bluuebunny/crossref_metadata_2025 huggingface dataset:
Regulation and function of innate and adaptive interleukin‐17‐producing cells
Authors: Hirota Keiji , Ahlfors Helena , Duarte João H , Stockinger Brigitta
Published: December 2011

Interleukin‐17 (IL‐17)‐mediated immune responses play a crucial role in the mucosal host defence against microbial and fungal pathogens. However, the chronic activation of IL‐17‐producing T helper cells can cause autoimmune disease. In addition, recent studies have highlighted key roles of innate cell‐mediated IL‐17 responses in various inflammatory settings. Besides inflammation, there have also been intriguing findings regarding the involvement of IL‐17 responses in the pathogenesis of cardiovascular diseases and tumour formation. Here, we discuss the latest discoveries in regulation and function of innate and adaptive IL‐17‐producing cells.
Craniocervical Traumatic Injuries: Evaluation and Surgical Decision Making
Authors: Joaquim Andrei F. , Patel Alpesh A.
Published: December 2011

We present a literature review of current approaches to craniocervical traumatic injuries. In an attempt to categorize the injuries that involve the upper cervical spine, we divide the injuries into two groups: (1) injuries affecting mainly bone structures and (2) predominantly ligamentous injury. This division is based on the principle that bone injuries have the potential to heal with conservative treatment whereas ligamentous injury would not heal properly, leading to an unstable spine. An accurate diagnosis and treatment are necessary to improve patient's outcome and avoid complications. As a general rule, ligamentous injuries are unstable lesions, requiring surgical treatment. Bony injuries can be conservatively treated, with surgery reserved for more unstable patterns (unstable C1 ring, displaced odontoid or C2 pars fractures).
Kinematic Evaluation of Association between Disc Bulge Migration, Lumbar Segmental Mobility, and Disc Degeneration in the Lumbar Spine Using Positional Magnetic Resonance Imaging
Authors: Hu Jonathan K. , Morishita Yuichiro , Montgomery Scott R. , Hymanson Henry , Taghavi Cyrus E. , Do Duc , Wang Jeff C.
Published: December 2011

Degenerative disc disease and disc bulge in the lumbar spine are common sources of lower back pain. Little is known regarding disc bulge migration and lumbar segmental mobility as the lumbar spine moves from flexion to extension. In this study, 329 symptomatic (low back pain with or without neurological symptoms) patients with an average age of 43.5 years with varying degrees of disc degeneration were examined to characterize the kinematics of the lumbar intervertebral discs through flexion, neutral, and extension weight-bearing positions. In this population, disc bulge migration associated with dynamic motion of the lumbar spine significantly increased with increased grade of disk degeneration. Although no obvious trends relating the migration of disc bulge and angular segmental mobility were seen, translational segmental mobility tended to increase with disc bulge migration in all of the degenerative disc states. It appears that many factors, both static (intervertebral disc degeneration or disc height) and dynamic (lumbar segmental mobility), affect the mechanisms of lumbar disc bulge migration.
Exact on-lattice stochastic reaction-diffusion simulations using partial-propensity methods
Authors: Ramaswamy Rajesh , Sbalzarini Ivo F.
Published: December 2011

Stochastic reaction-diffusion systems frequently exhibit behavior that is not predicted by deterministic simulation models. Stochastic simulation methods, however, are computationally expensive. We present a more efficient stochastic reaction-diffusion simulation algorithm that samples realizations from the exact solution of the reaction-diffusion master equation. The present algorithm, called partial-propensity stochastic reaction-diffusion (PSRD) method, uses an on-lattice discretization of the reaction-diffusion system and relies on partial-propensity methods for computational efficiency. We describe the algorithm in detail, provide a theoretical analysis of its computational cost, and demonstrate its computational performance in benchmarks. We then illustrate the application of PSRD to two- and three-dimensional pattern-forming Gray-Scott systems, highlighting the role of intrinsic noise in these systems.
Analytic second derivatives for the spin-free exact two-component theory
Authors: Cheng Lan , Gauss Jürgen
Published: December 2011

The formulation and implementation of the spin-free (SF) exact two-component (X2c) theory at the one-electron level (SFX2c-1e) is extended in the present work to the analytic evaluation of second derivatives of the energy. In the X2c-1e scheme, the four-component one-electron Dirac Hamiltonian is block diagonalized in its matrix representation and the resulting “electrons-only” two-component Hamiltonian is then used together with untransformed two-electron interactions. The derivatives of the two-component Hamiltonian can thus be obtained by means of simple manipulations of the parent four-component Hamiltonian integrals and derivative integrals. The SF version of X2c-1e can furthermore exploit available nonrelativistic quantum-chemical codes in a straightforward manner. As a first application of analytic SFX2c-1e second derivatives, we report a systematic study of the equilibrium geometry and vibrational frequencies for the bent ground state of the copper hydroxide (CuOH) molecule. Scalar-relativistic, electron-correlation, and basis-set effects on these properties are carefully assessed.
Structure, electronic, and optical properties of TiO2 atomic clusters: An ab initio study
Authors: Chiodo Letizia , Salazar Martin , Romero Aldo H. , Laricchia Savio , Sala Fabio Della , Rubio Angel
Published: December 2011

Atomic clusters of TiO2 are modeled by means of state-of-the-art techniques to characterize their structural, electronic and optical properties. We combine ab initio molecular dynamics, static density functional theory, time-dependent density functional theory, and many body techniques, to provide a deep and comprehensive characterization of these systems. TiO2 clusters can be considered as the starting seeds for the synthesis of larger nanostructures, which are of technological interest in photocatalysis and photovoltaics. In this work, we prove that clusters with anatase symmetry are energetically stable and can be considered as the starting seeds to growth much larger and complex nanostructures. The electronic gap of these inorganic molecules is investigated, and shown to be larger than the optical gap by almost 4 eV. Therefore, strong excitonic effects appear in these systems, much more than in the corresponding bulk phase. Moreover, the use of various levels of theory demonstrates that charge transfer effects play an important role under photon absorption, and therefore the use of adiabatic functionals in time dependent density functional theory has to be carefully evaluated.
Preferential solvation of lysozyme in water/ethanol mixtures
Authors: Ortore Maria Grazia , Mariani Paolo , Carsughi Flavio , Cinelli Stefania , Onori Giuseppe , Teixeira José , Spinozzi Francesco
Published: December 2011

We provide a quantitative description of the solvation properties of lysozyme in water/ethanol mixtures, which has been obtained by a simultaneous analysis of small-angle neutron scattering and differential scanning calorimetry experiments. All data sets were analyzed by an original method, which integrates the exchange equilibrium model between water and ethanol molecules at the protein surface and activity coefficients data of water/ethanol binary mixtures. As a result, the preferential binding of ethanol molecules at the protein surface was obtained for both native and thermal unfolded protein states. Excess solvation numbers reveal a critical point at ethanol molar fraction ≈0.06, corresponding to the triggering of the hydrophobic clustering of alcohol molecules detected in water/ethanol binary mixtures.
Study of self-generated magnetic fields in laser produced plasmas using a three-channel polaro-interferometer
Authors: Prasad Y. B. S. R. , Barnwal S. , Bolkhovitinov E. A. , Naik P. A. , Kamath M. P. , Joshi A. S. , Kumbhare S. R. , Rupasov A. A. , Gupta P. D.
Published: December 2011

Self-generated magnetic fields produced in laser plasmas at moderate laser intensities have been measured using a three-channel polaro-interferometer. The main elements of this device are two birefringent calcite wedges placed between two crossed polarizers. Using this device, the spatial profiles of (a) the rotation angle (polarometry), (b) the electron density (interferometry), and (c) the transmitted probe beam intensity (shadowgraphy) are recorded simultaneously using a digital camera with a large format CCD in a single laser shot. Magnetic fields of 2–4 MG had been estimated in aluminum plasma at laser intensities ∼1013 W/cm2. It is also possible to use this device in other configurations to get time resolved information.
Mach stem formation in explosion systems, which include high modulus elastic elements
Authors: Balagansky Igor A. , Hokamoto Kazuyuki , Manikandan Palavesamuthu , Matrosov Alexander D. , Stadnichenko Ivan A. , Miyoshi Hitoshi , Bataev Ivan A. , Bataev Anatoly A.
Published: December 2011

Results of experimental and numerical research of the Mach stem formation in explosion systems, which include high modulus elastic elements, are presented. The experimental data are discussed, and the analysis using ANSYS AUTODYN 11.0 is provided. It is shown that the phenomenon is reproduced for various high explosives. The Mach stem formation is observed in the conditions close to critical conditions of detonation transfer from an active to a passive HE charge. The best conditions for the Mach stem formation have been observed for TG-40/60 (Russian analog of Composition B) with silicon carbide insert heights of 16.5 mm, 18 mm, and 19.5 mm. The physical reason of the phenomenon is the propagation of a convergent detonation wave into highly compressed HE. The phenomenon is reproduced in numerical simulation with ANSYS AUTODYN 11.0. Calculated maximum value of pressure on the symmetry axis of passive HE charge was up to 1.25 Mbar. Results of metallographic analysis of steel identification specimen on the rear end of the passive HE charge indirectly confirm very high local pressures and temperatures for this scheme of explosion loading.
Ab initio calculations of the electronic states of AsH2 including dissociation characteristics
Authors: Alekseyev Aleksey B. , Buenker Robert J. , Liebermann Heinz–Peter
Published: December 2011

Multireference configuration interaction calculations have been carried out for low-lying electronic states of AsH2. Bending potentials for the ten lowest states of AsH2 are obtained in C2v symmetry for As–H distances fixed at the the ground state equilibrium value of 2.845 a0, as well as for the minimum energy path constrained to R1 = R2. The calculated equilibrium geometries for the $\tilde{X}\,^2B_1$X̃B12 ground state and the $\tilde{A}\,^2A_1$ÃA12 excited state agree very well with the previous experimental and theoretical results, whereas the data for the higher-lying states are obtained for the first time. Asymmetric potential energy surface (PES) cuts (at R1 = 2.845 a0, θ = 90.7°) and two-dimensional (2D) PESs for the lowest three states are also new. The calculated ab initio data are used for analysis of possible AsH2 photodissociation channels and predissociation effects. It is shown that the $\tilde{A}\,^2A_1 - \tilde{X}\,^2B_1$ÃA12−X̃B12 transition dipole moment decreases with increasing bending angle, which influences the intensity distribution in the $\tilde{A}(0,0,0) \rightarrow \tilde{X}$Ã(0,0,0)→X̃ emission spectrum ($v_2^{\prime \prime }$v2′′ bending series), shifting its maximum to smaller $v_2^{\prime \prime }$v2′′ quantum numbers.
Tunning of microstructure and thermoelectric properties of Ca3Co4O9 ceramics by high-magnetic-field sintering
Authors: Huang Yanan , Zhao Bangchuan , Fang Jun , Ang Ran , Sun Yuping
Published: December 2011

The structural, magnetic, electrical, and thermal transport properties of Ca3Co4O9 ceramics sintered under high magnetic field were investigated. Crystal grain texturing and densification were achieved through cold-pressing and high-magnetic-field sintering techniques. The c-axis of the layered crystal grain was partly oriented along the c-axis of the pressed samples via a cold-pressing technique, and the degree of orientation was further increased while applying the magnetic field in the sample sintering progress. The easy magnetization axis of Ca3Co4O9 polycrystalline ceramics was found to be the c-axis. The room-temperature resistivity along the ab-plane of the sample sintered under 8 T magnetic field was about 30% smaller than that of the sample sintered without magnetic field, and the Seebeck coefficient of the former reached 177.7 μV/K at the room temperature, which is about 50% larger than that of the latter. Consequently, for the sample sintered at 8 T magnetic field, the power factor along the ab-plane was enhanced by about 1.8 times compared to the sample without magnetic field sintering. The obtained result is suggested to originate from the variations of the carrier mobility and spin-orbital degeneracy due to high-magnetic-field sintering in the progress of the sample preparation.
Remote domain wall chirality measurement via stray field detection
Authors: Bashir M. A. , Bryan M. T. , Allwood D. A. , Schrefl T. , Claydon J. S. , Burnell G. , Marrows C. H.
Published: December 2011

We have calculated magnetostatic fields from transverse and vortex magnetic domain walls in a planar Ni81Fe19 nanowire using micromagnetic simulations. Magnetic fields were calculated either side of the wire in the wire plane. Asymmetries in the stray field from the two types of domain walls can be understood in terms of monopole, dipole and quadrupole contributions. These calculations indicate the required sensitivity of a nearby sensor for domain wall detection or being able to distinguish domain wall character. We demonstrate this by modeling the electrical response of a magnetoresistive multilayer element to a domain wall in a nearby magnetic nanowire.
Effects of frequency and temperature evolution of polar nanoregions on susceptibility dispersion and polarization mechanism in relaxors
Authors: Shi Y. P. , Soh A. K.
Published: December 2011

A generic theory for the frequency and temperature effects on the characteristic evolution of polar nanoregions (PNRs) is essential for improving and optimizing the design of relaxor-based piezoelectric and electrocaloric cooling devices. Pauli’s master equation was used to deduce analytical expressions for both the polarization dynamics and frequency-tunable susceptibility dispersions of relaxors. This was done by coupling the intrinsic equilibrium and dynamic factors of bulk relaxors and thin-films. It has been found that for relaxors to comply with Vogel–Fulcher relation, the evolution of PNR mean volume and coercive field of localized electric hysteresis for PNRs has to obey the classic Merz’s switching law. The evolution of PNR mean volume in Pb(Mg1/3Nb2/3)O3 crystal was calculated in the temperature range of 200–300 K and at different frequencies up to 1012 Hz. Our results were in good agreement with the mean-field percolation theory and experimental correlation lengths. Hence, the proposed theory may serve as a new basis for studying the relationship between macroscopic dielectric, electrocaloric as well as other important properties of relaxors and evolutions of their typical microstructures.
Monte Carlo computer simulations and electron microscopy of colloidal cluster formation via emulsion droplet evaporation
Authors: Schwarz Ingmar , Fortini Andrea , Wagner Claudia Simone , Wittemann Alexander , Schmidt Matthias
Published: December 2011

We consider a theoretical model for a binary mixture of colloidal particles and spherical emulsion droplets. The hard sphere colloids interact via additional short-ranged attraction and long-ranged repulsion. The droplet-colloid interaction is an attractive well at the droplet surface, which induces the Pickering effect. The droplet-droplet interaction is a hard-core interaction. The droplets shrink in time, which models the evaporation of the dispersed (oil) phase, and we use Monte Carlo simulations for the dynamics. In the experiments, polystyrene particles were assembled using toluene droplets as templates. The arrangement of the particles on the surface of the droplets was analyzed with cryogenic field emission scanning electron microscopy. Before evaporation of the oil, the particle distribution on the droplet surface was found to be disordered in experiments, and the simulations reproduce this effect. After complete evaporation, ordered colloidal clusters are formed that are stable against thermal fluctuations. Both in the simulations and with field emission scanning electron microscopy, we find stable packings that range from doublets, triplets, and tetrahedra to complex polyhedra of colloids. The simulated cluster structures and size distribution agree well with the experimental results. We also simulate hierarchical assembly in a mixture of tetrahedral clusters and droplets, and find supercluster structures with morphologies that are more complex than those of clusters of single particles.
An alternative approach to Schrödinger equations with a spatially varying mass
Authors: Çapak M. , Gönül B.
Published: December 2011

Extending the point canonical transformation approach in a manner distinct from the previous ones, we propose a unified approach of generating potentials of all classes having non-constant masses.
Band gaps in phononic crystals: Generation mechanisms and interaction effects
Authors: Croënne C. , Lee E. J. S. , Hu Hefei , Page J. H.
Published: December 2011

A wide range of mesoscopic phononic materials can exhibit frequency bands where transmission is forbidden, i.e. band gaps. Three different mechanisms for their origin can be distinguished, namely Bragg, hybridization and weak elastic coupling effects. Characteristic properties of gaps of different origins are investigated and compared, for a 3D crystal of tungsten carbide beads in water, a 2D crystal of nylon rods in water, and a 3D opal-like structure of weakly sintered aluminum beads. For the second type of crystal, it is shown that Bragg and hybridization gaps can be overlapped, allowing the study of the interaction between these two mechanisms. Atypical dispersion characteristics are demonstrated near the resonance frequency.
Resonant excitation of coupled Rayleigh waves in a short and narrow fluid channel clad between two identical metal plates
Authors: García-Chocano Victor M. , López-Rios Tomás , Krokhin Arkadii , Sánchez-Dehesa José
Published: December 2011

Transmission of ultrasonic waves through a slit between two water immersed brass plates is studied for sub-wavelength plate thicknesses and slit apertures. Extraordinary high absorption is observed at discrete frequencies corresponding to resonant excitation of Rayleigh waves on the both sides of the channel. The coupling of the Rayleigh waves occurs through the fluid and the corresponding contribution to the dispersion has been theoretically derived and also experimentally confirmed. Symmetric and anti-symmetric modes are predicted but only the symmetric mode resonances have been observed. It follows from the dispersion equation that the coupled Rayleigh waves cannot be excited in a channel with apertures less than the critical one. The calculated critical aperture is in a good agreement with the measured acoustic spectra. These findings could be applied to design a broadband absorptive metamaterial.
Bloch wave deafness and modal conversion at a phononic crystal boundary
Authors: Laude Vincent , Moiseyenko Rayisa P. , Benchabane Sarah , Declercq Nico F.
Published: December 2011

We investigate modal conversion at the boundary between a homogeneous incident medium and a phononic crystal, with consideration of the impact of symmetry on the excitation of Bloch waves. We give a quantitative criterion for the appearance of deaf Bloch waves, which are antisymmetric with respect to a symmetry axis of the phononic crystal, in the frame of generalized Fresnel formulas for reflection and transmission at the phononic crystal boundary. This criterion is used to index Bloch waves in the complex band structure of the phononic crystal, for directions of incidence along a symmetry axis. We argue that within deaf frequency ranges transmission is multi-exponential, as it is within frequency band gaps.
Individualism, innovation, and long-run growth
Authors: Gorodnichenko Yuriy , Roland Gerard
Published: December 2011

Countries having a more individualist culture have enjoyed higher long-run growth than countries with a more collectivist culture. Individualist culture attaches social status rewards to personal achievements and thus, provides not only monetary incentives for innovation but also social status rewards, leading to higher rates of innovation and economic growth.
Database independent proteomics analysis of the ostrich and human proteome
Authors: Altelaar A. F. Maarten , Navarro Danny , Boekhorst Jos , van Breukelen Bas , Snel Berend , Mohammed Shabaz , Heck Albert J. R.
Published: December 2011

Mass spectrometry (MS)-based proteome analysis relies heavily on the presence of complete protein databases. Such a strategy is extremely powerful, albeit not adequate in the analysis of unpredicted postgenome events, such as posttranslational modifications, which exponentially increase the search space. Therefore, it is of interest to explore “database-free” approaches. Here, we sampled the ostrich and human proteomes with a method facilitating de novo sequencing, utilizing the protease Lys-N in combination with electron transfer dissociation. By implementing several validation steps, including the combined use of collision-induced dissociation/electron transfer dissociation data and a cross-validation with conventional database search strategies, we identified approximately 2,500 unique de novo peptide sequences from the ostrich sample with over 900 peptides generating full backbone sequence coverage. This dataset allowed the appropriate positioning of ostrich in the evolutionary tree. The described database-free sequencing approach is generically applicable and has great potential in important proteomics applications such as in the analysis of variable parts of endogenous antibodies or proteins modified by a plethora of complex posttranslational modifications.
Incorporating microorganisms into polymer layers provides bioinspired functional living materials
Authors: Gerber Lukas C. , Koehler Fabian M. , Grass Robert N. , Stark Wendelin J.
Published: December 2011

Artificial two-dimensional biological habitats were prepared from porous polymer layers and inoculated with the fungus
Penicillium roqueforti
to provide a living material. Such composites of classical industrial ingredients and living microorganisms can provide a novel form of functional or smart materials with capability for evolutionary adaptation. This allows realization of most complex responses to environmental stimuli. As a conceptual design, we prepared a material surface with self-cleaning capability when subjected to standardized food spill. Fungal growth and reproduction were observed in between two specifically adapted polymer layers. Gas exchange for breathing and transport of nutrient through a nano-porous top layer allowed selective intake of food whilst limiting the microorganism to dwell exclusively in between a confined, well-enclosed area of the material. We demonstrated a design of such living materials and showed both active (eating) and waiting (dormant, hibernation) states with additional recovery for reinitiation of a new active state by observing the metabolic activity over two full nutrition cycles of the living material (active, hibernation, reactivation). This novel class of living materials can be expected to provide nonclassical solutions in consumer goods such as packaging, indoor surfaces, and in biotechnology.
Layer-by-layer crystallization of Co2FeSi Heusler alloy thin films
Authors: Fleet L R , Cheglakov G , Yoshida K , Lazarov V K , Nakayama T , Hirohata A
Published: December 2011

Grain-size evolution with increasing annealing time has been investigated in polycrystalline Co2FeSi films. The samples were prepared by sputtering giving differing grain sizes. Large grains were formed after annealing at 500 °C, with grains over 200 nm forming in the L21 phase in a layer-by-layer mode. Further annealing causes a decrease in the average grain size, agreeing well with previously reported results for Co2MnSi. Magnetic measurements showed moments with values of up to 75% of those predicted from the Slater–Pauling curve providing further evidence for the formation of the L21 phase.
Giant anomalous Hall effect in Fe-based microwires grown by focused-electron-beam-induced deposition
Authors: Córdoba R , Lavrijsen R , Fernández-Pacheco A , Ibarra M R , Schoenaker F , Ellis T , Barcones-Campo B , Kohlhepp J T , Swagten H J M , Koopmans B , Mulders J J L , Teresa J M De
Published: December 2011

We report the temperature dependence of the resistivity, the anisotropic magnetoresistance and the Hall effect of iron microwires grown by focused-electron-beam-induced deposition. By modifying the growth conditions in a controllable way, we study wires with iron compositions varying from 45% to 70%, which present different electrical conduction mechanisms, with resistivity values differing over three orders of magnitude. The magnetoresistance depends highly on the composition, and it can be understood by a subtle interplay between the anisotropic magnetoresistance and intergrain magnetoresistance due to their complex microstructure, consisting of an iron–carbon–oxygen amorphous matrix. A giant value for the anomalous Hall effect is found, which we explain by a large contribution of the skew scattering mechanism. The present results emphasize the correlation between the exotic microstructure of the microwires, and their magnetotransport properties.
Tuning of the size and the lattice parameter of ion-beam synthesized Pb nanoparticles embedded in Si
Authors: Wang Huan , Cuppens J , Biermans E , Bals S , Fernandez-Ballester L , Kvashnina K O , Bras W , Van Bael M J , Temst K , Vantomme A
Published: December 2011

The size and lattice constant evolution of Pb nanoparticles (NPs) synthesized by high fluence implantation in crystalline Si have been studied with a variety of experimental techniques. Results obtained from small-angle x-ray scattering showed that the Pb NPs grow with increasing implantation fluence and annealing duration. The theory of NP growth kinetics can be applied to qualitatively explain the size evolution of the Pb NPs during the implantation and annealing processes. Moreover, the lattice constant of the Pb NPs was evaluated by conventional x-ray diffraction. The lattice dilatation was observed to decrease with increasing size of the Pb NPs. Such lattice constant tuning can be attributed to the pseudomorphism caused by the lattice mismatch between the Pb NPs and the Si matrix.
Correlation between space charge accumulation in polyethylene and its fluorinated surface layer characteristics
Authors: An Zhenlian , Liu Chenxia , Chen Xuan , Zheng Feihu , Zhang Yewen
Published: December 2011

Polyethylene (PE) samples were surface fluorinated by the F2/N2 mixture for 30, 60, 120 or 240 min to investigate the influence of the fluorinated layer characteristics on space charge accumulation. After polarization at 50 kV mm−1 dc electrical field and 40 °C for 240 min, the charge amounts of the samples fluorinated for the different times, normalized to the charge amount of the original sample, are 1.17, 0.51, 0.49 and 0.22, respectively, showing significant suppression of the charge accumulation by the longer treatments, especially for the 240 min treatment. Infrared analyses and SEM cross-section images of the fluorinated samples indicate the increases in degree of fluorination and thicknesses of the fluorinated layer with the treatment time, and the fluorinated layer thicknesses were determined to be 0.39, 0.45, 0.65 and 0.80 µm. Surface energy calculations show that the polar component increased from 2.9 to 14.7 mJ m−2 after the 30 min treatment, and subsequently decreased to 11.8, 11.5 and 9.5 mJ m−2 for the longer treatments of 60, 120 and 240 min. This suggests a similar change in surface layer permittivity with the treatment time. The fluorinations led to the shift of thermally stimulated discharge current peak from 156 °C of the original sample to 145, 142, 144 and 149 °C of the fluorinated samples, and thus reduced the trap depth of the surface layer. But, the longer treatments of 60, 120 and 240 min significantly improved the barrier properties of the surface layer to the diffusion of the chemical species from the semi-conductive electrode to the PE by the decrease in free volume of the surface layer. The chemical species diffused into the sample surface layer reduced the depth of surface traps. The decrease in free volume is more important in suppressing the charge accumulation than the increase in surface layer permittivity and the change in surface trap, because it would reduce the charge transport in the surface layer and the charge direct injection at both electrodes.
Spatiotemporal changes in the pressure-driven current densities on DIII-D due to magnetic islands
Authors: Petty C.C. , Jayakumar R.J. , Makowski M.A. , Holcomb C.T. , Humphreys D.A. , La Haye R.J. , Luce T.C. , Politzer P.A. , Prater R. , Wade M.R. , Welander A.S.
Published: December 2011

Using direct analysis of the motional Stark effect (MSE) signals, an explicit measurement of the ‘missing’ bootstrap current density around the island location of a neoclassical tearing mode (NTM) is made for the first time. When the NTM is suppressed using co-electron cyclotron current drive, the measured changes in the current profile that restore the bootstrap current are also directly found from the MSE measurements. Additionally, direct analysis of helical perturbations in the MSE signals during slowly rotating ‘quasi-stationary’ modes shows the first explicit measurement of the deficit in the toroidal current density in the island O-point.
Effects of ELM mitigation coils on energetic particle confinement in ITER steady-state operation
Authors: Tani K. , Shinohara K. , Oikawa T. , Tsutsui H. , Miyamoto S. , Kusama Y. , Sugie T.
Published: December 2011

The effects of edge-localized mode (ELM) mitigation coils (ELM coils) on the loss of NBI-produced fast ions and fusion-produced alpha particles are investigated using an orbit following Monte Carlo code. The ELM mitigation coil field (EMC field) may cause a significant loss of fast ions produced by NBI on the order of 16.0–17.0% for a 9 MA steady-state ITER scenario. A significant transit-particle loss occurs in the case of the toroidal mode number n = 4 in which magnetic surfaces are ergodic near the plasma periphery. When the number of ELM coils in each toroidal row is nine, the main toroidal mode n = 4 is accompanied by a complementary mode n
c = 5. Concerning the resonance of fast-ion trajectories, the anti-resonant surfaces of n = 4 are very close to the resonant surfaces of n
c = 5 and vice versa. Since the effect of resonance on fast-ion trajectories dominates that of anti-resonance, a synergy effect of the main and complementary modes effectively enlarges the resonant regions. In a single n-mode EMC field, the resonant and anti-resonant regions are well separated. The peak heat load due to the loss of NB-produced fast ions near the upper ELM coils is as high as 1.0–1.5 MW m−2, which exceeds the allowable level in ITER. Rotation of the EMC field is essential for ITER to alleviate the local peak heat load. Most loss particles hit the inner side of the torus of the dome in the ITER divertor. The loss of alpha particles is also increased by the effect of the EMC field. The loss is still acceptably low at less than 1.0%.
Tokamak plasma response to droplet spraying from melted plasma-facing components
Authors: Tokar M.Z. , Coenen J.W. , Philipps V. , Ueda Y.
Published: December 2011

High-Z materials such as tungsten are currently the potentially best candidates for plasma-facing components (PFCs) in future fusion devices. However, the threat of melting under uncontrolled conditions and the associated material redistribution and loss can place strict limits on the lifetime of PFCs and plasma operation conditions. In particular, material losses in the form of fine sprayed droplets can provide a very intensive source of impurities in the plasma core. In this paper, the plasma response to radiation losses from impurity particles produced by droplet evaporation is modelled for the conditions found in the tokamak TEXTOR. The interplay between tungsten spraying and plasma behaviour, resulting in the reduction of power transferred to the limiter and diminution of droplet production, is taken into account. Calculations predict, in agreement with experimental observations, that this evolution results in a new steady state with significantly reduced central temperature and peaked impurity radiation profile. The efficiency of melt conversion into droplets, estimated by comparing experimental and computed plasma temperatures, is in reasonable agreement with the predictions from models for droplet generation.
Molecular hydrogen density measurements of short-pulse, high-density fuelling from a molecular cluster injector
Authors: Lundberg D.P. , Kaita R. , Majeski R.
Published: December 2011

A molecular cluster injector (MCI) has been developed to provide short-pulse, high-density fuelling for the lithium tokamak experiment (LTX). Using an electron-beam fluorescence method, the molecular density profiles produced by the injector are measured with sub-cm spatial resolution. The system, which is cryogenically cooled to promote the formation of molecular clusters, demonstrates a significant increase in molecular density relative to room-temperature supersonic gas injectors. The transient characteristics of short pulses (3–5 ms) are measured with 250 µs temporal resolution, and the jet shock structure is found to evolve significantly on that time scale. Supplemental measurements with a pressure transducer validate the electron-beam measurements. The measured density profiles are consistent with supersonic flows suitable for producing substantial populations of molecular clusters. The measured densities and flow rates are appropriate for high-density fuelling of LTX plasmas. The MCI will be used to investigate the physics of molecular cluster fuelling of LTX plasmas.
First mirrors in ITER: material choice and deposition prevention/cleaning techniques
Authors: Mukhin E.E. , Semenov V.V. , Razdobarin A.G. , Tolstyakov S. Yu. , Kochergin M.M. , Kurskiev G.S. , Podushnikova K.A. , Masyukevich S.V. , Kirilenko D.A. , Sitnikova A.A. , Chernakov P.V. , Gorodetsky A.E. , Bukhovets V.L. , Zalavutdinov R. Kh. , Zakharov A.P. , Arkhipov I.I. , Khimich Yu.P. , Nikitin D.B. , Gorshkov V.N. , Smirnov A.S. , Chernoizumskaja T.V. , Khilkevitch E.M. , Bulovich S.V. , Voitsenya V.S. , Bondarenko V.N. , Konovalov V.G. , Ryzhkov I.V. , Nekhaieva O.M. , Skorik O.A. , Vukolov K. Yu. , Khripunov V.I. , Andrew P.
Published: December 2011

We present here our recent results on the development and testing of the first mirrors for the divertor Thomson scattering diagnostics in ITER. The Thomson scattering system is based on several large-scale (tens of centimetres) mirrors that will be located in an area with extremely high (3–10%) concentration of contaminants (mainly hydrocarbons) and our main concern is to prevent deposition-induced loss of mirror reflectivity in the spectral range 1000–1064 nm. The suggested design of the mirrors—a high-reflective metal layer on a Si substrate with an oxide coating—combines highly stable optical characteristics under deposition-dominated conditions with excellent mechanical properties. For the mirror layer materials we consider Ag and Al allowing the possibility of sharing the Thomson scattering mirror collecting system with a laser-induced fluorescence system operating in the visible range. Neutron tests of the mirrors of this design are presented along with numerical simulation of radiation damage and transmutation of mirror materials. To provide active protection of the large-scale mirrors we use a number of deposition-mitigating techniques simultaneously. Two main techniques among them, plasma treatment and blowing-out, are considered in detail. The plasma conditions appropriate for mirror cleaning are determined from experiments using plasma-induced erosion/deposition in a CH4/H2 gas mixture. We also report data on the numerical simulation of plasma parameters of a capacitively-coupled discharge calculated using a commercial CFD-ACE code. A comparison of these data with the results for mirror testing under deuterium ion bombardment illustrates the possibility of using the capacitively-coupled discharge for in situ non-destructive deposition mitigation/cleaning.
Endpoint restriction estimates for the paraboloid over finite fields
Authors: Lewko Allison , Lewko Mark
Published: December 2011

We prove certain endpoint restriction estimates for the paraboloid over finite fields in three and higher dimensions. Working in the bilinear setting, we are able to pass from estimates for characteristic functions to estimates for general functions while avoiding the extra logarithmic power of the field size which is introduced by the dyadic pigeonhole approach. This allows us to remove logarithmic factors from the estimates obtained by Mockenhaupt and Tao in three dimensions and those obtained by Iosevich and Koh in higher dimensions.
Promoter architecture of mouse olfactory receptor genes
Authors: Plessy Charles , Pascarella Giovanni , Bertin Nicolas , Akalin Altuna , Carrieri Claudia , Vassalli Anne , Lazarevic Dejan , Severin Jessica , Vlachouli Christina , Simone Roberto , Faulkner Geoffrey J. , Kawai Jun , Daub Carsten O. , Zucchelli Silvia , Hayashizaki Yoshihide , Mombaerts Peter , Lenhard Boris , Gustincich Stefano , Carninci Piero
Published: December 2011

Odorous chemicals are detected by the mouse main olfactory epithelium (MOE) by about 1100 types of olfactory receptors (OR) expressed by olfactory sensory neurons (OSNs). Each mature OSN is thought to express only one allele of a single OR gene. Major impediments to understand the transcriptional control of OR gene expression are the lack of a proper characterization of OR transcription start sites (TSSs) and promoters, and of regulatory transcripts at OR loci. We have applied the nanoCAGE technology to profile the transcriptome and the active promoters in the MOE. nanoCAGE analysis revealed the map and architecture of promoters for 87.5% of the mouse OR genes, as well as the expression of many novel noncoding RNAs including antisense transcripts. We identified candidate transcription factors for OR gene expression and among them confirmed by chromatin immunoprecipitation the binding of TBP, EBF1 (OLF1), and MEF2A to OR promoters. Finally, we showed that a short genomic fragment flanking the major TSS of the OR geneOlfr160(M72) can drive OSN-specific expression in transgenic mice.
A transforming KIF5B and RET gene fusion in lung adenocarcinoma revealed from whole-genome and transcriptome sequencing
Authors: Ju Young Seok , Lee Won-Chul , Shin Jong-Yeon , Lee Seungbok , Bleazard Thomas , Won Jae-Kyung , Kim Young Tae , Kim Jong-Il , Kang Jin-Hyoung , Seo Jeong-Sun
Published: December 2011

The identification of the molecular events that drive cancer transformation is essential to the development of targeted agents that improve the clinical outcome of lung cancer. Many studies have reported genomic driver mutations in non-small-cell lung cancers (NSCLCs) over the past decade; however, the molecular pathogenesis of >40% of NSCLCs is still unknown. To identify new molecular targets in NSCLCs, we performed the combined analysis of massively parallel whole-genome and transcriptome sequencing for cancer and paired normal tissue of a 33-yr-old lung adenocarcinoma patient, who is a never-smoker and has no familial cancer history. The cancer showed no known driver mutation in EGFR or KRAS and no EML4-ALK fusion. Here we report a novel fusion gene between KIF5B and the RET proto-oncogene caused by a pericentric inversion of 10p11.22–q11.21. This fusion gene overexpresses chimeric RET receptor tyrosine kinase, which could spontaneously induce cellular transformation. We identified the KIF5B-RET fusion in two more cases out of 20 primary lung adenocarcinomas in the replication study. Our data demonstrate that a subset of NSCLCs could be caused by a fusion of KIF5B and RET, and suggest the chimeric oncogene as a promising molecular target for the personalized diagnosis and treatment of lung cancer.
Effectiveness of three instrumentation systems to remove Enterococcus faecalis from root canals
Authors: Matos Neto M. , Santos S. S. F. , Leão M. V. P. , Habitante S. M. , Rodrigues J. R. D. D. , Jorge A. O. C.
Published: December 2011

Matos Neto M, Santos SSF, Leão MVP, Habitante SM, Rodrigues JRDD, Jorge AOC. Effectiveness of three instrumentation systems to remove Enterococcus faecalis from root canals. International Endodontic Journal, 45, 435–438, 2012.

Aim  To assess the effectiveness of three systems of mechanical preparation to reduce Enterococcus faecalis within root canals.

Methodology  Twenty‐four human single‐rooted canine teeth were standardized to a length of 17 mm and the canal contents removed using a size 20 K‐file, as the last apical file. After irrigation and sterilization, the canals were contaminated with E. faecalis and incubated for 21 days at 37 °C with 5% CO2. Then, the teeth were divided into three groups for mechanical preparation with: ProTaper rotary system, ProTaper manual system and manual K‐files. Samples of the root canal contents, before and after the debridement, were collected with sterile paper points for 1 min. Then, the samples were diluted and plated in Brain Heart Infusion (BHI) agar. The colony‐forming units were counted and the percentage reduction calculated. The reduction and log CFU mL−1 were compared between groups using Wilcoxon nonparametric test and two‐way analysis of variance, respectively.

Results  There was a significant reduction in the number of CFU/mL (P = 0.000) before and after debridement for all the systems used. However, there was no significant difference between the systems.

Conclusion  All the three instrumentation systems reduced E. faecalis counts to a similar degree.
Speciation in the White‐breasted Nuthatch (Sitta carolinensis): a multilocus perspective
Authors: WALSTROM V. WOODY , KLICKA JOHN , SPELLMAN GARTH M.
Published: December 2011

Inferring the evolutionary and ecological processes that have shaped contemporary species distributions using the geographic distribution of gene lineages is the principal goal of phylogeographic research. Researchers in the field have recognized that inferences made from a single gene, often mitochondrial, can be informative regarding the pattern of diversification but lack conclusive information regarding the evolutionary mechanisms that led to the observed patterns. Here, we use a multilocus (20 loci) data set to explore the evolutionary history of the White‐breasted Nuthatch (Sitta carolinensis). A previous single‐locus study found S. carolinensis is comprised of four reciprocally monophyletic clades geographically restricted to the pine and oak forests of: (i) eastern North America, (ii) southern Rocky Mountain and Mexican Mountain ranges, (iii) Eastern Sierra Nevada and Northern Rocky Mountains and (iv) Pacific slope of North America. The diversification of the clades was attributed to the fragmentation of North American pine and oak woodlands in the Pliocene with subsequent divergences owing to the Pleistocene glacial cycles. Principal component, clustering and species tree analyses of the multilocus data resolved the same four groups or lineages found in the single‐locus study. Coalescent analyses and hypothesis testing of nested isolation and migration models indicate that isolation and not gene flow has been the major evolutionary mechanism responsible for shaping genetic variation, and all the divergence events within S. carolinensis have occurred in response to the Pleistocene glacial cycles.
Association of variants in innate immune genes with asthma and eczema
Authors: Sharma Sunita , Poon Audrey , Himes Blanca E. , Lasky‐Su Jessica , Sordillo Joanne E. , Belanger Kathleen , Milton Donald K. , Bracken Michael B. , Triche Elizabeth W. , Leaderer Brian P. , Gold Diane R. , Litonjua Augusto A.
Published: December 2011

To cite this article: Sharma S, Poon A, Himes BE, Lasky‐Su J, Sordillo JE, Belanger K, Milton DK, Bracken MB, Triche EW, Leaderer BP, Gold DR, Litonjua AA. Association of variants in innate immune genes with asthma and eczema. Pediatric Allergy Immunology 2012: 23: 315–323.

Background:  The innate immune pathway is important in the pathogenesis of asthma and eczema. However, only a few variants in these genes have been associated with either disease. We investigate the association between polymorphisms of genes in the innate immune pathway with childhood asthma and eczema. In addition, we compare individual associations with those discovered using a multivariate approach.

Methods:  Using a novel method, case control based association testing (C2BAT), 569 single nucleotide polymorphisms (SNPs) in 44 innate immune genes were tested for association with asthma and eczema in children from the Boston Home Allergens and Asthma Study and the Connecticut Childhood Asthma Study. The screening algorithm was used to identify the top SNPs associated with asthma and eczema. We next investigated the interaction of innate immune variants with asthma and eczema risk using Bayesian networks.

Results:  After correction for multiple comparisons, 7 SNPs in 6 genes (CARD25, TGFB1, LY96, ACAA1, DEFB1, and IFNG) were associated with asthma (adjusted p‐value<0.02), while 5 SNPs in 3 different genes (CD80, STAT4, and IRAKI) were significantly associated with eczema (adjusted p‐value < 0.02). None of these SNPs were associated with both asthma and eczema. Bayesian network analysis identified 4 SNPs that were predictive of asthma and 10 SNPs that predicted eczema. Of the genes identified using Bayesian networks, only CD80 was associated with eczema in the single‐SNP study. Using novel methodology that allows for screening and replication in the same population, we have identified associations of innate immune genes with asthma and eczema. Bayesian network analysis suggests that additional SNPs influence disease susceptibility via SNP interactions.

Conclusion:  Our findings suggest that innate immune genes contribute to the pathogenesis of asthma and eczema, and that these diseases likely have different genetic determinants.