bluuebunny/crossref_metadata_2025 huggingface dataset:
SLI1(YGR212W) is a major gene conferring resistance to the sphingolipid biosynthesis inhibitor ISP-1, and encodes an ISP-1 N-acetyltransferase in yeast
Authors: MOMOI Michiko , TANOUE Daisuke , SUN Yidi , TAKEMATSU Hiromu , SUZUKI Yusuke , SUZUKI Minoru , SUZUKI Akemi , FUJITA Tetsuro , KOZUTSUMI Yasunori
Published: June 2004

ISP-1 (myriocin) is a potent inhibitor of serine palmitoyltransferase, the primary enzyme of sphingolipid biosynthesis, and is a useful tool for studying the biological functions of sphingolipids in both mammals and yeast (Saccharomyces cerevisiae). In a previous study, we cloned yeast multicopy suppressor genes for ISP-1, and one of these, YPK1/SLI2, was shown to encode a serine/threonine kinase which is a yeast homologue of mammalian SGK1 (serum/glucocorticoid-regulated kinase 1). In the present study, another gene, termed SLI1 (YGR212W; GenBank accession number CAA97239.1), was characterized. Sli1p has weak similarity to Atf1p and Atf2p, which are alcohol acetyltransferases. Although a sli1-null strain grew normally, the IC50 of ISP-1 for the growth of this strain was markedly decreased compared with that for the parental strain, indicating that Sli1p is a major contributor to ISP-1 resistance in yeast. On a sli1-null background, the increase in resistance to ISP-1 induced by YPK1 gene transfection was almost abolished. These data indicate that Sli1p co-operates with Ypk1p in mediating resistance to ISP-1 in yeast. Sli1p was found to convert ISP-1 into N-acetyl-ISP-1 in vitro. Furthermore, N-acetyl-ISP-1 did not share the ability of ISP-1 to inhibit the growth of yeast cells, and the serine palmitoyltransferase inhibitory activity of N-acetyl-ISP-1 was much lower than that of ISP-1. These data suggest that Sli1p inactivates ISP-1 due to its N-acetyltransferase activity towards ISP-1.
Molecular evolution and structure–function relationships of crotoxin-like and asparagine-6-containing phospholipases A2 in pit viper venoms
Authors: CHEN Yi-Hsuan , WANG Ying-Ming , HSEU Ming-Jhy , TSAI Inn-Ho
Published: June 2004

Some myotoxic or neurotoxic PLA2s (phospholipases A2) from pit viper venoms contain characteristic N6 substitutions. Our survey of the venoms of more than ten pit viper genera revealed that N6-PLA2s exist only in limited Asian pit vipers of two genera, Protobothrops and Gloydius, and exist as either monomers or the basic subunits of heterodimers in some New World pit vipers. For the newly identified N6-PLA2s, the neuromuscular blocking activities were assayed with the chick biventer cervicis neuromuscular tissue, whereas the increased serum creatine kinase level assessed their myotoxicities. The purified N6-PLA2s from Protobothrops mangshanensis and Gloydius intermedius saxatilis were found to be presynaptic neurotoxins. In contrast, all N6-PLA2s from the venoms of Sistrurus miliarius strackeri, S. m. barbouri, Crotalus viridis viridis, C. lepidus lepidus, Cerrophidion godmani and Bothreichis schlegelii were myotoxins without neurotoxicity even in the presence of crotoxin A. Crotoxin-like complexes were for the first time purified from the venoms of Sitrurus catenatus tergeminus, C. mitchelli mitchelli, C. horridus atricaudatus, C. basiliscus and C. durissus cumanensis. The cDNAs encoding six novel N6-PLA2s and subunits of the crotoxin-like complex from S. c. tergeminus were cloned and fully sequenced. Phylogeny analysis showed that two structural subtypes of N6-PLA2s with either F24 or S24 substitution have been evolved in parallel, possibly descended respectively from species related to present-day Protobothrops and Gloydius. Calmodulin binds all the N6-PLA2s but crotoxin A may inhibit its binding to crotoxin B and to other neurotoxic N6-PLA2s. Structure–activity relationships at various regions of the PLA2 molecules were extensively discussed.
Conformational variation between allelic variants of cell-surface ovine prion protein
Authors: THACKRAY Alana M. , YANG Sujeong , WONG Edmond , FITZMAURICE Tim J. , MORGAN-WARREN Robert J. , BUJDOSO Raymond
Published: June 2004

The distribution of prion infectivity and PrPSc between peripheral lymphoid tissues suggests their possible haematogenic spread during the progression of natural scrapie in susceptible sheep. Since ovine PBMCs (peripheral blood mononuclear cells) express PrPC, they have the potential to carry or harbour disease-associated forms of PrP. To detect the possible presence of disease-associated PrP on the surface of blood cells, an understanding is required of the conformations that normal ovine cell-surface PrPC may adopt. In the present study, we have used monoclonal antibodies that recognize epitopes in either the N- or C-terminal portions of PrP to probe the conformations of PrPC on ovine PBMCs by flow cytometry. Although PBMCs from scrapie-susceptible and -resistant genotypes of sheep expressed similar levels of cell-surface PrPC, as judged by their reactivity with N-terminal-specific anti-PrP monoclonal antibodies, there was considerable genotypic heterogeneity in the region between helix-1 and residue 171. Cells from PrP-VRQ (V136R154Q171) sheep showed uniform reactivity with monoclonal antibodies that bound to epitopes around helix-1, whereas cells from PrP-ARQ (A136R154Q171) and PrP-ARR (A136R154R171) sheep showed variable binding. The region between β-strand-2 and residue 171, which includes a YYR motif, was buried or obscured in cell-surface PrPC on PBMCs from scrapie-susceptible and -resistant sheep. However, an epitope of PrPC that is influenced by residue 171 was more exposed on PBMCs from PrP-VRQ sheep than on PBMCs from the PrP-ARQ genotype. Our results highlight conformational variation between scrapie-susceptible and -resistant forms of cell-surface PrPC and also between allelic variants of susceptible genotypes.
TIRF imaging of docking and fusion of single insulin granule motion in primary rat pancreatic β-cells: different behaviour of granule motion between normal and Goto–Kakizaki diabetic rat β-cells
Authors: OHARA-IMAIZUMI Mica , NISHIWAKI Chiyono , KIKUTA Toshiteru , NAGAI Shintaro , NAKAMICHI Yoko , NAGAMATSU Shinya
Published: June 2004

We imaged and analysed the motion of single insulin secretory granules near the plasma membrane in live pancreatic β-cells, from normal and diabetic Goto–Kakizaki (GK) rats, using total internal reflection fluorescence microscopy (TIRFM). In normal rat primary β-cells, the granules that were fusing during the first phase originate from previously docked granules, and those during the second phase originate from ‘newcomers’. In diabetic GK rat β-cells, the number of fusion events from previously docked granules were markedly reduced, and, in contrast, the fusion from newcomers was still preserved. The dynamic change in the number of docked insulin granules showed that, in GK rat β-cells, the total number of docked insulin granules was markedly decreased to 35% of the initial number after glucose stimulation. Immunohistochemistry with anti-insulin antibody observed by TIRFM showed that GK rat β-cells had a marked decline of endogenous insulin granules docked to the plasma membrane. Thus our results indicate that the decreased number of docked insulin granules accounts for the impaired insulin release during the first phase of insulin release in diabetic GK rat β-cells.
Mycophenolate mofetil, an inhibitor of inosine monophosphate dehydrogenase, causes a paradoxical elevation of GTP in erythrocytes of renal transplant patients
Authors: GOLDSMITH David , CARREY Elizabeth A. , EDBURY Stephen , SMOLENSKI Ryszard T. , JAGODZINSKI Piotr. , SIMMONDS H. Anne
Published: June 2004

The immunosuppressant MMF (mycophenolate mofetil) has increasingly replaced AZA (azathioprine) in renal transplantation. MMF is a prodrug of MPA (mycophenolic acid), which inhibits lymphocyte IMPDH (inosine monophosphate dehydrogenase), thereby drastically decreasing GTP concentrations essential to lymphocyte proliferation in vitro and in vivo. Erythrocyte GTP concentrations are commonly elevated in severe renal disease, but normalize following successful engraftment. Consequently, elevated GTP in renal transplant recipients might signal impending loss of immunosuppression and graft failure. In the present study, we compared erythrocyte nucleotides and plasma metabolites in two groups of 25 patients after renal transplantation, both receiving prednisolone and cyclosporin A, but one group receiving MMF and the other AZA. No patients had recent allograft biopsy evidence of rejection. Erythrocyte GTP concentrations at MMF commencement were 50.4±23.4 μmol/l. An increase occurred during the first 3 months after transplant when MMF was used de novo, stabilizing at 146.7±62.9 μmol/l after 4 months. This was significantly higher (P=2.5×10−6) than erythrocyte GTP (40.4±15.9 μmol/l) in the AZA group, which was essentially unchanged from values immediately after successful transplantation. The effect of MMF on erythrocyte GTP levels was reversible, since GTP levels fell when MMF therapy was terminated. The results demonstrate paradoxically high GTP concentrations in erythrocytes of renal transplant patients receiving MMF. MPA may stabilize reticulocyte IMPDH, allowing the protein to persist during erythropoiesis. This behaviour is in marked contrast with the decrease in GTP levels seen in white blood cells of patients on chronic MMF therapy.
Electromechanical stiffening of rods and tubes
Authors: Zandi Roya , Golestanian Ramin , Rudnick Joseph
Published: June 2004

Electrostatic interactions are shown to exert a significant effect on the buckling instability of a rod. In particular, the threshold value of the compressional force needed to induce buckling is found to be independent of rod length for long charged rods. In the case of rods of intermediate length, the critical buckling force crosses over from the classic inverse-square length dependence to asymptotic length-independent form with increasing rod length. It is suggested that this effect leads to the possibility of electromechanical stiffening of nanotubes, which would allow relatively long segments of them to be used as atomic force probes.
Fifth-order contributions to ultrafast spectrally resolved vibrational echoes: Heme-CO proteins
Authors: Finkelstein Ilya J. , McClain Brian L. , Fayer M. D.
Published: June 2004

The fifth order contributions to the signals of ultrafast infrared spectrally resolved stimulated vibrational echoes at high intensities have been investigated in carbonmonoxy heme proteins. High intensities are often required to obtain good data. Intensity dependent measurements are presented on hemoglobin-CO (Hb–CO) and a mutant of myoglobin, H64V–CO. The spectrally resolved vibrational echoes demonstrate that fifth order effects arise at both the 1-0 and the 2-1 emission frequencies of the stretching mode of the CO chromophore bound at the active site of heme proteins. Unlike one-dimensional experiments, in which the signal is integrated over all emission frequencies, spectrally resolving the signal shows that the fifth order contributions have a much more pronounced influence on the 2-1 transition than on the 1-0 transition. By spectrally isolating the 1-0 transition, the influence of fifth order contributions to vibrational echo data can be substantially reduced. Analysis of fifth order Feynman diagrams that contribute in the vibrational echo phase-matched direction demonstrates the reason for the greater influence of fifth order processes on the 1-2 transition, and that the fifth order contributions are heterodyne amplified by the third order signal. Finally, it is shown that the anharmonic oscillations in vibrational echo data of Hb–CO that previous work had attributed strictly to fifth order effects arise even without fifth order contributions.
A multidimensional discrete variable representation basis obtained by simultaneous diagonalization
Authors: Dawes Richard , Carrington Tucker
Published: June 2004

Direct product basis functions are frequently used in quantum dynamics calculations, but they are poor in the sense that many such functions are required to converge a spectrum, compute a rate constant, etc. Much better, contracted, basis functions, that account for coupling between coordinates, can be obtained by diagonalizing reduced dimension Hamiltonians. If a direct product basis is used, it is advantageous to use discrete variable representation (DVR) basis functions because matrix representations of functions of coordinates are diagonal in the DVR. By diagonalizing matrices representing coordinates it is straightforward to obtain the DVR that corresponds to any direct product basis. Because contracted basis functions are eigenfunctions of reduced dimension Hamiltonians that include coupling terms they are not direct product functions. The advantages of contracted basis functions and the advantages of the DVR therefore appear to be mutually exclusive. A DVR that corresponds to contracted functions is unknown. In this paper we propose such a DVR. It spans the same space as a contracted basis, but in it matrix representations of coordinates are diagonal. The DVR basis functions are chosen to achieve maximal diagonality of coordinate matrices. We assess the accuracy of this DVR by applying it to model four-dimensional problems.
Properties of reactively radio frequency-magnetron sputtered (Zr,Sn)TiO4 dielectric films
Authors: Huang Cheng-Liang , Hsu Cheng-Hsing
Published: June 2004

Zirconium tin titanium oxide doped 1 wt % ZnO thin films on n-type Si substrate were deposited by rf magnetron sputtering at a fixed rf power of 350 W with various argon-oxygen (Ar/O2) mixture and different substrate temperatures. Electrical properties and microstructures of ZnO-doped (Zr0.8Sn0.2)TiO4 thin films prepared by rf magnetron sputtering on n-type Si(100) substrates at different Ar/O2 ratios and substrate temperatures have been investigated. The surface structural and morphological characteristics analyzed by x-ray diffraction, scanning electron microscopy, and atomic force microscope were sensitive to the deposition conditions, such as Ar/O2 ratio (100/0–80/20) and substrate temperature (350 °C–450 °C). The selected-area diffraction pattern showed that the deposited films exhibited a polycrystalline microstructure. All films exhibited ZST (111) orientation perpendicular to the substrate surface and the grain size as well as the deposition rate of the films increased with the increase of both the Ar partial pressure and the substrate temperature. At a Ar/O2 ratio of 100/0, rf power level of 350 W and substrate temperature of 450 °C, the Zr0.8Sn0.2TiO4 films with 6.44 μm thickness possess a dielectric constant of 42 (at 10 MHz), a dissipation factor of 0.065 (at 10 MHz), and a leakage current density of 2×10−7 A/cm2 at an electrical field of 1 kV/cm.
Preferential hydration and the exclusion of cosolvents from protein surfaces
Authors: Shimizu Seishi , Smith Derek J.
Published: June 2004

Protein stability is enhanced by the addition of osmolytes, such as sugars and polyols and inert crowders, such as polyethylene glycols. This stability enhancement has been quantified by the preferential hydration parameter which can be determined by experiments. To understand the mechanism of protein stability enhancement, we present a statistical mechanical analysis of the preferential hydration parameter based upon Kirkwood–Buff theory. Previously, the preferential hydration parameter was interpreted in terms of the number of hydration waters, as well as the cosolvent exclusion volume. It was not clear how accurate these interpretations were, nor what the relationship is between the two. By using the Kirkwood–Buff theory and experimental data, we conclude that the contribution from the cosolvent exclusion dominantly determines the preferential hydration parameters for crowders. For osmolytes, although the cosolvent exclusion largely determines the preferential hydration parameters, the contribution from hydration may not be negligible.
Optical emission from C60-molecule-coupled Si nanocrystallites
Authors: Wu X. L. , Liao M. X. , Deng S. S. , Siu G. G.
Published: June 2004

Using C60 molecule as a kind of surface-passivated agent to modify the electronic structure of Si nanocrystallites in porous silicon, we disclose that this kind of C60/nanocrystalline Si coupling system can show a strong blue emission at ∼460 nm when stored in air for more than one year. After a full characterization of the photoluminescence properties, we propose a luminescent center in the SiOx layer at the surface of a Si nanocrystallite. It is a pair consisting of an oxygen vacancy and an interstitial oxygen. The interstitial oxygen also forms a peroxy linkage with a neighboring lattice oxygen. Radiative recombination of carriers photogenerated from Si nanocrystallite cores in the luminescent centers results in the observed blue photoluminescence. Neutron irradiation experiments support our assignment of the blue emission mechanism. This work improves the understanding of the origin of blue emission from silicon/oxygen-related nanostructured materials.
Hexagonal-to-cubic phase transformation in GaN nanowires by Ga+ implantation
Authors: Dhara S. , Datta A. , Wu C. T. , Lan Z. H. , Chen K. H. , Wang Y. L. , Hsu C. W. , Shen C. H. , Chen L. C. , Chen C. C.
Published: June 2004

Hexagonal to cubic phase transformation is studied in focused ion beam assisted Ga+-implanted GaN nanowires. Optical photoluminescence and cathodoluminescence studies along with high-resolution transmission electron microscopic structural studies are performed to confirm the phase transformation. In one possibility, sufficient accumulation of Ga from the implanted source might have reduced the surface energy and simultaneously stabilized the cubic phase. Another potential reason may be that the fluctuations in the short-range order induced by enhanced dynamic annealing (defect annihilation) with the irradiation process stabilize the cubic phase and cause the phase transformation.
Enhancement of the recollision rate in diffusion-influenced reactions in an inhomogeneous medium
Authors: Buján-Nuñez M. C. , López-Quintela M. A.
Published: June 2004

Brownian dynamics simulations were performed to determine the first collision and recollision rates of spherical reagent particles in a reaction medium made heterogeneous by the presence of randomly located inert spherical obstacles in a continuum solvent. The recollision rate vp (and hence the overall reactive collision rate when activation energy is high) was always enhanced by the presence of obstacles, the degree of enhancement increasing with the volume fraction occupied by obstacles (φ) and with decreasing reagent concentration φR. Enhancement increased with obstacle size at high φR, and fell with increasing obstacle size at low φR. The vp-φR data follow a power law, where the scaling factor βp decreased with decreasing obstacle size and increasing φ, and the prefactor kp initially increased with φ and then fell (except for large obstacles). The behavior of βp appears to be largely due to the obstacles reducing the probability that reagent particles escape from each other after collision, while the dominant factors responsible for the behavior of kp appear to be initially the effect of obstacles in enhancing effective local reagent concentration, and then (for small obstacles), their reduction of the reagent-particle coordination number. As the energy of activation falls, the reactive collision rate becomes less influenced by the reagent recollision rate and more influenced by the rate of first collision. For low-activation-energy reactions, the presence of obstacles depresses the reactive collision rate if reagent concentration is low or if the obstacles are small and their concentration high. The fall in the reactive collision rate with decreasing activation energy is steeper, the lower the reagent concentration and the smaller the obstacles.
Cumulative isomerization probability studied by various transition state wave packet methods including the MCTDH algorithm. Benchmark: HCN→CNH isomerization
Authors: Lasorne B. , Gatti F. , Baloitcha E. , Meyer H.-D. , Desouter-Lecomte M.
Published: June 2004

The 3D cumulative isomerization probability N(E) for the transfer of a light particle between two atoms is computed by one time-independent and two time-dependent versions of the transition state wave packet (TSWP) method. The time-independent method is based on the direct expansion of the microcanonical projection operator on Chebyshev polynomials. In the time-dependent TSWP methods, the propagations are carried out by the split operator scheme and the multiconfiguration time-dependent Hartree (MCTDH) algorithm. This is the very first implementation of the TSWP method in the Heidelberg MCTDH package [G. W. Worth, M. H. Beck, A. Jäckle, and H.-D. Meyer, The MCDTH package, Version 8.2 (2000); H.-D Meyer, Version 8.3 (2002). See http://www.pci.uni-heidelberg.de/tc/usr/mctdh/]. The benchmark is the HCN→CNH isomerization for zero total angular momentum. Particular insights are given into the tunneling region. In larger systems, the time-dependent version of TSWP making use of the MCTDH algorithm will permit to treat more and more modes quantum mechanically, for very accurate results. Therefore, it was important to calibrate the implementation. Besides, we also assess the efficiency of a reduced dimensionality approach by comparing the new exact 3D calculations of N(E) for the HCN→CNH isomerization with results obtained via 1D or 2D active subspaces. This suggests that, it should be possible to take directly benefit of the present 3D approaches, adapted for triatomic Jacobi coordinates to compute N(E) for H-transfer in larger systems, via three active coordinates. The prerequisite is then the simplification of the reduced 3D kinetic energy operator with rigid constraint to take the form corresponding to a pseudo triatomic system in Jacobi coordinates with effective masses. This last step is checked in the methoxy radical and malonaldehyde. Finally, different ways to obtain reliable eigenvectors of the flux operator associated with a dividing surface are revisited.
On the interconversion pathway of HBO↔BOH
Authors: Peng Qian , Wang Yubin , Suo Bing , Shi Qizhen , Wen Zhenyi
Published: June 2004

The potential energy surfaces have been constructed for the A′1, A′3, and A″3 states of HBO by using the multireference perturbation theory with the basis set cc-pVTZ (6d,10f ). Two stationary points and a transition state have been characterized on all the three surfaces, which are in good agreement with available experiments and previous calculations. The interconversion pathways from metastable boron hydroxide BOH to the considerably more stable HBO are expounded based on the nature of the surfaces.
The relaxation time of the magnetization of uniaxial single-domain ferromagnetic particles in the presence of a uniform magnetic field
Authors: Kalmykov Yuri P.
Published: June 2004

The relaxation time of the magnetization of uniaxial single-domain ferromagnetic particles is evaluated for magnetic field applied to an arbitrary angle to the easy axis in the entire dissipation range, i.e., for very low damping (VLD), intermediate-to-high damping (IHD), and crossover values. The calculations are based on the Mel’nikov-Meshkov method [J. Chem. Phys. 85, 1018 (1986)] for bridging the VLD and IHD Kramers escape rates for mechanical particles (the Kramers turnover problem) as extended by Coffey et al. [Adv. Chem. Phys. 117, 483 (2001); Phys. Rev. E 63, 021102 (2001)] to the analogous magnetic spin problem. It is shown that the analytical results are in complete agreement with the relaxation time calculated numerically from the solution of the stochastic Landau-Lifshitz-Gilbert equation.
Observation of a reactive resonance in the integral cross section of a six-atom reaction: F+CHD3
Authors: Zhou Jingang , Lin Jim J. , Liu Kopin
Published: June 2004

The title reaction was investigated under crossed-beam conditions at collisional energies ranging from about 0.4 to 7.5 kcal/mol. Product velocity distributions were measured by a time-sliced, velocity-map imaging technique to explicitly account for the density-to-flux transformation factors. Both the state-resolved, pair-correlated excitation functions and vibrational branching ratios are presented for the two isotopic product channels. An intriguing resonance tunneling mechanism occurring near the reaction threshold for the HF+CD3 product channel is surmized, which echoes the reactive resonances found previously for the F+HD→HF+D reaction and more recently for the F+CH4 reaction.
Simple analytical approximations for eddy current profiling of the near-surface residual stress in shot-peened metals
Authors: Yu Feng , Nagy Peter B.
Published: June 2004

Because of their frequency-dependent penetration depth, eddy current measurements are capable of mapping the near-surface depth profile of the electrical conductivity. This technique can be used to nondestructively characterize the subsurface residual stress distribution in certain types of shot-peened metals, e.g., in nickel-base superalloys. For quantitative evaluation of the experimental results, analytical and computational techniques are needed to solve the direct and inverse problems, i.e., to predict the frequency-dependent apparent eddy current conductivity from the depth profile of the frequency-independent intrinsic electrical conductivity of the specimen and vice versa. Simple analytical approximations are presented for both the direct and inverse eddy current problems by exploiting two specific features of the subsurface electrical conductivity variation caused by near-surface residual stresses in shot-peened metals. First, compressive residual stresses are limited to a shallow surface region of depth, much less than typical probe coil diameters. Second, the change in electrical conductivity due to residual stresses is always very small, typically less than 1%. The proposed approximations are verified by numerical comparison to much more complicated numerical solutions.
The kinetic energy of carbon ions in vacuum arc plasmas: A comparison of measuring techniques
Authors: Anders André , Yushkov George Yu.
Published: June 2004

Ions in cathodic arc plasmas have high velocities attained by acceleration at cathode spots. Among other techniques, two time-of-flight setups had previously been used to determine ion velocities. These measurements showed significant discrepancies especially for some light cathode materials like carbon. To reconcile the differences, a thorough investigation was conducted using carbon as the cathode material. It is shown that systematic errors occur when the ion source time-of-flight system is not operated near perveance-matching conditions. The extracted ion beam is not parallel but divergent, and the Faraday cup detector measures only a fraction of the beam. In contrast, plasma source experiments without ion extraction are free of such distortions. In the absence of an external magnetic field, the average carbon ion energy has been determined to be in the range 18.5–20.5 eV for arc currents in the range 100–600 A, in agreement with previous plasma source measurements and other literature data.
Modeling the effect of subsurface interface defects on contact stiffness for ultrasonic atomic force microscopy
Authors: Sarioglu A. F. , Atalar A. , Degertekin F. L.
Published: June 2004

We present a model predicting the effects of mechanical defects at layer interfaces on the contact stiffness measured by ultrasonic atomic force microscopy (AFM). Defects at subsurface interfaces result in changes at the local contact stiffness between the AFM tip and the sample. Surface impedance method is employed to model the imperfections and an iterative algorithm is used to calculate the AFM tip-surface contact stiffness. The sensitivity of AFM to voids or delaminations and disbonds is investigated for film-substrate combinations commonly used in microelectronic structures, and optimum defect depth for maximum sensitivity is defined. The effect of contact force and the tip properties on the defect sensitivity are considered. The results indicate that the ultrasonic AFM should be suitable for subsurface detection and its defect sensitivity can be enhanced by adjusting the applied force as well as by judicious choice of the AFM tip material and geometry.
Mechanisms of injection enhancement in organic light-emitting diodes through insulating buffer
Authors: Zhao J. M. , Zhan Y. Q. , Zhang S. T. , Wang X. J. , Zhou Y. C. , Wu Y. , Wang Z. J. , Ding X. M. , Hou X. Y.
Published: June 2004

Three types of organic light-emitting diodes are fabricated. Tris-8-hydroxyquinoline aluminum (Alq3) is used as an electron-transporting layer (ETL) and sodium stearate (NaSt) as an electron-injecting buffer. The optimal thickness of NaSt for electron injection is different for cathodes of different metals, such as Mg, Al, and Ag. This is attributed to the different work functions of cathodes, which result in different initial barrier heights for electron injection from cathodes into ETL, and explained based on tunneling theory.
Identification of native defects around grain boundary in Pr-doped ZnO bicrystal using electron energy loss spectroscopy and first-principles calculations
Authors: Sato Yukio , Mizoguchi Teruyasu , Oba Fumiyasu , Yodogawa Masatada , Yamamoto Takahisa , Ikuhara Yuichi
Published: June 2004

Native defects and Pr dopant around grain boundaries in Pr-doped and undoped ZnO bicrystals were investigated by electron energy loss spectroscopy (EELS) with a focus on the relationship with the current–voltage characteristics. The Pr-doped bicrystal exhibited a nonlinear current–voltage characteristic, whereas the undoped bicrystal shows an ohmic characteristic. In the Pr-doped bicrystal, Pr was found to be present within 8nm around the grain boundary. EELS investigation of native defects combined with first-principles calculations indicated the presence of zinc vacancies in the vicinity of the Pr-doped grain boundary. The formation of zinc vacancies is considered to be the origin of the nonlinear current–voltage characteristic.
Vertical alignment of printed carbon nanotubes by multiple field emission cycles
Authors: Kim Yong C. , Sohn K. H. , Cho Y. M. , Yoo Eun H.
Published: June 2004

The effect of field emission cycles on printed carbon nanotubes was investigated using scanning electron microscopy and current–voltage measurement. After multiple emission cycles, the printed nanotubes irreversibly deformed to orient themselves parallel to the field direction and, from them, remarkably enhanced emission image with good uniformity was demonstrated. Corresponding gradual decrease in the field emission threshold and increase of field enhancement factor (β) were also observed during field emission cycles.
Atomic-scale characterization of perovskite superlattice using chemical lattice imaging and spatially resolved electron energy-loss spectroscopy
Authors: Kimoto K. , Matsui Y. , Yamada H. , Kawasaki M. , Yu X. , Kaneko Y. , Tokura Y.
Published: June 2004

The layered structure of a perovskite tricolor superlattice {SrTiO3(STO)∕LaAlO3(LAO)∕La0.6Sr0.4MnO3(LSMO)}n on an STO substrate is investigated using transmission electron microscopy (TEM) and electron energy-loss spectroscopy (EELS). Conventional TEM imaging is not effective for thickness evaluation, in which both LAO and LSMO layers show the same image contrast because of the similarity in their mean atomic numbers. We observe 001 lattice fringes, which are chemically sensitive in the case of the perovskite structure ABO3, since the 001 structure factor is proportional to the difference between A- and B-site atomic scattering factors. The thickness of each layer is evaluated with an accuracy of one unit cell. We also apply spatially resolved EELS to analyze the depth profile of Ti, Mn, and La contents.
Rotation of two-dimensional arrays of microparticles trappedby circularly polarized light
Authors: Miyakawa Kenji , Adachi Hiroto , Inoue Yoshinori
Published: June 2004

We investigate the creation and the rotation of the array of microparticles trapped by circularly polarized light. We find that a smooth rotation requires two-dimensional structure having a rotational symmetry along the light beam axis. We show that it is possible to control smoothly both the rate and the sense of rotation not only by varying the handedness and the power of the incident beam but also by varying the position of the beam focus.
Photovoltage study of charge injection from dye moleculesinto transparent hole and electron conductors
Authors: Mahrov B. , Boschloo G. , Hagfeldt A. , Dloczik L. , Dittrich Th.
Published: June 2004

Transient and spectral photovoltage (PV) have been investigated for charge injection from a dye [Ru(dcbpyH2)2(NCS)2] into transparent hole (CuSCN, CuI, CuAlO2) and electron (TiO2, SnO2:F) conductors. The PV signal rises to a maximum within 10ns to 10μs, depending on the transparent hole or electron conductor and on the mechanism of charge separation. The efficiency of hole and electron injection is of the same order while the effective lifetimes of injected charge vary between several μs and 1ms for the samples used. The thresholds for charge injection from the dye range between 1.6 and 1.8eV depending on the material on which the dye is adsorbed.
Integral and differential developments of the carrier density of states in intercalated layered crystals
Authors: Tovstyuk N. K.
Published: June 2004

The effect of the layered crystal intercalation on the functional dependence of the carrier density of states is analyzed. The conditions of thermodynamic stability of the intercalation process in relation to the Fermi energy and microscopic parameters are studied.
Evidence for a bound HeH2 halo molecule by diffraction from a transmission grating
Authors: Kalinin Anton , Kornilov Oleg , Rusin Lev. Yu , Toennies J. Peter
Published: June 2004

The HeH2 van der Waals complex has been identified in a molecular beam produced by a cryogenic (T0=24.7 K) free jet expansion of a 1% H2 mixture in 99% He4 gas. The weakly bound HeH2 complexes in the beam are identified via their first order diffraction angles after passing through a 100 nm period transmission grating. An electron impact mass spectrometer analysis of the diffraction patterns is used to discriminate against ion fragments of the constituent gas clusters.
Tetrasulfur, S4: Rotational spectrum, interchange tunneling, and geometrical structure
Authors: McCarthy M. C. , Thorwirth S. , Gottlieb C. A. , Thaddeus P.
Published: June 2004

The rotational spectrum of S4 has been observed for the first time in an electrical discharge through sulfur vapor. Two techniques have been used: Fourier transform microwave spectroscopy and long-path millimeter-wave absorption spectroscopy. Small, but systematic shifts of the measured transition frequencies of the normal isotopic species indicate that S4 has C2v symmetry but with a low-lying transition state of D2h symmetry, yielding interchange tunneling at 14.1(2) kHz in its ground vibrational state. From the rotational constants of the normal and the single S34 isotopic species, an experimental (r0) structure has been derived: S4 is a singlet planar trapezoid with a terminal bond length of 1.899(7) Å, a central bond of 2.173(32) Å, and an S-S-S angle of 103.9(8)°. Like thiozone (S3), S4 is a candidate for detection in the atmosphere of the Jovian moon Io and in other astronomical sources.
Historical demography of Müllerian mimicry in the neotropical
Heliconius
butterflies
Authors: Flanagan N. S. , Tobler A. , Davison A. , Pybus O. G. , Kapan D. D. , Planas S. , Linares M. , Heckel D. , McMillan W. O.
Published: June 2004

We compare the historical demographies of two Müllerian comimetic butterfly species:
Heliconius erato
and
Heliconius melpomene
. These species show an extensive parallel geographic divergence in their aposematic wing phenotypes. Recent studies suggest that this coincident mosaic results from simultaneous demographic processes shaped by extrinsic forces over Pleistocene climate fluctuations. However, DNA sequence variation at two rapidly evolving unlinked nuclear loci,
Mannose phosphate isomerase
(
Mpi
) and
Triose phosphate isomerase
(
Tpi
), show that the comimetic species have quite different quaternary demographies. In
H. erato
, despite ongoing lineage sorting across the Andes, nuclear genealogical estimates showed little geographical structure, suggesting high historical gene flow. Coalescent-based demographic analysis revealed population growth since the Pliocene period. Although these patterns suggest vicariant population subdivision associated with the Andean orogeny, they are not consistent with hypotheses of Pleistocene population fragmentation facilitating allopatric wing phenotype radiation in
H. erato
. In contrast, nuclear genetic diversity, θ,in
H. melpomene
was reduced relative to its comimic and revealed three phylogeographical clades. The pattern of coalescent events within regional clades was most consistent with population growth in relatively isolated populations after a recent period of restricted population size. These different demographic histories suggest that the wing-pattern radiations were not coincident in the two species. Instead, larger effective population size (
N
e
) in
H. erato
, together with profound population change in
H. melpomene
, supports an earlier hypothesis that
H. erato
diversified first as the model species of this remarkable mimetic association.
No evidence for new dopaminergic neurons in the adult mammalian substantia nigra
Authors: Frielingsdorf Helena , Schwarz Katherine , Brundin Patrik , Mohapel Paul
Published: June 2004

A recent report by Zhao
et al.
[Zhao, M., Momma, S., Delfani, K., Carlen, M., Cassidy, R. M., Johansson, C. B., Brismar, H., Shupliakov, O., Frisen, J. & Janson, A. M. (2003)
Proc. Natl. Acad. Sci. USA
100, 7925–7930] suggests that dopaminergic neurons, the cell type lost in Parkinson's disease, are continuously generated in the adult substantia nigra pars compacta. Using similar methodological procedures to label dividing cells, we found no evidence of new dopaminergic neurons in the substantia nigra, either in normal or 6-hydroxydopamine-lesioned hemi-Parkinsonian rodents, or even after growth factor treatment. Furthermore, we found no evidence of neural stem cells emanating from the cerebroventricular system and migrating to the substantia nigra. We conclude that it is unlikely that dopaminergic neurons are generated in the adult mammalian substantia nigra.
The integral membrane enzyme PagP alternates between two dynamically distinct states
Authors: Hwang Peter M. , Bishop Russell E. , Kay Lewis E.
Published: June 2004

PhoPQ-activated gene P (PagP) is an integral membrane enzyme that transfers the
sn
-1 palmitate chain from phospholipid to lipopolysaccharide in Gram-negative bacteria. A recent x-ray crystallographic study established that the
sn
-1 palmitate binds within a long cavity at the center of the PagP β barrel. The high mobility required to permit substrate entry into the central core of the barrel contrasts with the need to assemble a well defined structure in the peripheral loops, where many key catalytic residues are located. To gain insight into how dynamics relate to the function of PagP, the enzyme was reconstituted into CYFOS-7, a detergent that supports enzymatic activity. Under these conditions, PagP exists in equilibrium between two states, relaxed (R) and tense (T). The kinetics and thermodynamics of the interchange have been investigated by
1
H-
15
N NMR spectroscopy, with ΔH = -10.7 kcal/mol and ΔS = -37.5 cal/mol·K for the R→ T transition. A comparison of chemical shifts between the two states indicates that major structural changes occur in the large extracellular L1 loop and adjacent regions of the β barrel. In addition to the R,T interconversion, other conformational exchange processes are observed in the R state, showing it to be quite flexible. Thus a picture emerges in which substrate entry is facilitated by the mobility of the R state, whereas the relatively rigid T state adopts a radically different conformation in a region of the protein known to be essential for catalysis. The ability to switch between dynamically distinct states may be a key feature of the catalytic cycle of PagP.
The broad spectrum revisited: Evidence from plant remains
Authors: Weiss Ehud , Wetterstrom Wilma , Nadel Dani , Bar-Yosef Ofer
Published: June 2004

The beginning of agriculture is one of the most important developments in human history, with enormous consequences that paved the way for settled life and complex society. Much of the research on the origins of agriculture over the last 40 years has been guided by Flannery's [Flannery, K. V. (1969) in
The Domestication and Exploitation of Plants and Animals
, eds. Ucko, P. J. & Dimbleby, G. W. (Duckworth, London), pp. 73–100] “broad spectrum revolution” (BSR) hypothesis, which posits that the transition to farming in southwest Asia entailed a period during which foragers broadened their resource base to encompass a wide array of foods that were previously ignored in an attempt to overcome food shortages. Although these resources undoubtedly included plants, nearly all BSR hypothesis-inspired research has focused on animals because of a dearth of Upper Paleolithic archaeobotanical assemblages. Now, however, a collection of >90,000 plant remains, recently recovered from the Stone Age site Ohalo II (23,000 B.P.), Israel, offers insights into the plant foods of the late Upper Paleolithic. The staple foods of this assemblage were wild grasses, pushing back the dietary shift to grains some 10,000 years earlier than previously recognized. Besides the cereals (wild wheat and barley), small-grained grasses made up a large component of the assemblage, indicating that the BSR in the Levant was even broader than originally conceived, encompassing what would have been low-ranked plant foods. Over the next 15,000 years small-grained grasses were gradually replaced by the cereals and ultimately disappeared from the Levantine diet.
Extrageniculate mediation of unconscious vision in transcranial magnetic stimulation-induced blindsight
Authors: Ro Tony , Shelton Dominique , Lee Olivia L. , Chang Erik
Published: June 2004

The proposed neural mechanisms supporting blindsight, the above-chance performance of cortically blind patients on forced-choice visual discrimination tasks, are controversial. In this article, we show that although subjects were unable to perceive foveally presented visual stimuli when transcranial magnetic stimulation over the visual cortex induced a scotoma, responses nonetheless were delayed significantly by these unconscious distractors in a directed saccade but not in an indirect manual response task. These results suggest that the superior colliculus, which is involved with sensory encoding as well as with the generation of saccadic eye movements, is mediating the unconscious processing of the transcranial magnetic stimulation-suppressed distractors and implicate a role of the retinotectal pathway in many blindsight phenomena.
Identification of an evolutionarily divergent U11 small nuclear ribonucleoprotein particle in
Drosophila
Authors: Schneider Claudia , Will Cindy L. , Brosius Jürgen , Frilander Mikko J. , Lührmann Reinhard
Published: June 2004

Previous reports suggested that U11, in contrast to U12 or other small nuclear (sn)RNAs of the U12-type spliceosome, might be either highly divergent or absent in
Drosophila melanogaster
. Affinity purification of
Drosophila
U12-containing complexes has led to the identification of the fly U11 snRNA, which contains a potential U12-type 5′ splice-site-interacting sequence, but whose sequence and length differs significantly from vertebrate and plant U11. Analysis of U12-type introns revealed an A-rich region directly downstream of
Drosophila
, but not human, U12-type 5′ splice sites. This finding, coupled with the presence of a highly divergent U11 snRNA, and the apparent absence of
Drosophila
homologs of human U11 proteins, suggest that U12-type 5′ splice site recognition might be different in flies. A comparison of U11 snRNAs that we have identified from vertebrates, plants, and insects, suggests that an evolutionarily divergent U11 snRNA may be unique to
Drosophila
and not characteristic of insects in general.
Fine-root production dominates response of a deciduous forest to atmospheric CO
2
enrichment
Authors: Norby Richard J. , Ledford Joanne , Reilly Carolyn D. , Miller Nicole E. , O'Neill Elizabeth G.
Published: June 2004

Fine-root production and turnover are important regulators of the biogeochemical cycles of ecosystems and key components of their response to global change. We present a nearly continuous 6-year record of fine-root production and mortality from minirhizotron analysis of a closed-canopy, deciduous sweetgum forest in a free-air CO
2
enrichment experiment. Annual production of fine roots was more than doubled in plots with 550 ppm CO
2
compared with plots in ambient air. This response was the primary component of the sustained 22% increase in net primary productivity. Annual fine-root mortality matched annual production, and the mean residence time of roots was not altered by elevated CO
2
, but peak fine-root standing crop in midsummer was significantly higher in CO
2
-enriched plots, especially deeper in the soil profile. The preferential allocation of additional carbon to fine roots, which have a fast turnover rate in this species, rather than to stemwood reduces the possibility of long-term enhancement by elevated CO
2
of carbon sequestration in biomass. However, sequestration of some of the fine-root carbon in soil pools is not precluded, and there may be other benefits to the tree from a seasonally larger and deeper fine-root system. Root-system dynamics can explain differences among ecosystems in their response to elevated atmospheric CO
2
; hence, accurate assessments of carbon flux and storage in forests in a globally changing atmosphere must account for this unseen and difficult-to-measure component.
ADP-ribosylation factor 6 regulates tumor cell invasion through the activation of the MEK/ERK signaling pathway
Authors: Tague Sarah E. , Muralidharan Vandhana , D'Souza-Schorey Crislyn
Published: June 2004

Tumor cell invasion through the extracellular matrix is accompanied by the formation of invadopodia, which are actin-rich protrusions at the adherent surface of cells at sites of extracellular matrix degradation. Using the invasive human melanoma cell line LOX as a model system, we demonstrate that the ADP-ribosylation factor 6 (ARF6) GTPase is an important regulator of invadopodia formation and cell invasion. We show that ARF6 localizes to invadopodia of LOX cells. Sustained activation of ARF6 significantly enhances the invasive capacity of melanoma as well as breast tumor cell lines, whereas dominant negative ARF6 abolishes basal cell invasive capacity as well as invasion induced by growth factors. Furthermore, using biochemical assays, we show that enhanced invasive capacity is accompanied by the activation of endogenous ARF6. Finally, we provide evidence that ARF6-enhanced melanoma cell invasion depends on the activation of the extracellular signal-regulated kinase (ERK), and that the ARF6 GTPase cycle regulates ERK activation. This study describes a vital role for ARF6 in melanoma cell invasion and documents a link between ARF6-mediated signaling and ERK activation.