bluuebunny/crossref_metadata_2025 huggingface dataset:
A comparison of spectral sharp and smooth filters in the analysis of nonlinear interactions and energy transfer in turbulence
Authors: Domaradzki J. Andrzej , Carati Daniele
Published: August 2007

Energy transfer in turbulence is a result of nonlinear interactions among different scales of motion. For the purposes of quantitative analyses, various definitions of scales of motion can be used. This nonuniqueness leads to the possibility, raised in the literature on the subject, that properties of the energy transfer deduced from such analyses can be qualitatively affected by the scale definitions employed. We address this question by computing detailed energy exchanges between different scales of motion in direct numerical simulations databases of isotropic turbulence and employing different scale definitions. The scales of motion are defined by decomposing velocity fields using three specific filters: sharp spectral, Gaussian, and tangent hyperbolic. The traditional analysis of the energy transfer in terms of sharp spectral filters is generalized to smooth filters with broad support in the spectral space. The computed detailed energy transfer functions show only a minor quantitative dependence on the filter type. The qualitative conclusions obtained using sharp spectral filters are the same as for smooth filters, unless the latter has a very broad spectral support.
Optical and electrical properties of 4H-SiC epitaxial layer grown with HCl addition
Authors: Calcagno L. , Izzo G. , Litrico G. , Foti G. , La Via F. , Galvagno G. , Mauceri M. , Leone S.
Published: August 2007

The introduction of hydrogen chloride (HCl) in the deposition chamber during the growth of 4H-SiC epitaxial layers allows very high growth rates to be achieved. The properties of the epilayers and the growth rate depend on many parameters such as the growth temperature and the C/Si, Cl/Si, and Si∕H2 ratios. We have used optical and electrical measurements to investigate the effect of the Cl/Si and Si∕H2 ratio and growth temperature on the epitaxial growth process. The growth rate increases with increasing Si∕H2 ratio and higher growth rates are obtained when HCl is added to the gas flow. Optical microscopy shows an improvement of the surface morphology, and luminescence measurements reveal a decrease in the concentration of complex defects with increasing Cl/Si ratio in the range of 0.05–2.0 and with increasing growth temperature from 1550 °C to 1650 °C. The electrical measurements on the diodes realized on these epitaxial layers show a decrease of the leakage current with increasing Cl/Si ratio and growth temperature over the same range. Deep level transient spectroscopy measurements indicate that the deep level EH6∕7, which is one of the main levels responsible for the high value of leakage current measured in the Schottky diodes, is greatly reduced using HCl as a growth additive.
Terrylene in hexadecane revisited: A hole burning study
Authors: Sigl Alfred , Orrit Michel , Reinot Tonu , Jankowiak Ryszard , Friedrich Josef
Published: August 2007

Holes burnt into the absorption spectrum of terrylene in hexadecane have quite unusual features: spectral diffusion behavior under thermal cycles shows a narrowing regime at very low temperatures (2–5K) followed by a plateau region (up to about 13K) and a broadening regime (T>13K). Thermal line broadening (quasihomogeneous linewidth) shows a nonmonotonous behavior as a function of temperature: at around 4K there is a maximum followed by a flat minimum and the onset of strong broadening at higher temperatures. Finally, the central hole shows one-sided narrowly spaced side features. This behavior is interpreted within the frame of a two-site model. One of the two sites can be well described by a standard two level system; the other, however, shows characteristic features of a multilevel system. The two sites are characterized by strongly different optical linewidths, phototransformation yields, and thermal stabilities.
Measurement of temperature profiles in turbulent pipe flow of polymer and surfactant drag-reducing solutions
Authors: Gasljevic K. , Aguilar G. , Matthys E. F.
Published: August 2007

A device was built to measure temperature profiles of turbulent pipe flows of various drag-reducing fluids. It is easy to use and reliable. We measured temperature profiles over a range of conditions leading to accurate measurements down to y+≈10, for tests carried over Reynolds numbers (Re) between 10 000 and 90 000. The effects of high heat fluxes and buoyancy, in particular, were quantified to ascertain the parameter range for accurate measurements. Temperature profiles measured for type-A polymer solution and for cationic surfactant solutions allowed us to see strong similarity between velocity and temperature profiles for drag-reducing surfactant solutions. A comparison between the slopes of the thermal and velocity buffer layers resulted in calculated turbulent Prandtl numbers between 6 and 9 for those drag-reducing solutions. We also used this tool to investigate drag reduction for a nonionic surfactant solution, which showed a significantly different fan-type profile, and also for a type-B drag-reducing polymer solution (Xanthan gum).
Point interaction Hamiltonians in bounded domains
Authors: Blanchard Ph. , Figari R. , Mantile A.
Published: August 2007

Making use of recent techniques in the theory of self-adjoint extensions of symmetric operators, we characterize the class of point interaction Hamiltonians in a three-dimensional bounded domain with regular boundaries. In the particular case of one point interaction acting in the center of a ball, we obtain an explicit representation of the point spectrum of the operator together with the corresponding eigenfunctions. These operators are used to build up a model system where the dynamics of a quantum particle depends on the state of a quantum bit.
A water bag theory of autoresonant Bernstein-Greene-Kruskal modes
Authors: Khain P. , Friedland L.
Published: August 2007

The adiabatic water bag theory describing formation and passage through phase-space of driven, continuously phase-locked (autoresonant) coherent structures in plasmas [L. Friedland et al., Phys. Rev. Lett. 96, 225001 (2006)] and of the associated Bernstein-Greene-Kruskal (BGK) modes is developed. The phase-locking is achieved by using a chirped frequency ponderomotive drive, passing through kinetic Čerenkov-type resonances. The theory uses the adiabatic invariants (conserved actions of limiting trajectories) in the problem and, for a flat-top initial distribution of the electrons, reduces the calculation of the self-field of the driven BGK mode to solution of a few algebraic equations. The adiabatic multiwater bag extension of the theory for applications to autoresonant BGK structures with more general initial distributions is suggested. The results of the theories are in very good agreement with numerical simulations.
Linear and nonlinear instability in a cylindrical enclosure caused by a rotating magnetic field
Authors: Koal Kristina , Stiller Jörg , Grundmann Roger
Published: August 2007

Rotating magnetic fields generate a swirling motion in electrically conductive fluids. In previous theoretical and experimental studies this flow was found to be susceptible to non-normal nonlinear transition mechanisms, which are triggered by small perturbations. In this Brief Communication we present a numerical investigation of the transition in a closed cylindrical container. Depending on the magnetic Taylor number, three different scenarios have been identified: a single subcritical burst, a series of supercritical bursts and, at higher Taylor numbers, a sustained unsteady regime. In all three cases, the unsteady stages are governed by Taylor-Görtler vortices.
Inelastic strain relaxation in the Ge quantum dot array
Authors: Talochkin A. B. , Markov V. A. , Mashanov V. I.
Published: August 2007

Raman spectra of Si∕Ge∕Si (100) structures with Ge quantum dots (QDs) obtained by means of the low-temperature (200–300°C) molecular beam epitaxy are investigated. An extremely narrow Ge phonon line of the “anomalously” high intensity and a doublet structure of the Ge–Si mode are observed. These features are explained by the formation of a pure pseudomorphic state of a QD array to a Si substrate. Additional broad Ge phonon lines related to inelastic strain relaxation are found under the variation of growth conditions. The observed strain relaxation is strongly nonuniform for the two well known mechanisms of inelastic strain relaxation.
Iterative image-based modeling and control for higher scanning probe microscope performance
Authors: Clayton G. M. , Devasia S.
Published: August 2007

In this article, we develop an image-based approach to model and control the dynamics of scanning probe microscopes (SPMs) during high-speed operations. SPMs are key enabling tools in the experimental investigation and manipulation of nano- and subnanoscale phenomena; however, the speed at which the SPM probe can be positioned over the sample surface is limited due to adverse dynamic effects. It is noted that SPM speed can be increased using model-based control techniques. Modeling the SPM dynamics is, however, challenging because currently available sensing methods do not measure the SPM tip directly. Additionally, the resolution of currently available sensing methods is limited by noise at higher bandwidth. Our main contribution is an iterative image-based modeling method which overcomes these modeling difficulties (caused by sensing limitations). The method is applied to model an experimental scanning tunneling microscope (STM) system and to achieve high-speed imaging. Specifically, we model the STM up to a frequency of 2000Hz (corresponds to ∼2∕3 of the resonance frequency of our system) and achieve ∼1.2% error in 1nm square images at that same frequency.
Prediction study of structural and elastic properties under the pressure effect of M2GaC (M=Ti,V,Nb,Ta)
Authors: Bouhemadou A. , Khenata R.
Published: August 2007

Using first-principles density functional calculations, the effect of high pressures, up to 20 GPa, on the structural and elastic properties of M2GaC, with M=Ti, V, Nb, and Ta, were studied by means of the pseudopotential plane-waves method. Calculations were performed within the local density approximation to the exchange-correlation approximation energy. The lattice constants and the internal parameters are in agreement with the available results. The elastic constants and their pressure dependence are calculated using the static finite strain technique. We derived the bulk and shear moduli, Young’s moduli, and Poisson’s ratio for ideal polycrystalline M2GaC aggregates. We estimated the Debye temperature of M2GaC from the average sound velocity. This is a quantitative theoretical prediction of the elastic properties of Ti2GaC, V2GaC, Nb2GaC, and Ta2GaC compounds and it still awaits experimental confirmation.
Negative magnetoresistance of organic field effect transistors
Authors: Nishioka Masaya , Lee Yeon-Bae , Goldman A. M. , Xia Yu , Frisbie C. Daniel
Published: August 2007

The magnetoresistance (MR) of organic field effect transistors has been studied. Both pentacene film and tetracene single crystal devices exhibit negative MRs of up to 0.57% at 9T. This effect has been observed between 150 and 300K and is temperature dependent. The phenomenon may result from the action of the magnetic field on the hopping transport of carriers. However, the possibility of a magnetocapacitance effect that would increase the number of carriers cannot be ruled out.
Transparent organic light-emitting diodes using resonant tunneling double barrier structures
Authors: Ryu Seung Yoon , Jo Sung Jin , Kim Chang Su , Choi Sang Hun , Noh Joo Hyon , Baik Hong Koo , Jeong Hee Seong , Han Dong Won , Song Seung Yong , Lee Kyu Sung
Published: August 2007

A semitransparent cathode of indium tin oxide (ITO)/Ag/ITO was developed as a resonant tunneling double barrier structure for transparent organic light-emitting diodes. A weak negative differential resistance was observed in devices using a 100nm thick ITO/Ag/ITO layer as a cathode in combination with a thin LiF∕Al layer. The current injection of devices was dominated by resonant tunneling, which induced no luminance at low voltage. This was achieved by employing an e-beam evaporated ITO/Ag/ITO cathode due to the double quantum barriers of ITO and the quantum well of Ag. The authors also applied the multilayer cathode to small molecule devices, which showed the same resonant tunneling currents.
Ionized impurity scattering in n-doped C60 thin films
Authors: Harada Kentaro , Li Fenghong , Maennig Bert , Pfeiffer Martin , Leo Karl
Published: August 2007

Carrier transport in organic films is usually dominated by hopping process, leading to different temperature dependence from that of inorganic crystals. The aurhors demonstrate that n-doped C60 films show temperature dependence analogous to inorganic semiconductors. At low temperatures, the conductivity increases with temperature, around room temperature, a maximum is reached and then the conductivity decreases. These observations are confirmed by the dependence of mobility on doping level. In contrast to previous reports for organic thin films, the C60 films show a decrease of mobility with increasing doping levels, i.e., they follow the well-known Matthiessen rule which is generally observed in inorganic semiconductors.
In situ observation of nanoparticle ordering at the air-water-substrate boundary in colloidal solutions using x-ray nanobeams
Authors: Roth S. V. , Autenrieth T. , Grübel G. , Riekel C. , Burghammer M. , Hengstler R. , Schulz L. , Müller-Buschbaum P.
Published: August 2007

The nanoscale structuring during evaporation of a droplet consisting of an aqueous colloidal solution of 2nm gold nanoparticles in water on a silicon substrate is followed in real time. The authors investigated the transfer of lateral order and vertical layering as a function of time at the three-phase contact line air-solution substrate combining a nanometer-sized x-ray beam with a grazing incidence geometry. A pronounced retardation of vertical ordering is observed with respect to lateral ordering. While individual layers are deposited during evaporation of the solvent, the growth parallel to the substrate shows a strongly nondiffusive behavior.
Negative photoconduction of planar heterogeneous random network of ZnO-carbon nanotubes
Authors: Sen S. , Chowdhary D. , Kouklin N. A.
Published: August 2007

In this letter, the authors report on the effect of negative photoconduction observed in heterogeneous two-dimensional random networks comprising single-walled nanotubes and ZnO particles, and investigated by room temperature dc-photoconduction measurements. For this, two-terminal thin film devices engineered by solution coating of the nanotubes with ZnO microparticles consistently exhibited increase in the resistance versus decrease in the nanotubes alone with ultraviolet illumination, which is explained within the model of interface-mediated charging/discharging effects. The study suggests the possibility of engineering reduced-cost and multirange nanotube light sensors based on extrinsic carrier modulation via external gating at the interface.
Radiation detector resolution over a continuous energy range
Authors: Zhang Yanwen , Milbrath Brian D. , Weber William J. , Elfman Mikael , Whitlow Harry J.
Published: August 2007

An ion approach is demonstrated to determine energy resolution in both semiconductor detectors and scintillators over a continuous energy range. For semiconductors, the energy resolution of a silicon detector was measured as a function of helium ion energy, and the values from extrapolation to high energies are in good agreement with the literature data from alpha measurements. For scintillators, benchmark crystals subject to He+ irradiation were investigated, and the agreement of energy resolution between the ion and gamma measurements indicates that the ion approach can be used to predict the energy resolution of the candidate materials in thin-film form or small crystals when large crystals necessary for gamma-ray measurements are unavailable.
Domain wall displacement by current pulses injection in submicrometer Permalloy square ring structures
Authors: Vavassori P. , Metlushko V. , Ilic B.
Published: August 2007

The magnetoresistance in submicrometer Permalloy square ring structures has been experimentally measured and modeled. The authors show that using an external field they can place a head-to-head domain wall at a selected corner of the ring and sense its position by magnetoresistance. They finally demonstrate that a domain wall can be reversibly and controllably displaced by current pulses of different polarity. Their observations can be explained by a directional spin-torque effect.
Scanning mass spectrometer for quantitative reaction studies on catalytically active microstructures
Authors: Roos M. , Kielbassa S. , Schirling C. , Häring T. , Bansmann J. , Behm R. J.
Published: August 2007

We describe an apparatus for spatially resolving scanning mass spectrometry which is able to measure the gas composition above catalytically active microstructures or arrays of these microstructures with a lateral resolution of better than 100μm under reaction conditions and which allows us to quantitatively determine reaction rates on individual microstructures. Measurements of the three-dimensional gas composition at different vertical distances and separations between active structures allow the evaluation of gas phase mass transport effects. The system is based on a piezoelectrically driven positioning substage for controlled lateral and vertical positioning of the sample under a rigidly mounted capillary probe connecting to a mass spectrometer. Measurements can be performed at pressures in the range of <10−2–10mbars and temperatures between room temperature and 450°C. The performance of the setup is demonstrated using the CO oxidation reaction on Pt microstructures on Si with sizes between 100 and 300μm and distances in the same order of magnitude, evaluating CO2 formation and CO consumption above the microstructures. The rapidly decaying lateral resolution with increasing distance between sample and probe underlines the effects of (lateral) gas transport in the room between sample and probe. The reaction rates and apparent activation energy obtained from such measurements agree with previous data on extended surfaces, demonstrating the feasibility of determining absolute reaction rates on individual microstructures.
Rapid prototyping of three-dimensional microstructures from multiwalled carbon nanotubes
Authors: Hung Wei Hsuan , Kumar Rajay , Bushmaker Adam , Cronin Stephen B. , Bronikowski Michael J.
Published: August 2007

The authors report a method for creating three-dimensional carbon nanotube structures, whereby a focused laser beam is used to selectively burn local regions of a dense forest of multiwalled carbon nanotubes. Raman spectroscopy and scanning electron microscopy are used to quantify the threshold for laser burnout and depth of burnout. The minimum power density for burning carbon nanotubes in air is found to be 244μW∕μm2. We create various three-dimensional patterns using this method, illustrating its potential use for the rapid prototyping of carbon nanotube microstructures. Undercut profiles, changes in nanotube density, and nanoparticle formation are observed after laser surface treatment and provide insight into the dynamic process of the burnout mechanism.
Effects of polymer coating on the adsorption of gas molecules on carbon nanotube networks
Authors: Kim Sanghun , Lee Hyeong Rag , Yun Yong Ju , Ji Seungmuk , Yoo Kwonjae , Yun Wan Soo , Koo Ja-Yong , Ha Dong Han
Published: August 2007

Functionalization of carbon nanotubes (CNTs) with polymers such as polyethyleneimine or nafion was found to not change the adsorption properties of gas molecules on CNTs, although functionalization can remarkably enhance the sensitivity of gas sensors. Charge transfer between adsorbed molecules and single-walled carbon nanotubes (SWCNTs) at defect sites causes a steep and nonlinear conductance change at low gas concentrations, while molecules physically adsorbed on the pristine surfaces result in the linear electrical responses at higher concentrations. In addition, the molecular binding energies at defect sites of SWCNTs were measured to be 0.61eV for NO2 and 0.53eV for NH3.
Generation of high-quality lines and arrays using nanoparticle controlling processes
Authors: Huh Seung H. , Riu Doh H. , Naono Y. , Taguchi Y. , Kawabata S. , Nakajima A.
Published: August 2007

Highly reliable lines and arrays comprising the smallest metallic nanoparticles (NPs) were produced by using a combination of techniques such as lithography, lift-off, size selection, aerosol deposition, and NP colloids. The narrowest 80nm Au lines were produced by the deposition of only 4nm Au NPs, driven by two factors—NP kinetics and collision-induced surface melting. An array of unsupported free 30–100 Ni NPs and one of 20–40nm Ni NPs supported in holes were produced by the principles of hole-size-induced filtering and the binding of thiol groups.
Room temperature ferromagnetism in Mn-doped ZnO films mediated by acceptor defects
Authors: Xu Qingyu , Schmidt Heidemarie , Hartmann Lars , Hochmuth Holger , Lorenz Michael , Setzer Annette , Esquinazi Pablo , Meinecke Christoph , Grundmann Marius
Published: August 2007

Mn-doped ZnO films with preferred c-axis growth orientation were prepared by pulsed laser deposition under N2 atmosphere on a-plane sapphire substrates. Large positive magnetoresistance amounting to 60% was observed at 5K. Clear anomalous Hall effect was observed at 20K. Ferromagnetism with Curie temperature higher than 290K has been observed, and a deep acceptor trap due to Zn vacancies with a thermal activation energy amounting to 0.815eV has been detected by deep-level transient spectroscopy. For comparison, only paramagnetism was observed in Mn-doped ZnO films with donor traps prepared under O2 atmosphere. Their results clearly demonstrate that the ferromagnetism in Mn-doped ZnO originates from the parallel alignment of magnetic moments mediated by acceptor defects.
Electronic structures of N quantum dot molecule
Authors: Li Shu-Shen , Xia Jian-Bai
Published: August 2007

The electronic structures of N quantum dot molecules (QDMs) are investigated theoretically in the framework of effective-mass envelope function theory. The electron and hole energy levels are calculated. In the calculations, the effects of finite offset and valence-band mixing are taken into account. The theoretical method can be used to calculate the electronic structures of any QDM. The results show that (1) electronic energy levels decrease monotonically and the energy difference between the N QDMs decreases as the quantum dot (QD) radius increases; (2) the electron energy level is lower and quantum confinement is smaller for the larger N QDM; (3) the hole ground state energy level is lower for the one dot QDM than N (greater 1) QDMs if the QD radius is larger than about 5nm due to the valence-band mixing. The results are useful for the application of the N QDM to photoelectric devices.
Simultaneous in situ detection of alkaline phosphatase activity and polyphosphate in arbuscules within arbuscular mycorrhizal roots
Authors: Funamoto Rintaro , Saito Katsuharu , Oyaizu Hiroshi , Saito Masanori , Aono Toshihiro
Published: August 2007

Inorganic phosphate (Pi) metabolism in arbuscules of arbuscular mycorrhizal (AM) fungi is not well understood, although recent research has revealed that host plants absorb Pi around arbuscules with mycorrhiza-specific transporters. Therefore, we analysed the localisation of polyphosphate (polyP) and alkaline phosphatase (ALP) activity in arbuscules, which could be indicators of Pi metabolism. We developed a dual-labelling method for polyP and ALP activity, i.e. first labelling with fluorescent probes 4′,6-diamidino-2-phenyl-indole dihydrochloride (DAPI) and then labelling with enzyme-labelled fluorescence (ELF97). The dual-labelling method made it possible to observe polyP and ALP activity signals simultaneously in mycorrhizal roots. The dual-labelling method revealed that ALP activity was mainly observed in mature arbuscules where polyP was rarely observed. The expression of the AM fungal ALP gene was suppressed in the knockdown plants of an AM-inducible Pi-transporter, and there was much polyP in arbuscules that showed low ALP activity. These topological observations suggest that there may be some relationships between polyP metabolism and ALP activity in arbuscules, and that these are, in part, controlled by Pi uptake by plants via the AM-inducible Pi-transporter.
Corrigendum to: Plant isotopic composition provides insight into mechanisms underlying growth stimulation by AM fungi in a semiarid environment
Authors: Querejeta José I. , Allen Michael F. , Alguacil María M. , Roldán Antonio
Published: August 2007

We hypothesised that improved plant water status and enhanced transpiration are key mechanisms involved in plant growth stimulation by native arbuscular mycorrhizal fungi (AMF) in semiarid calcareous soils. Seedlings of the dryland shrubs Pistacia lentiscus L. and Retama sphaerocarpa L. were pre-inoculated with a mixture of eight native Glomus spp. fungi, or left un-inoculated, before transplanting into a degraded site in south-eastern Spain. Pre-inoculated Pistacia and Retama shrubs grew faster after transplanting, despite spontaneous colonisation of control plants by local AMF. Pre-inoculation enhanced shoot water content and shoot �15N in both shrub species. Increased potassium uptake and improved water relations were key mechanisms behind growth stimulation by native AMF in Pistacia. Shoot �18O (a proxy measure of stomatal conductance) was significantly less negative in AMF-inoculated than in control Pistacia seedlings, indicating enhanced cumulative transpiration in the former. In contrast, shoot �18O was unaffected by AMF inoculation in Retama, a leafless leguminous shrub with photosynthetic stems. Growth stimulation by native AMF in Retama was attributed to increased phosphorus uptake, enhanced atmospheric nitrogen fixation and a largely nutrient-mediated improvement of plant water status. Shoot �13C was not significantly influenced by AMF inoculation in either shrub species, thus suggesting roughly parallel upshifts in photosynthetic and transpiration rates which did not affect plant water use efficiency.
Resistance to radial CO2 diffusion contributes to between-tree variation in CO2 efflux of Populus deltoides stems
Authors: Steppe Kathy , Saveyn An , McGuire Mary Anne , Lemeur Raoul , Teskey Robert O.
Published: August 2007

Rates of CO2 efflux of stems and branches are highly variable among and within trees and across stands. Scaling factors have only partially succeeded in accounting for the observed variations. In this study, the resistance to radial CO2 diffusion was quantified for tree stems of an eastern cottonwood (Populus deltoides Bartr. ex Marsh.) clone by direct manipulation of the CO2 concentration ([CO2]) of xylem sap under controlled conditions. Tree-specific linear relationships between rates of stem CO2 efflux (JO) and xylem [CO2] were found. The resistance to radial CO2 diffusion differed 6-fold among the trees and influenced the balance between the amount of CO2 retained in the xylem v. that which diffused to the atmosphere. Therefore, we hypothesised that variability in the resistance to radial CO2 diffusion might be an overlooked cause for the inconsistencies and large variations in woody tissue CO2 efflux. It was found that transition from light to dark conditions caused a rapid increase in JO and xylem [CO2], both in manipulated trees and in an intact tree with no sap manipulation. This resulted in an increased resistance to radial CO2 diffusion during the dark, at least for trees with smaller daytime resistances. Stem diameter changes measured in the intact tree supported the idea that higher actual respiration rates occurred at night owing to higher metabolism in relation to an improved water status and higher turgor pressure.
Responses to chilling of two Eucalyptus globulus clones with contrasting drought resistance
Authors: Costa e Silva Filipe , Shvaleva Alla , Almeida M. Helena , Chaves M. Manuela , Pereira João S.
Published: August 2007

The effect of chilling on growth and plant hydraulic properties in a drought-resistant clone (CN5) and a drought-sensitive clone (ST51) of Eucalyptus globulus Labill. was evaluated. Chilling (10/5°C, day/night) led to a general decrease in growth of both clones and significant reductions in root hydraulic conductivity, rate of photosynthesis and stomatal conductance in comparison to plants grown at control temperature (24/16°C). The drought-resistant CN5 clone maintained higher root growth and lower leaf-to-root-area ratio than the drought-sensitive ST51 clone, in both temperature treatments. Conversely, ST51 exhibited greater carbon allocation to the foliage and higher hydraulic conductance than clone CN5 at both temperatures. Plants of both clones, when acclimated to chilling, maintained a higher hydraulic conductivity than control plants exposed to chilling temperatures without acclimation. Under chilling, the main differences between clones were a higher water status and anthocyanin concentration in CN5 plants, and a stronger inhibition of root growth in ST51 plants. Except for roots, the hypothesis of a lower depression of growth rate in the drought-resistant clone under chilling was not verified. However, higher root growth under low temperatures, as observed in CN5, can be an advantageous trait in Mediterranean-type environments, protecting trees against summer water-stress.
The maize Activator/Dissociation system is functional in hexaploid wheat through successive generations
Authors: Pastori Gabriela M. , Huttly Alison , West Jevon , Sparks Caroline , Pieters Alejandro , Luna Celina M. , Jones Huw D. , Foyer Christine H.
Published: August 2007

The aim of the present study was to provide useful background information and evidence of the functionality of the maize Activator/Dissociation (Ac/Ds) system in hexaploid wheat. Two transgenic parental wheat lines, one harbouring the immobilised Ac element (iAc) and the other the Ds element (pUbi[Ds-uidA]bar), were crossed. Transient GUS assays confirmed that the iAc transposase is active in hexaploid wheat. Selected F1 and F2 lines were analysed by PCR using primers specific to Ac, uidA and bar genes. The primer pair Ubi/bar-tag was used to detect excision of the Ds-uidA sequence, which occurred at a frequency of 39% in the F1 generation. Lines free of Ac and showing evidence of Ds excision were subject to Southern analysis, which indicated that at least one transposition event might have occurred in these lines. Although more evidence is required to unequivocally support the reintegration of the Ds element in the wheat genome, the evidence presented here nevertheless demonstrates the effectiveness and potential value of using this system to tag genes in wheat.
ALL1 fusion proteins induce deregulation of
EphA7
and ERK phosphorylation in human acute leukemias
Authors: Nakanishi Hiroshi , Nakamura Tatsuya , Canaani Eli , Croce Carlo M.
Published: August 2007

Erythropoietin-producing hepatoma-amplified sequence (Eph) receptor tyrosine kinases and their cell-surface-bound ligands, the ephrins, function as a unique signaling system triggered by cell-to-cell interaction and have been shown to mediate neurodevelopmental processes. In addition, recent studies showed deregulation of some of
Eph
/
ephrin
genes in human malignancies, suggesting the involvement of this signaling pathway in tumorigenesis. The
ALL1
(also termed
MLL
) gene on human chromosome 11q23 was isolated by virtue of its involvement in recurrent chromosome translocations associated with acute leukemias with poor prognosis. The translocations fuse
ALL1
to any of >50 partner genes and result in production of chimeric proteins composed of the ALL1 N terminus and the C terminus of the partner protein. The most common translocations in
ALL1
-associated leukemias are t(4;11) and t(9;11), which generate ALL1/AF4 and ALL1/AF9 fusion protein, respectively. In the present study, we sought to determine whether ALL1 fusion proteins are involved in regulation of
Eph
/
ephrin
genes. Screening of K562 cells producing recombinant ALL1/AF4 or ALL1/AF9 fusion protein revealed transcriptional up-regulation of the
EphA7
. Consistent with this finding, siRNA-mediated suppression of ALL1/AF4 in SEMK2 cells carrying the t(4;11) chromosome translocation resulted in down-regulation of
EphA7
. ChIP analysis demonstrated the occupancy of tagged ALL1 fusion proteins on the
EphA7
promoter, pointing to
EphA7
as a direct target of the formers. Further studies demonstrate that EphA7 up-regulation is accompanied by ERK phosphorylation. Finally, we show apoptotic cell death, specific for leukemic cells carrying the t(4;11) chromosome translocation, after treatment of the cells with an ERK phosphorylation blocker.
Automated
de novo
prediction of native-like RNA tertiary structures
Authors: Das Rhiju , Baker David
Published: August 2007

RNA tertiary structure prediction has been based almost entirely on base-pairing constraints derived from phylogenetic covariation analysis. We describe here a complementary approach, inspired by the Rosetta low-resolution protein structure prediction method, that seeks the lowest energy tertiary structure for a given RNA sequence without using evolutionary information. In a benchmark test of 20 RNA sequences with known structure and lengths of ≈30 nt, the new method reproduces better than 90% of Watson–Crick base pairs, comparable with the accuracy of secondary structure prediction methods. In more than half the cases, at least one of the top five models agrees with the native structure to better than 4 Å rmsd over the backbone. Most importantly, the method recapitulates more than one-third of non-Watson–Crick base pairs seen in the native structures. Tandem stacks of “sheared” base pairs, base triplets, and pseudoknots are among the noncanonical features reproduced in the models. In the cases in which none of the top five models were native-like, higher energy conformations similar to the native structures are still sampled frequently but not assigned low energies. These results suggest that modest improvements in the energy function, together with the incorporation of information from phylogenetic covariance, may allow confident and accurate structure prediction for larger and more complex RNA chains.
Breaking up the correlation between efficacy and toxicity for nonviral gene delivery
Authors: Breunig Miriam , Lungwitz Uta , Liebl Renate , Goepferich Achim
Published: August 2007

Nonviral nucleic acid delivery to cells and tissues is considered a standard tool in life science research. However, although an ideal delivery system should have high efficacy and minimal toxicity, existing materials fall short, most of them being either too toxic or little effective. We hypothesized that disulfide cross-linked low-molecular-weight (MW) linear poly(ethylene imine) (MW <4.6 kDa) would overcome this limitation. Investigations with these materials revealed that the extracellular high MW provided outstandingly high transfection efficacies (up to 69.62 ± 4.18% in HEK cells). We confirmed that the intracellular reductive degradation produced mainly nontoxic fragments (cell survival 98.69 ± 4.79%). When we compared the polymers in >1,400 individual experiments to seven commercial transfection reagents in seven different cell lines, we found highly superior transfection efficacies and substantially lower toxicities. This renders reductive degradation a highly promising tool for the design of new transfection materials.
Solvent coarse-graining and the string method applied to the hydrophobic collapse of a hydrated chain
Authors: Miller Thomas F. , Vanden-Eijnden Eric , Chandler David
Published: August 2007

With computer simulations of >100,000 atoms, the mechanism for the hydrophobic collapse of an idealized hydrated chain was obtained by tiling space with (0.2 nm)
3
cubes and projecting the atomistic water molecule positions onto this grid. With the coarse-grained field thus defined, the string method in collective variables was used to compute a minimum free-energy pathway (MFEP) for the collapsing chain. These calculations provide a proof of principle for a coarse-grained description of water solvent. Furthermore, the calculated MFEP characterizes the mechanism for the collapse of the hydrated chain by providing a path of maximum likelihood for dynamical trajectories. The reliability of the calculated MFEP was confirmed with the use of conventional molecular dynamics trajectories. Analysis of the MFEP provides atomistic confirmation for the mechanism of hydrophobic collapse proposed by ten Wolde and Chandler. In particular, we show that length-scale-dependent hydrophobic dewetting is the rate-limiting step in the hydrophobic collapse of the considered chain.
Determination of the effect of a single hemodialysis session on retrobulbar blood hemodynamics by color Doppler ultrasonography
Authors: Tosun Ö. , Davutluoglu B. , Arda K. , Boran M. , Yarangumeli A. , Kurt A. , Ozkan D.
Published: August 2007

Background: Retrobulbar hemodynamic alterations can occur during hemodialysis sessions, and patients with chronic renal failure may experience visual problems.

Purpose: To evaluate the effect of single-session hemodialysis on retrobulbar vessel hemodynamics by color Doppler ultrasonography.

Material and Methods: Thirty-five patients were included in the study. Retrobulbar blood flows were examined before and after dialysis sessions. Doppler spectral patterns of retrobulbar blood flow were evaluated. The t test for paired samples and the Wilcoxon matched-pairs signed-rank test were used for comparing the flow values before and after dialysis.

Results: Systolic and diastolic blood flow velocities of the ophthalmic artery, central retinal artery, central retinal vein, nasal posterior ciliary artery, and temporal posterior ciliary artery were found to be decreased bilaterally after hemodialysis sessions. No significant change was observed in resistivity index values after hemodialysis sessions.

Conclusion: Our findings reveal that retrobulbar circulation was disturbed after a single hemodialysis session.
Soft-copy reading in digital mammography of microcalcifications: diagnostic performance of a 5-megapixel cathode ray tube monitor versus a 3-megapixel liquid crystal display monitor in a clinical setting
Authors: Uematsu T. , Kasami M. , Uchida Y.
Published: August 2007

Background: A recent study using dedicated contrast-detail phantoms showed that the image quality of a 3-megapixel (M) monitor can approach that of a 5M monitor in digital mammography.

Purpose: To compare a 5M cathode ray tube (CRT) monitor with a 3M liquid crystal display (LCD) monitor for soft-copy reading of digital mammography of microcalcifications in a clinical setting.

Material and Methods: 100 screen-detected microcalcification lesions (34 malignant and 66 benign) without mass that had been evaluated with 11-gauge stereotactic vacuum-assisted breast biopsy or definitive surgery were recruited into the study. One radiologist analyzed the soft-copy mammograms on a 5M CRT monitor and a 3M LCD monitor with 5 months between interpretations and scored the likelihood of malignancy and calcification distribution on a five-point scale. Calcification morphology and breast density were scored on a four-point scale. Positive predictive value (PPV) and negative predictive value (NPV) were calculated on the basis of a Breast Imaging Reporting and Data System. The interpretation time was also measured.

Results: There was no significant difference in the likelihood of malignancy ( P = 0.655), calcification morphology ( P = 0.168), calcification distribution ( P = 0.11), and breast density ( P = 0.0608). The PPV and NPV of soft-copy reading on the 5M CRT monitor was 57% (30/53) and 91% (43/47), respectively, identical to the results using the 3M LCD monitor. The total interpretation time averaged 88 s for the 5M CRT monitor and 67 s for the 3M LCD monitor ( P<0.0001).

Conclusion: Soft-copy reading of a digital mammography of microcalcifications with a 3M LCD monitor was similar in diagnostic performance to a 5M CRT monitor in this study.
Preliminary study of hemodynamics in human carotid bifurcation by computational fluid dynamics combined with magnetic resonance angiography
Authors: Xue Yunjing , Gao Peyi , Lin Yan , Dai Chengbo
Published: August 2007

Background: A longstanding hypothesis that correlates fluid dynamic forces and atherosclerotic disease has led to numerous analytical, numerical, and experimental studies over the years because it is very difficult to measure the hemodynamic variables of blood in vivo.

Purpose: To investigate the technique of visualization and quantitation of hemodynamic variables at carotid artery bifurcation in vivo by combining computational fluid dynamics (CFD) and vascular imaging.

Material and Methods: Twenty-six healthy volunteers underwent magnetic resonance (MR) angiography of the bilateral carotid artery by a 3.0T whole-body scanner. Hemodynamic variables at these carotid bifurcations were calculated and visualized by combining vascular imaging post-processing and CFD.

Results: The average velocity of the carotid bifurcation in the systolic phase and the diastolic phase was 0.46±0.24 m/s and 0.23±0.05 m/s, respectively. Eddy current and back flows were observed at bifurcation and the lateral part of the proximal internal carotid arteries (ICA) and external carotid arteries (ECA), and the shapes of them changed with phases of the cardiac cycle, which were significant at the middle of the systolic phase and faded out quickly downstream of the ICA and ECA. The average range of wall shear stress (WSS) at the bifurcation was 4.36±1.32 Pa, and the maximum WSS was 18.02±4.11 Pa. The WSS map revealed a large region of low WSS at the carotid bulb and extended to the outer wall in the proximal end of the ICA (the lowest value was below 0.5 Pa), and there was also a small region of low WSS at the outer wall in the proximal end of the ECA.

Conclusion: CFD combined with vascular imaging can calculate and visualize hemodynamic variables at carotid bifurcation in vivo individually.
Radiological findings of primary retroperitoneal ewing sarcoma
Authors: Ulusan S. , Koc Z. , Tuba Canpolat E. , Çolakoglu T.
Published: August 2007

Ewing sarcomas are most commonly located in bone, while extraskeletal involvement of the retroperitoneum is extremely rare. We describe the radiologic and pathological findings in an adult patient with retroperitoneal extraskeletal Ewing sarcoma.
A class of perverse sheaves on a partial flag manifold
Authors: Lusztig G.
Published: August 2007

We introduce a class of perverse sheaves on a partial flag manifold of a connected reductive group

G
G

defined over a finite field which are equivariant for the action of the group of rational points of

G
G

. The definition of this class is similar to the definition of parabolic character sheaves.
Prevalence and regional variation in meticillin-resistant Staphylococcus aureus (MRSA) in the USA and comparative in vitro activity of tigecycline, a glycylcycline antimicrobial
Authors: Goff Debra A. , Dowzicky Michael J.
Published: August 2007

The Tigecycline Evaluation and Surveillance Trial (T.E.S.T.) is a surveillance study established in 2004 to monitor the activity of tigecycline, the first glycylcycline, and comparator agents [β-lactams (including penicillins, cephalosporins and carbapenems), glycopeptides, tetracyclines, fluoroquinolones and oxazolidinones] against Gram-positive and Gram-negative pathogens worldwide. This report examines 1692 isolates of Staphylococcus aureus collected in the continental United States between January 2004 and September 2005. Meticillin-resistant S. aureus (MRSA) accounted for 52.0 % of isolates. Prevalence of MRSA by state ranged from 12.5 % in New Hampshire to 100 % in Kentucky. All isolates were susceptible to tigecycline, linezolid and vancomycin. In vitro, tigecycline was potent against both meticillin-susceptible S. aureus (MSSA) (MIC50 and MIC90=0.12 μg ml−1) and MRSA (MIC50=0.12 μg ml−1; MIC90=0.25 μg ml−1). Only a single isolate was resistant to three or more antimicrobial classes. Ninety-six isolates (5.7 %) were susceptible to the complete antimicrobial panel.
Fatal post-traumatic zygomycosis in an immunocompetent young patient
Authors: Kontogiorgi Marina , Floros Ioannis , Koroneos Apostolos , Vamvouka Chrysanthi , Paniara Olga , Roussos Charis , Routsi Christina
Published: August 2007

Zygomycosis, a relatively uncommon infection, usually occurs among immunocompromised individuals. It has been reported only rarely in trauma patients. A fatal case is reported of pulmonary and rapidly progressive cutaneous zygomycosis in a young, otherwise healthy farmer, with multiple bone fractures, wounds and soft tissue injuries after an accident with an agricultural machine in the field. Rhizopus spp. was isolated from both cultures of bronchial washings and wound samples. The diagnosis was confirmed by histopathological examination of tissue specimens from a large wound. Despite systemic antifungal therapy and surgical debridement, the patient's condition deteriorated and he died from refractory septic shock.
Utility of mycobacterial interspersed repetitive unit typing for differentiating Mycobacterium tuberculosis isolates in Wuhan, China
Authors: Han Hui , Wang Fang , Xiao Yong , Ren Yi , Chao Yanjie , Guo Aizhen , Ye Lingxiang
Published: August 2007

Mycobacterial interspersed repetitive unit (MIRU) typing has been found to allow rapid, reliable, high-throughput genotyping of Mycobacterium tuberculosis, and may represent a feasible approach to study M. tuberculosis molecular epidemiology. To evaluate the use of MIRU typing in discriminating M. tuberculosis strains, isolates from 105 patients in Wuhan City, China, were genotyped by this method as compared to spoligotyping. MIRU typing identified 55 types that defined 21 clusters and 34 unique isolates. The discriminatory power was high [Hunter–Gaston discriminatory index (HGDI), 0.97]. Spoligotyping showed that 86 (81.9 %) of 105 isolates belonged to the Beijing family genotype. For Beijing family and non-Beijing strains, the discriminatory power of MIRU was high (HGDI, 0.95 and 0.98, respectively). Among the alleles of the MIRU loci for the Beijing family, only locus 26 was highly discriminative, but for non-Beijing strains, loci 10, 16 and 26 were highly discriminative. MIRU typing is a simple and fast method which may be used for preliminary screening of M. tuberculosis isolates in China.