bluuebunny/crossref_metadata_2025 huggingface dataset:
Laboratory experiments for intense vortical structures in turbulence velocity fields
Authors: Mouri Hideaki , Hori Akihiro , Kawashima Yoshihide
Published: May 2007

Vortical structures of turbulence, i.e., vortex tubes and sheets, are studied using one-dimensional velocity data obtained in laboratory experiments for duct flows and boundary layers at microscale Reynolds numbers from 332 to 1934. We study the mean velocity profile of intense vortical structures. The contribution from vortex tubes is dominant. The radius scales with the Kolmogorov length. The circulation velocity scales with the rms velocity fluctuation. We also study the spatial distribution of intense vortical structures. The distribution is self-similar over small scales and is random over large scales. Since these features are independent of the microscale Reynolds number and of the configuration for turbulence production, they appear to be universal.
Energy level alignment at Co/AlOx/pentacene interfaces
Authors: Popinciuc M. , Jonkman H. T. , van Wees B. J.
Published: May 2007

X-ray and ultraviolet photoemission spectroscopy (XPS and UPS) experiments were performed in order to study the energy level alignment and electronic structure at Co/AlOx/pentacene interfaces as a function of the aluminum oxide (AlOx) tunnel barrier thickness and the oxidation state of Co. XPS was used to determine the oxygen exposure for the optimum oxidation of 6, 8, and 10 Å thin layers of Al deposited on Co. The Fermi level (FL) position in the band gap of AlOx depends on the oxidation state of the underlying Co and on the thickness of the tunnel barrier. The energy level alignment at Co/AlOx interfaces is consistent with an interfacial dipole, its magnitude being sensitive to the oxidation of Co, and band bending phenomena in the thin AlOx tunnel barrier. UPS experiments revealed no chemical interaction at Co/AlOx/pentacene interface in contrast with hybridization effects found at Co/pentacene interface. The vacuum level of pentacene aligns with that of AlOx, following the position of AlOx energy levels with respect to FL. The hole injection barrier was found to increase with the thickness of the tunnel barrier and to decrease with the oxidation of Co at a fixed thickness of the AlOx layer.
Fourier analysis applied on in situ laser reflectometry during III-nitride metal organic chemical vapor deposition growth
Authors: Simbrunner C. , Sitter H. , Bonanni A.
Published: May 2007

In this article we present the Fourier analysis of kinetic reflectometry spectra acquired during metalorganic chemical vapor deposition. We can show that offset errors due to background radiation can be completely removed by the method itself without using filters or lock-in amplifiers. Additionally, calibration of the reflected intensity is needed as long as the response of the detector is linear to the reflected intensity of the sample. By analyzing the time dependent part of the signal growth rate, layer thickness and the refractive index of the growing layer can be deduced. We demonstrate that, by applying the method to the GaN:Mg δ-doping process, it is possible to obtain accurate information about the time, optical properties, and thickness of the grown multilayers with a resolution down to the monolayer range.
Cavity ring-down spectroscopy measurement of single aerosol particle extinction. II. Extinction of light by an aerosol particle in an optical cavity excited by a cw laser
Authors: Miller Johanna L. , Orr-Ewing Andrew J.
Published: May 2007

The authors present an analytical derivation of the scattered power from a spherical, homogeneous, nonabsorbing particle in a plane standing wave. The scattered power changes significantly with the position of the particle with respect to the peaks and nodes of the standing wave, even for particles whose diameters are many times the wavelength of the light. The analysis is applicable to continuous-wave cavity ring-down spectroscopy on aerosol particles, and the structure of the standing wave is expected to affect both the measured ring-down time and the shape of the ring-down trace. The dependence of the extinction on the phase of the standing wave at the location of the particle is captured in a parameter ζ which connects the current treatment to standard Mie scattering theory. Methods for calculating ζ are presented.
Defect reduction by periodic SiNx interlayers in gallium nitride grown on Si (111)
Authors: Zang K. Y. , Wang Y. D. , Wang L. S. , Chow S. Y. , Chua S. J.
Published: May 2007

Periodic SiNx interlayers were employed during the metal-organic chemical vapor deposition of epitaxial GaN on AlN buffer layers grown on Si (111) substrates. The growth and the evolution of defects were studied in this paper. A reduction of the threading dislocation density to ∼109cm−2 was observed on the surface of GaN by counting the surface pit density from the atomic force microscopy results. Besides the observation of the continuous bending and subsequent recombination of the threading dislocations related to the periodic conduction of the SiNx interlayer characterized using cross-sectional transmission electron microscopy, we observed a different behavior induced by the SiNx interlayers: Si-rich inverted hexagonal pyramids with their base on the (0001) plane and six sidewalls on the (101¯1) plane were found near the top surface of the GaN film at the location of SiNx insertion layer characterized using electron energy loss spectroscopy. The preferential deposition of the SiNx on the sidewalls of the pit defects leads to the subsequently selective growth of the GaN beyond the pit defects, which leads to the burying of the pits and the reduction of the pit defects within the film due to the micromasking effect of the SiNx.
Bimolecular recombination kinetics and interfacial electronic structures of poly[2-methoxy-5-(2-ethyl-hexyloxy)-p-phenylene vinylene] on gold studied using two-photon photoemission spectroscopy
Authors: Sohn Youngku , Stuckless John T.
Published: May 2007

Photoexcitation kinetics and interfacial electronic structures of poly[2-methoxy-5(2-ethylhexyloxy)-p-phenylene vinylene] (MEH-PPV) film on gold have been investigated using two-photon photoemission spectroscopy (2PPE). The authors directly probed a fixed intermediate state located at 0.95eV above the Fermi level (or 2.95eV below the vacuum level), assigned to a charged polaron. Based on the power law slope and the 2PPE spectra with laser intensity, they found that the polaron follows a second order bimolecular annihilation process. The 2PPE yield dramatically increases with increasing photon energy. They attribute this to an enhanced dissociation of hotter excitons at higher excitation levels. The work function of MEH-PPV/Au is measured to be 3.9eV, 1.2eV downshift from the clean gold, attributable to interface dipole effects. The energy gap between the intermediate polaron state and the hole polaron level is estimated to be 2.45eV.
Investigation of the photochemistry of the poly{p-phenylenevinylene} precursor system: Implications for nanolithography
Authors: Cotton D. V. , Fell C. J. , Belcher W. J. , Dastoor P. C.
Published: May 2007

The photochemistry of poly{p-phenylene[1-(tetrahydrothiophen-1-io)ethylene chloride]} (PPTEC), a water soluble precursor of the semiconducting polymer, poly{p-phenylenevinylene} (PPV), has been studied both under atmospheric conditions and in environments devoid of oxygen. UV-visible spectroscopy and photoluminescence data has been used to provide a picture of the mechanistic pathways involved in UV irradiation of the PPTEC material. A new quantitative model for the effect of UV irradiation upon film morphology is presented, which leads to insights for the improved control of the characteristics of PPV nanostructures produced via near-field scanning optical lithography.
Ultrafast repair of irradiated DNA: Nonadiabatic ab initio simulations of the guanine-cytosine photocycle
Authors: Markwick Phineus R. L. , Doltsinis Nikos L.
Published: May 2007

Nonadiabatic first-principles molecular dynamics simulations have been performed of the photoexcited Watson-Crick guanine-cytosine (GC) DNA base pair in the gas phase and in aqueous solution. An excited state coupled proton-electron transfer (CPET) from G to C along the central hydrogen bond is observed upon excitation of the ππ* state initially localized on G. In the resulting charge transfer state a conical intersection between the excited state and the ground state is easily accessible. Therefore radiationless decay is fast, of the order of 100fs, followed by a rapid CPET back reaction retrieving the initial Watson-Crick structure. A detailed analysis of the mechanism of nonradiative decay suggests a biexponential behavior in which out-of-plane motion plays a special role for the longer decay component.
Additive property of secondary relaxation processes in di-n-octyl and di-isooctyl phthalates: Signature of non-Johari-Goldstein relaxation
Authors: Kaminska Ewa , Kaminski Kamil , Paluch Marian , Ziolo Jerzy , Ngai K. L.
Published: May 2007

Broadband dielectric spectroscopy was used to study relaxation dynamics of supercooled di-n-octyl phthalate, di-isooctyl phthalate, and their mixtures. Additionally, low temperature measurements were performed to investigate the nature of the secondary relaxation processes in both glass formers. The authors found that the secondary relaxation observed in the mixture is the additive sum of the secondary relaxations of the two components. This experimental evidence indicates that these secondary relaxation processes are intramolecular in origin, and they are non-Johari-Goldstein secondary relaxations.
Normal and hyperspherical mode analysis of NO-doped Kr crystals upon Rydberg excitation of the impurity
Authors: Castro Palacio J. C. , Velazquez Abad L. , Lombardi A. , Aquilanti V. , Rubayo Soneíra J.
Published: May 2007

Molecular dynamics simulations and both normal mode and hyperspherical mode analyses of NO-doped Kr solid are carried out in order to get insights into the structural relaxation of the medium upon electronic excitation of the NO molecule. A combined study is reported on the time evolution of the cage radius and on the density of vibrational states, according to the hyperspherical and normal mode analyses. For the hyperspherical modes, hyper-radial and grand angular contributions are considered. For the normal modes, radial and tangential contributions are examined. Results show that the first shell radius dynamics is driven by modes with frequencies at ∼47 and ∼15cm−1. The first one is related to the ultrafast regime where a large part of the energy is transmitted to the lattice and the second one to relaxation and slow redistribution of the energy. The density of vibrational states γ(ω) is characterized by a broad distribution of bands peaking around the frequencies of ∼13, ∼19, ∼25, ∼31, ∼37, ∼47, and ∼103cm−1 (very small band). The dominant modes in the relaxation process were at 14.89, 23.49, and 53.78cm−1; they present the largest amplitudes and the greatest energy contributions. The mode at 14.89cm−1 is present in both the fit of the first shell radius and in the hyper-radial kinetic energy spectrum and resulted the one with the largest amplitude, although could not be revealed by the total kinetic energy power spectrum.
Single-crystal silicon/silicon dioxide multilayer heterostructures based on nanomembrane transfer
Authors: Peng Weina , Roberts Michelle M. , Nordberg Eric P. , Flack Frank S. , Colavita Paula E. , Hamers Robert J. , Savage Donald E. , Lagally Max G. , Eriksson Mark A.
Published: May 2007

A method to fabricate single-crystal Si∕SiO2 multilayer heterostructures is presented. Heterostructures are fabricated by repeated transfer of single crystal silicon nanomembranes alternating with deposition of spin-on-glass. Nanomembrane transfer produces multilayers with low surface roughness and smooth interfaces. To demonstrate interface quality, the specular reflectivities of one-, two-, and three-membrane heterostructures are measured. Comparison of the measured reflectivity with theoretical calculations shows good agreement. Nanomembrane stacking allows for the preprocessing of individual membranes with a high thermal budget before the low thermal budget assembly of the stack, suggesting a new avenue for the three dimensional integration of integrated circuits.
Hole scattering by confined optical phonons in silicon nanowires
Authors: Nawaz Mueen , Leburton Jean-Pierre , Jin Jianming
Published: May 2007

The authors provide a theoretical analysis of the influence of confinement on the hole-optical phonon interaction in freestanding Si nanowires. Their model based on deformation potential optical phonons shows that in narrow quantum wires, hole scattering is less frequent than when calculated with a bulk (continuous) phonon spectrum. In addition, scattering by confined optical phonons results in dissimilar rates for backward and forward events, in contrast with continuous phonons.
Degeneracy breaking of optical resonance modes in rolled-up spiral microtubes
Authors: Hosoda M. , Shigaki T.
Published: May 2007

The authors investigate the optical resonance modes (ORMs) generated in semiconductor microtubes of spiral symmetry by using finite-difference time-domain methods. Even though the tube-wall thickness is much smaller than the light wavelength, modes having an electric field parallel to the tube wall can loop around the tube periphery as ORMs. In addition, the degenerated ORMs present in conventional cylindrical cavities such as whispering gallery modes are broken and separated into two modes due to the spiral asymmetry of the rolled-up microtubes.
High resolution x-ray microscope
Authors: Gary C. K. , Park H. , Lombardo L. W. , Piestrup M. A. , Cremer J. T. , Pantell R. H. , Dudchik Y. I.
Published: May 2007

The authors present x-ray images of grid meshes and biological material obtained using a microspot x-ray tube with a multilayer optic and a 92-element parabolic compound refractive lens (CRL) made of a plastic containing only hydrogen and carbon. Images obtained using this apparatus are compared with those using an area source with a spherical lens and a spherical lens with multilayer condenser. The authors found the best image quality using the multilayer condenser with a parabolic lens, compared to images with a spherical lens and without the multilayer optics. The resolution was measured using a 155-element parabolic CRL and a multilayer condenser with the microspot tube. The experiment demonstrates about 1.1μm resolution.
Liquid state nuclear magnetic resonance at low fields using a nitrogen cooled superconducting quantum interference device
Authors: Zhang Yi , Qiu Longqing , Krause Hans-Joachim , Hartwig Stefan , Burghoff Martin , Trahms Lutz
Published: May 2007

Nuclear magnetic resonance (NMR) spectra of liquids were studied at fields from 470nTto65μT using a nitrogen cooled radio frequency superconducting quantum interference device. The authors demonstrated that low field NMR measurements with this device are feasible and may yield useful information. In particular, they determined the natural linewidth of distilled water to be 0.17±0.06Hz. In addition, they recorded J-coupled spectra of 2,2,2-trifluoroethanol in a measurement field regime that was determined to provide the best signal-to-noise ratio. Four peaks with frequency differences of about 2Hz were well separated.
Two-photon absorption based optical limiting and stabilization by using a CdTe quantum dot solution excited at optical communication wavelength of ∼1300nm
Authors: He Guang S. , Zheng Qingdong , Yong Ken-Tye , Ryasnyanskiy Aleksandr I. , Prasad Paras N. , Urbas Augustine
Published: May 2007

This letter presents the results of two-photon study of CdTe quantum dots (QDs) in chloroform. The measured two-photon absorption (2PA) spectrum shows that 2PA coefficient at ∼1300nm is ∼0.02cm∕GW. Based on a 1cm path-length CdTe QD solution sample of 8mg∕ml concentration, irradiated by a focused ∼1300nm laser beam of ∼160fs duration, the nonlinear transmission could be changed from ∼100% to ∼20% when the input pulse energy was varied from ∼50nJto∼10μJ, demonstrating a superior optical limiting performance. The input laser fluctuation was significantly reduced after passing through the sample, indicating a remarkable optical stabilization behavior.
Change of interface dipole energy with interfacial layer thickness and O2 plasma treatment in metal/organic interface
Authors: Kim Soo Young , Hong Kihyon , Lee Jong-Lam
Published: May 2007

The authors determined the interface dipole energies between interfacial layers with different thicknesses coated on indium tin oxides (ITOs) and 4,4′-bis[N-(1-naphtyl)-N-phenyl-amino]biphenyl using ultraviolet and synchrotron radiation photoemission spectroscopy. The interface dipole energy increased as a function of interfacial layer thickness up to 4nm. After O2 plasma treatment on thick-metal (>4nm) coated ITO, the work function and interface dipole energy increased. In thin-metal (<2nm) coated ITO, no change in the interface dipole energy was found though the work function increased. Thus, the O2 plasma treated thin (<2nm) interfacial layer reduced the hole injection barrier.
Mapping of individual carbon nanotubes in polymer/nanotube composites using electrostatic force microscopy
Authors: Jespersen Thomas Sand , Nygård Jesper
Published: May 2007

The authors demonstrate the use of electrostatic force microscopy (EFM) as a noninvasive tool for mapping individual single wall carbon nanotubes (SWCNTs) in spin cast polymer/SWCNT composites. The authors obtain the distribution of lengths and orientations of nanotubes in a poly-(methylmethacrylate)/SWCNT composite. By correlating the measured EFM amplitude with its dependence on SWCNT length and tip-tube separation they show that the technique can be used for mapping the three dimensional position of the SWCNTs in the polymer matrix. Finally the limitations of the technique are discussed.
Sellmeier equations for green, yellow, and orange colored HgGa2S4 crystals
Authors: Wang Tie-Jun , Kang Zhi-Hui , Zhang Hong-Zhi , Feng Zhi-Shu , Wu Feng-Guang , Zang Hai-Yan , Jiang Yun , Gao Jin-Yue , Andreev Yury , Lanskii Grigory , Atuchin Victor , Parasyuk Oleg
Published: May 2007

Modeling and experimental study on phase matching of second harmonic generation in different color HgGa2S4 crystals are carried out. Using the known Sellmeier equations, the dispersion relation with weighting proportionally to short-wavelength boundary of the crystal transparency band is proposed. Optimal dispersion relations and phase-matched conditions for different color HgGa2S4 crystals can be specified.
Tunability and ferroelectric relaxor properties of bismuth strontium titanate ceramics
Authors: Chen Wei , Yao Xi , Wei Xiaoyong
Published: May 2007

A systemic study was performed on bismuth strontium titanate (Sr1−1.5xBixTiO3, 0.04⩽x⩽0.25) ceramics. Dielectric properties were measured from 83to373K at different frequencies. A transformation from relaxor ferroelectrics to relaxor behavior was observed when x>0.10. Both diffuseness and relaxation degree increase as x rises. Tunability was found to increase with increasing x value until 0.07, and then decrease when Bi3+ content increases. Meanwhile, their figures of merit (defined as tunability/loss) shows a maximum at x=0.12. The change from relaxor ferroelectrics into relaxor behavior has a positive impact on the tunability of bismuth strontium titanate system.
High electron doping to a wide band gap semiconductor 12CaO∙7Al2O3 thin film
Authors: Miyakawa Masashi , Hirano Masahiro , Kamiya Toshio , Hosono Hideo
Published: May 2007

High-density electrons (∼1.9×1021cm−3) were doped into a polycrystalline film of a wide band gap (∼7eV) semiconductor 12CaO∙7Al2O3 (C12A7) by an in situ postdeposition reduction treatment using an oxygen-deficient C12A7 overlayer. The resultant film exhibits metallic conduction with a Hall mobility of ∼2.5cm2V−1s−1 and a conductivity of ∼800Scm−1. Optical analyses indicate that most of the doped electrons behave as free carriers with an effective mass of 0.82me and the estimated in-grain mobility is 5.2cm2V−1s−1, which agrees reasonably with the value obtained for high-quality single crystals.
Second order optical nonlinearity of ZnO∕ZnO:Al bilayers deposited on glass by low temperature radio frequency sputtering
Authors: Michelotti F. , Canali R. , Dominici L. , Belardini A. , Menchini F. , Schoer G. , Mueller J.
Published: May 2007

The authors report on the measurement of the second order nonlinear optical properties of ZnO films deposited by low temperature radio frequency sputtering on ZnO:Al coated glass substrates. They show that ZnO:Al plays a crucial role as a buffer layer for the successive growth of ZnO. The effect of aluminum doping on the relaxation of the stresses acts as a template for crystallization of ZnO, allowing us to obtain partially oriented ZnO films with relatively large nonlinear coefficients. The measurements of the second harmonic tensor by the Maker fringes method are in good agreement with results for the electro-optic coefficient obtained by nonlinear ellipsometry.
Photoluminescence properties of Cr2+:ZnSe films deposited by radio frequency magnetron cosputtering
Authors: Vivet N. , Morales M. , Levalois M. , Doualan J. L. , Moncorgé R.
Published: May 2007

Cr 2 + : Zn Se films were grown at room temperature by the radio frequency magnetron cosputtering technique. The structural characterization of the films shows that the corresponding films are well crystallized mainly in the cubic zinc-blende structure with strong ⟨111⟩ orientations. Using direct (1850nm) and indirect (visible) excitations, photoluminescence experiments in the midinfrared spectral region reveal that Cr is incorporated in the optically active Cr2+ state, and the shape of the spectra agrees with that reported for bulk materials. This study shows that magnetron cosputtering can provide viable structures for the realization of optically and electrically pumped midinfrared microlasers.
Opposite temperature effects of quantum-dot laser under dual-wavelength operation
Authors: Fan Hsueh-Shih , Su Yi-Shin , Chu Fei-Hung , Chang Fu-Yu , Lin Hao-Hsiung , Lin Ching-Fuh
Published: May 2007

The authors discover opposite temperature effects when the quantum-dot (QD) laser is controlled to simultaneously oscillate at two modes in the external cavity. The two modes correspond to the ground state and the first excited state of the QDs. Experiments show that the power of one mode increases, while the power of the other mode decreases as the temperature increases. The power variation between these two modes is similar to the situation of competition and anticompetition of laser modes. The physical reason is discussed in detail.
The interplay between microRNAs and the neurotrophin receptor tropomyosin-related kinase C controls proliferation of human neuroblastoma cells
Authors: Laneve Pietro , Di Marcotullio Lucia , Gioia Ubaldo , Fiori Micol E. , Ferretti Elisabetta , Gulino Alberto , Bozzoni Irene , Caffarelli Elisa
Published: May 2007

MicroRNAs (miRNAs) are tiny noncoding RNAs whose function as modulators of gene expression is crucial for the proper control of cell growth and differentiation. Although the profile of miRNA expression has been defined for many different cellular systems, the elucidation of the regulatory networks in which they are involved is only just emerging. In this work, we identify a crucial role for three neuronal miRNAs (9, 125a, and 125b) in controlling human neuroblastoma cell proliferation. We show that these molecules act in an additive manner by repressing a common target, the truncated isoform of the neurotrophin receptor tropomyosin-related kinase C, and we demonstrate that the down-regulation of this isoform is critical for regulating neuroblastoma cell growth. Consistently with their function, these miRNAs were found to be down-modulated in primary neuroblastoma tumors.
Decondensing the protamine domain for transcription
Authors: Martins Rui Pires , Krawetz Stephen A.
Published: May 2007

Potentiation is the transition from higher-order, transcriptionally silent chromatin to a less condensed state requisite to accommodating the molecular elements required for transcription. To examine the underlying mechanism of potentiation an ≈13.7-kb mouse protamine domain of increased nuclease sensitivity flanked by 5′ and 3′ nuclear matrix attachment regions was defined. The potentiated DNase I-sensitive region is formed at the pachytene spermatocyte stage with the recruitment to the nuclear matrix of a large ≈9.6-kb region just upstream of the domain. Attachment is then specified in the transcribing round spermatid, recapitulating the organization of the human cluster. In comparison to other modifiers that have no effect, i.e., histone methylation, HP1, and SATB1, topoisomerase engages nuclear matrix binding as minor marks of histone acetylation appear. Reorganization is marked by specific sites of topoisomerase II activity that are initially detected in leptotene–zygotene spermatocytes just preceding the formation of the DNase I-sensitive domain. This has provided a likely model of the events initiating potentiation, i.e., the opening of a chromatin domain.
High-speed mapping of synaptic connectivity using photostimulation in Channelrhodopsin-2 transgenic mice
Authors: Wang H. , Peca J. , Matsuzaki M. , Matsuzaki K. , Noguchi J. , Qiu L. , Wang D. , Zhang F. , Boyden E. , Deisseroth K. , Kasai H. , Hall W. C. , Feng G. , Augustine G. J.
Published: May 2007

To permit rapid optical control of brain activity, we have engineered multiple lines of transgenic mice that express the light-activated cation channel Channelrhodopsin-2 (ChR2) in subsets of neurons. Illumination of ChR2-positive neurons in brain slices produced photocurrents that generated action potentials within milliseconds and with precisely timed latencies. The number of light-evoked action potentials could be controlled by varying either the amplitude or duration of illumination. Furthermore, the frequency of light-evoked action potentials could be precisely controlled up to 30 Hz. Photostimulation also could evoke synaptic transmission between neurons, and, by scanning with a small laser light spot, we were able to map the spatial distribution of synaptic circuits connecting neurons within living cerebral cortex. We conclude that ChR2 is a genetically based photostimulation technology that permits analysis of neural circuits with high spatial and temporal resolution in transgenic mammals.
Comparison of coherent and spontaneous Raman microspectroscopies for noninvasive detection of single bacterial endospores
Authors: Petrov Georgi I. , Arora Rajan , Yakovlev Vladislav V. , Wang Xi , Sokolov Alexei V. , Scully Marlan O.
Published: May 2007

Single bacterial spores were analyzed by using nonlinear Raman microspectroscopy based on coherent anti-Stokes Raman scattering (CARS). The Raman spectra were retrieved from CARS spectra and found to be in excellent agreement with conventionally collected Raman spectra. The phase retrieval method based on maximum entropy model revealed significant robustness to external noise. The direct comparison of signal amplitudes exhibited a factor of 100 stronger CARS signal, as compared with the Raman signal.
Loss of erbB signaling in oligodendrocytes alters myelin and dopaminergic function, a potential mechanism for neuropsychiatric disorders
Authors: Roy Kristine , Murtie Joshua C. , El-Khodor Bassem F. , Edgar Nicole , Sardi S. Pablo , Hooks Bryan M. , Benoit-Marand Marianne , Chen Chinfei , Moore Holly , O'Donnell Patricio , Brunner Daniela , Corfas Gabriel
Published: May 2007

Several psychiatric disorders are associated with white matter defects, suggesting that oligodendrocyte (OL) abnormalities underlie some aspects of these diseases. Neuregulin 1 (NRG1) and its receptor, erbB4, are genetically linked with susceptibility to schizophrenia and bipolar disorder.
In vitro
studies suggest that NRG1-erbB signaling is important for OL development. To test whether erbB signaling contributes to psychiatric disorders by regulating the structure or function of OLs, we analyzed transgenic mice in which erbB signaling is blocked in OLs
in vivo
. Here we show that loss of erbB signaling leads to changes in OL number and morphology, reduced myelin thickness, and slower conduction velocity in CNS axons. Furthermore, these transgenic mice have increased levels of dopamine receptors and transporters and behavioral alterations consistent with neuropsychiatric disorders. These results indicate that defects in white matter can cause alterations in dopaminergic function and behavior relevant to neuropsychiatric disorders.
An adenosine-to-inosine tRNA-editing enzyme that can perform C-to-U deamination of DNA
Authors: Rubio Mary Anne T. , Pastar Irena , Gaston Kirk W. , Ragone Frank L. , Janzen Christian J. , Cross George A. M. , Papavasiliou F. Nina , Alfonzo Juan D.
Published: May 2007

Adenosine-to-inosine editing in the anticodon of tRNAs is essential for viability. Enzymes mediating tRNA adenosine deamination in bacteria and yeast contain cytidine deaminase-conserved motifs, suggesting an evolutionary link between the two reactions. In trypanosomatids, tRNAs undergo both cytidine-to-uridine and adenosine-to-inosine editing, but the relationship between the two reactions is unclear. Here we show that down-regulation of the
Trypanosoma brucei
tRNA-editing enzyme by RNAi leads to a reduction in both C-to-U and A-to-I editing of tRNA
in vivo
. Surprisingly,
in vitro
, this enzyme can mediate A-to-I editing of tRNA and C-to-U deamination of ssDNA but not both in either substrate. The ability to use both DNA and RNA provides a model for a multispecificity editing enzyme. Notably, the ability of a single enzyme to perform two different deamination reactions also suggests that this enzyme still maintains specificities that would have been found in the ancestor deaminase, providing a first line of evidence for the evolution of editing deaminases.
Midlife decline in declarative memory consolidation is correlated with a decline in slow wave sleep
Authors: Backhaus Jutta , Born Jan , Hoeckesfeld Ralf , Fokuhl Sylvia , Hohagen Fritz , Junghanns Klaus
Published: May 2007

Sleep architecture as well as memory function are strongly age dependent. Slow wave sleep (SWS), in particular, decreases dramatically with increasing age, starting already beyond the age of 30. SWS normally predominates during early nocturnal sleep and is implicated in declarative memory consolidation. However, the consequences of changes in sleep across the life span for sleep-associated memory consolidation have not been evaluated so far. Here, we compared declarative memory consolidation (for word-pair associates) during sleep in young and middle-aged healthy humans. The age groups (18–25 vs. 48–55 yr) did not differ with regard to learning performance before retention periods that covered, respectively, the first and second half of nocturnal sleep. However, after early retention sleep, where the younger subjects showed distinctly more SWS than the middle-aged (62.3 ± 3.7 min vs. 18.4 ± 7.2 min, P < 0.001), retrieval of the word pairs in the middle-aged was clearly worse than in the young (P < 0.001). In contrast, declarative memory retention did not differ between groups after late sleep, where retention was generally worse than after early sleep (P = 0.005). Retention of declarative memories was the same in both age groups when sleep periods containing equal amounts of SWS were compared, i.e., across late sleep in the young and across early sleep in the middle-aged. Our results indicate a decline in sleep-associated declarative memory consolidation that develops already during midlife and is associated with a decrease in early nocturnal SWS.
Acute exposure to stress improves performance in trace eyeblink conditioning and spatial learning tasks in healthy men
Authors: Duncko Roman , Cornwell Brian , Cui Lihong , Merikangas Kathleen R. , Grillon Christian
Published: May 2007

The present study investigated the effects of acute stress exposure on learning performance in humans using analogs of two paradigms frequently used in animals. Healthy male participants were exposed to the cold pressor test (CPT) procedure, i.e., insertion of the dominant hand into ice water for 60 sec. Following the CPT or the control procedure, participants completed a trace eyeblink conditioning task followed by a virtual navigation Morris water task (VNMWT). Hypothalamic-pituitary-adrenocortical (HPA) axis and sympathetic autonomic system (SAS) activity were assessed by measuring salivary cortisol, heart rate, and skin conductance at selected timepoints. Results revealed positive effects of stress on performance in both tasks. The stress group showed significantly more conditioned blinks than the control group during acquisition of trace eyeblink conditioning. The stress group also performed significantly better in the VNMWT than the control group, with the former showing significantly fewer failures to locate the hidden platform in the allotted time and smaller heading errors than the latter. Regression analyses revealed positive relationships between HPA axis and SAS activity during stress and eyeblink conditioning performance. Our results directly extend findings from animal studies and suggest potential physiological mechanisms underlying stress and learning.
Solution structure and backbone dynamics of the AF‐6 PDZ domain/Bcr peptide complex
Authors: Chen Quan , Niu Xiaogang , Xu Yingqi , Wu Jihui , Shi Yunyu
Published: May 2007

The human AF‐6, a scaffold protein between cell membrane‐associated proteins and the actin cytoskeleton, plays an important role in special cell–cell junctions and signal transduction. It can be phosphorylated by the protein kinase Bcr, which allows efficient binding of the C terminus of Bcr to the PDZ domain of AF‐6 and consequently enhances the binding affinity of AF‐6 to Ras. Formation of the AF‐6, Bcr, and Ras ternary complex results in down‐regulation of the Ras‐mediated signal transduction pathway. To better understand the molecular basis for the recognition of the AF‐6 PDZ domain and Bcr, we solve the solution structure of the AF‐6 PDZ domain complexed with the C‐terminal peptide of Bcr and explore the interactions between them in detail. Compared with previously reported structures, the complex exhibits a noncanonical binding mode of PDZ/peptide. Owing to the distinct residues involved in the AF‐6 PDZ domain and Bcr peptide interaction, the interaction mode does not adapt to the existing classification rules that have been put forward, based on the ligand or the PDZ domain specificity. Furthermore, the PDZ domain of AF‐6 can bind to the C terminus of Bcr efficiently after phosphorylation of AF‐6 by the Bcr kinase. The phosphorylation may induce a conformational change of AF‐6, which makes the binding surface on the PDZ domain accessible to Bcr for efficient binding. This study not only characterizes the structural details of the AF‐6 PDZ/Bcr peptide complex, but also provides a potential target for future drug design and disease therapy.
Conformational changes of glucose/galactose‐binding protein illuminated by open, unliganded, and ultra‐high‐resolution ligand‐bound structures
Authors: Borrok M. Jack , Kiessling Laura L. , Forest Katrina T.
Published: May 2007

D‐Glucose/D‐Galactose‐binding protein (GGBP) mediates chemotaxis toward and active transport of glucose and galactose in a number of bacterial species. GGBP, like other periplasmic binding proteins, can exist in open (ligand‐free) and closed (ligand‐bound) states. We report a 0.92 Å resolution structure of GGBP from Escherichia coli in the glucose‐bound state and the first structure of an open, unbound form of GGBP (at 1.55 Å resolution). These structures vary in the angle between the two structural domains; the observed difference of 31° arises from torsion angle changes in a three‐segment hinge. A comparison with the closely related periplasmic receptors, ribose‐ and allose‐binding proteins, shows that the GGBP hinge residue positions that undergo the largest conformational changes are different. Furthermore, the high‐quality data collected for the atomic resolution glucose‐bound structure allow for the refinement of specific hydrogen atom positions, the assignment of alternate side chain conformations, the first description of CO2 trapped after radiation‐induced decarboxylation, and insight into the role of the exo‐anomeric effect in sugar binding. Together, these structures provide insight into how the hinge‐bending movement of GGBP facilitates ligand binding, transport, and signaling.
Structure of the Q67H mutant of R67 dihydrofolate reductase‐NADP+ complex reveals a novel cofactor binding mode
Authors: Divya N. , Grifith E. , Narayana Narendra
Published: May 2007

Plasmid‐encoded bacterial R67 dihydrofolate reductase (DHFR) is a NADPH‐dependent enzyme unrelated to chromosomal DHFR in amino acid sequence and structure. R67 DHFR is insensitive to the bacterial drug trimethoprim in contrast to chromosomal DHFR. The crystal structure of Q67H mutant of R67 DHFR bound to NADP+ has been determined at 1.15 Å resolution. The cofactor assumes an extended conformation with the nicotinamide ring bound near the center of the active site pore, the ribose and pyrophosphate group (PPi) extending toward the outer pore. The ribonicotinamide exhibits anti conformation as in chromosomal DHFR complexes. The relative orientation between the PPi and the nicotinamide ribose differs from that observed in chromosomal DHFR–NADP+ complexes. The coenzyme displays symmetrical binding mode with several water‐mediated hydrogen bonds with the protein besides ionic, stacking, and van der Waals interactions. The structure provides a molecular basis for the observed stoichiometry and cooperativity in ligand binding. The ternary model based on the present structure and the previous R67 DHFR–folate complex provides insight into the catalytic mechanism and indicates that the relative orientation of the reactants in plasmid DHFR is different from that seen in chromosomal DHFRs.
Structural bases for substrate recognition and activity in Meaban virus nucleoside‐2′‐O‐methyltransferase
Authors: Mastrangelo Eloise , Bollati Michela , Milani Mario , Selisko Barbara , Peyrane Frederic , Canard Bruno , Grard Gilda , de Lamballerie Xavier , Bolognesi Martino
Published: May 2007

Viral methyltransferases are involved in the mRNA capping process, resulting in the transfer of a methyl group from S‐adenosyl‐L‐methionine to capped RNA. Two groups of methyltransferases (MTases) are known: (guanine‐N7)‐methyltransferases (N7MTases), adding a methyl group onto the N7 atom of guanine, and (nucleoside‐2′‐O‐)‐methyltransferases (2′OMTases), adding a methyl group to a ribose hydroxyl. We have expressed and purified two constructs of Meaban virus (MV; genus Flavivirus) NS5 protein MTase domain (residues 1–265 and 1–293, respectively). We report here the three‐dimensional structure of the shorter MTase construct in complex with the cofactor S‐adenosyl‐L‐methionine, at 2.9 Å resolution. Inspection of the refined crystal structure, which highlights structural conservation of specific active site residues, together with sequence analysis and structural comparison with Dengue virus 2′OMTase, suggests that the crystallized enzyme belongs to the 2′OMTase subgroup. Enzymatic assays show that the short MV MTase construct is inactive, but the longer construct expressed can transfer a methyl group to the ribose 2′O atom of a short GpppAC5 substrate. West Nile virus MTase domain has been recently shown to display both N7 and 2′O MTase activity on a capped RNA substrate comprising the 5′‐terminal 190 nt of the West Nile virus genome. The lack of N7 MTase activity here reported for MV MTase may be related either to the small size of the capped RNA substrate, to its sequence, or to different structural properties of the C‐terminal regions of West Nile virus and MV MTase‐domains.
Structure of the E. coli bifunctional GlmU acetyltransferase active site with substrates and products
Authors: Olsen Laurence R. , Vetting Matthew W. , Roderick Steven L.
Published: May 2007

The biosynthesis of UDP‐GlcNAc in bacteria is carried out by GlmU, an essential bifunctional uridyltransferase that catalyzes the CoA‐dependent acetylation of GlcN‐1‐PO4 to form GlcNAc‐1‐PO4 and its subsequent condensation with UTP to form pyrophosphate and UDP‐GlcNAc. As a metabolite, UDP‐GlcNAc is situated at a branch point leading to the biosynthesis of lipopolysaccharide and peptidoglycan. Consequently, GlmU is regarded as an important target for potential antibacterial agents. The crystal structure of the Escherichia coli GlmU acetyltransferase active site has been determined in complexes with acetyl‐CoA, CoA/GlcN‐1‐PO4, and desulpho‐CoA/GlcNAc‐1‐PO4. These structures reveal the enzyme groups responsible for binding the substrates. A superposition of these complex structures suggests that the 2‐amino group of GlcN‐1‐PO4 is positioned in proximity to the acetyl‐CoA to facilitate direct attack on its thioester by a ternary complex mechanism.
Structure of the PTB domain of tensin1 and a model for its recruitment to fibrillar adhesions
Authors: McCleverty Clare J. , Lin Diane C. , Liddington Robert C.
Published: May 2007

Tensin is a cytoskeletal protein that links integrins to the actin cytoskeleton at sites of cell‐matrix adhesion. Here we describe the crystal structure of the phosphotyrosine‐binding (PTB) domain of tensin1, and show that it binds integrins in an NPxY‐dependent fashion. Alanine mutagenesis of both the PTB domain and integrin tails supports a model of integrin binding similar to that of the PTB‐like domain of talin. However, we also show that phosphorylation of the NPxY tyrosine, which disrupts talin binding, has a negligible effect on tensin binding. This suggests that tyrosine phosphorylation of integrin, which occurs during the maturation of focal adhesions, could act as a switch to promote the migration of tensin–integrin complexes into fibronectin‐mediated fibrillar adhesions.
Crystal structure of the C‐terminal domain of splicing factor Prp8 carrying retinitis pigmentosa mutants
Authors: Zhang Lingdi , Shen Jingping , Guarnieri Michael T. , Heroux Annie , Yang Kui , Zhao Rui
Published: May 2007

Prp8 is a critical pre‐mRNA splicing factor. Prp8 is proposed to help form and stabilize the spliceosome catalytic core and to be an important regulator of spliceosome activation. Mutations in human Prp8 (hPrp8) cause a severe form of the genetic disorder retinitis pigmentosa, RP13. Understanding the molecular mechanism of Prp8's function in pre‐mRNA splicing and RP13 has been hindered by its large size (over 2000 amino acids) and remarkably low‐sequence similarity with other proteins. Here we present the crystal structure of the C‐terminal domain (the last 273 residues) of Caenorhabditis elegans Prp8 (cPrp8). The core of the C‐terminal domain is an α/β structure that forms the MPN (Mpr1, Pad1 N‐terminal) fold but without Zn2+ coordination. We propose that the C‐terminal domain is a protein interaction domain instead of a Zn2+‐dependent metalloenzyme as proposed for some MPN proteins. Mapping of RP13 mutants on the Prp8 structure suggests that these residues constitute a binding surface between Prp8 and other partner(s), and the disruption of this interaction provides a plausible molecular mechanism for RP13.
Pressure ulcer care in Spain: nurses’ knowledge and clinical practice
Authors: Pancorbo‐Hidalgo Pedro Luis , García‐Fernández Francisco Pedro , López‐Medina Isabel Maria , López‐Ortega Jesús
Published: May 2007

Aim.  This paper is a report of a study to determine: (a) Spanish nurses’ level of knowledge of existing guidelines for pressure ulcer prevention and treatment, (b) the level of implementation of this knowledge in clinical practice and (c) the professional and educational factors that influence knowledge and practice.

Background.  Improvement in pressure ulcer care depends both on the dissemination of knowledge and on its implementation in clinical practice. Studies carried out in several countries have demonstrated gaps in knowledge about recommendations for pressure ulcer care and deficiencies in their implementation.

Methods.  A survey was carried out between September 2001 and June 2002, targeting a cluster randomized sample of 2006 Registered Nurses and Licensed Practice Nurses working at hospitals, primary healthcare centres and elder care centres in Andalusia (Spain).

Results.  The response rate was 36·9% (n = 740). The level of knowledge of prevention interventions was 79·1%, while that of treatment interventions was 75·9%. The levels of implementation in clinical practice were notably lower: 68·1% for prevention, and 65·3% for treatment. Nurses holding a university degree obtained higher scores, and those who had received specific education in pressure ulcer care obtained higher scores both for knowledge and clinical practice. Taking part in research projects also improved knowledge implementation.

Conclusion.  Although most of the recommendations on pressure ulcer care found in guidelines are well known by nurses, there is a group of interventions about which they have insufficient knowledge and low implementation rates.
Nurses’ discourse in contraceptive prescribing: an analysis using Foucault's ‘procedures of exclusion’
Authors: Hayter Mark
Published: May 2007

Aim. This paper is a report of an analysis of the discourse about contraceptive efficacy and side effects used by nurses when prescribing contraception.

Background. All women seeking contraception should be informed of the efficacy and potential adverse effects of the particular method they are considering. This information facilitates an informed choice. Women also require this information in order to monitor for any side effects. Paradoxically, side effects are also a key factor in reducing adherence with contraceptive regimens. However, there is no literature that explores specifically how this issue is addressed in clinical consultations, or places these practices in a theoretical context.

Method. Forty‐nine consultations between nurses and women in sexual health clinics were audio‐recorded during 2002. Data were subject to a discourse analysis using Foucault's ‘procedures of exclusion’ to explore the discursive construction of contraceptive efficacy and side effects

Findings. The nurses employed specific discursive strategies when discussing contraception. When addressing efficacy, discourse centred on medico‐statistical facts, but side effects were described in lay terms that minimized their severity. Nurses contextualized contraceptive side effects within potential problems that women might experience in pregnancy, and also attempted to ‘normalize’ contraceptive‐related problems.

Conclusion. Discourse and its deployment play a key role in practitioner–client relationships that sexual health nurses need to become more aware of how they discuss clinical issues about contraception with women. Clinical data on contraceptive side‐effects are present in the literature, and it is important that sexual health nurses use this to help women make truly informed decisions.