bluuebunny/crossref_metadata_2025 huggingface dataset:
Oscillations, period doublings, and chaos in CO oxidation and catalytic mufflers
Authors: Marek Miloš , Schejbal Matyáš , Kočí Petr , Nevoral Vladislav , Kubíček Milan , Hadač Otto , Schreiber Igor
Published: September 2006

Early experimental observations of chaotic behavior arising via the period-doubling route for the CO catalytic oxidation both on Pt(110) and Pt∕γ-Al2O3 porous catalyst were reported more than 15 years ago. Recently, a detailed kinetic reaction scheme including over 20 reaction steps was proposed for the catalytic CO oxidation, NOx reduction, and hydrocarbon oxidation taking place in a three-way catalyst (TWC) converter, the most common reactor for detoxification of automobile exhaust gases. This reactor is typically operated with periodic variation of inlet oxygen concentration. For an unforced lumped model, we report results of the stoichiometric network analysis of a CO reaction subnetwork determining feedback loops, which cause the oscillations within certain regions of parameters in bifurcation diagrams constructed by numerical continuation techniques. For a forced system, numerical simulations of the CO oxidation reveal the existence of a period-doubling route to chaos. The dependence of the rotation number on the amplitude and period of forcing shows a typical bifurcation structure of Arnold tongues ordered according to Farey sequences, and positive Lyapunov exponents for sufficiently large forcing amplitudes indicate the presence of chaotic dynamics. Multiple periodic and aperiodic time courses of outlet concentrations were also found in simulations using the lumped model with the full TWC kinetics. Numerical solutions of the distributed model in two geometric coordinates with the CO oxidation subnetwork consisting of several tens of nonlinear partial differential equations show oscillations of the outlet reactor concentrations and, in the presence of forcing, multiple periodic and aperiodic oscillations. Spatiotemporal concentration patterns illustrate the complexity of processes within the reactor.
Doping effect on dark currents in In0.5Ga0.5As∕GaAs quantum dot infrared photodetectors grown by metal-organic chemical vapor deposition
Authors: Drozdowicz-Tomsia K. , Goldys E. M. , Fu Lan , Jagadish C.
Published: September 2006

Stacked self-assembled In0.5Ga0.5As∕GaAs quantum dot infrared photodetectors grown by low-pressure metal-organic chemical vapor deposition, with and without silicon dopants in the quantum dot layers, are investigated. The increase of dark currents observed at higher doping levels is attributed to higher defect density leading to stronger sequential resonant tunneling and to lowering of the operating temperature of the device.
Two- and one-dimensional light propagations and gain in layer-by-layer-deposited colloidal nanocrystal waveguides
Authors: Roither J. , Pichler S. , Kovalenko M. V. , Heiss W. , Feychuk P. , Panchuk O. , Allam J. , Murdin B. N.
Published: September 2006

Optical waveguides containing high percentages of colloidal nanocrystals have been fabricated by layer-by-layer deposition on planar and patterned glass substrates. The two- and one-dimensional waveguidings in these structures are demonstrated by propagation loss experiments. The experimental results obtained for various film thicknesses and widths of the waveguide stripes together with simulations of the light propagation indicate that the losses are dominated by surface roughness. The variable stripe length method is used to determine the optical gain of 230cm−1 from the amplified spontaneous emission. This high value makes the authors’ waveguide structures very promising for applications in amplifiers and lasers with reduced threshold powers.
Thermal responsive microlens arrays
Authors: Yang Han , Han Yong-Hao , Zhao Xiang-Wei , Nagai Keiji , Gu Zhong-Ze
Published: September 2006

The authors developed a technique to encapsulate poly-N-isopropylacrylamide (PNIPAAm) for fabrication of monodisperse microcapsules, whose size, embedding efficiency, and wall thickness are controllable. The monodisperse microcapsules were hexagonally packed to form microlens array (MLA) via a self-assembly process. Due to the thermal respondence of PNIPAAm, the imaging capability and light transportation of the MLA were simply controlled by temperature.
Electrical and optical properties of doped p-type GaN superlattices
Authors: Polyakov A. Y. , Smirnov N. B. , Govorkov A. V. , Dabiran Amir M. , Osinsky A. V. , Pearton S. J.
Published: September 2006

A comparison is reported of the electrical, photoelectrical, and microcathodoluminescence properties of bulk p-GaN films and p-type p-GaN(Mg)∕GaN superlattices grown by molecular beam epitaxy. It is shown that the microcathodoluminescence intensity is much lower and the photocurrent (both on samples with indium Ohmic contacts and on Au Schottky diodes) much higher for the doped superlattices due to the spatial separation of photoexcited electrons and holes in the doped and undoped layers and corresponding increase of the lifetime in comparison to the bulk samples. The in-plane conductivity in the doped superlattices is not enhanced significantly relative to conventional p-GaN, but the hole mobilities are increased (from 12to20cm2∕Vs).
Evaluation of Kelvin probe force microscopy for imaging grain boundaries in chalcopyrite thin films
Authors: Leendertz C. , Streicher F. , Lux-Steiner M. Ch. , Sadewasser S.
Published: September 2006

In view of the outstanding performance of polycrystalline thin film solar cells on the basis of Cu(In,Ga)Se2, the electrical activity at grain boundaries currently receives considerable attention. Recently, Kelvin probe force microscopy (KPFM) has been applied to characterize the properties of individual grain boundaries, observing a drop in the work function in many cases. We present finite element simulations of the electrostatic forces to assess the experimental resolution of KPFM. Depending on the tip-sample distance, the observed drop in the work function amounts to only a fraction of the real potential drop. The simulations are considered for different grain boundary models and consequences for the quantitative evaluation of experimental results are discussed.
Introduction: Self-organization in nonequilibrium chemical systems
Authors: Epstein Irving R. , Pojman John A. , Steinbock Oliver
Published: September 2006

The field of self-organization in nonequilibrium chemical systems comprises the study of dynamical phenomena in chemically reacting systems far from equilibrium. Systematic exploration of this area began with investigations of the temporal behavior of the Belousov-Zhabotinsky oscillating reaction, discovered accidentally in the former Soviet Union in the 1950s. The field soon advanced into chemical waves in excitable media and propagating fronts. With the systematic design of oscillating reactions in the 1980s and the discovery of Turing patterns in the 1990s, the scope of these studies expanded dramatically. The articles in this Focus Issue provide an overview of the development and current state of the field.
Spin reorientation transition in Fe-rich alloy films on W(110): The role of magnetoelastic anisotropy and structural transition
Authors: Lee Hangil , Baek I.-G. , Vescovo E.
Published: September 2006

Epitaxial Fe-rich alloy films of formulas Fe1−xNix, Fe1−xCox, and Fe1−xVx were grown on a W(110) substrate with a bcc structure without any structural transition at x<0.3. Using chemical pressure (inserting small amounts of Ni, Co, or V into Fe), the authors controlled the lattice constant of these alloy films and then measured the variation of spin reorientation thickness (tr) according to the alloy composition. The authors focused on the roles of the lattice constant of the film and the spin reorientation thickness that is closely related to the strain associated with the lattice mismatch between the thin film and the substrate.
Electronically excited states of tryptamine and its microhydrated complex
Authors: Schmitt Michael , Brause Robert , Marian Christel M. , Salzmann Susanne , Meerts W. Leo
Published: September 2006

The lowest electronically excited singlet states of tryptamine and the tryptamine (H2O)1 cluster have been studied, using time dependent density functional theory for determination of the geometries and multireference configuration interaction for the vertical and adiabatic excitation energies, the permanent dipole moments, and the transition dipole moment orientations. All molecular properties of the seven experimentally observed conformers of tryptamine could be reproduced with high accuracy. A strong solvent reorientation has been found upon electronic excitation of the 1:1 water cluster of tryptamine to the La and Lb states. The adiabatically lowest excited singlet state in case of the tryptamine monomer is the Lb state, while for the 1:1 water complex, the La is calculated below the Lb state.
Spectroscopic properties of Er3+ doped glass ceramics containing Sr2GdF7 nanocrystals
Authors: Qiao Xvsheng , Fan Xianping , Wang Minquan
Published: September 2006

The Er3+ doped transparent oxyfluoride glass ceramics containing Sr2GdF7 nanocrystals were prepared and their spectroscopic properties were discussed. The formation of Sr2GdF7 nanocrystals in the glass ceramics was confirmed by x-ray diffraction. The split peaks of the upconversion and near infrared emission bands of the Er3+ doped glass ceramics can be observed. The upconversion luminescence intensity of Er3+ in the glass ceramics increased significantly with the increasing heat treated temperature. The luminescence decay curves and time-resolved spectra indicated that the lifetime of the S3∕24 state of Er3+ in the glass ceramic was longer than that in the glass.
Multilayers with tailored blurred interfaces
Authors: Padiyath J. , Stahn J. , Horisberger M. , Böni P.
Published: September 2006

Monochromators used in neutron or x-ray experiments often have higher-order contributions, which have to be reduced by filters. Multilayer monochromators produced by dc-magnetron sputtering, with intentionally blurred interfaces, have reduced these higher-order contributions. The approach is to substitute the bilayer structure by several layers with individual thicknesses per period. A Ni∕Ti monochromator was prepared where higher-order contributions were reduced below 0.1% of the first-order reflectivity of 93% (measured up to the seventh order). In order to determine the lifetime of such a structure, the interdiffusion of the constituents was measured with thermal annealing (interface diffusion activation energy: 0.16(1)eV).
Wavelength dependence of thermo-optic coefficient of organically modified SiO2–ZrO2 hybrid films
Authors: Kang Eun-Seok , Takahashi Masahide , Tokuda Yomei , Yoko Toshinobu
Published: September 2006

Thermo-optic characteristics of organically modified SiO2–ZrO2 films prepared by a nonhydrolytic reaction have been investigated. The thermo-optic coefficient (dn∕dT) is negative on the order of −10−4∕K and varies with the wavelength as a function of the ZrO2 content in organically modified SiO2 material. As the amount of ZrO2 increases, the wavelength dependence of dn∕dT gradually varies from positive to negative. The magnitude and wavelength dependence of dn∕dT for organically modified SiO2–ZrO2 hybrid materials make these materials highly flexible for application in thermo-optic integrated devices.
Blob birth and transport in the tokamak edge plasma: Analysis of imaging data
Authors: Myra J. R. , D’Ippolito D. A. , Stotler D. P. , Zweben S. J. , LeBlanc B. P. , Menard J. E. , Maqueda R. J. , Boedo J.
Published: September 2006

High-speed high-spatial-resolution data obtained by the gas puff imaging (GPI) diagnostic on the National Spherical Torus Experiment [M. Ono, M.G. Bell, R.E. Bell et al. Plasma Phys. Control. Fusion 45, A335 (2003).] is analyzed and interpreted in light of recent theoretical models for electrostatic edge turbulence and blob propagation. The experiment is described in terms of theoretical regimes that predict different dependencies for the radial velocity of blob convection. Using the GPI data, atomic physics analysis, and blob tracking on a restricted dataset, it is shown that the observed blob velocities in the scrape-off layer are bounded by a theory-based minimum velocity associated with the sheath-connected regime. A similar maximum velocity bound associated with the resistive-ballooning regime is also observed. Turning to the question of blob creation, it is shown that blobs are born with a density and temperature characteristic of the plasma conditions where underlying linear edge drift-curvature instabilities are localized. Finally, statistical variations in blob properties and in the radial blob velocity for given edge conditions are significant, and tend to mask any systematic changes among discharges with different conditions.
Localization and cross section reconstruction of fluorescent targets in ex vivo breast tissue using independent component analysis
Authors: Alrubaiee M. , Xu M. , Gayen S. K. , Alfano R. R.
Published: September 2006

An information theory based approach is introduced for the detection and three-dimensional localization of fluorescent targets embedded in a turbid medium. The approach uses multisource illumination of the medium, multidetector transillumination acquisition of fluorescence signal, independent component analysis for target detection and localization, and a back-projection algorithm for reconstruction of target cross section. The efficacy of the approach is demonstrated by locating and estimating the cross section of a fluorescent target embedded in a 100×100×26mm3 ex vivo human breast tissue specimen and in a tissue-simulating turbid medium of thickness 50 times the transport mean free path.
Uniform glowlike plasma source assisted by preionization of spark in ambient air at atmospheric pressure
Authors: Qi Bing , Ren Chunsheng , Wang Dezhen , Li Shou-Zhe , Wang Kun , Zhang Yutao
Published: September 2006

The ultraviolet radiation produced by spark discharges is employed to supply preionization for the dielectric barrier discharge in ambient air at atmospheric pressure. The effect of ultraviolet preionization and overvoltage on improving the uniformity of the dielectric barrier discharge is investigated experimentally. Based on the emission spectra and voltage-current wave forms, the optical and electrical characteristics of the discharge are discussed.
High-performance ZnO nanowire field effect transistors
Authors: Chang Pai-Chun , Fan Zhiyong , Chien Chung-Jen , Stichtenoth Daniel , Ronning Carsten , Lu Jia Grace
Published: September 2006

ZnO nanowires with high crystalline and optical properties are characterized, showing strong effect of the surface defect states. In order to optimize the performance of devices based on these nanowires, a series of complementary metal-oxide semiconductor compatible surface passivation procedures is employed. Electrical transport measurements demonstrate significantly reduced subthreshold swing, high on/off ratio, and unprecedented field effect mobility.
Polymeric distributed feedback lasers by room-temperature nanoimprint lithography
Authors: Mele Elisa , Camposeo Andrea , Stabile Ripalta , Del Carro Pompilio , Di Benedetto Francesca , Persano Luana , Cingolani Roberto , Pisignano Dario
Published: September 2006

Room temperature nanoimprinting lithography is used to realize a distributed feedback laser by direct dry pressing of the conjugated polymer (poly[2-methoxy-5-(2-ethylhexyloxy)-1,4-phenylenevinylene]). The laser device exhibits emission at 630nm with a pump threshold of 25μJ∕cm2 and a polarization contrast of the emitted light as large as 0.91. Therefore, room temperature nanoimprint lithography turns out to be very effective for producing stable patterns on light-emitting polymers for the one-step fabrication of nanopatterned optoelectronic devices.
ZnTe nanowires grown on GaAs(100) substrates by molecular beam epitaxy
Authors: Janik E. , Sadowski J. , Dłużewski P. , Kret S. , Baczewski L. T. , Petroutchik A. , Łusakowska E. , Wróbel J. , Zaleszczyk W. , Karczewski G. , Wojtowicz T. , Presz A.
Published: September 2006

ZnTe nanowires with an average diameter of about 30nm and lengths above 1μm were grown on GaAs(100) substrate by molecular beam epitaxy. The growth process was based on the Au-catalyzed vapor-liquid-solid mechanism. A thin gold layer (3–20Å thick) annealed in high vacuum prior to the nanowire growth was used as a source of catalytic nanoparticles. The nanowires are inclined about 55° to the (100) substrate surface normal. They have a zinc-blende crystal structure and their growth axis is ⟨111⟩.
InSb and InSb:N multiple quantum dots
Authors: Hatami Fariba , Kim Seongsin M. , Yuen Homan B. , Harris James S.
Published: September 2006

The authors report the growth and structural properties of InSb and InSb:N quantum dots on InAs and GaAs substrates. Strain induced self-assembled quantum dots are grown using solid-source molecular beam epitaxy. For improved growth control, they developed a growth technique similar to atomic-layer epitaxial methods. InSb and InSb:N multiple quantum dots formed on both InAs and GaAs. They explain the formation of multiple quantum dots by the anisotropic distribution of strain energy within the quantum dot, the long adatom lifetime during atomic-layer epitaxy, and the low bond energy of InSb.
Silver nanocrystal superlattice coating for molecular sensing by surface-enhanced Raman spectroscopy
Authors: Qiu T. , Wu X. L. , Shen J. C. , Chu Paul K.
Published: September 2006

A nanotechnique to assemble silver nanocrystals and control the gaps precisely in the sub-10nm regime is demonstrated on an active coating exhibiting surface-enhanced Raman scattering (SERS). The silver nanocrystal superlattice coating boasts a high SERS enhancement factor, large dynamic range, and universal SERS activity. The observed SERS efficiency can be explained in terms of interparticle-coupling-induced Raman enhancement.
Analysis of the factors governing the enhanced photoluminescence brightness of Li-doped Y2O3:Eu thin-film phosphors
Authors: Cho Jun Yeol , Do Young Rag , Huh Young-Duk
Published: September 2006

The authors studied the Li concentration dependence of the internal efficiency and extraction efficiency contributions to the enhanced photoluminescence (PL) brightness of the Li-doped Y2O3:Eu thin films. Experiments conducted with excitation at a wavelength of 254nm showed that adding 20mol% Li2CO3 to conventional Y2O3:Eu thin films improved their PL brightness by a factor of over 7.0. This improvement is attributed to enhanced internal factors (crystallinity, grains, and substitution of interstitial oxygen) and the increased optical volume (thickness), as well as the reduction of photon trapping in the high-index guiding layers of the Y2O3:Eu thin films. They also discuss how to quantitatively determine the contributions of the internal efficiency, the extraction efficiency, and the optical volume to the enhanced PL brightness of the Li-doped Y2O3:Eu thin-film phosphors.
Generation of highly directional beam by k-space filtering using a metamaterial flat slab with a small negative index of refraction
Authors: Martínez Alejandro , Piqueras Miguel A. , Martí Javier
Published: September 2006

The authors show how a flat slab made of a metamaterial engineered to have a small negative index of refraction can be used to reshape radiation emitted from an isotropic source and produce a highly directional output beam. The slab makes a filtering of high transverse wave vectors of the input diverging beam. The predicted phenomenon is demonstrated at microwave frequencies using a two-dimensional photonic crystal made of alumina rods. Simulations using the finite-difference time-domain method support the experiments.
Quadratic autocorrelation of free-electron laser radiation and photocurrent saturation in two-photon quantum well infrared photodetectors
Authors: Schneider H. , Drachenko O. , Winnerl S. , Helm M. , Walther M.
Published: September 2006

Using the free-electron laser facility FELBE, the authors have studied the influence of the intensity on the quadratic autocorrelation measured with two-photon quantum well infrared photodetectors (QWIPs). At high illumination powers, the shape of the autocorrelation trace is affected by photocurrent saturation of the two-photon QWIP. They describe the saturation mechanism by different analytical models taking account of the photocurrent nonlinearity in analogy to linear QWIPs and give conditions where true quadratic behavior can be observed. While these studies were carried out at 77K, properties of two-photon QWIPs at room temperature will also be addressed.
Improving the power efficiency of white light-emitting diode by doping electron transport material
Authors: Huang Jinsong , Hou Wei-Jen , Li Juo-Hao , Li Gang , Yang Yang
Published: September 2006

Highly efficient white light emission was realized via the partial energy transfer from blue host polyfluorene (PF) to orange light emission dopant rubrene. A more balanced charge transport was achieved by adding an electron transport material, 2-(4-biphenylyl)-5-(4-tert-butylphenyl)-1,3,4-oxadiazole (PBD), into the PF-rubrene system to enhance the electron transportation. Efficiency improvement by as much as a factor of 2 has been observed through the addition of PBD. These devices can easily reach high luminance at low driving voltages, thus achieving high power efficiency at high luminance (14.8, 13.5, and 12.0lm∕W at the luminances of 1000, 2000, and 4000cd∕m2, respectively). Therefore, this performance is an important approach toward solid-state lighting application. The enhancement is mainly attributed to three factors: increased electron transport property of the host material, increased photoluminescence quantum efficiency, and the shifting of emission zone away from cathode contact. The reported efficiency is among the highest values reported in the white emission polymer light-emitting diodes.
Effects of pasture treatments on detached pasture litter mass, quality, litter loss, decomposition rates, and residence time in northern New South Wales
Authors: Lodge G. M. , King K. L. , Harden S.
Published: September 2006

Few data are available on litter quantity and quality and decomposition rates over time and what effects stocking rate, grazing method, legume introduction, and fertiliser application may have. Studies were conducted from spring 1997 to 2001 at 3 pasture sites in northern New South Wales to provide such data by examining the effects of pasture treatments on detached litter mass (kg DM/ha) and quality data (percent carbon (C), nitrogen (N) and C : N ratio) collected at 9 sampling times in 2 replicates of 5 (native pasture) or 4 (sown pasture) treatments and examined for differences over time using cubic spline analyses. For each site, decomposition bags were also used to assess differences among treatments for initial and final detached litter mass, organic matter (OM), N values, the relative rate of decomposition (g/g.day), and residence time (days) for periods March to June 1998, June to September 1998, and September to November 1998. Initial and final data were also collected for detached resident and subterranean clover (Trifolium subterraneum) litter for 6 sampling times from September 1998 to January 1999 for a reduced range of treatments at each site. Similar data were collected at each site for resident litter and grass green leaf material from January to April 1999.
Detached litter mass declined (P < 0.05) in unfertilised continuously grazed treatments (Barraba native pasture) and with high continuous stocking rate in the Nundle sown pasture. Litter quality was only significantly affected by grazing treatment at the Barraba native pasture site where the fertilised treatment oversown with subterranean clover tended to have low percent C and a lower C : N ratio and higher percent N and microbial biomass C than other treatments.
From autumn to spring 1998, the fertilised, oversown treatment at both native pasture sites generally had high litter DM, OM, and N losses and relative rates of decomposition compared with continuously grazed, unfertilised pasture. For the same period, at the Nundle sown pasture site, OM and N losses and the relative rate of decomposition were consistently higher, and residence time lower, in the continuously grazed, high stocking rate treatment compared with all other treatments. Compared with resident detached litter, both subterranean clover litter and green leaf material at the native pasture sites had higher relative decomposition rates and lower residence times. The implications of these data for the management of both native and sown pastures are discussed.
Expression of field resistance under Western Australian conditions to Sclerotinia sclerotiorum in Chinese and Australian Brassica napus and Brassica juncea germplasm and its relation with stem diameter
Authors: Li C. X. , Li Hua , Sivasithamparam K. , Fu T. D. , Li Y. C. , Liu S. Y. , Barbetti M. J.
Published: September 2006

Sclerotinia stem rot, caused by Sclerotinia sclerotiorum, has become one of the most serious disease problems in oilseed rape-growing areas in Australia. Sources of resistance to this disease have been sought worldwide. In this study, germplasm comprising 42 Brassica napus and 12 Brassica juncea accessions from China and Australia, was screened for resistance to Sclerotinia stem rot under Western Australian field conditions. Resistance was confirmed in some germplasm from China and new sources of resistance were identified in germplasm from Australia. Furthermore, our study found that the severity of stem lesions was related to stem diameter and percentage of the host plants that were dead. It was evident that both stem lesion length and percentage of plant death were at the lowest level when the stem diameter was approximately 10 mm. Smaller or greater stem diameter resulted both in increased stem lesion length and plant death. Stem diameter may be a useful parameter in breeding cultivars of oilseed Brassicas with Sclerotinia resistance.
The role of Pax-6 in lens regeneration
Authors: Madhavan Mayur , Haynes Tracy L. , Frisch Nicholas C. , Call Mindy K. , Minich Craig M. , Tsonis Panagiotis A. , Del Rio-Tsonis Katia
Published: September 2006

Pax-6 is a master regulator of eye development and is expressed in the dorsal and ventral iris during newt lens regeneration. We show that expression of Pax-6 during newt lens regeneration coincides with cell proliferation. By knocking down expression of Pax-6 via treatment with morpholinos, we found that proliferation of iris pigment epithelial cells was dramatically reduced both
in vitro
and
in vivo
, and, as a result, lens regeneration was significantly retarded. However, induction of dedifferentiation in the dorsal iris was not inhibited. Pax-6 knockdown early in lens regeneration resulted in inhibition of crystallin expression and retardation of lens fiber induction. Once crystallin expression and differentiation of lens fibers has ensued, however, loss of function of Pax-6 did not affect crystallin expression and lens fiber maintenance, even though the effects on proliferation persisted. These results conclusively show that Pax-6 is associated with distinct early events during lens regeneration, namely control of cell proliferation and subsequent lens fiber differentiation.
Transaldolase is essential for maintenance of the mitochondrial transmembrane potential and fertility of spermatozoa
Authors: Perl Andras , Qian Yueming , Chohan Kazim R. , Shirley Cynthia R. , Amidon Wendy , Banerjee Sanjay , Middleton Frank A. , Conkrite Karina L. , Barcza Maureen , Gonchoroff Nick , Suarez Susan S. , Banki Katalin
Published: September 2006

Fertility of spermatozoa depends on maintenance of the mitochondrial transmembrane potential (Δψm), which is generated by the electron-transport chain and regulated by an oxidation–reduction equilibrium of reactive oxygen intermediates, pyridine nucleotides, and glutathione (GSH). Here, we report that male mice lacking transaldolase (TAL)−/−are sterile because of defective forward motility. TAL−/−spermatozoa show loss of Δψmand mitochondrial membrane integrity because of diminished NADPH, NADH, and GSH. Mitochondria constitute major Ca2+stores; thus, diminished mitochondrial mass accounts for reduced Ca2+fluxing, defective forward motility, and infertility. Reduced forward progression of TAL-deficient spermatozoa is associated with diminished mitochondrial reactive oxygen intermediate production and Ca2+levels, intracellular acidosis, and compensatory down-regulation of carbonic anhydrase IV and overexpression of CD38 and γ-glutamyl transferase. Microarray analyses of gene expression in the testis, caput, and cauda epididymidis of TAL+/+, TAL+/−, and TAL−/−littermates confirmed a dominant impact of TAL deficiency on late stages of sperm-cell development, affecting the electron-transport chain and GSH metabolism. Stimulation ofde novoGSH synthesis by oralN-acetyl-cysteine normalized the low fertility rate of TAL+/−males without affecting the sterility of TAL−/−males. Whereas TAL−/−sperm failed to fertilize TAL+/+oocytesin vitro, sterility of TAL−/−sperm was circumvented by intracytoplasmic sperm injection, indicating that TAL deficiency influenced the structure and function of mitochondria without compromising the nucleus and DNA integrity. Collectively, these data reveal an essential role of TAL in sperm-cell mitochondrial function and, thus, male fertility.
Templated biomineralization on self-assembled protein fibers
Authors: Subburaman K. , Pernodet N. , Kwak S. Y. , DiMasi E. , Ge S. , Zaitsev V. , Ba X. , Yang N. L. , Rafailovich M.
Published: September 2006

Biological mineralization of tissues in living organisms relies on proteins that preferentially nucleate minerals and control their growth. This process is often referred to as “templating,” but this term has become generic, denoting various proposed mineral–organic interactions including both chemical and structural affinities. Here, we present an approach using self-assembled networks of elastin and fibronectin fibers, similar to the extracellular matrix. When induced onto negatively charged sulfonated polystyrene surfaces, these proteins form fiber networks of ≈10-μm spacing, leaving open regions of disorganized protein between them. We introduce an atomic force microscopy-based technique to measure the elastic modulus of both structured and disorganized protein before and during calcium carbonate mineralization. Mineral-induced thickening and stiffening of the protein fibers during early stages of mineralization is clearly demonstrated, well before discrete mineral crystals are large enough to image by atomic force microscopy. Calcium carbonate stiffens the protein fibers selectively without affecting the regions between them, emphasizing interactions between the mineral and the organized protein fibers. Late-stage observations by optical microscopy and secondary ion mass spectroscopy reveal that Ca is concentrated along the protein fibers and that crystals form preferentially on the fiber crossings. We demonstrate that organized versus unstructured proteins can be assembled mere nanometers apart and probed in identical environments, where mineralization is proved to require the structural organization imposed by fibrillogenesis of the extracellular matrix.
Characterization and prediction of protein–protein interactions within and between complexes
Authors: Sprinzak Einat , Altuvia Yael , Margalit Hanah
Published: September 2006

Databases of experimentally determined protein interactions provide information on binary interactions and on involvement in multiprotein complexes. These data are valuable for understanding the general properties of the interaction between proteins as well as for the development of prediction schemes for unknown interactions. Here we analyze experimentally determined protein interactions by measuring various sequence, genomic, transcriptomic, and proteomic attributes of each interacting pair in the yeast
Saccharomyces cerevisiae
. We find that dividing the data into two groups, one that includes binary interactions within protein complexes (stable) and another that includes binary interactions that are not within complexes (transient), enables better characterization of the interactions by the different attributes and improves the prediction of new interactions. This analysis revealed that most attributes were more indicative in the set of intracomplex interactions. Using this data set for training, we integrated the different attributes by logistic regression and developed a predictive scheme that distinguishes between interacting and noninteracting protein pairs. Analysis of the logistic-regression model showed that one of the strongest contributors to the discrimination between interacting and noninteracting pairs is the presence of distinct pairs of domain signatures that were suggested previously to characterize interacting proteins. The predictive algorithm succeeds in identifying both intracomplex and other interactions (possibly the more stable ones), and its correct identification rate is 2-fold higher than that of large-scale yeast two-hybrid experiments.
Direct spectroscopic detection of a C-H-cleaving high-spin Fe(IV) complex in a prolyl-4-hydroxylase
Authors: Hoffart Lee M. , Barr Eric W. , Guyer Robert B. , Bollinger J. Martin , Krebs Carsten
Published: September 2006

The Fe(II)- and α-ketoglutarate (αKG)-dependent dioxygenases use mononuclear nonheme iron centers to effect hydroxylation of their substrates and decarboxylation of their cosubstrate, αKG, to CO
2
and succinate. Our recent dissection of the mechanism of taurine:αKG dioxygenase (TauD), a member of this enzyme family, revealed that two transient complexes accumulate during catalysis in the presence of saturating substrates. The first complex contains the long-postulated C-H-cleaving Fe(IV)-oxo intermediate, J, and the second is an enzyme·product(s) complex. Here, we demonstrate the accumulation of two transient complexes in the reaction of a prolyl-4-hydroxylase (P4H), a functional homologue of human αKG-dependent dioxygenases with essential roles in collagen biosynthesis and oxygen sensing. The kinetic and spectroscopic properties of these two P4H complexes suggest that they are homologues of the TauD intermediates. Most notably, the first exhibits optical absorption and Mössbauer spectra similar to those of J and, like J, a large substrate deuterium kinetic isotope on its decay. The close correspondence of the accumulating states in the P4H and TauD reactions supports the hypothesis of a conserved mechanism for substrate hydroxylation by enzymes in this family.
Calcium-sensitive MRI contrast agents based on superparamagnetic iron oxide nanoparticles and calmodulin
Authors: Atanasijevic Tatjana , Shusteff Maxim , Fam Peter , Jasanoff Alan
Published: September 2006

We describe a family of calcium indicators for magnetic resonance imaging (MRI), formed by combining a powerful iron oxide nanoparticle-based contrast mechanism with the versatile calcium-sensing protein calmodulin and its targets. Calcium-dependent protein–protein interactions drive particle clustering and produce up to 5-fold changes in
T2
relaxivity, an indication of the sensors' potency. A variant based on conjugates of wild-type calmodulin and the peptide M13 reports concentration changes near 1 μM Ca
2+
, suitable for detection of elevated intracellular calcium levels. The midpoint and cooperativity of the response can be tuned by mutating the protein domains that actuate the sensor. Robust MRI signal changes are achieved even at nanomolar particle concentrations (<1 μM in calmodulin) that are unlikely to buffer calcium levels. When combined with technologies for cellular delivery of nanoparticulate agents, these sensors and their derivatives may be useful for functional molecular imaging of biological signaling networks in live, opaque specimens.
Bone morphogenetic protein antagonist gremlin 1 is widely expressed by cancer-associated stromal cells and can promote tumor cell proliferation
Authors: Sneddon Julie B. , Zhen Hanson H. , Montgomery Kelli , van de Rijn Matt , Tward Aaron D. , West Robert , Gladstone Hayes , Chang Howard Y. , Morganroth Greg S. , Oro Anthony E. , Brown Patrick O.
Published: September 2006

Although tissue microenvironments play critical roles in epithelial development and tumorigenesis, the factors mediating these effects are poorly understood. In this work, we used a genomic approach to identify factors produced by cells in the microenvironment of basal cell carcinoma (BCC) of the skin, one of the most common human cancers. The global gene expression programs of stromal cell cultures derived from human BCCs showed consistent, systematic differences from those derived from nontumor skin. The gene most consistently expressed at a higher level in BCC tumor stromal cells compared with those from nontumor skin was
GREMLIN 1
, which encodes a secreted antagonist of the bone morphogenetic protein (BMP) pathway. BMPs and their antagonists are known to play a crucial role in stem and progenitor cell biology as regulators of the balance between expansion and differentiation. Consistent with the hypothesis that BMP antagonists might have a similar role in cancer, we found
GREMLIN 1
expression in the stroma of human BCC tumors but not in normal skin
in vivo
. Furthermore, BMP 2 and 4 are expressed by BCC cells.
Ex vivo
, BMP inhibits, and Gremlin 1 promotes, proliferation of cultured BCC cells. We further found that
GREMLIN 1
is expressed by stromal cells in many carcinomas but not in the corresponding normal tissue counterparts that we examined. Our data suggest that BMP antagonists may be important constituents of tumor stroma, providing a favorable microenvironment for cancer cell survival and expansion in many cancers.
Primary bacteraemia caused by Rhizobium radiobacter in a patient with solid tumours
Authors: Christakis G. B. , Alexaki P. , Alivizatos A. S. , Chalkiopoulou I. , Athanasiou A. E. , Zarkadis I. K.
Published: September 2006

A case of Rhizobium radiobacter primary bacteraemia in a patient with solid tumours is reported. Corticosteroid therapy and diabetes mellitus were the predisposing factors. The patient was treated successfully with amikacin and piperacillin/tazobactam. The clinical isolate was identified as R. radiobacter by 16S rRNA gene sequencing. Phytopathogenicity tests and a PCR assay demonstrated that the organism was not a plant pathogen.
Antifungal activity of the essential oil of Thymus pulegioides on Candida, Aspergillus and dermatophyte species
Authors: Pinto Eugénia , Pina-Vaz Cidália , Salgueiro Lígia , Gonçalves Maria José , Costa-de-Oliveira Sofia , Cavaleiro Carlos , Palmeira Ana , Rodrigues Acácio , Martinez-de-Oliveira José
Published: September 2006

The composition of the essential oil of Thymus pulegioides and its antifungal activity on Candida, Aspergillus and dermatophyte fungal strains were studied. Essential oil from the aerial parts of the plant was obtained by hydrodistillation and analysed by GC and GC-MS. The oil showed high contents of carvacrol and thymol. The MIC and minimal lethal concentration were used to evaluate the antifungal activity against Candida (seven clinical isolates and four ATCC type strains), Aspergillus [five clinical isolates, and two Colección Española de Cultivos Tipo (CECT) and two ATCC type strains] and five clinical dermatophyte strains. Antifungal activity was evaluated for the essential oil and for its main components. To clarify its mechanism of action on yeasts and filamentous fungi, flow-cytometric studies of cytoplasmic membrane integrity were performed, and the effect on the amount of ergosterol was investigated. Results showed that T. pulegioides essential oil exhibited a significant activity against clinically relevant fungi, mainly due to lesion formation in the cytoplasmic membrane and a considerable reduction of the ergosterol content. The present study indicates that T. pulegioides essential oil has considerable antifungal activity, deserving further investigation for clinical applications.
Molecular characterization of clinical isolates of M non-typable group A streptococci from invasive disease cases
Authors: Tanna Asha , Emery Michaela , Dhami Chenchal , Arnold Eve , Efstratiou Androulla
Published: September 2006

Currently there are 93 validated M serotypes of Streptococcus pyogenes, Lancefield group A streptococcus (GAS), and >130 emm genotypes. A marked increase in the number of non-typable GAS isolates (2 % in 2000, 4 % in 2001 and 9 % in 2002) from invasive disease cases referred to the authors' reference laboratory was noted during 2000–2002. A total of 217 (92 %) were from blood cultures, 14 (6 %) from deep abscesses and five (2 %) from aspirates. The clinical manifestations included bacteraemia, septicaemia, cellulitis, meningitis, necrotizing fasciitis and toxic-shock syndrome. In order to establish whether this increase was due to the emergence of novel types or the unavailability of M-typing sera, these isolates were subjected to emm sequencing. A total of 144 isolates (61 %) belonged to M types for which sera were no longer available; 112 (48 %) belonged to higher M types, including emm83.1 (9 %), emm94 (8 %) emm87 (6 %) and emm89 (6 %); and 32 (13 %) belonged to lower M types that were not commonly isolated in the UK, and included M25, M43, M49, M64, M73 and M74. Sixty-six (28 %) of the isolates belonged to newly designated emm types. Other isolates belonged to the novel emm types st2147, STNS1033 and st854, recently registered in the Centers for Disease Control (CDC) database by other laboratories. One novel emm type, st2161, was isolated from an injecting drug user. There were differences in the type distribution of these isolates according to geographic location. However, 90 % of emm93, one of seven predominant emm types identified amongst the collection of M non-typable (MNT) isolates, were isolated from the London region.
Clonal analysis of Inquilinus limosus isolates from six cystic fibrosis patients and specific serum antibody response
Authors: Schmoldt Sabine , Latzin Philipp , Heesemann Juergen , Griese Matthias , Imhof Axel , Hogardt Michael
Published: September 2006

Inquilinus limosus is a novel Gram-negative bacterium of the subdivision α-Proteobacteria recently found in the airways of patients with cystic fibrosis (CF). Here, the authors report on the clinical courses of six CF patients colonized with I. limosus. Five patients suffered from either an acute respiratory exacerbation or a progressive loss of pulmonary function, whereas one patient was in a stable clinical situation. This study focused on two aims: (i) the clonal analysis of I. limosus isolates by random amplified polymorphic DNA (RAPD)-PCR, and (ii) the clarification of whether the presence of I. limosus in the respiratory tract is associated with a specific serum antibody response. Serum IgG was detected by immunoblotting using I. limosus whole-cell-lysate proteins as antigens. Sera from healthy blood donors (n=10) and from CF patients colonized with Pseudomonas aeruginosa (n=10) were found to be immunoblot negative. All six Inquilinus-positive patients raised serum IgG antibodies against various I. limosus antigens. Surprisingly, in one patient, a specific I. limosus serum antibody response was already detected 1 year prior to Inquilinus-positive sputum cultures. Two prominent antigens were characterized by MALDI-MS: a 23 kDa protein revealed homology to the outer membrane lipoprotein OmlA of Actinobacillus pleuropneumoniae, and an 18 kDa protein to a protein-tyrosine phosphatase of Burkholderia cepacia. In conclusion, detection of I. limosus is accompanied by a specific serum antibody response and may reflect the infectious/pathogenic potential of I. limosus. Moreover, IgG immunoblotting may be useful to detect early infection with I. limosus and may support the selective cultivation of this novel emerging pathogen.
Detection of antibodies against Mycobacterium leprae culture filtrate protein-10 in leprosy patients
Authors: Parkash Om , Kumar Ajay , Nigam Astha , Girdhar Bhawneshwar K.
Published: September 2006

The prevalence of IgG antibodies againstMycobacterium lepraerecombinant culture filtrate protein-10 (rCFP-10) was investigated in serum samples from 56 leprosy patients, 15 tuberculosis (TB) patients, 14 other skin-diseased patients and 20 healthy subjects. On classifying the patients into bacterial index (BI)-positive and BI-negative groups, the assay showed 83.3 % (15/18) sensitivity for detection of BI-positive leprosy patients. On the other hand, the sensitivity for detection of BI-negative patients was 18.4 % (7/38). None of the 15 TB patients and 14 other skin-diseased patients was positive; however, only one out of 20 healthy individuals was positive, indicating that antibody response to culture filtrate protein-10 (CFP-10) was highly specific (98.0 %; 48/49). Statistically, the performance of the CFP-10-based assay was found to be comparable (P>0.05) with that of an anti-phenolic glycolipid-I (PGL-I) antibody-detecting assay. Thus,M. lepraeCFP-10 is potentially a specific antigen for measuring antibody response in BI-positive leprosy patients. Being a secreted antigen, CFP-10 may act as a marker for the viability ofM. lepraeinside the host, and hence its serological potential is worth exploring for application in monitoring the response of patients with BI-positive leprosy (a highly infectious form) during the course of chemotherapy. When comparing the bacteriological and serological results, an agreement of 82.1 % showed that seropositivity toM. lepraeCFP-10 corresponded well with bacteriological criteria. Hence, CFP-10 seems to be a suitable antigen for classification of leprosy patients into BI-positive and BI-negative groups.
Topoisomerase mutations and efflux are associated with fluoroquinolone resistance in Enterococcus faecalis
Authors: Oyamada Yoshihiro , Ito Hideaki , Inoue Matsuhisa , Yamagishi Jun-ichi
Published: September 2006

To understand better the mechanisms of fluoroquinolone resistance in Enterococcus faecalis, fluoroquinolone-resistant mutants isolated from Ent. faecalis ATCC 29212 by stepwise selection with sparfloxacin (SPX) and norfloxacin (NOR) were analysed. The results showed the following. (i) In general, fluoroquinolone-resistance mechanisms in Ent. faecalis are similar to those in other Gram-positive bacteria, such as Staphylococcus aureus and Streptococcus pneumoniae, namely, mutants with amino acid changes in both GyrA and ParC exhibited high fluoroquinolone resistance, and single GyrA mutants and a single ParC mutant were more resistant to SPX and NOR, respectively, than the parent strain, indicating that the primary targets of SPX and NOR in Ent. faecalis are DNA gyrase and topoisomerase IV, respectively. (ii) Alterations in GyrB (ΔKGA, residues 395–397) and ParE (Glu-459 to Lys) were associated with fluoroquinolone resistance in some mutants. Moreover, the facts that the NOR MIC, but not the SPX MIC, decreased in the presence of multidrug efflux pump inhibitors, that NOR accumulation decreased in the cells, and that the EmeA mRNA expression level did not change, strongly suggested that a NorA-like efflux pump, rather than EmeA, was involved in resistance to NOR.
The DNA-binding domain of CaNdt80p is required to activate CDR1 involved in drug resistance in Candida albicans
Authors: Wang Jang-Shiun , Yang Yun-Liang , Wu Chin-Jung , Ouyang Karen J. , Tseng Kuo-Yun , Chen Chia-Geun , Wang Hsin , Lo Hsiu-Jung
Published: September 2006

CaNdt80p, theCandida albicanshomologue of theSaccharomyces cerevisiaetranscription factor ScNdt80p, has been identified as a positive regulator ofCDR1, which encodes an efflux pump involved in drug resistance inC. albicans. To investigate the involvement of the putative DNA-binding domain of CaNdt80p in drug resistance, chimeras of CaNdt80p and ScNdt80p were constructed. Interestingly, the DNA-binding domain of ScNdt80p could functionally complement that of CaNdt80p to activateCDR1p–lacZinS. cerevisiae. Consistently, CaNdt80p containing a mutation in the DNA-binding domain failed to activateCDR1p–lacZinS. cerevisiae. Furthermore, a copy ofCaNDT80with the same mutation also failed to complement the drug-sensitive phenotype caused by a null mutation inC. albicans. Thus, the DNA-binding domain of CaNdt80p is critical for its function in drug resistance inC. albicans.