bluuebunny/crossref_metadata_2025 huggingface dataset:
Nonlinear structure of the electromagnetic waves in underdense plasmas
Authors: Shokri B. , Niknam A. R.
Published: November 2006

The interaction of a high-frequency electromagnetic wave with a collisionless unmagnetized nonisothermal plasma, taking into account the ponderomotive force per unit volume acting on the plasma electrons, is studied. The electron density distribution is found. Obtaining the nonlinear differential and integral equations for the electric field and using the Maxwell equations, we investigate the electric and magnetic field profiles in plasma. It is shown that the profiles of the electric and magnetic field departure from a sinusoidal shape and the electron density becomes highly peaked for the higher electromagnetic energy flux.
Multidimensional infrared spectroscopy of water. II. Hydrogen bond switching dynamics
Authors: Loparo Joseph J. , Roberts Sean T. , Tokmakoff Andrei
Published: November 2006

We use multidimensional infrared spectroscopy of the OH stretch of HOD in D2O to measure the interconversion of different hydrogen bonding environments. The OH stretching frequency distinguishes hydrogen bonded (HB) and non-hydrogen-bonded (NHB) configurations by their absorption on the low (red) and high (blue) sides of the line shape. Measured asymmetries in the two dimensional infrared OH line shapes are manifestations of the fundamentally different spectral relaxations of HB and NHB. HB oscillators exhibit coherent oscillations within the hydrogen-bonded free energy well before undergoing activated barrier crossing, resulting in the exchange of hydrogen bonded partners. Conversely, NHB oscillators rapidly return to HB frequencies within 150fs. These results support a picture where NHB configurations are only visited transiently during large fluctuations about a hydrogen bond or during the switching of hydrogen bonding partners. The results are not consistent with the presence of entropically stabilized dangling hydrogen bonds or a conceptual picture of water as a mixture of environments with varying hydrogen bond strength separated by barriers >kT.
Low-frequency Raman study of hollow multiwalled nanotubes grown by Fe-catalyzed chemical vapor deposition
Authors: Santangelo S. , Messina G. , Donato M. G. , Lanza M. , Milone C. , Pistone A.
Published: November 2006

In this work, it is shown that some Raman-active modes may be detected, below 500cm−1, in the spectrum of nanotubes synthesized by iron catalyzed chemical vapor deposition. By comparatively discussing results of Raman, high-resolution transmission electron microscopy, and thermogravimetric analyses, demonstration is given that these spectral features originate from scattering by nanoparticles of iron catalyst encapsulated within the tubes under nonstationary growth regime. Their intensity progressively weakens with increasing carbon supply rate until bands disappear as stationary conditions are reached.
Time-dependent analysis of the resistivity of post-disruption tokamak plasmas
Authors: Bakhtiari M. , Whyte D. G.
Published: November 2006

The effect of neutrals on plasma resistivity due to electron-neutral collisions is studied with respect to its effect on tokamak disruptions. The resistivity of the tokamak plasma after the thermal quench is critical in determining the current quench rate, the plasma temperature, and runaway electron generation in tokamaks through the electric field, all features which are important for mitigating the damaging effect of disruptions. It is shown that the plasma resistivity during tokamak disruptions is a time-dependent parameter which may vary with disruption time scales due to the increasing fraction of neutrals. However the effect of neutrals on resistivity is found to be small for the expected neutral fraction, mostly due to power balance considerations between radiation and Ohmic heating in the plasma.
Thermoacoustically driven pulse tube refrigeration below 80K by introducing an acoustic pressure amplifier
Authors: Bao Rui , Chen Guobang , Tang Ke , Cao Weihua , Jin Tao
Published: November 2006

A copper tube of 3.3m in length and 8mm in inner diameter, acting as an acoustic pressure amplifier, was incorporated in a standing-wave thermoacoustically driven pulse tube refrigerator system. The enhancement of pressure ratio from 1.129 to 1.152 by the acoustic pressure amplifier has been obtained. As a result, a cooling temperature as low as 79.7K and a tripled coefficient of performance improvement at 120K were reached.
Markovian approximation in a coarse-grained description of atomic systems
Authors: Hijón Carmen , Serrano Mar , Español Pep
Published: November 2006

The Markovian assumption stating that memory effects can be neglected is a crucial assumption in the theory of coarse-graining. We investigate the coarse-graining of a one-dimensional chain of oscillators where the atoms are grouped into clusters or blobs. When the interaction between oscillators is through Hookean springs, the cluster dynamics is non-Markovian, as has been recently noted by Cubero and Yaliraki [J. Chem. Phys. 122, 03418 (2005)]. When the oscillators interact through a nonlinear potential of the Lennard-Jones type, the dynamics turns out to be Markovian. The different behavior in both types of interactions is attributed to the persistence of sound waves in the harmonic case, which are strongly suppressed in the nonlinear case.
Rewritable photonic circuits
Authors: Intonti Francesca , Vignolini Silvia , Türck Volker , Colocci Marcello , Bettotti Paolo , Pavesi Lorenzo , Schweizer Stefan L. , Wehrspohn Ralf , Wiersma Diederik
Published: November 2006

The authors present a technique that allows to modify the local characteristics of two-dimensional photonic crystals by controlled microinfiltration of liquids. They demonstrate experimentally that by addressing and infiltrating each pore with a simple liquid, e.g., water, it is possible to write pixel by pixel optical devices of any geometry and shape. Calculations confirm that the obtained structures indeed constitute the desired resonators and waveguide structures.
Electrochemically induced flowerlike gold nanoarchitectures and their strong surface-enhanced Raman scattering effect
Authors: Duan Guotao , Cai Weiping , Luo Yuanyuan , Li Zhigang , Li Yue
Published: November 2006

The authors report the fabrication of gold flowerlike nanoarchitectures (FNs) on indium tin oxide coated glass substrate using a low-cost electrochemical strategy at a proper current density and polyvinylpyrrolidone concentration in electrolyte. The FNs are grown and built with the blocks of two-dimensional flakelike nanostructures. Importantly, such FNs show strong surface-enhanced Raman scattering (SERS) effect associated with their geometries, which is much stronger than that from other particle films. The minimum concentration of detectable rhodamine 6G molecules can be down to 10−12M. These FNs with strong SERS effect could be used in chemical analysis, biosensors, and nanodevices with molecule-level detection.
Radial moduli of individual single-walled carbon nanotubes with and without electric current flow
Authors: Wang Hui-Yao , Zhao M. , Mao Scott X.
Published: November 2006

Although the radial elastic moduli of single-walled carbon nanotubes (SWCNTs) were studied by simulation or calculation, no experimental results were presented. The authors have studied the radial deformability of different diameters of SWCNTs with and without current flow using nanoindentation with rigid silicon and diamond tips under atomic force microscopy. The radial elastic moduli of SWCNT deduced by the Hertz model were found to be strongly dependent on the diameter, i.e., SWCNTs with smaller diameter have larger moduli. The radial stiffness was also shown to be larger for a SWCNT with current than that without current.
Enhanced differential conductance through light induced current switching in Mn12 acetate molecular junctions
Authors: Ni C. , Shah S. , Hendrickson D. , Bandaru P. R.
Published: November 2006

The authors have observed through electrical transport measurements enhanced differential conductance (G=dI∕dV), up to 2e2∕h (∼77μA∕V), through the Mn12O12(O2CCH3)16(H2O)4∙2CH3COOH∙4H2O: “Mn12–Ac” molecule. At room temperature, under optical illumination, electrical switching, accompanied by a 60-fold increase of G through Mn12–Ac, was seen. The temperature dependence of G was used to determine the activation energy for molecular conduction to be ∼0.4eV. Their results provide evidence for the possible use of Mn12–Ac as a conducting wire, in addition to its proposed utility for information storage, for implementing multifunctional molecular electronics.
p
H
-adaptive microlenses using pinned liquid-liquid interfaces actuated by pH-responsive hydrogel
Authors: Dong Liang , Jiang Hongrui
Published: November 2006

The authors report on variable-focus liquid microlenses self-adaptive to environmental pH. The microlens is formed via a water-oil interface stably pinned at a hydrophobic-hydrophilic contact line along an aperture in a flexible slip. A set of hydrogel microposts is photopatterned in a microfluidic chamber around the aperture; the microposts autonomously respond to the environmental pH variation by expanding or contracting, thus deforming the aperture slip and tuning the curvature of the water-oil interface and the focal length of the microlens. A single microlens has a tunable focal length from −7.6mm to −∞ (divergent) and from 8.5mm to +∞ (convergent).
Broadband inelastic light scattering of a relaxor ferroelectric 0.71Pb(Ni1∕3Nb2∕3)O3-0.29PbTiO3
Authors: Tsukada Shinya , Ike Yuji , Kano Jun , Sekiya Tadashi , Shimojo Yoshihito , Wang Ruiping , Kojima Seiji
Published: November 2006

Brillouin and Raman scatterings of a 0.71Pb(Ni1∕3Nb2∕3)O3-0.29PbTiO3 single crystal have been measured to investigate broadband inelastic spectra. The two different central peaks related to fast and slow relaxation processes have been observed separately. These two processes are attributed to the thermally activated switching of polarization in polar nanoregions. By the analysis of modified superparaelectric model, the activation energies of fast and slow relaxation processes are determined to be 3.66×103 and 4.31×102K, respectively. The fast process with the lower activation energy probably originated from 180° switching, whereas the slow one with the higher energy from non-180° switching.
Ballistic electron spectroscopy
Authors: Hohls F. , Pepper M. , Griffiths J. P. , Jones G. A. C. , Ritchie D. A.
Published: November 2006

The authors demonstrate the feasibility of ballistic electron spectroscopy as a tool for mesoscopic physics. A quantum dot is utilized as an energy-selective detector of nonequilibrium ballistic electrons injected into a two-dimensional electron system. In this letter they use a second quantum dot as the electron injector to evaluate the scheme. They propose an application in the study of interacting one- and zero-dimensional systems.
Charged particle dynamics and molecular kinetics in the hydrogen postdischarge plasma
Authors: Diomede P. , Longo S. , Capitelli M.
Published: November 2006

The afterglow of a parallel plate radio frequency discharge in hydrogen is studied by numerical modelling to compare ion dynamics and chemical effects on the behavior of negative ions. While the ion dynamics requires a kinetic description of space dependent plasma relaxation (at least 1D), chemical effects require a vibrational kinetics of hydrogen molecules. Since previous models did not include both features it has not been possible until now to realize both effects in a single simulation. We apply an updated version of the 1D Bari model which includes a 1.5D (1Dr2Dv) Particle in Cell/Monte Carlo (PIC/MC) multispecies module coupled to the space and time dependent master equation for H2(X1Σg+,v=0,…,14) vibrational level population. Negative ion fronts are described in hydrogen for the first time and their impact on the plasma limiting surfaces produces a negative ion current evolution compatible with experimental findings. In the same conditions, the attachment rate overshoot is found to contribute about 7% to the average ion density in the plasma.
Self-consistent radial electric field in collisional screw-pinches and axisymmetric closed field line configurations in the absence of fluctuations
Authors: Simakov Andrei N. , Catto Peter J.
Published: November 2006

Collisional plasma confined by magnetic fields in a screw-pinch and any axisymmetric, up-down symmetric closed magnetic field line configuration (such as a dipole or a field reversed configuration) is considered, and equations governing the evolution of the self-consistent radial electric field and flow are derived for each case, provided that effects of plasma fluctuations are negligible.
200
nm
deep ultraviolet photodetectors based on AlN
Authors: Li J. , Fan Z. Y. , Dahal R. , Nakarmi M. L , Lin J. Y. , Jiang H. X.
Published: November 2006

High quality AlN epilayers were grown on sapphire substrates by metal organic vapor deposition and exploited as active deep ultraviolet (DUV) optoelectronic materials through the demonstration of AlN metal-semiconductor-metal (MSM) photodetectors. DUV photodetectors with peak responsivity at 200nm with a very sharp cutoff wavelength at 207nm have been attained. The AlN MSM photodetectors are shown to possess outstanding features that are direct attributes of the fundamental properties of AlN, including extremely low dark current, high breakdown voltage, and high DUV to visible rejection ratio and high responsivity. The results demonstrate the high promise of AlN as an active material for DUV device applications.
Dielectric function of Cu, Ag, and Au obtained from reflection electron energy loss spectra, optical measurements, and density functional theory
Authors: Werner Wolfgang S. M.
Published: November 2006

Pairs of reflection electron energy loss spectra recorded at different incident energies are decomposed to give the energy loss distribution in individual inelastic collisions at the surface and in the bulk of the solid. The resulting single scattering loss distributions are fitted to a Drude-Lindhard model for the dielectric function in the spectral range between the near visible and soft x-ray regions. Good agreement is found between the retrieved optical constants, density functional theory calculations, and optical measurements, rendering this type of analysis promising for the investigation of surface plasmons and determination of optical constants of individual nanostructures.
Method for sensing the self-assembly of polyelectrolyte monolayers using scanning probe microscope cantilever
Authors: Ganesan P. G. , Wang X. , Nalamasu O.
Published: November 2006

Sensing self-assembly of polyelectrolyte is critical to exert greater control over layer thickness and properties. The authors demonstrate the use of a scanning probe microscope cantilever-based micromechanical device to sense the self-assembly of polyethyleneimine and polyacrylic acid. A change in mass of the cantilever due to the assembly was recorded by analyzing resonance frequency shift. Experimental results show three orders more sensitive than the conventional quartz crystal sensor. The ratio between the mass of the adsorbed polyelectrolyte and the mass of the polyelectrolyte monolayer is used to evaluate surface coverage as a parameter of critical importance for nanobiotechnology applications.
A graph-theoretic method for detecting potential Turing bifurcations
Authors: Mincheva Maya , Roussel Marc R.
Published: November 2006

The conditions for diffusion-driven (Turing) instabilities in systems with two reactive species are well known. General methods for detecting potential Turing bifurcations in larger reaction schemes are, on the other hand, not well developed. We prove a theorem for a graph-theoretic condition originally given by Volpert and Ivanova [Mathematical Modeling (Nauka, Moscow, 1987) (in Russian), p. 57] for Turing instabilities in a mass-action reaction-diffusion system involving n substances. The method is based on the representation of a reaction mechanism as a bipartite graph with two types of nodes representing chemical species and reactions, respectively. The condition for diffusion-driven instability is related to the existence of a structure in the graph known as a critical fragment. The technique is illustrated using a substrate-inhibited bifunctional enzyme mechanism which involves seven chemical species.
Control of spiral breakup by an alternating advective field
Authors: Zhang Hong , Chen Jiang-Xing , Li You-Quan , Xu Jiang-Rong
Published: November 2006

The control of spiral breakup due to Doppler instability is investigated. It is found that applying an alternating advective field with suitable amplitude and period can prevent the breakup of spiral waves. Further numerical simulations show that the growing meandering behavior of a spiral tip caused by decreasing the excitability of the medium can be efficiently suppressed by the alternating advective field, which inhibits the breakup of spiral waves eventually.
Fine wire resistance thermometer amplifier for atmospheric measurements
Authors: Harrison R. G. , Rogers G. W.
Published: November 2006

An improved amplifier for atmospheric fine wire resistance thermometry is described. The amplifier uses a low excitation current (50μA). This is shown to ensure negligible self-heating of the low mass fine wire resistance sensor, compared with measured nocturnal surface air temperature fluctuations. The system provides sufficient amplification for a ±50°C span using a ±5V dynamic range analog-to-digital converter, with a noise level of less than 0.01°C. A Kelvin four-wire connection cancels the effect of long lead resistances: a 50m length of screened cable connecting the Reading design of fine wire thermometer to the amplifier produced no measurable temperature change at 12bit resolution.
Implementing both short- and long-working-distance optical trappings into a commercial microscope
Authors: Kraikivski Pavel , Pouligny Bernard , Dimova Rumiana
Published: November 2006

Optical tweezers are now a widespread tool based on three-dimensional trapping by a tightly focused single laser beam. This configuration only works with large numerical aperture and short-working-distance (SWD) objectives, restricting optical manipulation to the high magnification end of the microscope nosepiece. Certain applications of optical trapping demand long-working distances (LWDs) at moderate magnification, imposing a more complex two-beam trapping configuration. In this article, we describe a complete setup that incorporates both SWD and LWD optical trapping functionalities into a single Axiovert 200M Zeiss microscope. We evaluate the performance of the setup in both trapping modes with latex particles, either fluorescent or not, of different sizes, in the 1–20μm range. We provide practical information allowing for optimal configuration of the two-beam geometry, in relation with longitudinal and lateral stabilities of the trap.
Regioselective Conversion of Unsymmetrical Terminal Epoxides into Vicinal Chlorohydrins Using Dimethoxyboron Chloride
Authors: Roy Chandra D.
Published: November 2006

A highly regioselective synthesis of chlorohydrins by chlorinative cleavage of unsymmetrical epoxides utilizing dimethoxyboron chloride is described. Except for styrene oxide, all the terminal epoxides were regioselectively cleaved following a predominantly SN2-type reaction pathway favouring the formation of primary chlorides. In the case of styrene oxide, a benzylic epoxide, (MeO)2BCl transfers the chlorine at the benzylic position, by following an apparent SN1-type mechanism.
Synthesis of New Substituted 4,5-Dihydro-3H-spiro[1,5]-benzoxazepine-2,4′-piperidine and Biological Properties
Authors: Laras Younes , Pietrancosta Nicolas , Moret Vincent , Marc Sylvain , Garino Cédrik , Rolland Amandine , Monnier Valérie , Kraus Jean-Louis
Published: November 2006

The reduction of substituted spiro-piperidinyl chromanone oximes with DIBAH reagents has been known to afford the corresponding substituted 4,5-dihydro-3H-spiro[1,5]-benzoxazepine-2,4′-piperidine. The position and electronic effects of the substituents on the aryl moiety control the observed rearrangement. Spiro-benzoxazepine analogue 5j represents a key intermediate for the creation of a library of diverse potential bioactive drugs. With three functional groups that could be selectively and orthogonally protected, many different substituents can be introduced. The obtained analogues were assayed as the possible aspartyl protease inhibitors HIV protease (HIV-1), and β-secretase (BACE-1).
Self-diffusion of Ag+ and Na+ in molten Ca(NO3)2-KNO3
Authors: Welch BJ , Angell CA
Published: November 2006

In order to explore the
behaviour of diffusing ionic species in a molten salt in which non-Arrhenius behaviour of other transport properties is
established, the diffusivities in dilute solution of Ag+ and Na+ in 38.1 mol%
Ca(NO3)2+ 61.9 mol% KNO3 have been measured.
For both ions limited radio-tracer diffusion coefficients, determined using a
diffusion-out-of-capillary method, are reported. D(Ag+) has also
been measured by chronopotentiometry, by which means
the range and reliability of the measurements were considerably extended. Chronopotentiometric and tracer data agree within expected
errors of measurement. Both ionic diffusivities show a non-Arrhenius
temperature dependence which is indistinguishable in magnitude from that of the
electrical conductance of the solvent melt.
The aggregation of copper phthalocyanine dyes
Authors: Gruen LC
Published: November 2006

The visible absorption
spectra of two reactive dyes based on the copper

phthalocyanine chromophore have been investigated as a function of
concentration, temperature, pH, ionic strength, and solvent. The persistence of
isosbestic points indicates that an equilibrium
exists, over the concentration range investigated, between two forms of the dye
only, namely dimer and monomer. The addition of urea exerts a relatively small
disaggregating influence on this equilibrium. On the other hand decrease in
dielectric constant substantially changes the equilibrium in favour of the
monomeric species.
Reactions with thioethoxide ion in dimethylformamide. II. O-Alkyl cleavage of methylene ethers, methyl esters, and aryloxyacetates
Authors: Feutrill GI , Mirrington RN
Published: November 2006

Reaction of
1,3-benzodioxole with sodium thioethoxide in DMF gave
a good yield of ethyl o-hydroxyphenoxymethyl sulphide (3), which was converted into
catechol nearly quantitatively by acid treatment. The same reagent converted
methyl p-anisate
into p-hydroxybenzoic
acid, and methyl p-chlorophenoxyacetate
to p-chlorophenol in good yield,
indicating its usefulness in cleaving methyl esters and aryloxyacetates
respectively.
Synthesis of 2-Benzamido-2-mercaptopropanoic acid from 4-Methyl-2-phenyl-2-oxazolin-5-one
Authors: Pojer PM , Rae ID
Published: November 2006

The structures of the
dimers of N-substituted pyruvamides
are confirmed to be the pyrrolidinones (6).
4-Chloro-4-methyl-2-phenyl-2-oxazolin-5-one reacts with a-toluenethiol
to give a thiol ester which can be converted into
2-benzamido-2-benzyl-thiopropanoic acid. Reaction of the chlorooxazolinone
with thioacetic acid gives 4-acetylthio-4-methyl-2-phenyl-2-oxazolin-one
which is converted into 2-benzamido-2-mercaptopropanoic acid. The mercapto acid
is oxidized by iron(111) chloride-ether to a mixture of disulphides.
Terpenoid chemistry. XX. Myoporone and dehydromyoporone, toxic furanoid ketones from Myoporum and Eremophila species
Authors: Blackburne ID , Park RJ , Sutherland MD
Published: November 2006

Certain samples of
essential oils from Myoporum deserti, M. betcheanum,
M. acuminatum,
Eremophila maculata, and E. latrobei
have been shown to contain myoporone and/or
10,ll-dehydromyoporone. The ambiguity regarding the stereochemistry of myoporone (previously known from M, bontioides)
has been resolved,(-)-myoporone being shown to
possess the S configuration by degradation to (S)-(+)-2-methylglutaric acid. (-)-Dehydromyoporone, m.p. 32.5-33.5, [x]D ? 15�, has the S
configuration as shown by degradation to (S)-(-)-3-methyladipic acid and hydrogenation
to (S)-(-)-myoporone, m.p. 17.5-19�, [x]D-5.3�. Both
ketones activate the typical ngaione pathology on intraperitoneal
injection into mice but myoporone is not toxic to
sheep. Myoporone from Myoporum
species shows wide variations in optical purity.
Global modulation of chromatin dynamics mediated by dephosphorylation of linker histone H1 is necessary for erythroid differentiation
Authors: Yellajoshyula Dhananjay , Brown David T.
Published: November 2006

Differentiation of metazoan cells involves dramatic changes in gene expression patterns and proliferative capacity driven primarily by epigenetic mechanisms. Here we used
in vivo
photobleaching techniques and biochemical assays to investigate the contribution of alterations in chromatin dynamics to the differentiation of murine erythroleukemia (MEL) cells, a model system for erythroid development. As MEL cells differentiate the binding affinity of all linker histone variants increases, indicative of an overall decrease in chromatin flexibility. Changes in H1
0
binding properties depend on phosphorylation at one or more of three cyclin-dependent kinase sites. The presence of constructs mimicking constitutively phosphorylated H1 results in a significant inhibition in the acquisition of commitment to terminal cell division and the expression of erythroid-specific properties. These data indicate that the progressive loss of cdk activity associated with MEL cell differentiation leads to the accumulation of dephosphorylated linker histones and restricted chromatin flexibility and that these are necessary events in the progression of erythroid differentiation. We present additional data indicating that the presence of phosphorylated H1 has a dominant effect on the binding behavior of other linker histones and propose a model for the role of linker histone phosphorylation in which these modifications act within the context of assembled chromatin.
Direct observation of DNA bending/unbending kinetics in complex with DNA-bending protein IHF
Authors: Kuznetsov Serguei V. , Sugimura Sawako , Vivas Paula , Crothers Donald M. , Ansari Anjum
Published: November 2006

Regulation of gene expression involves formation of specific protein–DNA complexes in which the DNA is often bent or sharply kinked. Kinetics measurements of DNA bending when in complex with the protein are essential for understanding the molecular mechanism that leads to precise recognition of specific DNA-binding sites. Previous kinetics measurements on several DNA-bending proteins used stopped-flow techniques that have limited time resolution of few milliseconds. Here we use a nanosecond laser temperature-jump apparatus to probe, with submillisecond time resolution, the kinetics of bending/unbending of a DNA substrate bound to integration host factor (IHF), an architectural protein from
Escherichia coli
. The kinetics are monitored with time-resolved FRET, with the DNA substrates end-labeled with a FRET pair. The temperature-jump measurements, in combination with stopped-flow measurements, demonstrate that the binding of IHF to its cognate DNA site involves an intermediate state with straight or, possibly, partially bent DNA. The DNA bending rates range from ≈2 ms
−1
at ≈37°C to ≈40 ms
−1
at ≈10°C and correspond to an activation energy of ≈14 ± 3 kcal/mol. These rates and activation energy are similar to those of a single A:T base pair opening inside duplex DNA. Thus, our results suggest that spontaneous thermal disruption in base-paring, nucleated at an A:T site, may be sufficient to overcome the free energy barrier needed to partially bend/kink DNA before forming a tight complex with IHF.
Characterization of ANIT-Induced Toxicity using Precision-Cut Rat and Dog Liver Slices Cultured in a Dynamic Organ Roller System
Authors: Amin K. , Ip C. , Sato B. , Le T. , Green C. E. , Tyson C. A. , Behrsing H. P.
Published: November 2006

This article describes the toxicity of α-naphthylisothiocyanate (ANIT), a compound known to induce dose-dependent hepatobiliary toxicity in vivo, using the slice model. Liver slices (200 μm thick) from male Sprague–Dawley rats and male beagle dogs were cultured for 7 days while exposed to a range of ANIT concentrations (1– 100 μM for rat and 4–320 μM for dog). Tissues (and medium for dog) were evaluated using a panel of clinically relevant biomarkers for liver and histological endpoints to assess viability and proliferation. ANIT increased slice levels of enzyme biomarkers corresponding to biliary markers. At high concentrations (80–100 μM for rat, 320 μM for dog) a diminution of tissue enzyme levels was observed, corresponding to severe hepatobiliary injury. By days 5 and 7, biochemical markers in the medium of dog slices indicated an elevation of hepatocellular and biliary markers. Histologically for both species, minimal hepatocellular injury was noted, but proliferation of biliary epithelial cells (BEC) was observed using 5-bromo-2-deoxyuridine (BrdU) immunostaining. In rat slices, ANIT increased the expression of inducible nitrous oxide synthase (iNOS) within 12 hrs of exposure. In summary, additional experimentation using slice culture may further demonstrate its value in screening compounds that cause hepatobiliary toxicity.
Frequent p53 and H-ras Mutations in Benzene- and Ethylene Oxide-Induced Mammary Gland Carcinomas from B6C3F1 Mice
Authors: Houle Christopher D. , Ton Thai-Vu T. , Clayton Natasha , Huff James , Hong Hue-Hua L. , Sills Robert C.
Published: November 2006

Benzene and ethylene oxide are multisite carcinogens in rodents and classified as human carcinogens by the National Toxicology Program. In 2-year mouse studies, both chemicals induced mammary carcinomas. We examined spontaneous, benzene-, and ethylene oxide-induced mouse mammary carcinomas for p53 protein expression, using immunohistochemistry, and p53 (exons 5–8) and H -ras (codon 61) mutations using cycle sequencing techniques. p53 protein expression was detected in 42% (8/19) of spontaneous, 43% (6/14) of benzene-, and 67% (8/12) of ethylene oxide-induced carcinomas. However, semiquantitative evaluation of p53 protein expression revealed that benzene- and ethylene oxide-induced carcinomas exhibited expression levels five- to six-fold higher than spontaneous carcinomas. p53 mutations were found in 58% (7/12) of spontaneous, 57% (8/14) of benzene-, and 67% (8/12) of ethylene oxide-induced carcinomas. H -ras mutations were identified in 26% (5/19) of spontaneous, 50% (7/14) of benzene-, and 33% (4/12) of ethylene oxide-induced carcinomas. When H- ras mutations were present, concurrent p53 mutations were identified in 40% (2/5) of spontaneous, 71% (5/7) of benzene-, and 75% (3/4) of ethylene oxide-induced carcinomas. Our results demonstrate that p53 and H -ras mutations are relatively common in control and chemically induced mouse mammary carcinomas although both chemicals can alter the mutational spectra and more commonly induce concurrent mutations.
The Application of Critical Social Theory to National Security Research
Authors: Tootell Holly
Published: November 2006

High‐tech solutions to national security, specifically Location‐Based Services (LBS), are attracting increased attention from citizens as they become more pervasive. The connection between LBS and national security has been made in previous ICT studies but has been limited to either the technological or the privacy impact of LBS. They have not addressed the use of LBS from a ‘lifeworld’ perspective. To do this Habermas’s Critical Social Theory (CST) is proposed as a method suitable for investigating the social impact of the technologies and identifying factors driving governments to adopt such technologies. The theory is applied to the national security context.
PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences
Authors: Katoh Kazutaka , Toh Hiroyuki
Published: November 2006

Motivation: To construct a multiple sequence alignment (MSA) of a large number (>∼10 000) of sequences, the calculation of a guide tree with a complexity of O(N2) to O(N3), where N is the number of sequences, is the most time-consuming process.

Results: To overcome this limitation, we have developed an approximate algorithm, PartTree, to construct a guide tree with an average time complexity of O(N log N). The new MSA method with the PartTree algorithm can align ∼60 000 sequences in several minutes on a standard desktop computer. The loss of accuracy in MSA caused by this approximation was estimated to be several percent in benchmark tests using Pfam.

Availability: The present algorithm has been implemented in the MAFFT sequence alignment package ().

Contact:  katoh@bioreg.kyushu-u.ac.jp

Supplementary information: Supplementary information is available at Bioinformatics online.
Characterization of the Drosophila myeloid leukemia factor
Authors: Martin‐Lannerée Séverine , Lasbleiz Christelle , Sanial Matthieu , Fouix Sylvaine , Besse Florence , Tricoire Hervé , Plessis Anne
Published: November 2006

In human, the myeloid leukemia factor 1 (hMLF1) has been shown to be involved in acute leukemia, and mlf related genes are present in many animals. Despite their extensive representation and their good conservation, very little is understood about their function. In Drosophila, dMLF physically interacts with both the transcription regulatory factor DREF and an antagonist of the Hedgehog pathway, Suppressor of Fused, whose over‐expression in the fly suppresses the toxicity induced by polyglutamine. No connection between these data has, however, been established. Here, we show that dmlf is widely and dynamically expressed during fly development. We isolated and analyzed the first dmlf mutants: embryos lacking maternal dmlf product have a low viability with no specific defect, and dmlf‐– adults display weak phenotypes. We monitored dMLF subcellular localization in the fly and cultured cells. We were able to show that, although generally nuclear, dMLF can also be cytoplasmic, depending on the developmental context. Furthermore, two differently spliced variants of dMLF display differential subcellular localization, allowing the identification of regions of dMLF potentially important for its localization. Finally, we demonstrate that dMLF can act developmentally and postdevelopmentally to suppress neurodegeneration and premature aging in a cerebellar ataxia model.
Function and stress tolerance of seed mitochondria
Authors: Macherel David , Benamar Abdelilah , Avelange‐Macherel Marie‐Hélène , Tolleter Dimitri
Published: November 2006

Seeds of higher plant are desiccation tolerant, which suggests that their mitochondria exhibit particular properties. Insight into the function of seed mitochondria, especially in legume and model plants, has been fostered by the development of proteomics. Seed mitochondria are functional at the onset of imbibition, and their integrity and performance systematically improves during germination. This suggests that repair and biogenesis mechanisms exist, and this is supported by morphological and biochemical evidence. Seed mitochondria generate and operate in a hypoxic environment. They accumulate stress proteins, such as a small heat‐shock protein and a late embryogenesis abundant protein. The mitochondria of pea (Pisum sativum L.) seed also display a biased phospholipid composition likely to favour desiccation tolerance. These specific biochemical properties surely contribute to the remarkable tolerance of seed mitochondria to extreme temperatures. Recent progress towards the resolution of the seed mitochondrial proteome is discussed in light of the growing body of genomic data.
Advanced radiogasometric method for the determination of the rates of photorespiratory and respiratory decarboxylations of primary and stored photosynthates under steady‐state photosynthesis
Authors: Pärnik Tiit , Keerberg Olav
Published: November 2006

An advanced radiogasometric method for the study of plant leaf CO2 exchange is presented. The method enables determination of the rates of CO2 fixation, photorespiration and respiration in the light under steady‐state photosynthesis and discrimination between primary and stored photosynthates as substrates of photorespiratory and respiratory decarboxylations. The method is based on the analysis of the time curves of 14CO2 evolution from labeled primary and stored photosynthates in leaves previously exposed to 14CO2. The molar rates of different decarboxylation reactions are calculated from the initial slopes of the curves taking into account the specific radioactivity of CO2 fed to leaves and/or evolved from leaves. To estimate the contribution of primary and stored photosynthates, the measurements of 14CO2 evolution are performed after feeding plant leaves for different periods with 14CO2. Photorespiration and respiration are distinguished on the basis of data obtained from measurements of 14CO2 evolution under normal (210 ml l−1) and low (15 ml l−1) concentrations of oxygen. A principally new method for the determination of the rate of intracellular refixation of respiratory CO2 has been developed. The method is based on the measurements of 14CO2 evolution from leaves into the medium of very high concentrations (30 ml l−1) of 12CO2, where the probability of refixation of 14CO2 evolved inside the cell is close to zero. The results obtained were comparable with the data derived from parallel refixation measurements by means of gasometric methods. As an example of application, the data on CO2 exchange in leaves of two contrasting groups of C3‐species, differing in the ability of starch accumulation, are presented.
Genome size and recombination in angiosperms: a second look
Authors: ROSS‐IBARRA J.
Published: November 2006

Despite dramatic differences in genome size – and thus space for recombination to occur – previous workers found no correlation between recombination rate and genome size in flowering plants. Here I re‐investigate these claims using phylogenetic comparative methods to test a large data set of recombination data in angiosperms. I show that genome size is significantly correlated with recombination rate across a wide sampling of species and that change in genome size explains a meaningful proportion (∼20%) of variation in recombination rate. I show that the strength of this correlation is comparable with that of several characters previously linked to evolutionary change in recombination rate, but argue that consideration of processes of genome size change likely make the observed correlation a conservative estimate. And finally, although I find that recombination rate increases less than proportionally to change in genome size, several mechanistic and theoretical arguments suggest that this result is not unexpected.
Prenatal period to adolescence: the variable presentations of congenital cystic adenomatoid malformation
Authors: ASLAN AYSE TANA , YALCIN EBRU , SOYER TUTKU , DOGRU DENIZ , TALIM BERIL , CIFTCI ARBAY OZDEN , OZCELIK UGUR , KIPER NURAL
Published: November 2006

Background: Congenital cystic adenomatoid malformation (CCAM) of the lung is a rare but potentially life‐threatening pulmonary anomaly.

Methods: Seven patients operated on with the diagnosis of CCAM were reviewed to determine the clinical presentation, age at diagnosis, histopathologic types and the postoperative course.

Results: Cough and respiratory distress were common clinical findings in the patients in the present study. Two of the patients had congenital respiratory distress. The patient who was diagnosed at 15 years had cough, hemoptysis and anorexia for the last 4 months. One patient who received the diagnosis of CCAM prenatally was asymptomatic until she was operated on, on the 45th postnatal day. All patients but one were operated on and histopathological diagnosis was made for each of them between the ages of 4 days to 12 months. Four patients were diagnosed as having CCAM type I, and three patients had CCAM type II histopathologically. Duration of postoperative follow up was between 3 months and 15 years. Neither patient had complaints during that period.

Conclusion: CCAM can present at different ages and in various clinical presentations. There can even be asymptomatic patients who receive their diagnosis during the prenatal period. The possibility of an underlying CCAM should be considered in infants with recurrent chest infections or persistent abnormalities on chest X‐ray following an acute infection. CCAM should also be considered in cases with lung abscess, even in adolescents with no past history of pulmonary complaints.
Newborn hearing screening in a single private Japanese obstetric hospital
Authors: TSUCHIYA HIROYUKI , GOTO KOKO , YUNOHARA NAOKI , MATSUOKA MARIKO , NISHIOKA MASAYO , NAKAMURA YASUKO , FUKUDA YOKO , ENDO FUMIO , MATSUI KAZUO
Published: November 2006

Background: Hearing loss is one of the most common abnormalities present at birth. The authors examined the frequency of newborn hearing disturbance at a single obstetric hospital to exclude technical varieties or varieties of subjects which are inevitable in multiple institutional cooperative studies.

Methods: The newborns were examined with an automated auditory brainstem response screener, the ALGO 2e, on day 4 post‐partum. This Screener uses 35 dB near hearing level click stimuli and provides a PASS/REFER result that requires no interpretation. The PASS result is accepted as adequate evidence of hearing and REFER result as required further diagnostic testing to determine hearing status. Screenings of REFER outcomes were repeated at 1 month of age. Comparisons were made of the results and the Japanese multiple institutional trials by Mann–Whitney U‐test.

Results: The authors screened 8979 out of 13 494 neonates born from July 1999 to October 2004. The neonates with unilateral or bilateral REFER outcomes were 37 cases (0.41% of the total examined) on day 4, and 31 cases (0.35%) at 1 month of age. Five of the 31 neonates had PASS outcomes at 6 months of age. Among the 31 REFER neonates, eight (25.8%) had otolaryngeal complications.

Conclusion: In the present study, screening results at 1 month of age resembled the final diagnosis obtained at 6 months of age; out of 31 REFER cases, 26 cases were diagnosed with hearing loss. In contrast, in the multiple institutional study, both unilateral and bilateral REFER rates were much higher than the rates of final hearing loss. Concerning the final diagnoses of bilateral hearing loss, the authors’ results (0.10%) and the multiple institutional studies’ results (0.05% in low‐risk and 2.19% in high‐risk neonates) were comparable to the results reported in the USA. To expand the newborn hearing screening program, it is crucial that authority and institutions concerned promote the development of a national or prefecture‐based early hearing loss identification and intervention network.
Umbilical serum concentrations of chemokines (RANTES and MGSA/GRO‐α) in preterm and term neonates
Authors: KRÓLAK‐OLEJNIK BARBARA , BECK BRYGIDA , OLEJNIK IGOR
Published: November 2006

Background: The objective of this study was to explore the relationship between labor (preterm and term) and umbilical blood serum regulated on activation, normal T cell expressed and secreted (RANTES) and melanoma growth stimulatory activity/growth‐related oncogene‐a (MSGA/GRO‐α) concentration, and to determine whether early sepsis and pneumonia are associated with changes in concentrations of the chemokines (RANTES and MSGA/GRO‐α) in umbilical blood serum.

Methods: Umbilical blood was obtained from 67 neonates in the following groups: (i) preterm neonates with early sepsis; (ii) preterm neonates with pneumonia; (iii) non‐infected preterm neonates; and (iv) full‐term healthy neonates. RANTES and MGSA/GRO‐α concentrations were determined by use of a commercially available immunoassay kit.

Results: Non‐infected preterm neonates had lower RANTES concentrations than healthy term neonates. Preterm infected neonates (pneumonia or sepsis) did not have higher RANTES concentrations than non‐infected preterm neonates. In contrast, non‐infected preterm neonates had higher MSGA/GRO‐α concentrations than full‐term healthy neonates. And preterm neonates with sepsis had higher MGSA/GRO‐α concentrations than preterm ones with pneumonia and non‐infected preterm ones.

Conclusions: Preterm neonates had constitutively lower RANTES concentrations than term ones and it seems that during infection RANTES concentrations did not increase. MGSA/GRO‐a concentrations were constitutively higher in preterm than term neonates, and septic events further increased its concentrations in preterm neonates.
Immune components (IgA, IgM, IgG, immune cells) of colostrum of Bangladeshi mothers
Authors: ISLAM SK NAZRUL , AHMED LUTHFOR , KHAN Md. NAZRUL ISLAM , HUQUE SAIFUL , BEGUM ANWARA , YUNUS ABUL BASHAR MOHAMMED
Published: November 2006

Background: Colostrum is the first defense for neonates. It is rich in immune components including immunoglobulins and viable immune cells. In the present study, human colostrum collected from 105 postpartum mothers was analyzed for its IgA, IgM, IgG levels, and peripheral immune cells.

Methods: Enzyme‐linked immunosorbent assay was used to analyze the serum immunoglobulin concentrations. Immune cells were estimated by counting 200 cells.

Results: IgA was the dominant immunoglobulin and ranged from 2.84 to 8.69 g/L (mean 5.61 g/L). Mean IgM and IgG concentrations were 0.4 g/L (0.16–0.66 g/L) and 0.095 g/L (0.04–0.15 g/L), respectively. Neutrophil–macrophage (neu‐mac) predominated in cell count (59%) followed by lymphocyte–plasma cells (lymph‐plasma; 40%). The influence of maternal nutritional status, age, parity and income levels on the colostral immunological factors was studied. No significant association could be traced for immunoglobulin content, suggesting that maternal characteristics do not have any bearing on the immunoglobulin content of colostrum. Mean value of eosinophils was found to be higher among the underweight than the normal mothers (F= 3.143, r=−0.101). Maternal age was positively correlated with eosinophil (F= 3.296, r= 0.162). Concentration of neu‐mac had a positive significant correlation with parity (t=−2.07, r= 0.205), while it was negatively significant for lymphocyte–plasma cells (t= 2.073, r=−0.101). However, the correlation coefficients of the immunologic parameters with other maternal characteristics were statistically insignificant.

Conclusion: Colostrum has enough humoral and cellular elements to protect babies. Therefore, immune protection derived from breastfeeding depends on the immunoglobulin level of the colostrum as well as the amount of colostrum ingested.
Punishing Those Responsible for the Prison Abuses at Abu Ghraib: The Influence of the Negative Reciprocity Norm (NRN)
Authors: Eder Paul , Aquino Karl , Turner Carl , Reed Americus
Published: November 2006

The negative reciprocity norm (NRN) is the personal moral code specifying retaliation as a proper response to wrongdoing (Eisenberger, Lynch, Aselage, & Rohdieck, 2004). We examined the role of negative reciprocity in interpreting and reacting to the prison abuses at Abu Ghraib. Results showed that people who believed that American soldiers behaved wrongly at Abu Ghraib were more likely to view punishing the soldiers responsible as a highly moral response and were less likely to contribute money to a charitable organization that helps American soldiers. These relationships were only present among those highly endorsing the negative reciprocity norm.