bluuebunny/crossref_metadata_2025 huggingface dataset:
Two-photon absorption spectra of carotenoids compounds
Authors: Vivas Marcelo Gonçalves , Silva Daniel Luiz , Boni Leonardo de , Zalesny Robert , Bartkowiak Wojciech , Mendonca Cleber Renato
Published: May 2011

Carotenoids are biosynthetic organic pigments that constitute an important class of one-dimensional π-conjugated organic molecules with enormous potential for application in biophotonic devices. In this context, we studied the degenerate two-photon absorption (2PA) cross-section spectra of two carotenoid compounds (β-carotene and β-apo-8′-carotenal) employing the conventional and white-light-continuum Z-scan techniques and quantum chemistry calculations. Because carotenoids coexist at room temperature as a mixture of isomers, the 2PA spectra reported here are due to samples containing a distribution of isomers, presenting distinct conjugation length and conformation. We show that these compounds present a defined structure on the 2PA spectra, that peaks at 650 nm with an absorption cross-section of approximately 5000 GM, for both compounds. In addition, we observed a 2PA band at 990 nm for β-apo-8′-carotenal, which was attributed to a overlapping of 11Bu+-like and 21Ag–-like states, which are strongly one- and two-photon allowed, respectively. Spectroscopic parameters of the electronic transitions to singlet-excited states, which are directly related to photophysical properties of these compounds, were obtained by fitting the 2PA spectra using the sum-over-states approach. The analysis and interpretations of the 2PA spectra of the investigated carotenoids were supported by theoretical predictions of one- and two-photon transitions carried out using the response functions formalism within the density functional theory framework, using the long-range corrected CAM-B3LYP functional.
Temperature-induced migration of a bubble in a soft microcavity
Authors: Selva Bertrand , Cantat Isabelle , Jullien Marie-Caroline
Published: May 2011

We perform studies of pancake-like shaped bubbles submitted to a temperature gradient in a micrometric height Hele-Shaw cell. We show that under the experimental conditions, usually found in microfluidic devices, the temperature-induced dilation of the cavity overcomes the thermocapillary convection due to surface tension variation, effectively driving the bubble toward the cold side of the cavity. The bubble velocity is experimentally characterized as a function of the bubble radius, the temperature gradient, and the initial Hele-Shaw cell thickness. We propose a theoretical prediction of the bubble velocity, based on the analytical resolution of the hydrodynamical problem. The equations set closure is ensured by the pressure value near the bubble and by the dissipation in the moving meniscus.
Korteweg-de Vries Burgers equation for magnetosonic wave in plasma
Authors: Hussain S. , Mahmood S.
Published: May 2011

Korteweg-de Vries Burgers (KdVB) equation for magnetosonic wave propagating in the perpendicular direction of the magnetic field is derived for homogeneous electron-ion magneto-plasmas. The dissipation in the system is taken into account through the kinematic viscosity of the ions. The effects of kinematic viscosity of ions, plasma density, and magnetic field strength on the formation of magnetosonic shocks are investigated. It is found that the shock strength is enhanced with the increase in the plasma density of the system. However, the increase in magnetic field strength decreases the amplitude of magnetosonic shock wave. The critical value of the dissipative coefficient to form oscillatory profile and monotonic shock is also discussed. The numerical results have also been plotted by taking the parameters from laboratory plasma experiments.
Buneman instability in a magnetized current-carrying plasma with velocity shear
Authors: Che H. , Goldman M. V. , Newman D. L.
Published: May 2011

Buneman instability is often driven in magnetic reconnection. Understanding how velocity shear in the beams driving the Buneman instability affects the growth and saturation of waves is relevant to turbulence, heating, and diffusion in magnetic reconnection. Using a Mathieu-equation analysis for weak cosine velocity shear together with Vlasov simulations, the effects of shear on the kinetic Buneman instability are studied in a plasma consisting of strongly magnetized electrons and cold unmagnetized ions. In the linearly unstable phase, shear enhances the coupling between oblique waves and the sheared electron beam, resulting in a wider range of unstable eigenmodes with common lower growth rates. The wave couplings generate new features of the electric fields in space, which can persist into the nonlinear phase when electron holes form. Lower hybrid instabilities simultaneously occur at k||/k⊥~me/mi with a much lower growth rate and are not affected by the velocity shear.
Vibrational and rotational cooling of NO+ in collisions with He
Authors: Stoecklin T. , Voronin A.
Published: May 2011

A quantum mechanical investigation of the vibrational and rotational deactivation of NO+ in collisions with He atoms in the cold and ultracold regime is presented. Ab initio potential energy calculations are carried out at BCCD(T) level and a new global 3D potential energy surface (PES) is obtained by fitting ab initio points within the reproducing kernel Hilbert space method. As a first test of this PES the bound state energies of the 3He–NO+ and 4He–NO+ complexes are calculated and compared to previous rigid rotor calculations. The efficiency of the vibrational and the rotational cooling of this molecular ion using a buffer gas of helium is then investigated by performing close coupling scattering calculations for collision energy ranging from 10−6 to 2000 cm−1. The calculations are performed for the two isotopes 3He and 4He and the results are compared to the available experimental data.
Power loss of a single electron charge distribution confined in a quantum plasma
Authors: Mehramiz A. , Mahmoodi J. , Sobhanian S.
Published: May 2011

The dielectric tensor for a quantum plasma is derived by using a linearized quantum hydrodynamic theory. The wave functions for a nanostructure bound system have been investigated. Finally, the power loss for an oscillating charge distribution of a mixed state will be calculated, using the dielectric function formalism.
An alternative to the plasma emission model: Particle-in-cell, self-consistent electromagnetic wave emission simulations of solar type III radio bursts
Authors: Tsiklauri David
Published: May 2011

High-resolution (sub-Debye length grid size and 10 000 particle species per cell), 1.5D particle-in-cell, relativistic, fully electromagnetic simulations are used to model electromagnetic wave emission generation in the context of solar type III radio bursts. The model studies generation of electromagnetic waves by a super-thermal, hot beam of electrons injected into a plasma thread that contains uniform longitudinal magnetic field and a parabolic density gradient. In effect, a single magnetic line connecting Sun to Earth is considered, for which five cases are studied. (i) We find that the physical system without a beam is stable and only low amplitude level electromagnetic drift waves (noise) are excited. (ii) The beam injection direction is controlled by setting either longitudinal or oblique electron initial drift speed, i.e., by setting the beam pitch angle (the angle between the beam velocity vector and the direction of background magnetic field). In the case of zero pitch angle, i.e., when v→b·E→⊥=0, the beam excites only electrostatic, standing waves, oscillating at local plasma frequency, in the beam injection spatial location, and only low level electromagnetic drift wave noise is also generated. (iii) In the case of oblique beam pitch angles, i.e., when v→b·E→⊥=0, again electrostatic waves with same properties are excited. However, now the beam also generates the electromagnetic waves with the properties commensurate to type III radio bursts. The latter is evidenced by the wavelet analysis of transverse electric field component, which shows that as the beam moves to the regions of lower density and hence lower plasma frequency, frequency of the electromagnetic waves drops accordingly. (iv) When the density gradient is removed, an electron beam with an oblique pitch angle still generates the electromagnetic radiation. However, in the latter case no frequency decrease is seen. (v) Since in most of the presented results, the ratio of electron plasma and cyclotron frequencies is close to unity near the beam injection location, in order to prove that the electromagnetic emission, generated by the non-zero pitch angle beam, oscillates at the plasma frequency, we also consider a case when the magnetic field (and the cyclotron frequency) is ten times smaller. Within the limitations of the model, the study presents the first attempt to produce synthetic (simulated) dynamical spectrum of the type III radio bursts in the fully kinetic plasma model. The latter is based on 1.5D non-zero pitch angle (non-gyrotropic) electron beam that is an alternative to the plasma emission classical mechanism for which two spatial dimensions are needed.
Excitation of surface plasma waves by a density modulated electron beam at a conductor-dusty plasma interface
Authors: Gupta Ruby , Sharma Suresh C. , Prakash Ved
Published: May 2011

A density modulated electron beam propagating through a conductor-dusty plasma interface drives electromagnetic surface plasma waves (SPWs) to instability via Cerenkov and cyclotron interaction. The SPWs propagate across an external magnetic field parallel to the interface. Numerical calculations of the growth rate and unstable mode frequencies have been carried out for the typical parameters of the SPWs. The frequency and the growth rate of the unstable wave instability increase with the relative density of negatively charged dust grains δ (= nio/neo, where nio is the ion plasma density and neo is the electron plasma density). The phase velocity of the unstable waves also increases with δ. In addition, the growth rate of the instability increases with the beam density and scales as one-third power of the beam density in Cerenkov interaction and square root of beam density in fast cyclotron interaction. Moreover, the dispersion relation of SPWs has been retrieved in the absence of the modulated beam and without dust grains.
Excitation of ion rarefaction waves in a low pressure plasma by applying a short high negative voltage pulse
Authors: Kar S. , Mukherjee S. , Saxena Y. C.
Published: May 2011

The ion rarefaction response to a high negative voltage pulse (U0 >> kTe/e) applied to a metal plate immersed in a low pressure argon plasma, for time duration lower than ion plasma period, is experimentally examined. In the present experiment the pulse duration is kept intermediate between the ion and electron plasma response times. Such a pulse duration is chosen so that ions are collectively undisturbed and, according to general understanding, no force is given to ions. Hence no ion rarefaction wave should be excited. But contrary to the general understanding, excitation of a rarefaction wave is observed. The results indicate that the speed of the rarefaction waves for various conditions (like plasma density, applied pulse magnitude, and pulse duration) is supersonic. After a distance from the exciter (biased plate), typically three-fourth of the exciter diameter, the rarefaction waves are turned into ion acoustic waves. The experimental results indicate that even though the bias durations are shorter than the ion plasma period, if the bias magnitude is large enough, some collective plasma behavior can still be excited.
Laser beat wave terahertz generation in a clustered plasma in an azimuthal magnetic field
Authors: Bhasin Lalita , Tripathi Deepak , Uma R. , Tripathi V. K.
Published: May 2011

Laser beat wave excitation of terahertz radiation in a rippled density clustered plasma, in the presence of an azimuthal magnetic field, is investigated. The lasers exert a beat ponderomotive force on cluster electrons, imparting them an oscillatory velocity with a significant transverse component due to the azimuthal magnetic field. The oscillatory velocity beats with the cluster density ripple and produces a nonlinear current, driving terahertz radiation. The terahertz field turns out to have ring shaped distribution. Its amplitude is enhanced by the cluster plasma resonance when 4π3nc0rc03ne/(ω2-ωpe2/3)>n0/ω2.
In situ electro-mechanical experiments and mechanics modeling of tensile cracking in indium tin oxide thin films on polyimide substrates
Authors: Peng Cheng , Jia Zheng , Bianculli Dan , Li Teng , Lou Jun
Published: May 2011

Indium tin oxide (ITO) thin films supported by polymer substrates have been widely used as transparent electrodes/interconnects in flexible electronics. Understanding the electro-mechanical behaviors of such material system is crucial for reliable operation of flexible devices under large deformation. In this paper, we performed in situ mechanical and electrical tests of ITO thin films with two different thicknesses (200 and 80 nm) deposited on polyimide substrates inside a scanning electron microscope. The crack initiation and propagation, crack density evolution and the corresponding electrical resistance variation were systematically investigated. It was found that cracks initiated at a higher tensile strain level and saturated with a higher density in thinner ITO films. Integrated with a coherently formulated mechanics model, the cohesive toughness and fracture strength of ITO thin films and the ITO/polyimide interfacial toughness were quantitatively determined. The experimentally observed thickness dependence of the saturated crack density in ITO thin films was also quantitatively verified by the model.
Structure and hydration of the C4H4•+ ion formed by electron impact ionization of acetylene clusters
Authors: Momoh Paul O. , Hamid Ahmed M. , Abrash Samuel A. , Samy El-Shall M.
Published: May 2011

Here we report ion mobility experiments and theoretical studies aimed at elucidating the identity of the acetylene dimer cation and its hydrated structures. The mobility measurement indicates the presence of more than one isomer for the C4H4•+ ion in the cluster beam. The measured average collision cross section of the C4H4•+ isomers in helium (38.9 ± 1 Å2) is consistent with the calculated cross sections of the four most stable covalent structures calculated for the C4H4•+ ion [methylenecyclopropene (39.9 Å2), 1,2,3-butatriene (41.1 Å2), cyclobutadiene (38.6 Å2), and vinyl acetylene (41.1 Å2)]. However, none of the single isomers is able to reproduce the experimental arrival time distribution of the C4H4•+ ion. Combinations of cyclobutadiene and vinyl acetylene isomers show excellent agreement with the experimental mobility profile and the measured collision cross section. The fragment ions obtained by the dissociation of the C4H4•+ ion are consistent with the cyclobutadiene structure in agreement with the vibrational predissociation spectrum of the acetylene dimer cation (C2H2)2•+ [R. A. Relph, J. C. Bopp, J. R. Roscioli, and M. A. Johnson, J. Chem. Phys. 131, 114305 (2009)]10.1063/1.3212595. The stepwise hydration experiments show that dissociative proton transfer reactions occur within the C4H4•+(H2O)n clusters with n ≥ 3 resulting in the formation of protonated water clusters. The measured binding energy of the C4H4•+H2O cluster, 38.7 ± 4 kJ/mol, is in excellent agreement with the G3(MP2) calculated binding energy of cyclobutadiene•+·H2O cluster (41 kJ/mol). The binding energies of the C4H4•+(H2O)n clusters change little from n = 1 to 5 (39–48 kJ/mol) suggesting the presence of multiple binding sites with comparable energies for the water–C4H4•+ and water–water interactions. A significant entropy loss is measured for the addition of the fifth water molecule suggesting a structure with restrained water molecules, probably a cyclic water pentamer within the C4H4•+(H2O)5 cluster. Consequently, a drop in the binding energy of the sixth water molecule is observed suggesting a structure in which the sixth water molecule interacts weakly with the C4H4•+(H2O)5 cluster presumably consisting of a cyclobutadiene•+ cation hydrogen bonded to a cyclic water pentamer. The combination of ion mobility, dissociation, and hydration experiments in conjunction with the theoretical calculations provides strong evidence that the (C2H2)2•+ ions are predominantly present as the cyclobutadiene cation with some contribution from the vinyl acetylene cation.
An infinite-dimensional calculus for generalized connections on hypercubic lattices
Authors: Mendes R. Vilela
Published: May 2011

A space for gauge theories is defined, using projective limits as subsets of Cartesian products of homomorphisms from a lattice on the structure group. In this space, non-interacting and interacting measures are defined as well as functions and operators. From projective limits of test functions and distributions on products of compact groups, a projective gauge triplet is obtained, which provides a framework for the infinite-dimensional calculus in gauge theories. The gauge measure behavior on non-generic strata is also obtained.
A versatile low-temperature setup for the electrical characterization of single-molecule junctions
Authors: Martin Christian A. , Smit Roel H. M. , Egmond Ruud van , van der Zant Herre S. J. , van Ruitenbeek Jan M.
Published: May 2011

We present a modular high-vacuum setup for the electrical characterization of single molecules down to liquid helium temperatures. The experimental design is based on microfabricated mechanically controllable break junctions, which offer control over the distance of two electrodes via the bending of a flexible substrate. The actuator part of the setup is divided into two stages. The slow stage is based on a differential screw drive with a large bending range. An amplified piezoceramic actuator forms the fast stage of the setup, which can operate at bending speeds of up to 800 μm/s. In our microfabricated break junctions this is translated into breaking speeds of several 10 nm/s, sufficient for the fast acquisition of large statistical datasets. The bandwidth of the measurement electronics has been optimized to enable fast dI/dV spectroscopy on molecular junctions with resistances up to 100 MΩ. The performance of the setup is demonstrated for a π-conjugated oligo(phenylene-ethynylene)-dithiol molecule.
In situ investigation of hydrogen interacting with Si(100)
Authors: Brückner Sebastian , Döscher Henning , Kleinschmidt Peter , Hannappel Thomas
Published: May 2011

Silicon surfaces are subject to intense interaction with hydrogen ambient common in vapor phase epitaxy. We distinguish characteristic configurations of vicinal Si(100) by in situ reflectance anisotropy spectroscopy: covered by protective oxides, cleaned by thermal annealing, and the formation of monohydrides during cooling. Even above 1000 K, most dangling bonds of the (2×1)-reconstructed surface are saturated by hydrogen, while stability of Si–H bonds in the process gas ambient requires temperatures well below 750 K. Adjustment of hydrogen coverage employing alternative process gases provides experimental access to hydrogen adsorption and desorption characteristics valid for annealing in vapor phase epitaxy ambient.
Ultrathin aluminum sample cans for single crystal inelastic neutron scattering
Authors: Stone M. B. , Loguillo M. J. , Abernathy D. L.
Published: May 2011

Single crystal inelastic neutron scattering measurements are often performed using a sample environment for controlling sample temperature. One difficulty associated with this is establishing appropriate thermal coupling from the sample to the temperature controlled portion of the sample environment. This is usually accomplished via a sample can which thermally couples the sample environment to the sample can and the sample can to the sample via an exchange gas. Unfortunately, this can will contribute additional background signal to one's measurement. We present here the design of an ultrathin aluminum sample can based upon established technology for producing aluminum beverage cans. This design minimizes parasitic sample can scattering. Neutron scattering measurements comparing a machined sample can to our beverage can design clearly indicate a large reduction in scattering intensity and texture when using the ultrathin sample can design. We also examine the possibility of using standard commercial beverage cans as sample cans.
Free-surface liquid jet impingement on rib patterned superhydrophobic surfaces
Authors: Maynes D. , Johnson M. , Webb B. W.
Published: May 2011

We report experimental results characterizing the dynamics of a liquid jet impinging normally on hydrophilic, hydrophobic, and superhydrophobic surfaces spanning the Weber number (based on the jet velocity and diameter) range from 100 to 1900. The superhydrophobic surfaces are fabricated with both hydrophobically coated silicon and polydimethylsiloxane that exhibit alternating microribs and cavities. For all surfaces a transition from a thin radially moving liquid sheet occurs. This takes the form of the classical hydraulic jump for the hydrophilic surfaces but is markedly different for the hydrophobic and superhydrophobic surfaces, where the transition is significantly influenced by surface tension and a break-up into droplets is observed at high Weber number. For the superhydrophobic surfaces, the transition exhibits an elliptical shape with the major axis being aligned parallel to the ribs, concomitant with the frictional resistance being smaller in the parallel direction than in the transverse direction. However, the total projected area of the ellipse exhibits a nearly linear dependence on the jet Weber number, and was nominally invariant with varying hydrophobicity and relative size of the ribs and cavities. For the hydrophobic and superhydrophobic scenarios, the local Weber number based on the local radial velocity and local depth of the radially moving liquid sheet is observed to be of order unity at the transition location. The results also reveal that for increasing relative size of the cavities, the ratio of the ellipse axis (major-to-minor) increases.
Au nanorods can be used for long-term cell imaging?
Authors: Wu Xi , Yang Fei , Ming Tian , Xiong Rongling , Wang Peinan , Chen Jiyao
Published: May 2011

The photostability of Au nanorods in human hepatocellular carcinoma cells under two-photon excitation was investigated to evaluate their potential in cell imaging. The photoluminescence images of the intracellular Au nanorods under the two-photon excitation of an 800 nm femtosecond laser were photobleached rapidly, which is due to the melting of Au nanorods. The images lost their brightness for more than 50% after 15 micrograph scans for the nanorod incubation concentrations of 10, 20, and 40 pM. The confocal reflectance image can prevent the image photobleaching and thus is suitable for long-term cell imaging with Au nanorods.
The NanoBeamBalance: A passive, tensile-test device for the atomic force microscope
Authors: Wenger M. P. E. , Mesquida P.
Published: May 2011

An add-on device is presented, which significantly expands the force measurement capabilities of the atomic force microscope (AFM). The device consists of a completely passive mechanism, which translates the vertical motion of the AFM tip in force measurements into a horizontal motion of two sample support pads. The advantage is that it is much easier to deposit microscopic samples from suspension onto flat surfaces than to attach them reliably between tip and a surface. The working-principle and the design of the device is comprehensively described and demonstrated on the example of collagen fibres with a diameter of a few μm. Well-defined tensile measurements in longitudinal direction were performed, showing that the tensile stiffness of collagen fibres from rat tail tendon decreases by a factor of 5 when rehydrated from a dried sample and slowly increases upon cross-linking with glutaraldehyde.
High resolution multiple excitation spot optical microscopy
Authors: Dilipkumar Shilpa , Mondal Partha Pratim
Published: May 2011

We propose fundamental improvements in three-dimensional (3D) resolution of multiple excitation spot optical microscopy. The excitation point spread function (PSF) is generated by two interfering counter-propagating depth-of-focus beams along the optical axis. Detection PSF is obtained by coherently interfering the emitted fluorescent light (collected by both the objectives) at the detector. System PSF shows upto 14-fold reduction in focal volume as compared to confocal, and almost 2-fold improvement in lateral resolution. Proposed PSF has the ability to simultaneously excite multiple 3D-spots of sub-femtoliter volume. Potential applications are in fluorescence microscopy and nanobioimaging.
Optimizing lightwave transmission through a nano-tip
Authors: Xie Xiangsheng , Chen Yongzhu , Zhang Peiqing , Guan Yefeng , Zhou Jianying , Wong Kam Sing , Yan Li , Kurizki Gershon
Published: May 2011

Optical microscopy with spatial resolution below the diffraction limit is at present attracting extensive attentions. Further advancement of the near-field scanning optical microscopy (NSOM), a practical super-resolution microscopy, is mainly limited by the low transmission of optical power through the nano-meter apex. This work shows that lightwave can be efficiently delivered to a sub-100 nm apex inside a tapered metallic guiding structure. The enhanced light delivery, about 5-fold, is made possible with an adaptive optimization of the transmission via a spatial light phase-modulator. Numerical simulation shows the mechanism for the efficient light delivery to be the selective excitation of predominantly the lowest-order transverse component of standing wavevector with proper input wavefront modulation, hence favoring the transmission of lightwave in the longitudinal direction. The demonstration of such efficient focusing, to about full-width at half-maximum of a quarter wavelength, has a direct and immediate application in the improvement of the existing NSOMs.
System-level feedbacks make the anaphase switch irreversible
Authors: He Enuo , Kapuy Orsolya , Oliveira Raquel A. , Uhlmann Frank , Tyson John J. , Novák Béla
Published: May 2011

The mitotic checkpoint prevents a eukaryotic cell from commencing to separate its replicated genome into two daughter cells (anaphase) until all of its chromosomes are properly aligned on the metaphase plate, with the two copies of each chromosome attached to opposite poles of the mitotic spindle. The mitotic checkpoint is exquisitely sensitive in that a single unaligned chromosome, 1 of a total of ∼50, is sufficient to delay progression into anaphase; however, when the last chromosome comes into alignment on the metaphase plate, the mitotic checkpoint is quickly satisfied, and the replicated chromosomes are rapidly partitioned to opposite poles of the dividing cell. The mitotic checkpoint is also curious in the sense that, before metaphase alignment, chromosomes that are not being pulled in opposite directions by the mitotic spindle activate the checkpoint, but during anaphase, these same tensionless chromosomes can no longer activate the checkpoint. These and other puzzles associated with the mitotic checkpoint are addressed by a proposed molecular mechanism, which involves two positive feedback loops that create a bistable response of the checkpoint to chromosomal tension.
The need for academic generalists
Authors: Kelly Regis B. , Crawford Douglas
Published: May 2011

Academia should be willing to shoulder some of the responsibility for the current dearth of new therapeutic drugs. Our research funding is predicated on the assumption that it will bring value to society, but our emphasis on scientific specialization hinders our ability to add value when a broader vision is required. A solution is the creation of an academy of science generalists motivated to bring together clinical and basic scientists, academia and the private sector, government legislators and industry. A small investment in academic generalists could yield benefits far beyond its modest cost.
Genetic characterization of enzymes involved in the priming steps of oxytetracycline biosynthesis in Streptomyces rimosus
Authors: Wang Peng , Gao Xue , Chooi Yit-Heng , Deng Zixin , Tang Yi
Published: May 2011

Tetracyclines are clinically important aromatic polyketides whose biosynthesis is catalysed by bacterial type II polyketide synthases (PKSs). Tetracyclines are biosynthesized starting with an amide-containing malonamate starter unit and the resulting C-2 carboxyamide is critical for the antibiotic activities. In this work, we genetically verified that an amidotransferase, OxyD, and a thiolase, OxyP, are involved in the biosynthesis and incorporation of the starter unit. First, two mutations, R248T and D268N, were found to be present in OxyD* encoded in Streptomyces rimosus ATCC 13224, a strain that produces the acetate-primed 2-acetyl-2-decarboxyamido-oxytetracycline (ADOTC) instead of the malonamate-primed oxytetracycline (OTC). Homology modelling suggested that in particular D268N may inactivate OxyD. Complementation of S. rimosus ATCC 13224 with wild-type OxyD restored OTC biosynthesis, thereby confirming the essential role of OxyD in the synthesis of the amide starter unit. Second, using a series of knockout and complementation approaches, we demonstrated that OxyP is most likely involved in maintaining fidelity of the amide-priming process via hydrolysis of the competing acetate priming starter units. While the inactivation of OxyP does not eliminate OTC biosynthesis, the ratio of acetate-primed ADOTC to malonamate-primed OTC is significantly increased. This suggests that OxyP plays an ancillary role in OTC biosynthesis and is important for minimizing the levels of ADOTC, a shunt product that has much weaker antibiotic activities than OTC.
Tannerella forsythia invasion in oral epithelial cells requires phosphoinositide 3-kinase activation and clathrin-mediated endocytosis
Authors: Mishima Elina , Sharma Ashu
Published: May 2011

Tannerella forsythia, a Gram-negative anaerobe implicated in periodontitis, has been detected within human buccal epithelial cells and shown to invade oral epithelial cellsin vitro. We have previously shown that this bacterium triggers host tyrosine kinase-dependent phosphorylation and actin-dependent cytoskeleton reorganization for invasion. On the bacterial side, the leucine-rich repeat cell-surface BspA protein is important for entry. The present study was undertaken to identify host signalling molecules duringT. forsythiaentry into human oral and cervical epithelial cells. Specifically, the roles of phosphatidylinositol 3-kinase (PI3K), Rho-family GTPases, cholesterol-rich membrane microdomains and the endocytic protein clathrin were investigated. For this purpose, cell lines were pretreated with chemical inhibitors or small interfering RNAs (siRNAs) that target PI3Ks, Rho GTPases, clathrin and cholesterol (a critical component of ‘lipid rafts’), and the resulting effects onT. forsythiauptake were determined. Our studies revealed thatT. forsythiaentry is dependent on host PI3K signalling, and that purified BspA protein causes activation of this lipid kinase. Bacterial entry also requires the cooperation of host Rac1 GTPase. Finally, our findings indicate an important role for clathrin and cholesterol-rich lipid microdomains in the internalization process
Distinctive Photosystem II Photoinactivation and Protein Dynamics in Marine Diatoms
Authors: Wu Hongyan , Cockshutt Amanda M. , McCarthy Avery , Campbell Douglas A.
Published: May 2011

Diatoms host chlorophyll a/c chloroplasts distinct from green chloroplasts. Diatoms now dominate the eukaryotic oceanic phytoplankton, in part through their exploitation of environments with variable light. We grew marine diatoms across a range of temperatures and then analyzed their PSII function and subunit turnover during an increase in light to mimic an upward mixing event. The small diatom Thalassiosira pseudonana initially responds to increased photoinactivation under blue or white light with rapid acceleration of the photosystem II (PSII) repair cycle. Increased red light provoked only modest PSII photoinactivation but triggered a rapid clearance of a subpool of PsbA. Furthermore, PsbD and PsbB content was greater than PsbA content, indicating a large pool of partly assembled PSII repair cycle intermediates lacking PsbA. The initial replacement rates for PsbD (D2) were, surprisingly, comparable to or higher than those for PsbA (D1), and even the supposedly stable PsbB (CP47) dropped rapidly upon the light shift, showing a novel aspect of rapid protein subunit turnover in the PSII repair cycle in small diatoms. Under sustained high light, T. pseudonana induces sustained nonphotochemical quenching, which correlates with stabilization of PSII function and the PsbA pool. The larger diatom Coscinodiscus radiatus showed generally similar responses but had a smaller allocation of PSII complexes relative to total protein content, with nearly equal stiochiometries of PsbA and PsbD subunits. Fast turnover of multiple PSII subunits, pools of PSII repair cycle intermediates, and photoprotective induction of nonphotochemical quenching are important interacting factors, particularly for small diatoms, to withstand and exploit high, fluctuating light.
Quantification of the Brassinosteroid Insensitive1 Receptor in Planta
Authors: Wilma van Esse G. , Westphal Adrie H. , Surendran Ramya Preethi , Albrecht Catherine , van Veen Boudewijn , Borst Jan Willem , de Vries Sacco C.
Published: May 2011

In plants, green fluorescent protein (GFP) is routinely used to determine the subcellular location of fusion proteins. Here, we show that confocal imaging can be employed to approximate the number of GFP-labeled protein molecules present in living Arabidopsis (Arabidopsis thaliana) root cells. The technique involves calibration with soluble GFP to provide a usable protein concentration range within the confocal volume of the microscope. As a proof of principle, we quantified the Brassinosteroid Insensitive1 (BRI1) receptor fused to GFP, under control of its own promoter. The number of BRI1-GFP molecules per root epidermal cell ranges from 22,000 in the meristem and 130,000 in the elongation zone to 80,000 in the maturation zone, indicating that up to 6-fold differences in BRI1 receptor content exist. In contrast, when taking into account differences in cell size, BRI1-GFP receptor density in the plasma membrane is kept constant at 12 receptors μm−2 in all cells throughout the meristem and elongation zone. Only the quiescent center and columella cells deviate from this pattern and have 5 to 6 receptors μm−2. Remarkably, root cell sensitivity toward brassinosteroids appears to coincide with uniform meristem receptor density.
Genetic relationships between Japanese native and commercial breeds using 70 chicken autosomal SNP genotypes by the DigiTag2 assay
Authors: Shimogiri T. , Nishida N. , Kudo M. , Niwa K. , Nishibori M. , Kinoshita K. , Okamoto S. , Maeda Y. , Tokunaga K. , Yasue H.
Published: May 2011

Recently, single nucleotide polymorphisms (SNPs) have been used to identify genes or genomic regions responsible for economic traits, including genetic diseases in domestic animals, and to examine genetic diversity of populations. In this study, we genotyped 70 chicken autosomal SNPs using DigiTag2 assay to understand the genetic structure of the Japanese native chicken breeds Satsumadori and Ingie, and the relationship of these breeds with other established breeds, Rhode Island Red (RIR), commercial broiler and layer. Five breeds, each consisting of approximately 20 chickens, were subjected to the assay, revealing the following: Average expected heterozygosities of broiler, Satsumadori, RIR, layer and Ingie were 0.265, 0.254, 0.244, 0.179 and 0.176, respectively. Phylogenetic analysis using the concatenated 70 autosomal SNP genotypes distinguished all chickens and formed clusters of chickens belonging to the respective breeds. In addition, the 2‐D scatter plot of the first two principal components was consistent with the phylogenic tree. Taken together with the pairwise Fst distances, broiler and RIR were closely positioned near each other, while Ingie was positioned far from the other breeds. Structure analysis revealed that the probable number of genetic clusters (K) was six and four with maximum likelihood and ΔK values, respectively. The clustering with maximum likelihood revealed that, in addition to the clustering of the other five breeds, the Satsumadori was subdivided into two genetic clusters. The clustering with ΔK value indicated that the broiler and Rhode Island Red were assigned to the same genetic cluster.
Health‐related quality of life of adolescents with overweight or obesity in the north of Jordan
Authors: Al‐Akour N. A. , Khader Y. S. , Khassawneh M. Y. , Bawadi H.
Published: May 2011

Background  Previous studies showed that overweight and obesity in children and adolescents are associated with impaired health‐related quality of life (QOL). The objective of this study was to describe health‐related QOL among Jordanian adolescents who were overweight or obese.

Methods  This is a cross‐sectional study conducted among Jordanian students aged between 13 and 18 years in three educational directorates in Irbid City in the north of Jordan. Using simple random sampling, two male schools and two female schools were selected from the list of each directorate to represent all schools in north of Jordan. In each selected school, all adolescents aged 13–18 years were visited in their classes and were invited to participate in the study. Of the total number of 1561 subjects, 1433 (91.8%) agreed to participate in the study. The short‐form 15‐item Pediatric Quality of Life Inventory version 4.00 was used to measure health‐related QOL among participants. Body mass index (BMI) was calculated and interpreted according to the BMI‐for‐age growth charts of the Center for Disease Control and Prevention guidelines.

Results  This study included 707 boys and 726 girls; 17.6% of participants were overweight and 7.8% were obese. For boys and girls, adolescents who were overweight or obese had significantly lower average scores for psychosocial health summary scale and physical functioning scale. Female gender, age of 16–18 years, fathers' education of high school or less and unemployed fathers (for social functioning and physical functioning) were significantly associated with decreased average scores of all scales and subscales of Pediatric Quality of Life Inventory.

Conclusions  Compared with healthy adolescents, adolescents who were overweight or obese reported significantly lower health‐related QOL in all domains. Girls reported greater effect of overweight and obesity on their health‐related QOL.
The effect of the classical and medium chain triglyceride ketogenic diet on vitamin and mineral levels
Authors: Christodoulides S. S. , Neal E. G. , Fitzsimmons G. , Chaffe H. M. , Jeanes Y. M. , Aitkenhead H. , Cross J. H.
Published: May 2011

Background:  The risk of nutritional deficiency in children on restrictive dietary treatments and a lack of ketogenic diet (KD)‐specific UK supplements raises concerns about micronutrient status. Vitamin A, E, zinc, selenium and magnesium levels were therefore examined in children with intractable epilepsy treated with the KD.

Methods:  Plasma vitamins A and E, zinc, selenium and magnesium levels were measured at baseline and after 3, 6 and 12 months on the classical (n = 46) or medium chain triglyceride (MCT) (n = 45) KD in children aged 2–16 years, as part of a randomised trial, and pairwise comparisons with baseline were performed.

Results:  Data were available from 91 children. From baseline to 12 months, mean plasma vitamin A decreased from 1.41 μmol L−1 to 1.13 μmol L−1 in the classical group (P < 0.001) but increased from 1.52 μmol L−1 to 1.81 μmol L−1 in the MCT group (P < 0.001). Mean plasma vitamin E increased from 22.7 μmol L−1 to 33.2 μmol L−1 in the classical group (P < 0.001) and from 22.3 μmol L−1 to 23.3 μmol L−1 in the MCT group (P < 0.05). No significant change in plasma zinc was seen at 12 months, although mean plasma selenium decreased from 0.95 μmol L−1 to 0.88 μmol L−1 in the group as a whole (P < 0.05). Mean plasma magnesium decreased from 0.87 mmol L−1 to 0.83 mmol L−1 in the group as a whole (P < 0.001); when subdivided by KD type, this was limited to the classical group.

Conclusions:  Changes in plasma vitamins A and E and the decline in magnesium status after 12 months of KD treatment suggest that micronutrient status may be suboptimal in this group and that available formulations for KD supplementation may need reviewing.
Pharmacokinetics and pharmacodynamics of A77 1726 and leflunomide in domestic cats
Authors: MEHL M. L. , TELL L. , KYLES A. E. , CHEN Y.‐J. , CRAIGMILL A. , GREGORY C. R.
Published: May 2011

Mehl, M. L., Tell, L., Kyles, A. E., Chen, Y.‐J., Craigmill, A., Gregory, C. R. Pharmacokinetics and pharmacodynamics of A77 1726 and leflunomide in domestic cats. J. vet. Pharmacol. Therap. 35, 139–146.

The pharmacokinetics and pharmacodynamics of A77 1726 and leflunomide after intravenous (i.v.) and oral (p.o.) administration were evaluated in adult cats. Three treatments were administered: a single i.v. dose of A77 1726 (4 mg/kg), a single oral dose of leflunomide (4 mg/kg), and multiple oral doses of leflunomide (2 mg/kg). Mean pharmacokinetic parameter values after a single i.v. dose of A77 1726 were distribution (A) and elimination (B) intercepts (15.2 μg/mL and 34.5 μg/mL, respectively), distribution and elimination half‐lives (1.5 and 71.8 h, respectively), area under the curve (AUC0→∞; 3723 μg*h/mL), mean residence time (MRT; 93 h), clearance (Clobs; 1.1 mL/kg/h), and volume of distribution at steady state (Vdss; 97 mL/kg). Mean pharmacokinetic parameter values after a single oral dose of leflunomide were absorption and elimination rate constants (0.3 1/h and 0.01 1/h, respectively), absorption and elimination half‐lives (2.3 and 59.1 h, respectively), AUC0→∞ (3966 μg*h/mL), and maximum observed plasma concentration (Cmax; 38 μg/mL). The bioavailability after a single oral dose of leflunomide was 100%. The mean ± SD A77 1726 concentration that inhibited 50% lymphocytes (EC50) was 16 ± 13.5 μg/mL. The mean ± SD maximum A77 1726 concentration (ECmax) was 61.0 ± 23.9 μg/mL.
Long‐term outcome of chronic hepatitis C in a population‐based cohort and impact of antiviral therapy: a propensity‐adjusted analysis
Authors: Di Martino V. , Crouzet J. , Hillon P. , Thévenot T. , Minello A. , Monnet E.
Published: May 2011

Summary.  This population‐based study aimed to assess the determinants of the outcome of chronic hepatitis C with analysis of the impact of antiviral therapy with or without sustained virological response (SVR) on cirrhosis decompensation, hepatocellular carcinoma, liver‐related and non‐liver‐related mortality. A total of 1159 HCV‐positive patients newly detected between 1994 and 2001 were included. For each outcome, the prognostic effect of patients’ baseline characteristics was estimated by time‐dependent Cox models using age as the time‐scale and adjusting for treatment received during follow‐up. The impact of antiviral therapy was assessed by using a propensity score in a sample including 184 patients treated in the first 24 months following diagnosis who were matched to 184 untreated patients. At the end of a 59‐month median follow‐up, 100 cases of compensated disease, 58 liver cancer and 163 deaths (55 liver related) were recorded. The 5‐year rates of decompensated cirrhosis, hepatocellular carcinoma, liver‐related and non‐liver‐related death were 4.4%, 2.7%, 5.0% and 8.9%, respectively. Multivariate analyses identified two variables with pejorative influence: alcohol consumption (RR = 4.29 for CD; RR = 5.76 for HCC; RR = 6.69 for liver‐related death; P < 0.0001); HCV diagnosis unrelated to systematic screening (RR = 2.25 for CD; RR = 3.05 for HCC; RR = 4.31 for liver‐related death, P < 0.03). In the matched subset, no significant benefit of antiviral therapy was observed. Nevertheless, among the 144 patients who achieved SVR, no death was observed. This population‐based study showed substantial rates of decompensated cirrhosis, hepatocellular carcinoma and non‐liver‐related mortality. Alcohol consumption and absence of systematic screening were significant determinants of poor outcome, whereas treatment did not have significant influence.
A Mechanism for the Action of the Compound DA‐6034 on NF‐κB Pathway Activation in Helicobacter pylori‐Infected Gastric Epithelial Cells
Authors: Ko S. H. , Yoo D. Y. , Kim Y.‐J. , Choi S. M. , Kang K. K. , Kim H. , Kim N. , Kim J. S. , Kim J. M.
Published: May 2011

DA‐6034 is a synthetic derivative of eupatilin, a flavonoid with anti‐inflammatory effects. The aim of this study was to investigate the effects of DA‐6034 on the interactions between IκB kinase (IKK) and heat shock protein 90 (Hsp90), and activation of the nuclear factor‐kappaB (NF‐κB) signalling pathway in human gastric epithelial cells infected with Helicobacter pylori. MKN‐45 gastric epithelial cell line was treated with DA‐6034 and H. pylori. DA‐6034 significantly inhibited NF‐κB activation and upregulated the expressions of interleukin‐8 (IL‐8) and monocyte chemoattractant protein‐1 in MKN‐45 cells infected with H. pylori. However, DA‐6034 did not influence activator protein‐1 DNA binding activity in H. pylori‐infected gastric epithelial cells. Pretreatment with DA‐6034 attenuated the H. pylori‐induced increase in IKK activity, and Hsp90 was associated with IKK‐α and IKK‐γ in MKN‐45 cells. Treatment with DA‐6034 dissociated the Hsp90 and IKK‐γ complex in H. pylori‐infected cells, leading to the inhibition of IL‐8 expression. These results suggest that the eupatilin derivative 7‐carboxymethyloxy‐3′,4′,5‐trimethoxy flavone has anti‐inflammatory activity in gastric epithelial cells infected with H. pylori through the promotion of the dissociation of the IKK‐γ–Hsp90 complex and suppression of NF‐κB signalling.
Lessons from a transplant patient with diarrhea, cryptosporidial infection, and possible mycophenolate mofetil‐associated colitis
Authors: Frei P. , Weber A. , Geier A. , Mertens J.C. , Kohler S. , Rogler G. , Müllhaupt B.
Published: May 2011

P. Frei, A. Weber, A. Geier, J.C. Mertens, S. Kohler, G. Rogler, B. Müllhaupt. Lessons from a transplant patient with diarrhea, cryptosporidial infection, and possible mycophenolate mofetil‐associated colitis. Transpl Infect Dis 2011: 13: 416–418. All rights reserved

Abstract: Diarrhea in a transplant recipient may be caused by infection, metabolic problems, or adverse drug effects. The immunosuppressive drug most frequently associated with diarrhea in transplant recipients is mycophenolate mofetil (MMF). We present the case of a patient with 2 potential explanations for diarrhea lasting several weeks, which occurred years after liver transplantation. Whereas stool samples were positive for cryptosporidia, the histopathological findings were compatible with MMF colitis. However, diarrhea resolved after treatment of cryptosporidial infection, despite continued MMF medication. This case shows that histopathological findings of MMF colitis may be misleading and do not prove that diarrhea is drug induced.