Linear stability of a two-layer film flow down an inclined channel: A second-order weighted residual approach
Authors: Amaouche M. , Mehidi N. , Amatousse N.
Published: August 2007

Our interest is with the long-wavelength instability in a two-dimensional gravity-driven flow of two superposed, incompressible, immiscible, and viscous fluids bounded by an upper and a lower rigid plate. Approximate boundary-layer-like equations valid up to second order in the channel width-to-wavelength ratio are first derived. An extension of the weighted residual approach first suggested by Ruyer-Quil and Manneville [Eur. Phys. J. B 15, 357 (2000)] to model the single-layer flow is then presented. It is shown that a suitable choice of trial and weighted functions allows us to lower appreciably the dimensionality of the problem. Marginal stability results clearly indicate that unlike the Shkadov approach, which gives erroneous critical conditions, the proposed second-order model, its simplified version corresponding to parabolic velocity profiles and referred to as the one-mode Galerkin approach, and the lubrication theory (long wave expansion procedure) are all in good agreement with the Orr-Sommerfeld equations near criticality where the viscous effects are dominant. The one-mode Galerkin model is therefore sufficient to correctly predict the near-critical behavior of the long wave interfacial mode. As inertia increases, the lubrication theory provides results that diverge. The Shkadov approach gives bad results as well while the second-order weighted residual model and its simplified version continue to follow the numerical results up to moderate Reynolds numbers, the approximation being better for the former than for the latter.
Resonance energy transfer: Spectral overlap, efficiency, and direction
Authors: Andrews David L. , Rodríguez Justo
Published: August 2007

The efficiency and directedness of resonance energy transfer, by means of which electronic excitation passes between molecular units or subunits, fundamentally depend on the spectral features of donor and acceptor components. In particular, the flow of energy between chromophores in complex energy harvesting materials is crucially dependent on a spectral overlap integral reflecting the relative positioning and shapes of the absorption and fluorescence bands. In this paper, analytical results for this integral are derived for bands of Gaussian and log normal line shape; the methods also prove applicable to double Gaussian curves under suitable conditions. Underlying principles have been ascertained through further development of theory, with physically reasonable assumptions. Consideration of the Gaussian case, widely applicable to spectra of symmetric form, reveals that the directional efficiency of energy transfer depends equally on a frequency shift characterizing the spectroscopic gradient and the Stokes shift. On application to tryptophan residues, calculations based on a minimal parameter set give excellent agreement with experiment. Finally, an illustrative application highlights the critical role that the spectroscopic gradient and Stokes shift can exercise in extended, multichromophore energy harvesting systems.
A stabilized finite element method for global analysis of convective instabilities in nonparallel flows
Authors: Mittal Sanjay , Kumar Bhaskar
Published: August 2007

A new scheme for the global analysis of convective instabilities in nonparallel flows is proposed. The linearized perturbation equations for an incompressible flow are written in a moving frame of reference that travels with the perturbation. In the moving frame, the base flow varies with time. However, at t=0, it is the same as the one in the stationary frame. Therefore, this analysis for determining the global convective instability is valid in an instantaneous sense. A stabilized finite element method is utilized to discretize these equations. A subspace iteration procedure is utilized to solve the resulting generalized eigenvalue problem. The scheme is applied to assess the stability of uniform flow past a circular cylinder. The critical Re for the onset of convective instability is found to be approximately 4. The results are in excellent agreement with the direct numerical simulation of the linearized flows equations. Unlike local analysis, the proposed method gives the global eigenmode and the corresponding growth rate.
Continuing nonlinear growth of Tollmien-Schlichting waves
Authors: Lifshitz Yuli , Degani David
Published: August 2007

This brief paper is concerned with the effect of mean flow distortions on spatially growing Tollmien-Schlichting waves in the Blasius boundary layer. It is shown that the coherent Reynolds stresses arising from the waves affect the mean flow by tending to reverse the sign of the cross-stream derivative of vorticity in the critical layer. If the wave amplitude is high enough to initiate the reversal, it further contributes to the wave amplification. That, in turn, increases the region of the vorticity derivative with opposite sign.
Structural relaxation of an unentangled polymer in terms of a simple phenomenological approach
Authors: Andreozzi Laura , Autiero Ciro , Faetti Massimo , Zulli Fabio
Published: August 2007

The enthalpy relaxation mechanism of a low molecular weight synthesis of polymethylmethacrylate was investigated by means of calorimetric experiments. The data were analyzed in terms of a kinetic approach treating nonlinearity in a different manner with respect to the Tool-Narayanaswamy-Moynihan model. The relaxation isotherms recorded at four different temperatures were well reproduced by this approach that, however, failed in describing the relaxation asymmetry towards the equilibrium after opposite temperature jumps. A modification of the model was proposed with an additional free parameter accounting for the stretching of the relaxation function. In this way all the experimental data were reproduced fairly well.
Two staged laser acceleration with a static magnetic field
Authors: Chen Z. , Ho Y. K. , Kong Q. , Wang P. X. , Wang W. , Xu J. J.
Published: August 2007

The use of a static magnetic field with a modest intensity in the conventional vacuum laser acceleration scheme has been investigated. It has been found that the applied magnetic field can break the symmetry of the laser acceleration and deceleration phases experienced by the electrons after they leave the focal region, allowing the electrons to be accelerated in the focal region to gain more energy from the combined fields of the laser and the static magnetic field. The later process is the second stage acceleration taking place in the region outside the laser focal area. Explanations of these interaction features based on analytical calculations and simulations are presented.
Paramagnetic defects and amorphous network reconstruction of magnetron sputtered a-SiO2:Ge films
Authors: Pereira R. N. , Skov Jensen J. , Chevallier J. , Bech Nielsen B. , Nylandsted Larsen A.
Published: August 2007

We have investigated the paramagnetic defects and the structure of magnetron sputtered amorphous SiO2 films containing 3.8at.% Ge (a-SiO2:Ge) over the 500–1000°C annealing temperature range using electron paramagnetic resonance (EPR), Fourier-transform infrared (FTIR) absorption, and transmission electron microscopy (TEM). The EPR spectra of as-grown a-SiO2:Ge films reveal three different defects: Si-E′ centers with g‖=2.0019 and g⊥=2.0004, •Ge≡Si3 dangling bonds with g‖=2.001 and g⊥=2.024, and •Si≡Si2O or •Si≡SiO2 defects with g=2.004. While the Si-E′ and g=2.004 lines are removed by heat treatments at 500°C, the signal from •Ge≡Si3 dangling bonds persists up to annealing temperatures of 700°C. The structural changes induced upon annealing on the a-SiO2:Ge films have been studied by monitoring the frequency and linewidth of the asymmetric stretching vibration of the Si–O–Si linkage using FTIR. We find that the rearrangement of the amorphous oxide network occurs primarily within the 500–700°C temperature range and no further significant recovery happens upon annealing at temperatures above 700°C, in line with the EPR results. TEM images reveal the formation of Ge nanocrystals (Ge ncs) with diameters of 2–4nm already upon heat treatments at 500°C. Moreover, it is shown that the mean size of the Ge ncs increases quite significantly as the temperature of the heat treatments increases. The mean diameter of Ge ncs observed after annealing at temperatures above 600°C is above that expected for Ge ncs with efficient photoluminescence properties. The implications of our experimental results for the understanding of the quenching of the photoluminescence from quantum-confined excitons within Ge ncs are briefly discussed.
Control of polarization and mode mapping of small volume high Q micropillars
Authors: Daraei A. , Sanvitto D. , Timpson J. A. , Fox A. M. , Whittaker D. M. , Skolnick M. S. , Guimarães P. S. S. , Vinck H. , Tahraoui A. , Fry P. W. , Liew S. L. , Hopkinson M.
Published: August 2007

We show that the polarization of the emission of a single quantum dot embedded within a microcavity pillar of elliptical cross section can be completely controlled and even switched between two orthogonal linear polarizations by changing the coupling of the dot emission with the polarized photonic modes. We also measure the spatial profile of the emission of a series of pillars with different ellipticities and show that the results can be well described by simple theoretical modeling of the modes of an infinite length elliptical cylinder.
Angle-resolved absolute out-of-band radiation studies of a tin-based laser-produced plasma source
Authors: Morris O. , Hayden P. , O’Reilly F. , Murphy N. , Dunne P. , Bakshi V.
Published: August 2007

Out-of-band radiation emitted from an extreme ultraviolet laser-produced plasma, formed on a solid tin target, was measured over several angles between 25° and 85° with respect to the target normal for six energy bands between 200 and 1000nm. The optical and target system was rotated with respect to the detector and the intensity of the radiation was measured using an absolutely calibrated filter/photodiode combination. The emission was dominated by radiation in the 214nm band. A cosine function fitted to the angular distribution of the total radiation yielded an exponent of 0.23±0.02.
Photovoltaic and photoconductivity effect in thin-film phototransistors based on a heterocyclic spiro-type molecule
Authors: Saragi Tobat P. I. , Londenberg Joscha , Salbeck Josef
Published: August 2007

We reported on photovoltaic and photoconductivity effects as the underlying mechanism in thin-film phototransistors based on 2,2′,6,6′-Tetraphenyl-4,4′-spirobi[cyclopenta[2,1-b;3,4-b′]dithiophene]. The responsivity and the ratio of photocurrent to dark current were 25 A/W and 290, respectively. Our devices also exhibited a field-effect mobility of (1−2)×10−4 cm2∕V s and an ON/OFF ratio of ∼103. Hysteresis in the transfer curve was observed after the curves were measured from the ON-state to the OFF-state and vice versa. In this case, the gate voltage (at drain bias −20 V and drain current −1 nA) shifted by 8 V at an optical power of ∼20 μW.
La 0.8 Sr 0.2 MnO 3 buffer layer effects on microstructure, leakage current, polarization, and magnetic properties of BiFeO3 thin films
Authors: Habouti S. , Shiva R. K. , Solterbeck C-H. , Es-Souni M. , Zaporojtchenko V.
Published: August 2007

BiFeO 3 thin films were processed on La0.8Sr0.2MnO3 (LSMO) buffered silicon substrate via chemical solution deposition. Short-wave ultraviolet assisted pyrolysis was conducted in oxygen atmosphere in order to improve microstructure. A fine, homogeneous, and phase-pure grain structure with smooth topography was obtained. X-ray photoelectron spectroscopy analysis indicates diffusion of lanthanum and manganese from LSMO into the BiFeO3 film leading to a diffuse interface. Nevertheless, improved polarization and leakage resistance properties were obtained. For the first time polarization switching was obtained in sol-gel BiFeO3 films using capacitance-voltage (C−V) curves. This has been imputed to homogeneous local electrical properties of the film, corroborated by surface scanning potential microscopy investigations. The leakage current mechanisms were investigated as function of temperature, and could be interpreted in terms of the Frenkel-Poole mechanism with a trap depth of 1.6 eV. Finally, the magnetic properties of the LSMO∕BiFeO3 heterostructure are presented in comparison to those of BiFeO3 on platinized silicon. An exchange coupling between BiFeO3 and LSMO layers is suggested.
Effect of interlayer strain interaction on the island composition and ordering in Ge/Si(001) island superlattices
Authors: De Seta M. , Capellini G. , Evangelisti F. , Ferrari C. , Lazzarini L. , Salviati G. , Peng R. W. , Jiang S. S.
Published: August 2007

In this article we present a quantitative study of the influence of the number and the thickness of the silicon spacer layer on the optical and structural properties of single and multilayers of self-assembled Ge/Si(001) islands. By means of cathodoluminescence spectroscopy, high resolution x-ray diffraction, and transmission electron microscopy, we will show that the island composition and strain status of single-layer samples do not depend on the silicon cap-layer thickness. On the contrary, we found that the strain interaction existing between island layers separated by a silicon spacer layer 33 nm thick (i.e., ∼3 times the mean island height), enhances the SiGe intermixing during the deposition of subsequent layers bringing to a composition inhomogeneity of the intermixed islands of about 18% along the stack. This inhomogeneity is not present in samples having a thicker spacer layer (60 nm) although the strain interaction between different layers is strong enough to drive the island stacking along the vertical direction. We conclude that the latter spacer layer thickness allows us to obtain a highly ordered three-dimensional superlattice of an island having a homogeneous size and composition along the stack itself.
Semiclassical initial value calculations of the collinear helium atom
Authors: Harabati C. , Kay K. G.
Published: August 2007

Semiclassical calculations using the Herman-Kluk initial value treatment are performed to determine energy eigenvalues of bound and resonance states of the collinear helium atom. Both the eZe configuration (where the classical motion is fully chaotic) and the Zee configuration (where the classical dynamics is nearly integrable) are treated. The classical motion is regularized to remove singularities that occur when the electrons collide with the nucleus. Very good agreement is obtained with quantum energies for bound and resonance states calculated by the complex rotation method.
Theoretical analysis of breakdown probabilities and jitter in single-photon avalanche diodes
Authors: Tan S. L. , Ong D. S. , Yow H. K.
Published: August 2007

A simple random ionization path length model is used to investigate the breakdown probabilities and jitter in single photon avalanche diodes (SPADs) with submicron multiplication widths. The simulation results show that increasing the multiplication width may not necessarily increase the breakdown probability relative to the breakdown voltage, as the effect of dead space becomes more dominant in thinner multiplication regions at realistic ionization threshold energies for GaAs. On the other hand, reducing the multiplication width results in smaller breakdown time and jitter, despite the increased dead space. The effect of dead space in degrading breakdown time and jitter is relatively weak and further compensated by the stronger influence of large feedback ionization at high fields. Thus, SPAD designs that can minimize the dark count rate may potentially benefit from enhanced breakdown probability, breakdown time, and jitter by reducing the thickness of the multiplication region.
Control of in-plane and out-of-plane texture in shear mode piezoelectric ZnO films by ion-beam irradiation
Authors: Yanagitani Takahiko , Kiuchi Masato
Published: August 2007

ZnO polycrystalline films have a strong tendency to grow their c-axis perpendicular to the film surface, even on an amorphous substrate. However, unusual (101¯0) preferred orientations in which the c-axis lies in the substrate plane are often observed when the film is exposed to ion irradiation during its growth. To investigate the effect of ion irradiation on the (101¯0) preferred orientation, ZnO films were fabricated using a 0–1 keV oxygen ion-beam-assisted electron-beam evaporation of zinc. The results clearly indicated that the tendency of (101¯0) preferred orientation was enhanced with increasing ion energy and amount of ion irradiation. This demonstrated that the ion bombardment induced the (0001) preferred orientation to change into a (101¯0) preferred orientation which corresponds to the ion channeling direction. An in-plane preferred orientation was also obtained, probably because of deviations in the incident ion-beam direction from 5° to the substrate surface normal. These in-plane textured (101¯0) ZnO films, fabricated under the ion-beam irradiation of 0.5–1 keV, excited a shear acoustic wave without any longitudinal wave. The highest shear mode electromechanical coupling coefficient was found to be k15=0.16 in the film with ion-beam irradiation of 1 keV. This k15 value corresponds to 60% of that in a ZnO single crystal (k15=0.26).
Role of oxygen desorption during vacuum annealing in the improvement of electrical properties of aluminum doped zinc oxide films synthesized by sol gel method
Authors: Zhu Mingwei , Huang Hui , Gong Jun , Sun Chao , Jiang Xin
Published: August 2007

Aluminum doped zinc oxide (ZAO) films were prepared by sol gel dip-coating process. Several annealing treatments were carried out to improve the conductivity of ZAO films. The results show that the annealing temperature and the cooling rate have significant effects on the resistivity of ZAO films. A minimum resistivity of 5.97×10−3Ωcm with the transmission in visible light region above 85% can be obtained after vacuum annealing. The desorption of oxygen that is chemisorbed on the surface and at the grain boundary is thought to be responsible for the observed improvement.
Study of ferroelectric properties in sodium nitrite:poly(vinyl alcohol) nanocomposite films
Authors: Sekhar K. C. , Nath R.
Published: August 2007

The ferroelectric properties of sodium nitrite (NaNO2):poly(vinyl alcohol) nanocomposite films prepared by the solvent cast method have been studied. The optimization of the ferroelectric properties of the composite films as a function of the composition gave 50wt% to be the optimum value. The enhanced remanent polarization was observed in the composite in the frequency range of 10Hz–1kHz. The stability of the ferroelectric polarization shows improvement over the pure NaNO2 films. The x-ray diffraction study revealed that the strain is reduced in the composite films. The images of field emission scanning electron microscope showed the nanosize and uniform distribution of particles in 50wt% composite. The improved values of the polarization and stability have been attributed to the reduced strain in the composite. The ferroelectric phase transition peak was observed in the differential scanning calorimetry (DSC) scan. The ferroelectric phase transition temperature of the composite film obtained from the capacitance-voltage (C–V) measurements agrees well with the DSC measurements.
Mechanism and sensitivity of the intrinsic charge detection of biomolecular interactions by field effect devices
Authors: Wunderlich B. K. , Neff P. A. , Bausch A. R.
Published: August 2007

For many biotechnological applications a quantitative and label-free detection of biomolecular interactions is becoming of outstanding importance. The here presented analytical description of the direct charge detection by field effect devices introduces a straightforward tool for quantitative analysis. By combined measurements of the pH and electrolyte concentration response the absolute amount of adsorbed surface charge can now be determined.
Anomalous strain dependent effective masses in (111) Si nanowires
Authors: Peng G. W. , Feng Y. P.
Published: August 2007

First-principles methods are employed to investigate the effect of strain on the carrier effective masses in (111) Si nanowires (SiNWs). It is found that the electron effective masses of SiNWs depend strongly on the applied axial strain. Within a certain range of strain, the electron effective masses are significantly enhanced. Most remarkably, the electron effective masses are anomalous and become infinity at a critical point of strain. This effect is associated with how strain changes the band structure with a single minimum to that with double minima or vice versa. The hole effective masses, on the other hand, decrease with the increase of the tensile strain, as a result of the strain-induced band energy shift in the vicinity of the valence band maximum. It is also shown that the band gaps of SiNWs with diameters ⩾1.16nm increase with the increase of the tensile strain. The tunability of the effective masses and band gaps with strain would be useful in tailoring the transport properties of SiNWs.
Optimization of electrical characteristics of TiO2-incorporated HfO2 n-type doped gallium arsenide metal oxide semiconductor capacitor with silicon interface passivation layer
Authors: Park Sung Il , Ok Injo , Kim Hyoung-Sub , Zhu Feng , Zhang Manhong , Yum Jung Hwan , Han Zhao , Lee Jack C.
Published: August 2007

Structural approach of TiO2-incorporated HfO2 multimetal dielectric n-type doped gallium arsenide (n-GaAs) metal oxide semiconductor capacitors and their electrical characteristics are investigated. Top TiO2 with bottom HfO2 bilayer dielectric shows excellent C-V characteristics and the lowest hysteresis. Scaling down of this TiO2∕HfO2 dielectric results in substantial reduction in hysteresis and equivalent oxide thickness compared to HfO2 dielectric. Reduced hysteresis is believed to be due to lower trap density of TiO2 than HfO2.
Behavior of hydrogen in InN investigated in real time exploiting spectroscopic ellipsometry
Authors: Losurdo Maria , Giangregorio Maria M. , Bruno Giovanni , Kim Tong-Ho , Choi Soojeong , Brown April S. , Pettinari Giorgio , Capizzi Mario , Polimeni Antonio
Published: August 2007

The interaction of hydrogen with InN epitaxial films has been investigated by exposing InN to a remote hydrogen plasma and monitoring changes in the InN optical properties in real time via spectroscopic ellipsometry. Atomic hydrogen reacts swith InN causing nitrogen depletion with formation of indium clusters at the sample surface. After terminating the hydrogenation process, the hydrogen remains stable in the InN host lattice at T<200°C, while at higher temperatures it partially desorbs as NHx and InHx (x=1–3).
Nanoscale disorder in high critical field, carbon-doped MgB2 hybrid physical-chemical vapor deposition thin films
Authors: Zhu Y. , Larbalestier D. C. , Voyles P. M. , Pogrebnyakov A. V. , Xi X. X. , Redwing J. M.
Published: August 2007

Carbon-doped MgB2 thin films deposited by hybrid physical-chemical vapor deposition (HPCVD) can have Hc2(0K)∼70T, anomalously high compared to bulk samples which have Hc2 about half this value. Using transmission electron microscopy, the authors show that the carbon content in HPCVD-grown Mg(B1−xCx)2 grains is x⩽5%, and that most carbon forms an amorphous intergranular phase. The authors also find extensive structural disorder, including rotations about the c axis and small tilts of the c axis, with a domain size of 5–20nm. The authors propose that strong electron scattering from the nanoscale disorder is responsible for the very high Hc2 in such films.
Carbon nanotube biosensors: The critical role of the reference electrode
Authors: Minot Ethan D. , Janssens Anne M. , Heller Iddo , Heering Hendrik A. , Dekker Cees , Lemay Serge G.
Published: August 2007

Carbon nanotube transistors show tremendous potential for electronic detection of biomolecules in solution. However, the nature and magnitude of the sensing signal upon molecular adsorption have so far remained controversial. Here, the authors show that the choice of the reference electrode is critical and resolves much of the previous controversy. The authors eliminate artifacts related to the reference electrode by using a well-defined reference electrode to accurately control the solution potential. Upon addition of bovine serum albumin proteins, the authors measure a transistor threshold shift of −15mV which can be unambiguously attributed to the adsorption of biomolecules in the vicinity of the nanotube.
Thermal energy harvesting device using ferromagnetic materials
Authors: Ujihara M. , Carman G. P. , Lee D. G.
Published: August 2007

A unique concept for harvesting electrical energy from thermal energy is presented. A thermomechanical actuator was fabricated using ferromagnetic material. The device converts thermal energy into mechanical energy, which can be converted into electrical energy using piezoelectric materials. Magnetic force and operating frequency were measured on the device. Results show that the current power density at ΔT=50K is between 1.85 and 3.61mW∕cm2. A thermal finite element analysis model is also presented to understand the influence of thermal interface, suggesting that increases of 18.5mW∕cm2 or higher are achievable.
Surface texturing by solution deposition for omnidirectional antireflection
Authors: Tao Meng , Zhou Weidong , Yang Hongjun , Chen Li
Published: August 2007

Surface texturing by solution deposition has been developed for antireflection in solar cells. The surface texture is formed by a monolayer of microscale silica particles partially immersed into a spin-on-glass film with a thickness less than the height of the particles. When the silica particles have a spherical shape, the low reflectance from this coating becomes omnidirectional, a desirable feature in fixed-orientation solar panels. It has been experimentally found that the coating improves the transmittance of a quartz wafer in the spectral range of 400–1100nm and in the incident-angle range of surface normal to at least 30°. The surface texture can be applied to different types of solar cells as an add-on coating.
Torsional stiffening of carbon nanotube systems
Authors: Jeong Byeong-Woo , Lim Jang-Keun , Sinnott Susan B.
Published: August 2007

The torsional responses of hollow and filled carbon nanotubes under a combination of tension and torsion are examined using classical molecular dynamics simulations. The critical torsional moment and shear modulus are predicted to significantly increase as a result of coupling between tension and torsion. In particular, the simulations predict that the torsional responses under this type of combined loading are beyond the linear responses of the nanotubes. Importantly, the coupling effect between tension and torsion also increases the torsional stiffness and oscillation frequency of the nanotubes.
Nonlinear optical scattering and absorption in bismuth nanorod suspensions
Authors: Sivaramakrishnan S. , Muthukumar V. S. , Sivasankara Sai S. , Venkataramaniah K. , Reppert Jason , Rao Apparao M , Anija M. , Philip Reji , Kuthirummal Narayanan
Published: August 2007

The authors present the results of optical limiting measurements of ∼10nm wide bismuth nanorods suspended in chloroform. Their Z-scan measurements reveal that optical limiting under 532nm excitation stems from a strong nonlinear scattering (NLS) subsequent to nonlinear absorption (NLA) by suspension. On the other hand, the optical limiting is entirely due to NLA when excited with 1064nm excitation in the nanosecond regime. The occurrence of NLS at one wavelength and absence at another is unusual, especially when compared to the behavior of carbon nanotubes under similar conditions, in which NLS is dominant at both wavelengths.
High resolution spectroscopic and microscopic signatures of ordered growth of ferrous sulfate in SO2 assisted corrosion of Fe3O4(100)
Authors: Stoltz D. , Önsten A. , Karlsson U. O. , Göthelid M.
Published: August 2007

The authors present a high-resolution core-level photoemission study of a Fe3O4(100) surface exposed to 50L (1L=10−6mbars) of H2O and 50L of SO2. S 2p core-level spectra reveal the presence of SO3 and SO4 species. An additional peak in the Fe 3p core-level spectrum shows that they bond with iron from the substrate. Complementary scanning tunneling microscopy of the same surface demonstrates formation of a long-range ordered sulfate locked in the (2×2)R45°-surface potential.
Generation of high-power laser light with Gigahertz splitting
Authors: Unks B. E. , Proite N. A. , Yavuz D. D.
Published: August 2007

We demonstrate the generation of two high-power laser beams whose frequencies are separated by the ground state hyperfine transition frequency in Rb87. The system uses a single master diode laser appropriately shifted by high frequency acousto-optic modulators and amplified by semiconductor tapered amplifiers. This produces two 1W laser beams with a frequency spacing of 6.834GHz and a relative frequency stability of 1Hz. We discuss possible applications of this apparatus, including electromagnetically induced transparencylike effects and ultrafast qubit rotations.
The Increasing Importance of Geographical Proximity in Knowledge Production: An Analysis of US Patent Citations, 1975–1997
Authors: Sonn Jung Won , Storper Michael
Published: August 2007

Much literature suggests that knowledge-production activities are still heavily dependent upon geographically proximate sources of information, in spite of rapid development in telecommunications technology. Some analysts believe that the importance of proximity in knowledge production will eventually disappear with the continued development of telecommunications. The authors analyse patent citations and find that, after controlling for the existing distribution of knowledge-production activities, the proportion of local citations has increased over time. This finding reinforces the notion that in contemporary knowledge production and innovation the role for geographical proximity is increasing.
Complexity Measures as a Basis for Mass Customization of Novel Designs
Authors: Gero John S , Sosa Ricardo
Published: August 2007

In this paper we present a computational approach to the integration of mass customization into the design of novel solutions. We propose the use of entropy as a function of the diversity of solutions that can be generated within a design space. This work demonstrates that the potential of design systems to generate novel solutions can be estimated using complexity measures. This principle is implemented in an evolutionary system for the design of automotive instrument panels that display situation-relevant information in configurations that adapt to traffic conditions and driving actions. This sample application shows that the application of complexity maximization as a selection criterion in evolutionary design systems yields a large variety of solutions of high fitness. We also present guidelines for future developments.
Apparent Afterimage Size, Emmert's Law, and Oculomotor Adjustment
Authors: Lou Liang
Published: August 2007

The apparent size of an afterimage viewed from distances between 5 cm and 580 cm was matched to that of a size-adjustable stimulus at a fixed distance (20, 30, 90, and 200 cm). The experiment was conducted under normal indoor illumination with a procedure that facilitated matching for angular size. The matched size was found to increase with focal distance within 1 m and very little beyond 1 m. Similar results were obtained with an equivalent series of real stimuli subtending a constant visual angle. These findings suggest a scaling in perceived angular size in proportion to the oculomotor adjustments for accommodation and convergence. The observations of perceived angular size of the afterimage complement what Emmert's law is meant to describe (perceived object size of the afterimage), even though as the focal distance decreases it may be increasingly difficult to tease out perceived object size and perceived angular size with the matching procedure.
How Does the Purpose of Inspection Influence the Potency of Visual Salience in Scene Perception?
Authors: Foulsham Tom , Underwood Geoffrey
Published: August 2007

Salience-map models have been taken to suggest that the locations of eye fixations are determined by the extent of the low-level discontinuities in an image. While such models have found some support, an increasing emphasis on the task viewers are performing implies that these models must combine with cognitive demands to describe how the eyes are guided efficiently. An experiment is reported in which eye movements to objects in photographs were examined while viewers performed a memory-encoding task or one of two search tasks. The objects depicted in the scenes had known salience ranks according to a popular model. Participants fixated higher-salience objects sooner and more often than lower-salience objects, but only when memorising scenes. This difference shows that salience-map models provide useful predictions even in complex scenes and late in viewing. However, salience had no effects when searching for a target defined by category or exemplar. The results suggest that salience maps are not used to guide the eyes in these tasks, that cognitive override by task demands can be total, and that modelling top – down search is important but may not be easily accomplished within a salience-map framework.
Attentional Filtering of Transients Allows for a Recovery from Change Blindness
Authors: Becker Mark W , Vera Sara
Published: August 2007

Previous reports suggest that introducing distracting visual transients during a change-detection task can result in change blindness. In four experiments, we found that presenting the distracting transients repeatedly prior to the change produces a recovery from change blindness. This recovery from change blindness is not due solely to low-level neural adaptation of transient detectors, but instead seems to be based on attentional filtering of the distracting transient signals. This attentional filtering can be object-based rather than location-based. In addition, we found that the ability to achieve this attentional filtering depends critically on presenting the to-be-ignored transient signals prior to the time of the change.
Evolution of a fluorinated green fluorescent protein
Authors: Yoo Tae Hyeon , Link A. James , Tirrell David A.
Published: August 2007

The fluorescence of bacterial cells expressing a variant (GFPm) of the green fluorescent protein (GFP) was reduced to background levels by global replacement of the leucine residues of GFPm by 5,5,5-trifluoroleucine. Eleven rounds of random mutagenesis and screening via fluorescence-activated cell sorting yielded a GFP mutant containing 20 amino acid substitutions. The mutant protein in fluorinated form showed improved folding efficiency both
in vivo
and
in vitro
, and the median fluorescence of cells expressing the fluorinated protein was improved ≈650-fold in comparison to that of cells expressing fluorinated GFPm. The success of this approach demonstrates the feasibility of engineering functional proteins containing many copies of abiological amino acid constituents.
Quantitative assessment of protein function prediction from metagenomics shotgun sequences
Authors: Harrington E. D. , Singh A. H. , Doerks T. , Letunic I. , von Mering C. , Jensen L. J. , Raes J. , Bork P.
Published: August 2007

To assess the potential of protein function prediction in environmental genomics data, we analyzed shotgun sequences from four diverse and complex habitats. Using homology searches as well as customized gene neighborhood methods that incorporate intergenic and evolutionary distances, we inferred specific functions for 76% of the 1.4 million predicted ORFs in these samples (83% when nonspecific functions are considered). Surprisingly, these fractions are only slightly smaller than the corresponding ones in completely sequenced genomes (83% and 86%, respectively, by using the same methodology) and considerably higher than previously thought. For as many as 75,448 ORFs (5% of the total), only neighborhood methods can assign functions, illustrated here by a previously undescribed gene associated with the well characterized heme biosynthesis operon and a potential transcription factor that might regulate a coupling between fatty acid biosynthesis and degradation. Our results further suggest that, although functions can be inferred for most proteins on earth, many functions remain to be discovered in numerous small, rare protein families.
Development at the wildland–urban interface and the mitigation of forest-fire risk
Authors: Spyratos Vassilis , Bourgeron Patrick S. , Ghil Michael
Published: August 2007

This work addresses the impacts of development at the wildland–urban interface on forest fires that spread to human habitats. Catastrophic fires in the western United States and elsewhere make these impacts a matter of urgency for decision makers, scientists, and the general public. Using a simple fire-spread model, along with housing and vegetation data, we show that fire size probability distributions can be strongly modified by the density and flammability of houses. We highlight a sharp transition zone in the parameter space of vegetation flammability and house density. Many actual fire landscapes in the United States appear to have spreading properties close to this transition. Thus, the density and flammability of buildings should be taken into account when assessing fire risk at the wildland–urban interface. Moreover, our results highlight ways for regulation at this interface to help mitigate fire risk.
TCR-based lineage tracing: no evidence for conversion of conventional into regulatory T cells in response to a natural self-antigen in pancreatic islets
Authors: Wong Jamie , Mathis Diane , Benoist Christophe
Published: August 2007

Foxp3-expressing regulatory T (T reg) cells derive primarily from selection in the thymus. Yet conversion of mature conventional CD4+ T (T conv) cell lymphocytes can be achieved in several conditions, such as transforming growth factor β treatment, homeostatic expansion, or chronic exposure to low-dose antigen. Such conversion might provide a means to generate peripheral tolerance by “converting” potentially damaging T cells that react to self-antigens. We tested this hypothesis in mice transgenic for the BDC2.5 T cell receptor (TCR), which is representative of a diabetogenic specificity that is naturally present in NOD mice and reactive against a pancreatic self-antigen. In the thymus, before any exposure to antigen, clonotype-positive T reg and T conv cells express a second TCRα chain derived from endogenous loci. High-throughput single-cell sequencing of secondary TCRs of the Vα2 family showed their joining CDR3α regions to be very different in T reg and T conv cell thymocytes. These specific CDR3α motifs, thus, provided a “tag” with which to test the actual impact of T conv to T reg cell conversion in response to peripheral self-antigen; should the autoreactive clonotypic TCR induce T conv to T reg cell conversion upon encounter of cognate antigen in the pancreas or draining lymph node, one would expect to detect tag CDR3α motifs from T conv cells in the T reg cell populations. Sequencing large numbers of peripheral BDC+Vα2+ cells showed that little to no conversion occurs in response to this pancreatic autoantigen.
MyD88-5 links mitochondria, microtubules, and JNK3 in neurons and regulates neuronal survival
Authors: Kim Younghwa , Zhou Ping , Qian Liping , Chuang Jen-Zen , Lee Jessica , Li Chenjian , Iadecola Costantino , Nathan Carl , Ding Aihao
Published: August 2007

The innate immune system relies on evolutionally conserved Toll-like receptors (TLRs) to recognize diverse microbial molecular structures. Most TLRs depend on a family of adaptor proteins termed MyD88s to transduce their signals. Critical roles of MyD88-1–4 in host defense were demonstrated by defective immune responses in knockout mice. In contrast, the sites of expression and functions of vertebrate MyD88-5 have remained elusive. We show that MyD88-5 is distinct from other MyD88s in that MyD88-5 is preferentially expressed in neurons, colocalizes in part with mitochondria and JNK3, and regulates neuronal death. We prepared MyD88-5/GFP transgenic mice via a bacterial artificial chromosome to preserve its endogenous expression pattern. MyD88-5/GFP was detected chiefly in the brain, where it associated with punctate structures within neurons and copurified in part with mitochondria. In vitro, MyD88-5 coimmunoprecipitated with JNK3 and recruited JNK3 from cytosol to mitochondria. Hippocampal neurons from MyD88-5–deficient mice were protected from death after deprivation of oxygen and glucose. In contrast, MyD88-5–null macrophages behaved like wild-type cells in their response to microbial products. Thus, MyD88-5 appears unique among MyD88s in functioning to mediate stress-induced neuronal toxicity.