bluuebunny/crossref_metadata_2025 huggingface dataset:
A yellow-emitting Ce3+ phosphor, La1−xCexSr2AlO5, for white light-emitting diodes
Authors: Im Won Bin , Kim Young-Il , Fellows Natalie N. , Masui Hisashi , Hirata G. A. , DenBaars Steven P. , Seshadri Ram
Published: September 2008

A yellow-emitting phosphor, La1−xCex3+Sr2AlO5, is reported that displays a peak in the excitation at 450nm and a peak in the emission at 556nm. When this phosphor is pumped by a blue InGaN light-emitting diode (λmax=450nm) we obtain white light with color rendering index (Ra) between 81 and 85 and color temperatures between 4200 and 5500K, suggesting that this material is competitive as a blue-pumped yellow phosphors.
Microlens coupled interdigital photoconductive switch
Authors: Matthäus Gabor , Nolte Stefan , Hohmuth Rico , Voitsch Martin , Richter Wolfgang , Pradarutti Boris , Riehemann Stefan , Notni Gunther , Tünnermann Andreas
Published: September 2008

A large-area terahertz emitter based on an interdigital finger electrode photoconductive switch on low-temperature grown GaAs attached to a hexagonal microlens array is demonstrated. The hexagonal arranged microlenses direct the incident IR excitation pulses into specified electrode gaps, resulting in constructive interference in the terahertz far field. Using a Ti:sapphire oscillator running at 80MHz with 150fs pulses, 6.5μmTHz average power at 540mW optical excitation is obtained. The maximum IR-to-terahertz conversion efficiency achieved is ⩾1.35×10−5.
Three-dimensional imaging of aerosol particles with scanning proton microprobe in a confocal arrangement
Authors: Žitnik M. , Pelicon P. , Grlj N. , Karydas A. G. , Sokaras D. , Schütz R. , Kanngießer B.
Published: September 2008

We have reconstructed three-dimensional (3D) element-specific distributions of aerosol microparticles captured in a thick quartz filter. The characteristic x rays were induced by a proton microprobe and detected by a Si(Li) spectrometer equipped with a polycapillary lens. Combining a fine microbeam scanning in the lateral plane with the sample movement parallel to the beam axis, the aerosol particles were driven across the sensitive microvolume and for Fe, Ca, S, and Si a sequence of two-dimensional lateral x-ray images was recorded. This is the first example of an x-ray element selective 3D imaging of a few micrometer sized objects with a proton beam.
Strong vertical light output from thin silicon rich oxide/SiO2 multilayers via in-plane modulation of photonic crystal patterns
Authors: Ren Fang-Fang , Yu M. B. , Ye J. D. , Chen Q. , Tan S. T. , Lo G. Q. , Kwong D. L.
Published: September 2008

Three-dimensional-confined structures with triangular-lattice air-hole photonic crystal patterns were fabricated to enhance the light output from silicon rich oxide/SiO2 multilayer stack. The intensity and profile of spontaneous emission were found to be efficiently modulated by controlling the optical modes of the periodic arrays via varying their structural parameters. With lattice constant/radius of 700nm∕280nm, the photoluminescence intensity was found to be enhanced by nearly nine times in the vertical direction. The mechanisms for different enhancement features have been theoretically analyzed based on coherent scattering and quantum electrodynamic effects, well supporting the experimental observation.
Surface stress induced structural transformations and pseudoelastic effects in palladium nanowires
Authors: Lao Jijun , Moldovan Dorel
Published: September 2008

Using molecular dynamics simulations, we investigate the surface stress induced structural transformations and pseudoelastic behaviors in palladium nanowires. For wires with a ⟨100⟩ initial orientation, the simulations indicate that when the cross-sectional area is less than 2.18×2.18nm2, the nanowire undergoes spontaneous reversible phase transformation from fcc to body-centered tetragonal structure. In wires with larger cross-sectional areas, the structural transformation is achieved via spontaneous reversible lattice reorientation. In both cases, under tensile loading and unloading, Pd nanowires reverse between the corresponding transformed structure and the original structure, exhibiting pseudoelastic behaviors characterized by fully recoverable strains of up to 50%.
A planar layer configuration for surface plasmon interference nanoscale lithography
Authors: Sreekanth K. V. , Murukeshan V. M. , Chua J. K.
Published: September 2008

A planar layer configuration for surface plasmon interference lithography to realize one-dimensional periodic nanostructure is proposed and numerically demonstrated in this letter. High electric field distribution compared to conventional prism based configuration is found to be achievable with this and hence facilitate high contrast and high resolution features with good exposure depth. Finite-difference time-domain simulation results indicate that the feature size approximately at sub-65-nm is achievable by using silver metal layer and a p-polarized 427 nm wavelength illumination. Simulated resist profiles, using cellular automata model, obtained through this proposed configuration is also presented.
Cooling an optical fiber to 4.5 K by indirect thermal contact with a liquid-helium flow and spectroscopic temperature measurements
Authors: Hashimoto Daisuke , Shimizu Kaoru
Published: September 2008

We have made it possible to cool a 10-m-long optical fiber to 4.5 K in a compact helium-flow cryostat. The cryostat is vacuum loaded and the cooling principle is based on thermal contact with a copper holder cooled by the liquid-helium flow. To measure the temperature directly, we employed two different spectroscopic methods depending on the temperature regions. One was photon-counting Raman spectroscopy and the other was Brillouin spectroscopy. We used certain devices to improve the cooling efficiency and confirmed that the fiber was uniformly cooled to 4.5 K.
Thick YBa2Cu3O7−x+BaSnO3 films with enhanced critical current density at high magnetic fields
Authors: Varanasi C. V. , Burke J. , Wang H. , Lee J. H. , Barnes P. N.
Published: September 2008

The thickness dependence was studied for the critical current density (Jc) of YBa2Cu3O7−x(YBCO)+BaSnO3 (BSO) nanocomposite films. These films showed a significantly reduced decline of the Jc with thickness, especially at high magnetic fields. For example, a 2 μm thick YBCO+BSO film had a Jc∼3×105 A/cm2 at 5 T as compared to a typical Jc of 2.4×103 A/cm2 at 5 T for a 300 nm thick YBCO film. The thick YBCO+BSO films maintained high Tc (>88 K) and had a high density (2.5×1011/cm2) of continuous BSO nanocolumns that likely contributed for the observed Jc enhancements.
Solid phase epitaxy of ferrimagnetic Y3Fe5O12 garnet thin films
Authors: Krockenberger Y. , Matsui H. , Hasegawa T. , Kawasaki M. , Tokura Y.
Published: September 2008

Epitaxial Y3Fe5O12 thin films were grown on (111) Gd3Ga5O12 substrates by pulsed laser deposition and subsequent annealing above 1270 K. The as-grown films deposited at temperatures below 1070 K were amorphous and the absence of trivalent iron ions has been verified by electron spin resonance spectroscopy. The ex situ annealing above 1270 K in oxygen atmosphere converted the films into epitaxial ones with ferrimagnetic properties. The higher temperature annealing up to 1670 K enabled the higher TC and the shorter lattice constant approaching those of bulk, while the saturation magnetization stayed at 2μB/f.u. at 300 K. Slightly expanded lattice constants and reduced saturation magnetization values may originate from oxygen deficient crystal structures. Nonetheless, the epitaxial films preserved a fairly smooth surface with a root mean square roughness below 2 nm.
Design of a simple annular electron beam source and its operating characteristics in single and repetitive shot modes
Authors: Li Limin , Liu Lie , Xu Qifu , Wen Jianchun , Liu Yonggui
Published: September 2008

In this work, design and performance of an annular carbon fiber cathode are presented. Measurements on this cathode were performed in a single high-voltage pulse generator (600 kV, 50 ns, and 50 Ω) and a repetitive one (350 kV, <10 ns, 180 Ω, and 100 Hz), respectively. In a single pulse regime, emphasis was placed on the uniformity of electron beam extracted from this cathode. It was found that this cathode could deliver uniform electron beams with current densities exceeding kA/cm2. Cesium iodide (CsI) coating eliminated hot spots on the cathode surface, significantly improving the uniformity of electron emission. Under repetitively pulsed operation, this cathode exhibited a good shot-to-shot reproducibility at the pressure of 1.5×10−4 Torr, suggesting an ability of surviving even in poor vacuum. However, once the base pressure rose up to 3.76×10−4 Torr, the cathode performance gradually degraded as the pulse shot proceeded. Besides, some possible explanations for these experimental results are presented. These results show that given proper diode design, carbon fiber with CsI coating has great promise as electron emitter producing high-current electron beams.
Exploring the origin of the internal rotational barrier for molecules with one rotatable dihedral angle
Authors: Liu Shubin , Govind Niranjan , Pedersen Lee G.
Published: September 2008

Continuing our recent endeavor, we systematically investigate in this work the origin of internal rotational barriers for small molecules using the new energy partition scheme proposed recently by one of the authors [S. B. Liu, J. Chem. Phys. 126, 244103 (2007)], where the total electronic energy is decomposed into three independent components, steric, electrostatic, and fermionic quantum. Specifically, we focus in this work on six carbon, nitrogen, and oxygen containing hydrides, CH3CH3, CH3NH2, CH3OH, NH2NH2, NH2OH, and H2O2, with only one rotatable dihedral angle ∠H–X–Y–H (X,Y=C,N,O). The relative contributions of the different energy components to the total energy difference as a function of the internal dihedral rotation will be considered. Both optimized-geometry (adiabatic) and fixed-geometry (vertical) differences are examined, as are the results from the conventional energy partition and natural bond orbital analysis. A wealth of strong linear relationships among the total energy difference and energy component differences for different systems have been observed but no universal relationship applicable to all systems for both cases has been discovered, indicating that even for simple systems such as these, there exists no omnipresent, unique interpretation on the nature and origin of the internal rotation barrier. Different energy components can be employed for different systems in the rationalization of the barrier height. Confirming that the two differences, adiabatic and vertical, are disparate in nature, we find that for the vertical case there is a unique linear relationship applicable to all the six molecules between the total energy difference and the sum of the kinetic and electrostatic energy differences. For the adiabatic case, it is the total potential energy difference that has been found to correlate well with the total energy difference except for ethane whose rotation barrier is dominated by the quantum effect.
Ultrafast electron dynamics and cubic optical nonlinearity of freestanding thin film of double walled carbon nanotubes
Authors: Kamaraju N. , Kumar Sunil , Karthikeyan B. , Moravsky Alexander , Loutfy R. O. , Sood A. K.
Published: September 2008

Ultrafast degenerate pump-probe experiments performed on a freestanding film of double walled carbon nanotubes near the first metallic transition energy of outer tube show ultrafast (97 fs) photobleaching followed by a photoinduced absorption with a slow relaxation of 1.8 ps. Femtosecond closed and open aperture z-scan experiments carried out at the same excitation energy show saturation absorption and negative cubic nonlinearity. From these measurements, real and imaginary part of the third order nonlinear susceptibility are estimated to be Re(χ(3))∼−2.2×10−9 esu and Im(χ(3))∼4.5×10−11 esu.
Spin polarization tuning in Mn5−xFexGe3
Authors: Stroppa A. , Kresse G. , Continenza A.
Published: September 2008

Experimentally, the intermetallic compound Mn4FeGe3 has been recently shown to exhibit enhanced magnetic properties and spin polarization compared to the Mn5Ge3 parent compound. The present ab initio study focuses on the effect of Fe substitution on the electronic and magnetic properties of the compound. Our calculations reveal that the changes on the Fermi surface of the doped compound are remarkable, and provide explanations for the enhanced spin polarization observed. Finally, we show that it is indeed possible to tune the degree of spin polarization upon Fe doping, thus making the Mn5−xFexGe3 intermetallic alloy very promising for future spintronic applications.
Wavevector-dependent quantum-size effect in electron decay length at Pb thin film surfaces
Authors: Liu Xin , Zhang S. B. , Ma X. C. , Jia Jin-Feng , Xue Qi-Kun , Bao Xin-He , Li Wei-Xue
Published: September 2008

The physical origin of quantum-size effects (QSEs) and its impact on the decay length of electrons in Pb thin films are studied by first-principles calculations. We show that QSE is not only size but also wavevector dependent: being maximum at Γ¯ due to strong interlayer coupling between pz orbitals, but could be vanishingly small at other symmetry points due to weak interlayer coupling between px,y orbitals. The electron decay length also exhibits systematic oscillations with film thickness and the Γ¯ valley has the slowest decay.
Decay dynamics of quantum dots influenced by the local density of optical states of two-dimensional photonic crystal membranes
Authors: Julsgaard B. , Johansen J. , Stobbe S. , Stolberg-Rohr T. , Sünner T. , Kamp M. , Forchel A. , Lodahl P.
Published: September 2008

We have performed time-resolved spectroscopy on InAs quantum dot ensembles in photonic crystal membranes. The influence of the photonic crystal is investigated by varying the lattice constant systematically. We observe a strong slow down of the quantum dots’ spontaneous emission rates as the two-dimensional bandgap is tuned through their emission frequencies. The measured band edges are in full agreement with theoretical predictions. We characterize the multiexponential decay curves by their mean decay time and find enhancement of the spontaneous emission at the bandgap edges and strong inhibition inside the bandgap in good agreement with local density of states calculations.
Slope parameters at metal-organic interfaces
Authors: Zhou Y. C. , Tang J. X. , Liu Z. T. , Lee C. S. , Lee S. T.
Published: September 2008

Carrier injection barriers are often described as linear functions of metal’s work function or electronegativity. Slope of these functions are called the slope parameters of the organic materials. Using either the work function or the electronegativity relation has led to different slope parameters. This work discusses the discrepancy in the relation between the two slope parameters in literature. Using updated data, we analyzed the relation between work function and electronegativity. The slope parameters of different organics are compiled, analyzed, and found to follow a linear relation with the inverse of the organics’ band gaps.
Determining the static dielectric permittivity of ion conducting materials when obscured by electrode polarization
Authors: Gråsjö Johan , Welch Ken , Strømme Maria
Published: September 2008

A method is derived for the determination of the static dielectric permittivity of ion conducting materials when this parameter is obscured by electrode polarization in as-recorded low frequency dielectric spectra. The method requires permittivity measurements at two different electrode separations, and is applicable when the electric fields created by charge separation near the electrode surfaces do not induce nonlinear effects in the frequency region where electrode polarization begins to affect the dielectric response. The performance of the method is illustrated by the analysis of an ion conducting cellulose gel biosynthesized by the Acetobacter. xylinum bacterium. The method opens up possibilities to obtain more detailed information about dynamic processes in ion conducting materials from dielectric spectroscopy.
Theoretical investigation of sheath expansion and implant fluence uniformity in enhanced glow discharge plasma immersion ion implantation
Authors: Kwok Dixon T. K. , Lu Qiu Yuan , Li Liu He , Fu Ricky K. Y. , Chu Paul K.
Published: September 2008

In enhanced glow discharge plasma immersion ion implantation that involves a small-pointed anode and large area tabular cathode, the high negative substrate bias acts as the plasma producer and supplies the implantation voltage. An electric field is created to focus the electrons and the electron-focusing field in turn enhances the glow discharge process. The sheath physics is theoretically investigated using numerical simulation based on the multiple-grid particle-in-cell code. Electron focusing is corroborated and the plasma sheath has enough expansion when t=40μs so that a uniform distribution of the incident ion fluence is attained.
Superlateral growth of a-Ge film by excimer laser annealing
Authors: Yeh Wenchang , Chen Hsinchi , Huang Hsiangen , Hsiao Chihping , Jeng Jengywan
Published: September 2008

90 - nm -thick a-Ge films were melted and solidified by excimer laser annealing method. The superlateral growth (SLG) distance increased from 0.5to4.1μm with increasing absorption coefficient of the light-absorptive underlayer. Real-time reflectivity measurement revealed that the increase in the SLG distance resulted from an increase in the Ge film solidification term from 60to650ns. The SLG velocity calculated from the proportionality constant of the SLG distance and the solidification term was 6–7m∕s. It was shown that SLG grains exhibit a single-crystalline structure.
In situ tuning of a photonic band gap with laser pulses
Authors: Pasquazi A. , Stivala S. , Assanto G. , Amendola V. , Meneghetti M. , Cucini M. , Comoretto D.
Published: September 2008

We report on light-induced optical tuning of colloidal photonic crystals doped with gold nanoparticles (Au-nps). By resonantly exciting the Au-np surface plasmon absorption with picosecond pulses at 0.53μm in a standard pump-probe setup, we observed permanent changes in the stop band resonance around 1.7μm, with blue wavelength shifts as large as 30nm and associated to a nanoparticle reshaping. Fine tuning was achieved by controlling either the pulse energy or the irradiation time.
Thermal conductivity of perovskite ferroelectrics
Authors: Tachibana Makoto , Kolodiazhnyi Taras , Takayama-Muromachi Eiji
Published: September 2008

Thermal conductivities of BaTiO3, PbTiO3, KNbO3, KTaO3, NaNbO3, and Pb(Mg1∕3Nb2∕3)O3 (PMN) single crystals have been measured from 2to390K. Pronounced jumps are found at structural transitions in BaTiO3 and KNbO3. A low-temperature anomaly from soft optical phonons is observed in KTaO3. For PMN and NaNbO3, glasslike behavior is observed in both the thermal conductivity and heat capacity measurements. We associate the glasslike behavior in NaNbO3 with the phase separation phenomena reported in recent studies.
Terahertz emission from black silicon
Authors: Hoyer P. , Theuer M. , Beigang R. , Kley E.-B.
Published: September 2008

We report on a terahertz emitter made out of black silicon. The black surface structure absorbs the whole optical pump power in the very surface. In contrast to expectations for indirect semiconductors, the black structure shows an emission in the terahertz range. The emitted radiation of the black silicon crystal is characterized for different parameters using terahertz time-domain spectroscopy.
Trap distribution and the impact of oxygen-induced traps on the charge transport in poly(3-hexylthiophene)
Authors: Schafferhans Julia , Baumann Andreas , Deibel Carsten , Dyakonov Vladimir
Published: September 2008

The trap distribution in the conjugated polymer poly(3-hexylthiophene) was investigated by fractional thermally stimulated current measurements. Two defect states with activation energies of about 50 and 105 meV and Gaussian energy distributions were revealed. The first is assigned to the tail of the intrinsic density of states, whereas the concentration of the second trap is directly related to oxygen exposure. The impact of the oxygen induced traps on the charge transport was examined by performing photo-induced charge carrier extraction by linearly increasing voltage measurements that exhibited a strong decrease in the mobility with air exposure time.
The neutrophil gelatinase-associated lipocalin (NGAL), a NF-κB-regulated gene, is a survival factor for thyroid neoplastic cells
Authors: Iannetti Alessio , Pacifico Francesco , Acquaviva Renato , Lavorgna Alfonso , Crescenzi Elvira , Vascotto Carlo , Tell Gianluca , Salzano Anna Maria , Scaloni Andrea , Vuttariello Emilia , Chiappetta Gennaro , Formisano Silvestro , Leonardi Antonio
Published: September 2008

NF-κB is constitutively activated in primary human thyroid tumors, particularly in those of anaplastic type. The inhibition of NF-κB activity in the human anaplastic thyroid carcinoma cell line, FRO, leads to an increased susceptibility to chemotherapeutic drug-induced apoptosis and to the blockage of their ability to form tumors in nude mice. To identify NF-κB target genes involved in thyroid cancer, we analyzed the secretome of conditioned media from parental and NF-κB-null FRO cells. Proteomic analysis revealed that the neutrophil gelatinase-associated lipocalin (NGAL), a protein involved in inflammatory and immune responses, is secreted by FRO cells whereas its expression is strongly reduced in the NF-κB-null FRO cells. NGAL is highly expressed in human thyroid carcinomas, and knocking down its expression blocks the ability of FRO cells to grow in soft agar and form tumors in nude mice. These effects are reverted by the addition of either recombinant NGAL or FRO conditioned medium. In addition, we show that the prosurvival activity of NGAL is mediated by its ability to bind and transport iron inside the cells. Our data suggest that NF-κB contributes to thyroid tumor cell survival by controlling iron uptake via NGAL.
Inhibition of the mTORC1 pathway suppresses intestinal polyp formation and reduces mortality in
Apc
Δ716
mice
Authors: Fujishita Teruaki , Aoki Koji , Lane Heidi A. , Aoki Masahiro , Taketo Makoto M.
Published: September 2008

The mammalian target of rapamycin (mTOR) is a serine/threonine kinase that regulates cell growth via mTOR complex 1 (mTORC1), whose activation has been implicated in many human cancers. However, mTORC1's status in gastrointestinal tumors has not been characterized thoroughly. We have found that the mTORC1 pathway is activated with increased expression of the mTOR protein in intestinal polyps of the
Apc
Δ716
heterozygous mutant mouse, a model for human familial adenomatous polyposis. An 8-week treatment with RAD001 (everolimus) suppressed the mTORC1 activity in these polyps and inhibited proliferation of the adenoma cells as well as tumor angiogenesis, which significantly reduced not only the number of polyps but also their size. β-Catenin knockdown in the colon cancer cell lines reduced the mTOR level and thereby inhibited the mTORC1 signaling. These results suggest that the Wnt signaling contributes to mTORC1 activation through the increased level of mTOR and that the activation plays important roles in the intestinal polyp formation and growth. Indeed, long-term RAD001 treatment significantly reduced mortality of the
Apc
Δ716
mice. Thus, we propose that the mTOR inhibitors may be efficacious for therapy and prevention of colonic adenomas and cancers with Wnt signaling activation.
Alteration of citrine structure by hydrostatic pressure explains the accompanying spectral shift
Authors: Barstow Buz , Ando Nozomi , Kim Chae Un , Gruner Sol M.
Published: September 2008

A protein molecule is an intricate system whose function is highly sensitive to small external perturbations. However, no examples that correlate protein function with progressive subangstrom structural perturbations have thus far been presented. To elucidate this relationship, we have investigated a fluorescent protein, citrine, as a model system under high-pressure perturbation. The protein has been compressed to produce deformations of its chromophore by applying a high-pressure cryocooling technique. A closely spaced series of x-ray crystallographic structures reveals that the chromophore undergoes a progressive deformation of up to 0.8 Å at an applied pressure of 500 MPa. It is experimentally demonstrated that the structural motion is directly correlated with the progressive fluorescence shift of citrine from yellow to green under these conditions. This protein is therefore highly sensitive to subangstrom deformations and its function must be understood at the subangstrom level. These results have significant implications for protein function prediction and biomolecule design and engineering, because they suggest methods to tune protein function by modification of the protein scaffold.
The structure of a folding intermediate provides insight into differences in immunoglobulin amyloidogenicity
Authors: Feige Matthias J. , Groscurth Sandra , Marcinowski Moritz , Yew Zu Thur , Truffault Vincent , Paci Emanuele , Kessler Horst , Buchner Johannes
Published: September 2008

Folding intermediates play a key role in defining protein folding and assembly pathways as well as those of misfolding and aggregation. Yet, due to their transient nature, they are poorly accessible to high-resolution techniques. Here, we made use of the intrinsically slow folding reaction of an antibody domain to characterize its major folding intermediate in detail. Furthermore, by a single point mutation we were able to trap the intermediate in equilibrium and characterize it at atomic resolution. The intermediate exhibits the basic β-barrel topology, yet some strands are distorted. Surprisingly, two short strand-connecting helices conserved in constant antibody domains assume their completely native structure already in the intermediate, thus providing a scaffold for adjacent strands. By transplanting these helical elements into β
2
-microglobulin, a highly homologous member of the same superfamily, we drastically reduced its amyloidogenicity. Thus, minor structural differences in an intermediate can shape the folding landscape decisively to favor either folding or misfolding.
Forest commons and local enforcement
Authors: Chhatre Ashwini , Agrawal Arun
Published: September 2008

This article examines the relationship between local enforcement and forests used as commons. It uses a unique multicountry dataset, created over the past 15 years by the International Forestry Resources and Institutions Research Program. Drawing on original enforcement and forest commons data from 9 countries, we find that higher levels of local enforcement have a strong and positive but complex relationship to the probability of forest regeneration. This relationship holds even when the influence of a number of other factors such as user group size, subsistence, and commercial importance of forests, size of forest, and collective action for forest improvement activities is taken into account. Although several of the above factors have a statistically significant relationship to changes in the condition of forest commons, differences in levels of local enforcement strongly moderate their link with forest commons outcomes. The research, using data from diverse political, social, and ecological contexts, shows both the importance of enforcement to forest commons and some of the limits of forest governance through commons arrangements.
Rhinovirus-induced lower respiratory illness is increased in asthma and related to virus load and Th1/2 cytokine and IL-10 production
Authors: Message Simon D. , Laza-Stanca Vasile , Mallia Patrick , Parker Hayley L. , Zhu Jie , Kebadze Tatiana , Contoli Marco , Sanderson Gwen , Kon Onn M. , Papi Alberto , Jeffery Peter K. , Stanciu Luminita A. , Johnston Sebastian L.
Published: September 2008

Acute exacerbations are the major cause of asthma morbidity, mortality, and health-care costs and are difficult to treat and prevent. The majority of asthma exacerbations are associated with rhinovirus (RV) infection, but evidence supporting a causal relationship is weak and mechanisms are poorly understood. We hypothesized that in asthmatic, but not normal, subjects RV infection would induce clinical, physiologic, and pathologic lower airway responses typical of an asthma exacerbation and that these changes would be related to virus replication and impaired T helper 1 (Th1)/IL-10 or augmented Th2 immune responses. We investigated physiologic, virologic, and immunopathologic responses to experimental RV infection in blood, induced sputum, and bronchial lavage in 10 asthmatic and 15 normal volunteers. RV infection induced significantly greater lower respiratory symptoms and lung function impairment and increases in bronchial hyperreactivity and eosinophilic lower airway inflammation in asthmatic compared with normal subjects. In asthmatic, but not normal, subjects virus load was significantly related to lower respiratory symptoms, bronchial hyperreactivity, and reductions in blood total and CD8
+
lymphocytes; lung function impairment was significantly related to neutrophilic and eosinophilic lower airway inflammation. The same virologic and clinical outcomes were strongly related to deficient IFN-γ and IL-10 responses and to augmented IL-4, IL-5, and IL-13 responses. This study demonstrates increased RV-induced clinical illness severity in asthmatic compared with normal subjects, provides evidence of strong relationships between virus load, lower airway virus-induced inflammation and asthma exacerbation severity, and indicates augmented Th2 or impaired Th1 or IL-10 immunity are likely important mechanisms.
HCMV gH/gL/UL128–131 interferes with virus entry into epithelial cells: Evidence for cell type-specific receptors
Authors: Ryckman Brent J. , Chase Marie C. , Johnson David C.
Published: September 2008

Human cytomegalovirus (HCMV) forms two different membrane protein complexes, gH/gL/gO and gH/gL/UL128/UL130/UL131, that function in different cell types. gH/gL/gO appears to be important for HCMV entry into or spread between fibroblasts, processes that occur at neutral pH. We demonstrated that HCMV entry into epithelial and endothelial cells requires gH/gL/UL128–131 and involves endocytosis and low pH. A complex of all five HCMV proteins, gH, gL, UL128, UL130, and UL131, is the functionally important mediator of this entry pathway into epithelial/endothelial cells. Here, we report that expression of gH/gL/UL128–131 in ARPE-19 epithelial cells causes the cells to be resistant to HCMV infection. Another HCMV glycoprotein, gB, did not interfere, and expression of all five gH/gL/UL128–131 proteins was required for this interference. gH/gL/UL128–131 interference was at the stage of virus entry into cells rather than the initial adsorption onto cell surfaces or after-entry defects. By contrast, expression of gH/gL/UL128–131 in primary human fibroblasts did not block HCMV infection. Previously, interference by retrovirus and herpes-simplex-virus entry mediators resulted from sequestration or obstruction of receptors. We concluded that epithelial cells express gH/gL/UL128–131 receptors that mediate HCMV entry. Fibroblasts either lack the gH/gL/UL128–131 receptors, the receptors are more numerous, or fibroblasts express other functional receptors.
Molecular signatures of ribosomal evolution
Authors: Roberts Elijah , Sethi Anurag , Montoya Jonathan , Woese Carl R. , Luthey-Schulten Zaida
Published: September 2008

Ribosomal signatures, idiosyncrasies in the ribosomal RNA (rRNA) and/or proteins, are characteristic of the individual domains of life. As such, insight into the early evolution of the domains can be gained from a comparative analysis of their respective signatures in the translational apparatus. In this work, we identify signatures in both the sequence and structure of the rRNA and analyze their contributions to the universal phylogenetic tree using both sequence- and structure-based methods. Domain-specific ribosomal proteins can be considered signatures in their own right. Although it is commonly assumed that they developed after the universal ribosomal proteins, we present evidence that at least one may have been present before the divergence of the organismal lineages. We find correlations between the rRNA signatures and signatures in the ribosomal proteins showing that the rRNA signatures coevolved with both domain-specific and universal ribosomal proteins. Finally, we show that the genomic organization of the universal ribosomal components contains these signatures as well. From these studies, we propose the ribosomal signatures are remnants of an evolutionary-phase transition that occurred as the cell lineages began to coalesce and so should be reflected in corresponding signatures throughout the fabric of the cell and its genome.
Identification of cardioviruses related to Theiler's murine encephalomyelitis virus in human infections
Authors: Chiu Charles Y. , Greninger Alexander L. , Kanada Kimberly , Kwok Thomas , Fischer Kael F. , Runckel Charles , Louie Janice K. , Glaser Carol A. , Yagi Shigeo , Schnurr David P. , Haggerty Tom D. , Parsonnet Julie , Ganem Don , DeRisi Joseph L.
Published: September 2008

Cardioviruses comprise a genus of picornaviruses that cause severe illnesses in rodents, but little is known about the prevalence, diversity, or spectrum of disease of such agents among humans. A single cardiovirus isolate, Saffold virus, was cultured in 1981 in stool from an infant with fever. Here, we describe the identification of a group of human cardioviruses that have been cloned directly from patient specimens, the first of which was detected using a pan-viral microarray in respiratory secretions from a child with influenza-like illness. Phylogenetic analysis of the nearly complete viral genome (7961 bp) revealed that this virus belongs to the Theiler's murine encephalomyelitis virus (TMEV) subgroup of cardioviruses and is most closely related to Saffold virus. Subsequent screening by RT-PCR of 719 additional respiratory specimens [637 (89%) from patients with acute respiratory illness] and 400 cerebrospinal fluid specimens from patients with neurological disease (aseptic meningitis, encephalitis, and multiple sclerosis) revealed no evidence of cardiovirus infection. However, screening of 751 stool specimens from 498 individuals in a gastroenteritis cohort resulted in the detection of 6 additional cardioviruses (1.2%). Although all 8 human cardioviruses (including Saffold virus) clustered together by phylogenetic analysis, significant sequence diversity was observed in the VP1 gene (66.9%–100% pairwise amino acid identities). These findings suggest that there exists a diverse group of novel human Theiler's murine encephalomyelitis virus-like cardioviruses that hitherto have gone largely undetected, are found primarily in the gastrointestinal tract, can be shed asymptomatically, and have potential links to enteric and extraintestinal disease.
Long-distance pollen flow assessment through evaluation of pollinator foraging range suggests transgene escape distances
Authors: Pasquet Rémy S. , Peltier Alexis , Hufford Matthew B. , Oudin Emeline , Saulnier Jonathan , Paul Lénaic , Knudsen Jette T. , Herren Hans R. , Gepts Paul
Published: September 2008

Foraging range, an important component of bee ecology, is of considerable interest for insect-pollinated plants because it determines the potential for outcrossing among individuals. However, long-distance pollen flow is difficult to assess, especially when the plant also relies on self-pollination. Pollen movement can be estimated indirectly through population genetic data, but complementary data on pollinator flight distances is necessary to validate such estimates. By using radio-tracking of cowpea pollinator return flights, we found that carpenter bees visiting cowpea flowers can forage up to 6 km from their nest. Foraging distances were found to be shorter than the maximum flight range, especially under adverse weather conditions or poor reward levels. From complete flight records in which bees visited wild and domesticated populations, we conclude that bees can mediate gene flow and, in some instances, allow transgene (genetically engineered material) escape over several kilometers. However, most between-flower flights occur within plant patches, while very few occur between plant patches.
Bisphenol A prevents the synaptogenic response to estradiol in hippocampus and prefrontal cortex of ovariectomized nonhuman primates
Authors: Leranth Csaba , Hajszan Tibor , Szigeti-Buck Klara , Bober Jeremy , MacLusky Neil J.
Published: September 2008

Exposure measurements from several countries indicate that humans are routinely exposed to low levels of bisphenol A (BPA), a synthetic xenoestrogen widely used in the production of polycarbonate plastics. There is considerable debate about whether this exposure represents an environmental risk, based on reports that BPA interferes with the development of many organs and that it may alter cognitive functions and mood. Consistent with these reports, we have previously demonstrated that BPA antagonizes spine synapse formation induced by estrogens and testosterone in limbic brain areas of gonadectomized female and male rats. An important limitation of these studies, however, is that they were based on rodent animal models, which may not be representative of the effects of human BPA exposure. To address this issue, we examined the influence of continuous BPA administration, at a daily dose equal to the current U.S. Environmental Protection Agency's reference safe daily limit, on estradiol-induced spine synapse formation in the hippocampus and prefrontal cortex of a nonhuman primate model. Our data indicate that even at this relatively low exposure level, BPA completely abolishes the synaptogenic response to estradiol. Because remodeling of spine synapses may play a critical role in cognition and mood, the ability of BPA to interfere with spine synapse formation has profound implications. This study is the first to demonstrate an adverse effect of BPA on the brain in a nonhuman primate model and further amplifies concerns about the widespread use of BPA in medical equipment, and in food preparation and storage.
Three-dimensional analysis of tokamaks and stellarators
Authors: Garabedian Paul R.
Published: September 2008

The NSTAB equilibrium and stability code and the TRAN Monte Carlo transport code furnish a simple but effective numerical simulation of essential features of present tokamak and stellarator experiments. When the mesh size is comparable to the island width, an accurate radial difference scheme in conservation form captures magnetic islands successfully despite a nested surface hypothesis imposed by the mathematics. Three-dimensional asymmetries in bifurcated numerical solutions of the axially symmetric tokamak problem are relevant to the observation of unstable neoclassical tearing modes and edge localized modes in experiments. Islands in compact stellarators with quasiaxial symmetry are easier to control, so these configurations will become good candidates for magnetic fusion if difficulties with safety and stability are encountered in the International Thermonuclear Experimental Reactor (ITER) project.
Mitochondrial localization of human frataxin is necessary but processing is not for rescuing frataxin deficiency in
Trypanosoma brucei
Authors: Long Shaojun , Jirků Milan , Ayala Francisco J. , Lukeš Julius
Published: September 2008

Trypanosoma brucei
, the agent of human sleeping sickness and ruminant nagana, is the most genetically tractable representative of the domain Excavata. It is evolutionarily very distant from humans, with a last common ancestor over 1 billion years ago. Frataxin, a highly conserved small protein involved in iron-sulfur cluster synthesis, is present in both organisms, and its deficiency is responsible for Friedreich's ataxia in humans. We have found that
T. brucei
growth-inhibition phenotype caused by down-regulated frataxin is rescued by means of human frataxin. The rescue is fully dependent on the human frataxin being imported into the trypanosome mitochondrion. Processing of the imported protein by mitochondrial processing peptidase can be blocked by mutations in the signal peptide, as in human cells. Although in human cells frataxin must be processed to execute its function, the same protein in the
T. brucei
mitochondrion is functional even in the absence of processing. Our results illuminate remarkable conservation of the mechanisms of mitochondrial protein import and processing.
Andrimid producers encode an acetyl-CoA carboxyltransferase subunit resistant to the action of the antibiotic
Authors: Liu Xinyu , Fortin Pascal D. , Walsh Christopher T.
Published: September 2008

Andrimid is a hybrid nonribosomal peptide-polyketide antibiotic that blocks the carboxyl-transfer reaction of bacterial acetyl-CoA carboxylase (ACC) and thereby inhibits fatty acid biosynthesis with submicromolar potency. The andrimid biosynthetic gene cluster from
Pantoea agglomerans
encodes an
admT
gene with homology to the acetyl-CoA carboxyltransferase (CT) β-subunit gene
accD. Escherichia coli
cells overexpressing
admT
showed resistance to andrimid. Co-overproduction of AdmT with
E. coli
CT α-subunit AccA allowed for the
in vitro
reconstitution of an active heterologous tetrameric CT A
2
T
2
complex. A subsequent andrimid-inhibition assay revealed an IC
50
of 500 nM for this hybrid A
2
T
2
in contrast to that of 12 nM for
E. coli
CT A
2
D
2
. These results validated that AdmT is an AccD homolog that confers resistance in the andrimid producer. Mutagenesis studies guided by the x-ray crystal structure of the
E. coli
A
2
D
2
complex disclosed a single amino acid mutation of AdmT (L203M) responsible for 5-fold andrimid sensitivity (IC
50
= 100 nM). Complementarily, the
E. coli
AccD mutant M203L became 5-fold more resistant in the CT assays. This observation allowed for bioinformatic identification of several
Vibrio cholerae
strains in which
accD
genes encode the Met↔Leu switches, and their occurrences correlate predictively with sensitivities to andrimid
in vivo
.
Expression of liver X receptor β is essential for formation of superficial cortical layers and migration of later-born neurons
Authors: Fan Xiaotang , Kim Hyun-Jin , Bouton Didier , Warner Margaret , Gustafsson Jan-Åke
Published: September 2008

Liver X receptor (LXR) β regulates cholesterol levels in the brain and is essential for maintenance of motor neurons in the spinal cord and dopaminergic neurons in the substantia nigra. Here, we have examined the expression pattern of LXRβ protein in the cerebral cortex and looked for defects in cortical development in LXRβ knockout (LXRβ
−/−
) mice. LXRβ protein was widely expressed in the mouse brain at later embryonic stages, and the expression pattern in the cerebral cortex was developmentally regulated. In normal postnatal mice, LXRβ was localized mainly in the upper layers of the cerebral cortex. In LXRβ
−/−
mice layers II and III were thinner with fewer neurons. Layer I was slightly thicker, whereas layers IV–VI were essentially normal. Consistent with this finding, Brn2 and NeuN expression were decreased in the upper layers in the LXRβ
−/−
neonatal cortex. The number of S-phase progenitor cells in the cortex between embryonic day (E) 12.5 to E16.5, was similar in WT and LXRβ
−/−
littermates but BrdU birth dating revealed that late-generated neurons labeled by BrdU injections administered at E14.5 or E16.5, and destined to cortical layers II/III, were disorganized and failed to migrate. The defect in migration appears to be caused by a reduction in the number of vertical processes emanating from the radial glia. These processes are the architectural guides for later-born migrating neurons. Taken together, these findings suggest that LXRβ expression in the cerebral cortex is involved in cortex lamination and is essential for the migration of late-generated neocortical neurons.
Efficacy of Adding 2% (w/v) Chlorhexidine Gluconate to 70% (v/v) Isopropyl Alcohol for Skin Disinfection Prior to Peripheral Venous Cannulation
Authors: Small Heather , Adams Debra , Casey Anna L. , Crosby Cynthia T. , Lambert Peter A. , Elliott Thomas
Published: September 2008

We undertook a clinical trial to compare the efficacy of 2% (w/v) chlorhexidine gluconate in 70% (v/v) isopropyl alcohol with the efficacy of 70% (v/v) isopropyl alcohol alone for skin disinfection to prevent peripheral venous catheter colonization and contamination. We found that the addition of 2% chlorhexidine gluconate reduced the number of peripheral venous catheters that were colonized or contaminated.
A Novel Class of mRNA-containing Cytoplasmic Granules Are Produced in Response to UV-Irradiation
Authors: Gaillard Hélène , Aguilera Andrés
Published: September 2008

Nucleic acids are substrates for different types of damage, but little is known about the fate of damaged RNAs. We addressed the existence of an RNA-damage response in yeast. The decay kinetics of GAL1p-driven mRNAs revealed a dose-dependent mRNA stabilization upon UV-irradiation that was not observed after heat or saline shocks, or during nitrogen starvation. UV-induced mRNA stabilization did not depend on DNA repair, damage checkpoint or mRNA degradation machineries. Notably, fluorescent in situ hybridization revealed that after UV-irradiation, polyadenylated mRNA accumulated in cytoplasmic foci that increased in size with time. In situ colocalization showed that these foci are not processing-bodies, eIF4E-, eIF4G-, and Pab1-containing bodies, stress granules, autophagy vesicles, or part of the secretory or endocytic pathways. These results point to the existence of a specific eukaryotic RNA-damage response, which leads to new polyadenylated mRNA-containing granules (UV-induced mRNA granules; UVGs). We propose that potentially damaged mRNAs, which may be deleterious to the cell, are temporarily stored in UVG granules to safeguard cell viability.
In Vitro Budding of Intralumenal Vesicles into Late Endosomes Is Regulated by Alix and Tsg101
Authors: Falguières Thomas , Luyet Pierre-Philippe , Bissig Christin , Scott Cameron C. , Velluz Marie-Claire , Gruenberg Jean
Published: September 2008

Endosomes along the degradation pathway leading to lysosomes accumulate membranes in their lumen and thus exhibit a characteristic multivesicular appearance. These lumenal membranes typically incorporate down-regulated EGF receptor destined for degradation, but the mechanisms that control their formation remain poorly characterized. Here, we describe a novel quantitative biochemical assay that reconstitutes the formation of lumenal vesicles within late endosomes in vitro. Vesicle budding into the endosome lumen was time-, temperature-, pH-, and energy-dependent and required cytosolic factors and endosome membrane components. Our light and electron microscopy analysis showed that the compartment supporting the budding process was accessible to endocytosed bulk tracers and EGF receptor. We also found that the EGF receptor became protected against trypsin in our assay, indicating that it was sorted into the intraendosomal vesicles that were formed in vitro. Our data show that the formation of intralumenal vesicles is ESCRT-dependent, because the process was inhibited by the K173Q dominant negative mutant of hVps4. Moreover, we find that the ESCRT-I subunit Tsg101 and its partner Alix control intralumenal vesicle formation, by acting as positive and negative regulators, respectively. We conclude that budding of the limiting membrane toward the late endosome lumen, which leads to the formation of intraendosomal vesicles, is controlled by the positive and negative functions of Tsg101 and Alix, respectively.