bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of second-order split operator and Chebyshev propagator in wave packet based state-to-state reactive scattering calculations
Authors: Sun Zhigang , Lee Soo-Y. , Guo Hua , Zhang Dong H.
Published: May 2009

A detailed comparison of the time-dependent wave packet method using the split operator propagator and recently introduced Chebyshev real wave packet approach for calculating reactive scattering processes is reported. As examples, the state-to-state differential cross sections of the H+H′D(v0=0,j0=1)→H′D+H/H′H+D reaction, the state-to-state reaction probabilities of the O16+O352 (v0=0,j0=0)→O17+O16O18/O18+O16O17 reaction, the H+O2→O+HO reaction, and the F+HD→HF+D reaction are calculated, using an efficient reactant-coordinate-based method on an L-shape grid which allows the extraction of the state-to-state information of the two product channels simultaneously. These four reactions have quite different dynamic characteristics and thus provide a comprehensive picture of the relative advantages of these two propagation methods for describing reactive scattering dynamics. The results indicate that the Chebyshev real wave packet method is typically more accurate, particularly for reactions dominated by long-lived resonances. However, the split operator approach is often more cost effective, making it a method of choice for fast reactions. In addition, our results demonstrate accuracy of the reactant-coordinate-based method for extracting state-to-state information.
Whispering gallery modes in indium oxide hexagonal microcavities
Authors: Dong Hongxing , Chen Zhanghai , Sun Liaoxin , Lu Jian , Xie Wei , Tan H. Hoe , Jagadish Chennupati , Shen Xuechu
Published: May 2009

We report on the use of In2O3 nanowires with hexagonal cross section as optical whispering gallery resonators. The single-crystal In2O3 nanowires were fabricated by an in situ thermal oxidation method. Whispering gallery modes (WGMs) in the visible spectral range were directly observed at room temperature. Due to the slight tapering of the nanowires, the energies and orders of the WGMs were modulated when excitations were scanned along the c-axis (length) of the nanowires. The experimental results were explained and fitted well with a plane wave interference model and Cauchy dispersion formula for refractive indices.
Optimizing the switching function for nonequilibrium free-energy calculations: An on-the-fly approach
Authors: Lindberg Gerrick E. , Berkelbach Timothy C. , Wang Feng
Published: May 2009

Using nonequilibrium switching simulations to determine the free-energy difference between two thermodynamic states has gained tremendous popularity since Jarzynski’s identity was proposed. The efficiency of a nonequilibrium switching simulation depends on the switching function. A well selected switching function can significantly minimize the associated dissipative work and reduce the computational cost of nonequilibrium free-energy simulations. In this paper, a method for estimating an efficient switching function during a nonequilibrium free-energy simulation is presented. The switching rate depends on the fluctuation of the fictitious force and a relaxation time. This method is similar to a prior method described by de Koning [J. Chem. Phys. 122, 104106 (2005)], except in our approach the switching rate is determined on-the-fly without the need for trial pulls. Our method can be easily incorporated into any existing implementation of the nonequilibrium switching method. The on-the-fly approach was used to determine the transformation free energy between two types of Einstein crystals and the isothermal free energy of expansion of a van der Waals gas. For both of the test cases, our on-the-fly method is found to provide a switching function much more superior than the standard one.
Assignment of photoelectron spectra of (TiO2)n with n=1–3
Authors: Liu Yuzhen , Yuan Yongbo , Wang Zhoubin , Deng Kaiming , Xiao Chuanyun , Li Qunxiang
Published: May 2009

This paper reports a comprehensive study of (TiO2)n (n=1–3) clusters on their structures, vertical electron affinities (VEA) and adiabatic electron affinities (AEA), and excited states that are further correlated with experimental photoelectron spectra (PES). Local density functional and time-dependent density functional methods (TTDFT) with 6–31G(d) basis set are used. For (TiO2)n with n=1 and 3, the ground-state geometries are found to have C2v and Cs structures, respectively, in both neutral and anionic charge states. For neutral (TiO2)2, the most stable structure corresponds to a C2h conformation. For anionic (TiO2)2−, two isomers with C2h and C2v symmetries are identified to be nearly isoenergetic. This conclusion is supported by reoptimization at CCSD/6–31G(d) level and single-point calculation at CCSD(T)/6-311+G(d) level. Hence, they are competitive candidates for the ground-state structure of (TiO2)2−. For TiO2 and (TiO2)3, the calculated VEA and AEA values agree well with the experimental data. For (TiO2)2, the VEA and AEA obtained with the C2v structure agree well with the experimental data while those with the C2h structure do not. The subsequent assignment of PES indicates that it is the C2v isomer of (TiO2)2− that represents the structure from which the photoexcitation in experimental PES takes place. TDDFT is used to determine the excited states of (TiO2)n (n=1–3) and the calculated excitation energies are in good agreement with PES experiment.
Quantum coherence and electric field control of the photodetached electron on elastic surface
Authors: Wang Lifei , Wang Yanwei , Ran Shiyong , Yang Guangcan
Published: May 2009

The quantum dynamics of the photodetached electron of H− in electric field near a surface are studied in the time domain. The evolution of wave packet for different manifold eigenstates with limited lifetimes is obtain analytically. It is found that the quantum coherence and temporal evolution of surface electronic wave packet can be controlled by the laser central energy and electric field. The correspondence between classical and quantum mechanics is shown explicitly in the system. Numerical simulation shows that the temporal evolution of photodetached electronic wave packet on elastic surface exhibits some similar properties of time-resolved two-photon photoemission signal of surface electron.
Appropriate choice of channel ratio in thin-film transistors for the exact determination of field-effect mobility
Authors: Okamura Koshi , Nikolova Donna , Mechau Norman , Hahn Horst
Published: May 2009

Field-effect mobilities are the most important figures of merit to evaluate the feasibility of semiconductors for thin-film transistors (TFTs). They are, however, sometimes extracted from TFTs with the active semiconductor area undefined and in small channel ratios without the effect of the fringing electric field at the ends of source/drain electrodes taken into account. In this letter, it is demonstrated that the field-effect mobilities extracted from undefined nanoparticulate zinc oxide (ZnO) TFTs at the channel ratio of 2.5 are overestimated by 418%, and the choice of large channel ratios gives the real value of field-effect mobilities.
Mechanism of electrohydrodynamic printing based on ac voltage without a nozzle electrode
Authors: Nguyen Vu Dat , Byun Doyoung
Published: May 2009

The electrohydrodynamic (EHD) spraying technique has been applied to inkjet printing technology for fabrication of printed electronics. The conventional EHD inkjet device is based on dc voltage and requires two electrodes: a nozzle electrode and an extractor electrode. This study notes several drawbacks of the dc-based EHD printing device such as electrical breakdown and demonstrates stable jetting by using the extractor electrode alone without the nozzle electrode and ac voltage. The continuous ejection of droplets can be obtained only by ac voltage, showing consistent ejection at every peak of electrical signal. The suggested EHD inkjet device prevents electrical breakdown.
Time dependence of effective slip on textured hydrophobic surfaces
Authors: Govardhan R. N. , Srinivas G. S. , Asthana A. , Bobji M. S.
Published: May 2009

In this paper, we present results on water flow past randomly textured hydrophobic surfaces with relatively large surface features of the order of 50 μm. Direct shear stress measurements are made on these surfaces in a channel configuration. The measurements indicate that the flow rates required to maintain a shear stress value vary substantially with water immersion time. At small times after filling the channel with water, the flow rates are up to 30% higher compared with the reference hydrophilic surface. With time, the flow rate gradually decreases and in a few hours reaches a value that is nearly the same as the hydrophilic case. Calculations of the effective slip lengths indicate that it varies from about 50 μm at small times to nearly zero or “no slip” after a few hours. Large effective slip lengths on such hydrophobic surfaces are known to be caused by trapped air pockets in the crevices of the surface. In order to understand the time dependent effective slip length, direct visualization of trapped air pockets is made in stationary water using the principle of total internal reflection of light at the water-air interface of the air pockets. These visualizations indicate that the number of bright spots corresponding to the air pockets decreases with time. This type of gradual disappearance of the trapped air pockets is possibly the reason for the decrease in effective slip length with time in the flow experiments. From the practical point of usage of such surfaces to reduce pressure drop, say, in microchannels, this time scale of the order of 1 h for the reduction in slip length would be very crucial. It would ultimately decide the time over which the surface can usefully provide pressure drop reductions.
Optical memory of silicon nanocrystals with submicron spatial resolution and very high thermal stability
Authors: Nikitin Timur , Khriachtchev Leonid , Räsänen Markku , Novikov Sergei
Published: May 2009

Crystallization of Si nanostructures in free-standing Si/SiO2 superlattice films by a strongly focused laser beam is studied. The structural change is obtained in small areas of submicron sizes, which is detectable by camera photographs and by Raman scattering and transmission measurements. The obtained optical changes are stable at very high temperatures as shown by prolonged furnace annealing at 1200 °C. An approach based on silicon stress state is also presented, which allows erasing and rewriting data readable by Raman spectroscopy. These results can be used for nonvolatile data storage.
Experimental investigation of hybrid single-electron turnstiles with high charging energy
Authors: Kemppinen A. , Kafanov S. , Pashkin Yu. A. , Tsai J. S. , Averin D. V. , Pekola J. P.
Published: May 2009

We present an experimental study of hybrid turnstiles with high charging energies in comparison to the superconducting gap. The device is modeled with the sequential tunneling approximation. The backtunneling effect is shown to limit the amplitude of the gate drive and thereby the maximum pumped current of the turnstile. We compare results obtained with sine and square wave drive and show how a fast rise time can suppress errors due to leakage current. Quantized current plateaus up to 160 pA are demonstrated.
Nonvolatile memory device based on Ag nanoparticle: Characteristics improvement
Authors: Mukherjee Biswanath , Mukherjee Moumita
Published: May 2009

A single layer memory device based on silver nanoparticles has been fabricated. The device exhibits electrical bistability and nonvolatile memory phenomenon. The performance of the device improved (in terms of On/Off ratio, switching cycles, and retention time) when an additional polymer (PMMA) layer was deposited prior to nanoparticles deposition. The retention time and switching cycles of the device improved a lot and on/off current ratio of the device increased by more than three orders of magnitude. The ability to write, erase, read, and refresh the electrical states of the polymer-nanoparticle composite fulfills the functionality of a dynamic random access memory.
Simultaneous measurement of force and tunneling current at room temperature
Authors: Sawada Daisuke , Sugimoto Yoshiaki , Morita Ken-ichi , Abe Masayuki , Morita Seizo
Published: May 2009

We have performed simultaneous scanning tunneling microscopy and atomic force microscopy measurements in the dynamic mode using metal-coated Si cantilevers at room temperature. Frequency shift (Δf) and time-average tunneling current (⟨It⟩) images are obtained by tip scanning on the Si(111)-(7×7) surface at constant height mode. By measuring site-specific Δf(⟨It⟩) versus tip-surface distance curves, we derive the force (tunneling current) at the closest separation between the sample surface and the oscillating tip. We observe the drop in the tunneling current due to the chemical interaction between the tip apex atom and the surface adatom, which was found recently, and estimate the value of the chemical bonding force. Scanning tunneling spectroscopy using the same tip shows that the tip is metallic enough to measure local density of states of electrons on the surface.
Logic inverters composed of controlled depletion-mode and enhancement-mode ZnO nanowire transistors
Authors: Jo Gunho , Hong Woong-Ki , Maeng Jongsun , Choe Minhyeok , Park Woojin , Lee Takhee
Published: May 2009

We demonstrate ZnO nanowire logic inverters consisting of n-channel depletion-mode (D-mode) transistors and n-channel enhancement-mode (E-mode) transistors that are selectively controlled by smooth- and corrugated-surface ZnO nanowires grown on two different types of substrates via a vapor transport method. Our inverter circuits, by combination of both D-mode and E-mode ZnO nanowire devices, show desired voltage transfer characteristics with a high gain and robust noise margin in a simple circuit design with less power dissipation, which makes them superior to logic inverters based on single-mode nanowire transistors.
Demonstration of high-Q (>8600) three-dimensional photonic crystal nanocavity embedding quantum dots
Authors: Tandaechanurat A. , Ishida S. , Aoki K. , Guimard D. , Nomura M. , Iwamoto S. , Arakawa Y.
Published: May 2009

The authors report on an experimental demonstration of coupling of quantum dots with a point-defect nanocavity in woodpile three-dimensional (3D) photonic crystal (PhC) with the highest quality (Q) factor among those for 3D PhC cavities. The Q factor of more than 8600 was achieved by stacking 25 layers using a micromanipulation technique. The size of the square-shaped defect cavity was optimized to tune the cavity mode to the midgap frequency of the complete photonic bandgap to achieve high Q.
Optical isolation based on nonreciprocal phase shift induced by interband photonic transitions
Authors: Yu Zongfu , Fan Shanhui
Published: May 2009

Photonic transitions in waveguides can create nonreciprocal phase response for counterpropagating modes. Such effect can be used in Mach–Zehnder interferometers to form optical isolators and circulators. Performance of such device is analyzed using coupled mode theory given the experimentally available modulation in silicon. The proposed scheme can provide a broadband (>0.8 THz), high contrast ratio (>20 dB) optical isolation at telecommunication wavelength.
Marangoni convection in a binary liquid layer with Soret effect at small Lewis number: Linear stability analysis
Authors: Shklyaev S. , Nepomnyashchy A. A. , Oron A.
Published: May 2009

We consider surface-tension-driven convection in a layer of a binary mixture. A linear stability problem is studied in the presence of both thermocapillary and solutocapillary effects. Assuming the Lewis and Biot numbers to be small, we develop the long wave theory and find both monotonic and oscillatory modes. Three various modes of oscillatory convection exist depending on the ratio between the small parameters. In the case of finite but sufficiently small values of the Biot and Lewis numbers, linear stability thresholds are determined numerically. The numerical results agree well with those found analytically.
Retarding potential and induction charge detectors in tandem for measuring the charge and mass of nanodroplets
Authors: Gamero-Castaño Manuel
Published: May 2009

The determination of the mass of a nanoparticle via time-of-flight typically requires a direct measurement of its charge. This can be done with a differential retarding potential analyzer and an induction charge detector operating in tandem. The spectrometer described in this article selects a particle with a specified retarding potential from a beam and directs it to an induction charge detector where both its velocity and charge are measured. The retarding potential, velocity, and charge also yield the particle’s mass. The particle is analyzed without the need to collect it, and therefore can be employed in a subsequent experiment. The high charge sensitivity of the induction charge detector and the capability for working at low retarding potentials make the characterization of electrosprayed nanodroplets possible for the first time.
Transitions between semiconductor and metal induced by mixed deformation in carbon nanotube devices
Authors: Ren Yun , Chen Ke-Qiu , Wan Qing , Zou B. S. , Zhang Yan
Published: May 2009

By applying nonequilibrium Green’s functions in combination with the density-functional theory, we investigate the electronic transport properties of molecular junctions constructed by (8,0) and (9,0) carbon nanotubes with radial and elongation deformation. The results show that the transitions between semiconductor and metal can be induced by the combination of both radial and elongation deformation. The results also show that the electronic transport properties of molecular junction can be modulated by deformation degree. A mechanism for the transitions is suggested.
Erratic dislocations within funnel defects in AlN templates for AlGaN epitaxial layer growth
Authors: Hawkridge M. E. , Liliental-Weber Z. , Kim H. J. , Choi S. , Yoo D. , Ryou J.-H. , Dupuis R. D.
Published: May 2009

We report our transmission electron microscopy observations of erratic dislocation behavior within funnel-like defects on top of AlN templates filled with AlGaN from an overlying epitaxial layer. This dislocation behavior is observed in material where phase separation is also observed. Several bare AlN templates were examined to determine the formation mechanism of the funnels. Our results suggest that they are formed prior to epitaxial layer deposition due to the presence of impurities during template regrowth. We discuss the erratic dislocation behavior in relation to the presence of the phase-separated material and the possible effects of these defects on the optoelectronic properties.
Stability of a ferroelectric phase with electrical domains in multilayers
Authors: Misirlioglu I. B.
Published: May 2009

Multilayer BaTiO3–SrTiO3 and PbTiO3–SrTiO3 structures with different electrical domain states are studied using a Landau–Ginzburg–Devonshire free energy. Polarizations in the layers are computed for multidomain and single-domain states where the paraelectric-to-ferroelectric volumetric layer ratio is varied. It is shown that the ferroelectric layers with electrical domains are thermodynamically more stable than the single-domain ferroelectric state. High domain wall energies result in the stabilization of the paraelectric state in the ferroelectric layers for large depolarizing fields. It is concluded that the stability of single-domain state ferroelectric layers correspond to a very small paraelectric-to-ferroelectric ratio after which multidomain ferroelectric state is favored.
Microstructure and magnetic properties of L1-FePt thin films prepared under high pressures
Authors: Li Xiaohong , Wang Fengqing , Liu Yanguo , Xu Lei , Zhao Jingwei , Liu Baoting , Zhang Xiangyi
Published: May 2009

The ultrafine grain size with a narrow size distribution is a critical issue for the development of L10-FePt thin films as ultrahigh density magnetic recording media. In this study, we succeeded in reducing both the grain size and the ordered domain size of L10-FePt thin films and simultaneously improving the size uniformity by annealing disordered FePt thin films at a high pressure of 1 GPa. This is attributed to the fact that high pressure promotes the nucleation of the L10 ordered domains and inhibits the growth of both the grains and the ordered domains during the L10 ordering transition.
Anisotropic c-axis pinning in interfacial self-assembled nanostructured trifluoracetate-YBa2Cu3O7−x films
Authors: Gutierrez J. , Puig T. , Gibert M. , Moreno C. , Romà N. , Pomar A. , Obradors X.
Published: May 2009

An all chemical route has been used to produce substrates—nanostructured by self-assembled oxide nanoislands—and to grow YBa2Cu3O7−x (YBCO) films on top. A great increase in the superconducting properties has been observed at high temperatures and magnetic fields parallel to the YBa2Cu3O7−x c-axis. The vortex pinning properties and the defects induced in the YBa2Cu3O7−x matrix have been investigated. We show that extended defects along the c-axis, induced in the YBCO matrix by the interfacial nanostructures, lay at the origin of the improved performances.
Comment on “Facile strategy and mechanism for orthorhombic SnO2 thin films” [Appl. Phys. Lett. 89, 231902 (2006)]
Authors: Reid Scott A.
Published: May 2009

Recent studies have reported thin films containing a significant fraction of the high-pressure orthorhombic phase of tin dioxide (o-SnO2). Although the generation of a pure film containing this metastable phase is an important goal, a careful examination of claims to that effect show that this goal remains to be achieved.
Formation of a localized acceleration potential during magnetic reconnection with a guide field
Authors: Egedal J. , Daughton W. , Drake J. F. , Katz N. , Lê A.
Published: May 2009

Magnetic reconnection near the surface of the sun and in the Earth’s magnetotail is associated with the production of highly energetic electrons. Direct acceleration in the reconnection electric field has been proposed as a possible mechanism for energizing these electrons. Here, however, we use kinetic simulations of guide-field reconnection to show that in two-dimensional (2D) reconnection the parallel electric field, E∥ in the reconnection region is localized and its structure does not permit significant energization of the electrons. Rather, a large fraction of the electrons become trapped due to a sign reversal in E∥, imposing strict constraints on their motions and energizations. Given these new results, simple 2D models, which invoke direct acceleration for energizing electrons during a single encounter with a reconnection region, need to be revised.
Aluminum induced in situ crystallization of amorphous SiC
Authors: Wang Li , Dimitrijev Sima , Tanner Philip , Zou Jin
Published: May 2009

Experimental evidence of aluminum induced in situ crystallization of amorphous SiC is presented. The deposition of SiC films on Si substrates was performed using low pressure chemical vapor deposition method at 600 °C with concurrent supply of Al(CH3)3 and H3SiCH3. Transmission electron micrographs confirm the presence of nanocrystals, whereas capacitance-voltage measurements demonstrate that the deposited films are p type doped. A crystallization mechanism is proposed based on the classic theory of nucleation in the growth rate limited regime. The introduction of Al(CH3)3 enhances the surface reaction and increases the supersaturation, which reduces the activation energy for nucleation.
Copper in plants: acquisition, transport and interactions
Authors: Yruela Inmaculada
Published: May 2009

Copper is an essential metal for plants. It plays key roles in photosynthetic and respiratory electron transport chains, in ethylene sensing, cell wall metabolism, oxidative stress protection and biogenesis of molybdenum cofactor. Thus, a deficiency in the copper supply can alter essential functions in plant metabolism. However, copper has traditionally been used in agriculture as an antifungal agent, and it is also extensively released into the environment by human activities that often cause environmental pollution. Accordingly, excess copper is present in certain regions and environments, and exposure to such can be potentially toxic to plants, causing phytotoxicity by the formation of reactive oxygen radicals that damage cells, or by the interaction with proteins impairing key cellular processes, inactivating enzymes and disturbing protein structure. Plants have a complex network of metal trafficking pathways in order to appropriately regulate copper homeostasis in response to environmental copper level variations. Such strategies must prevent accumulation of the metal in the freely reactive form (metal detoxification pathways) and ensure proper delivery of this element to target metalloproteins. The mechanisms involved in the acquisition and the distribution of copper have not been clearly defined, although emerging data in last decade, mainly obtained on copper uptake, and both intra- and intercellular distribution, as well as on long-distance transport, are contributing to the understanding of copper homeostasis in plants and the response to copper stress. This review gives an overview of the current understanding of main features concerning copper function, acquisition and trafficking network as well as interactions between copper and other elements.
Identification of ARIA regulating endothelial apoptosis and angiogenesis by modulating proteasomal degradation of cIAP-1 and cIAP-2
Authors: Ikeda Koji , Nakano Ritsuko , Uraoka Maki , Nakagawa Yusuke , Koide Masahiro , Katsume Asako , Minamino Keizo , Yamada Eri , Yamada Haruhiko , Quertermous Thomas , Matsubara Hiroaki
Published: May 2009

Endothelial apoptosis is a pivotal process for angiogenesis during embryogenesis as well as postnatal life. By using a retrovirus-mediated signal sequence trap method, we identified a previously undescribed gene, termed ARIA (apoptosis regulator through modulating IAP expression), which regulates endothelial apoptosis and angiogenesis. ARIA was expressed in blood vessels during mouse embryogenesis, as well as in endothelial cells both in vitro and in vivo. ARIA is a unique protein with no homology to previously reported conserved domain structures. Knockdown of ARIA in HUVECs by using small interfering RNA significantly reduced endothelial apoptosis without affecting either cell migration or proliferation. ARIA knockdown significantly increased inhibitor of apoptosis (cIAP)-1 and cIAP-2 protein expression, although their mRNA expression was not changed. Simultaneous knockdown of cIAP-1 and cIAP-2 abolished the antiapoptotic effect of ARIA knockdown. Using yeast 2-hybrid screening, we identified the interaction of ARIA with 20S proteasome subunit α-7. Thereafter, we found that cIAP-1 and cIAP-2 were degraded by proteasomes in endothelial cells under normal condition. Overexpression of ARIA significantly reduced cIAP-1 expression, and this reduction was abolished by proteasomal inhibition in BAECs. Also, knockdown of ARIA demonstrated an effect similar to proteasomal inhibition with respect to not only expression but also subcellular localization of cIAP-1 and cIAP-2. In vivo angiogenesis studied by Matrigel-plug assay, mouse ischemic retinopathy model, and tumor xenograft model was significantly enhanced by ARIA knockdown. Together, our data indicate that ARIA is a unique factor regulating endothelial apoptosis, as well as angiogenesis, presumably through modulating proteasomal degradation of cIAP-1 and cIAP-2 in endothelial cells.
Tec kinase Itk in γδT cells is pivotal for controlling IgE production in vivo
Authors: Felices Martin , Yin Catherine C. , Kosaka Yoko , Kang Joonsoo , Berg Leslie J.
Published: May 2009

In conventional αβ T cells, the Tec family tyrosine kinase Itk is required for signaling downstream of the T cell receptor (TCR). Itk also regulates αβ T cell development, lineage commitment, and effector function. A well established feature ofItk−/−mice is their inability to generate T helper type 2 (Th2) responses that produce IL-4, IL-5, and IL-13; yet these mice have spontaneously elevated levels of serum IgE and increased numbers of germinal center B cells. Here we show that the source of this phenotype is γδ T cells, as normal IgE levels are observed inItk−/−Tcrd−/−mice. When stimulated through the γδ TCR, Itk−/−γδ T cells produce high levels of Th2 cytokines, but diminished IFNγ. In addition, activated Itk−/−γδ T cells up-regulate costimulatory molecules important for B cell help, suggesting that they may directly promote B cell activation and Ig class switching. Furthermore, we find that γδ T cells numbers are increased inItk−/−mice, most notably the Vγ1.1+Vδ6.3+subset that represents the dominant population of γδ NKT cells.Itk−/−γδ NKT cells also have increased expression of PLZF, a transcription factor required for αβ NKT cells, indicating a common molecular program between αβ and γδ NKT cell lineages. Together, these data indicate that Itk signaling regulates γδ T cell lineage development and effector function and is required to control IgE production in vivo.
The type III TGF-β receptor regulates epithelial and cancer cell migration through β-arrestin2-mediated activation of Cdc42
Authors: Mythreye Karthikeyan , Blobe Gerard C.
Published: May 2009

Loss of expression of the TGF-β superfamily coreceptor, the type III TGF-β receptor (TβRIII or betaglycan), occurs in a broad spectrum of human cancers including breast, lung, ovarian, pancreatic, prostate, and renal cell cancer. TβRIII suppresses cancer progression in vivo, at least in part, by reducing cancer cell motility. However, the mechanism by which TβRIII regulates migration is unknown. Here, we demonstrate an unexpected TGF-β signaling independent role for TβRIII in activating Cdc42, altering the actin cytoskeleton and reducing directional persistence to inhibit random migration of both cancer and normal epithelial cells. Functionally, TβRIII through its interaction with the scaffolding protein β-arrestin2, activates Cdc42 and inhibits migration. These studies identify a TGF-β independent homeostatic function for TβRIII in regulating cell migration.
Sustained activation of XBP1 splicing leads to endothelial apoptosis and atherosclerosis development in response to disturbed flow
Authors: Zeng Lingfang , Zampetaki Anna , Margariti Andriana , Pepe Anna Elena , Alam Saydul , Martin Daniel , Xiao Qingzhong , Wang Wen , Jin Zheng-Gen , Cockerill Gillian , Mori Kazutoshi , Li Yi-shuan Julie , Hu Yanhua , Chien Shu , Xu Qingbo
Published: May 2009

X-box binding protein 1 (XBP1) is a key signal transducer in endoplasmic reticulum stress response, and its potential role in the atherosclerosis development is unknown. This study aims to explore the impact of XBP1 on maintaining endothelial integrity related to atherosclerosis and to delineate the underlying mechanism. We found that XBP1 was highly expressed at branch points and areas of atherosclerotic lesions in the arteries of
ApoE
−/−
mice, which was related to the severity of lesion development. In vitro study using human umbilical vein endothelial cells (HUVECs) indicated that disturbed flow increased the activation of XBP1 expression and splicing. Overexpression of spliced XBP1 induced apoptosis of HUVECs and endothelial loss from blood vessels during ex vivo cultures because of caspase activation and down-regulation of VE-cadherin resulting from transcriptional suppression and matrix metalloproteinase-mediated degradation. Reconstitution of VE-cadherin by Ad-VEcad significantly increased Ad-XBP1s-infected HUVEC survival. Importantly, Ad-XBP1s gene transfer to the vessel wall of
ApoE
−/−
mice resulted in development of atherosclerotic lesions after aorta isografting. These results indicate that XBP1 plays an important role in maintaining endothelial integrity and atherosclerosis development, which provides a potential therapeutic target to intervene in atherosclerosis.
Ablation of cholesterol biosynthesis in neural stem cells increases their VEGF expression and angiogenesis but causes neuron apoptosis
Authors: Saito Kanako , Dubreuil Veronique , Arai Yoko , Wilsch-Bräuninger Michaela , Schwudke Dominik , Saher Gesine , Miyata Takaki , Breier Georg , Thiele Christoph , Shevchenko Andrej , Nave Klaus-Armin , Huttner Wieland B.
Published: May 2009

Although sufficient cholesterol supply is known to be crucial for neurons in the developing mammalian brain, the cholesterol requirement of neural stem and progenitor cells in the embryonic central nervous system has not been addressed. Here we have conditionally ablated the activity of squalene synthase (SQS), a key enzyme for endogenous cholesterol production, in the neural stem and progenitor cells of the ventricular zone (VZ) of the embryonic mouse brain. Mutant embryos exhibited a reduced brain size due to the atrophy of the neuronal layers, and died at birth. Analyses of the E11.5–E15.5 dorsal telencephalon and diencephalon revealed that this atrophy was due to massive apoptosis of newborn neurons, implying that this progeny of the SQS-ablated neural stem and progenitor cells was dependent on endogenous cholesterol biosynthesis for survival. Interestingly, the neural stem and progenitor cells of the VZ, the primary target of SQS inactivation, did not undergo significant apoptosis. Instead, vascular endothelial growth factor (VEGF) expression in these cells was strongly upregulated via a hypoxia-inducible factor-1–independent pathway, and angiogenesis in the VZ was increased. Consistent with an increased supply of lipoproteins to these cells, the level of lipid droplets containing triacylglycerides with unsaturated fatty acyl chains was found to be elevated. Our study establishes a direct link between intracellular cholesterol levels, VEGF expression, and angiogenesis. Moreover, our data reveal a hitherto unknown compensatory process by which the neural stem and progenitor cells of the developing mammalian brain evade the detrimental consequences of impaired endogenous cholesterol biosynthesis.
Multicenter Study of the Impact of Community-Onset Clostridium difficile Infection on Surveillance for C. difficile Infection
Authors: Dubberke Erik R. , Butler Anne M. , Hota Bala , Khan Yosef M. , Mangino Julie E. , Mayer Jeanmarie , Popovich Kyle J. , Stevenson Kurt B. , Yokoe Deborah S. , McDonald L. Clifford , Jernigan John , Fraser Victoria J. ,   Prevention Epicenters Program from the Centers for Disease Control and Prevention
Published: May 2009

Objective.

To evaluate the impact of cases of community-onset, healthcare facility (HCF)-associated Clostridium difficile infection (CDI) on the incidence and outbreak detection of CDI.

Design.

A retrospective multicenter cohort study.

Setting.

Five university-affiliated, acute care HCFs in the United States.

Methods.

We collected data (including results of C. difficile toxin assays of stool samples) on all of the adult patients admitted to the 5 hospitals during the period from July I, 2000, through June 30, 2006. CDI cases were classified as HCF-onset if they were diagnosed more than 48 hours after admission or as community-onset, HCF-associated if they were diagnosed within 48 hours after admission and if the patient had recently been discharged from the HCF. Four surveillance definitions were compared: cases of HCF-onset CDI only (hereafter referred to as HCF-onset CDI) and cases of HCF-onset and community-onset, HCF-associated CDI diagnosed within 30, 60, and 90 days after the last discharge from the study hospital (hereafter referred to as 30-day, 60-day, and 90-day CDI, respectively). Monthly CDI rates were compared. Control charts were used to identify potential CDI outbreaks.

Results.

The rate of 30-day CDI was significantly higher than the rate of HCF-onset CDI at 2 HCFs (P < .01 ). The rates of 30-day CDI were not statistically significantly different from the rates of 60-day or 90-day CDI at any HCF. The correlations between each HCF's monthly rates of HCF-onset CDI and 30-day CDI were almost perfect (ρ range, 0.94-0.99; P < .001). Overall, 12 time points had a CDI rate that was more than 3 standard deviations above the mean, including 11 time points identified using the definition for HCF-onset CDI and 9 time points identified using the definition for 30-day CDI, with discordant results at 4 time points (k = 0.794; P < .001).

Conclusions.

Tracking cases of both community-onset and HCF-onset, HCF-associated CDI captures significantly more CDI cases, but surveillance of HCF-onset, HCF-associated CDI alone is sufficient to detect an outbreak.
Prospective Evaluation of Colonization with Extended-Spectrum β-Lactamase (ESBL)–Producing Enterobacteriaceae Among Patients at Hospital Admission and of Subsequent Colonization with ESBL-Producing Enterobacteriaceae Among Patients During Hospitalization
Authors: Friedmann Reuven , Raveh David , Zartzer Esther , Rudensky Bernard , Broide Ellen , Attias Denise , Yinnon Amos M.
Published: May 2009

Objective.

To determine the rates of and risk factors for carriage and acquisition of extended-spectrum (β-lactamase (ESBL)-producing Enterobacteriaceae during hospitalization.

Design.

Cohort study.

Setting.

Shaare Zedek Medical Center, a 550-bed teaching hospital.

Methods.

During a 5-month period (February 1-June 30, 2004), 167 (8%) of 1,985 newly admitted general medical patients were enrolled in our study. Nasal, oropharyngeal, and rectal swab specimens were obtained at admission and every 2-3 days until hospital discharge or death. Enterobacteriaceae isolates were tested for ESBL, andStaphylococcus aureusisolates were tested for methicillin resistance.

Results.

Of the 167 patients enrolled in our study, 15 (9%) were identified as nasal carriers of methicillin-resistantS. aureus(MRSA) at admission, and 13 (8%) were rectal carriers of ESBL-producing Enterobacteriaceae at admission. Univariate risk factors for rectal carriage of ESBL-producing Enterobacteriaceae included female sex (odds ratio [OR], 11 [95% confidence interval {CI}, 1.4—238];P< .05), nursing home residence (OR, 6.9 [95% CI, 1.8-27];P< .01), recent antibiotic treatment (OR, 9.8 [95% CI, 1.7-74];P< .05), and concomitant nasal carriage of MRSA and/or ESBL-producing Enterobacteriaceae (OR, 5.8 [95% CI, 1.2-26];P< .01). Multivariate risk factors were female sex and recent antibiotic treatment. During hospitalization, 35 (21%) of 167 patients had acquired rectal carriage of ESBL-producing Enterobacteriaceae (P= .002, for trend analysis). Of the 12 patients who were still in the hospital 2 weeks after admission, 4 (33%) were carriers of ESBL-producing Enterobacteriaceae. Univariate risk factors for acquisition included an age of older than 65 years (P< .005), nursing home residence (OR 2.6, [95% CI, 0.98-2.6]), impaired cognition (OR, 4.8 [95% CI, 1.9-12]), recent antibiotic treatment (OR, 2.7 [95% CI, 0.9-8.3]), respiratory assistance (OR, 4.2 [95% CI, 1.2-14]), and prolonged hospitalization. Multivariate risk factors were an age of older than 65 years and broad-spectrum antibiotic therapy.

Conclusions.

Rectal carriage of ESBL-producing Enterobacteriaceae occurred in 13 (8%) of 167 patients at admission to the medical departments of our hospital and in 4 (33%) of 12 patients still remaining in our hospital after 2 weeks.
Association Between Physician Caseload and Patient Outcome for Sepsis Treatment
Authors: Chen Chao-Hung , Chen Yi-Hua , Lin Hsiu-Chen , Lin Herng-Ching
Published: May 2009

Objective.

The purpose of this study was to investigate whether physicians with larger sepsis caseloads provide better outcomes, defined as lower in-hospital mortality rates, for patients with sepsis.

Design.

Retrospective cross-sectional study.

Method.

This study used pooled data from the 2002-2004 Taiwan National Health Insurance Research Database. A total of 48,336 patients hospitalized with a principal diagnosis of septicemia were selected and assigned to 1 of 4 caseload groups on the basis of their treating physician's sepsis caseload during the 3 years reflected in the pooled data (low caseload, less than 39 cases; medium caseload, 39–88 cases; high caseload, 89–176 cases; and very high caseload, more than 176 cases). Generalized estimating equation models were used for analysis.

Results.

Receipt of treatment from physicians in the very high, high, and medium caseload groups decreased patients' odds of inhospital mortality by 49% (95% confidence interval [CI], 0.41-0.67; P < .001 ), 40% (95% CI, 0.53-0.68; P < .001 ), and 18% (95% CI, 0.73-0.92; P < .001), respectively, compared with the odds for patients treated by low-caseload physicians. These findings persisted after partitioning out systematic physician-specific and hospital-specific variation and isolating the effects of most hospital, physician, and patient confounders.

Conclusion.

Patients treated by physicians who had a larger sepsis caseload had a substantially lower in-hospital mortality rate than did patients treated by physicians in the other caseload groups, and the difference was statistically significant. This result supports the “practice makes perfect” hypothesis.
Self-Protection as a Driver for Hand Hygiene Among Healthcare Workers
Authors: Borg Michael A. , Benbachir Mohamed , Cookson Barry D. , Redjeb Saida Ben , Elnasser Ziad , Rasslan Ossama , Gür Deniz , Daoud Ziad , Bagatzouni Despo Pieridou
Published: May 2009

A total of 2,725 healthcare workers in 8 Mediterranean countries replied to a self-assessment questionnaire that assessed their perceptions on hand hygiene. Responses revealed that rates of hand hygiene compliance before patient contact were significantly less than rates after patient contact (P < .001) and that use of soap and water was preferred over use of alcohol-based hand rub. These findings suggest that self-protection could be a major subliminal driver for performance of hand hygiene.
Trends in Antibacterial Use in Hospitalized Pediatric Patients in United States Academic Health Centers
Authors: Pakyz Amy L. , Gurgle Holly E. , Ibrahim Omar M. , Oinonen Michael J. , Polk Ronald E.
Published: May 2009

Trends in pediatric antibacterial use were examined in 20 academic health centers during the period 2002-2007. There was a significant increase in the use of linezolid (P < .001) and of macrolides (P = .001) and a significant decrease in the use of aminoglycosides (P < .001) and of first-generation cephalosporins (P < .001).
Solenoid-free plasma startup in NSTX using transient CHI
Authors: Raman R. , Jarboe T.R. , Mueller D. , Nelson B.A. , Bell M.G. , Bell R. , Gates D. , Gerhardt S. , Hosea J. , Kaita R. , Kugel H. , LeBlanc B. , Maingi R. , Maqueda R. , Menard J. , Nagata M. , Ono M. , Paul S. , Roquemore L. , Sabbagh S. , Soukhanovskii V. , Taylor G.
Published: May 2009

Experiments in NSTX have now demonstrated the coupling of toroidal plasmas produced by the technique of coaxial helicity injection (CHI) to inductive sustainment and ramp-up of the toroidal plasma current. In these discharges, the central Ohmic transformer was used to apply an inductive loop voltage to discharges with a toroidal current of about 100 kA created by CHI. The coupled discharges have ramped up to >700 kA and transitioned into an H-mode demonstrating compatibility of this startup method with conventional operation. The electron temperature in the coupled discharges reached over 800 eV and the resulting plasma had low inductance, which is preferred for long-pulse high-performance discharges. These results from NSTX in combination with the previously obtained record 160 kA non-inductively generated startup currents in an ST or tokamak in NSTX demonstrate that CHI is a viable solenoid-free plasma startup method for future STs and tokamaks.
Flexible structural protein alignment by a sequence of local transformations
Authors: Rocha Jairo , Segura Joan , Wilson Richard C. , Dasgupta Swagata
Published: May 2009

Motivation: Throughout evolution, homologous proteins have common regions that stay semi-rigid relative to each other and other parts that vary in a more noticeable way. In order to compare the increasing number of structures in the PDB, flexible geometrical alignments are needed, that are reliable and easy to use.

Results: We present a protein structure alignment method whose main feature is the ability to consider different rigid transformations at different sites, allowing for deformations beyond a global rigid transformation. The performance of the method is comparable with that of the best ones from 10 aligners tested, regarding both the quality of the alignments with respect to hand curated ones, and the classification ability. An analysis of some structure pairs from the literature that need to be matched in a flexible fashion are shown. The use of a series of local transformations can be exported to other classifiers, and a future golden protein similarity measure could benefit from it.

Availability: A public server for the program is available at http://dmi.uib.es/ProtDeform/.

Contact:  jairo@uib.es

Supplementary information: All data used, results and examples are available at http://dmi.uib.es/people/jairo/bio/ProtDeform.Supplementary data are available at Bioinformatics online.
Efficient designs for sampling and subsampling in fisheries research based on ranked sets
Authors: Wang You-Gan , Ye Yimin , Milton David A.
Published: May 2009

Wang, Y-G., Ye, Y., and Milton, D. A. 2009. Efficient designs for sampling and subsampling in fisheries research based on ranked sets. – ICES Journal of Marine Science, 66: 928–934. Sampling strategies are developed based on the idea of ranked set sampling (RSS) to increase efficiency and therefore to reduce the cost of sampling in fishery research. The RSS incorporates information on concomitant variables that are correlated with the variable of interest in the selection of samples. For example, estimating a monitoring survey abundance index would be more efficient if the sampling sites were selected based on the information from previous surveys or catch rates of the fishery. We use two practical fishery examples to demonstrate the approach: site selection for a fishery-independent monitoring survey in the Australian northern prawn fishery (NPF) and fish age prediction by simple linear regression modelling a short-lived tropical clupeoid. The relative efficiencies of the new designs were derived analytically and compared with the traditional simple random sampling (SRS). Optimal sampling schemes were measured by different optimality criteria. For the NPF monitoring survey, the efficiency in terms of variance or mean squared errors of the estimated mean abundance index ranged from 114 to 199% compared with the SRS. In the case of a fish ageing study for Tenualosa ilisha in Bangladesh, the efficiency of age prediction from fish body weight reached 140%.
Adaptive social immunity in leaf-cutting ants
Authors: Walker Tom N. , Hughes William O. H.
Published: May 2009

Social insects have evolved a suite of sophisticated defences against parasites. In addition to the individual physiological immune response, social insects also express ‘social immunity’ consisting of group-level defences and behaviours that include allogrooming. Here we investigate whether the social immune response of the leaf-cutting ant
Acromyrmex echinatior
reacts adaptively to the virulent fungal parasite,
Metarhizium anisopliae
. We ‘immunized’ mini-nests of the ants by exposing them twice to the parasite and then compared their social immune response with that of naive mini-nests that had not been experimentally exposed to the parasite. Ants allogroomed individuals exposed to the parasite, doing this both for those freshly treated with the parasite, which were infectious but not yet infected, and for those treated 2 days previously, which were already infected but no longer infectious. We found that ants exposed to the parasite received more allogrooming in immunized mini-nests than in naive mini-nests. This increased the survival of the freshly treated ants, but not those that were already infected. The results thus indicate that the social immune response of this leaf-cutting ant is adaptive, with the group exhibiting a greater and more effective response to a parasite that it has previously been exposed to.