bluuebunny/crossref_metadata_2025 huggingface dataset:
A role for p38 MAPK in head and neck cancer cell growth and tumor‐induced angiogenesis and lymphangiogenesis
Authors: Leelahavanichkul Kantima , Amornphimoltham Panomwat , Molinolo Alfredo A. , Basile John R. , Koontongkaew Sittichai , Gutkind J. Silvio
Published: October 2013

We have recently gained a remarkable understanding of the mutational landscape of head and neck squamous cell carcinoma (HNSCC). However, the nature of the dysregulated signaling networks contributing to HNSCC progression is still poorly defined. Here, we have focused on the role of the family of mitogen activated kinases (MAPKs), extracellular regulated kinase (ERK), c‐Jun terminal kinase (JNK) and p38 MAPK in HNSCC. Immunohistochemical analysis of a large collection of human HNSCC tissues revealed that the levels of the phosphorylated active form of ERK1/2 and JNK were elevated in less than 33% and 16% of the cases, respectively. Strikingly, however, high levels of active phospho‐p38 were observed in most (79%) of hundreds of tissues analyzed. We explored the biological role of p38 in HNSCC cell lines using three independent approaches: treatment with a specific p38 inhibitor, SB203580; a retro‐inhibition strategy consisting in the use of SB203580 combined with the expression of an inhibitor‐insensitive mutant form of p38α; and short‐hairpin RNAs (shRNAs) targeting p38α. We found that specific blockade of p38 signaling significantly inhibited the proliferation of HNSCC cells both in vitro and in vivo. Indeed, we observed that p38 inhibition in HNSCC cancer cells reduces cancer growth in tumor xenografts and a remarkable decrease in intratumoral blood and lymphatic vessels. We conclude that p38α functions as a positive regulator of HNSCC in the context of the tumor microenvironment, controlling cancer cell growth as well as tumor‐induced angiogenesis and lymphangiogenesis.
The elastocapillary Landau–Levich problem
Authors: Dixit Harish N. , Homsy G. M.
Published: October 2013

We study the classical Landau–Levich dip-coating problem for the case in which the interface possesses both elasticity and surface tension. The aim of the study is to develop a complete asymptotic theory of the elastocapillary Landau–Levich problem in the limit of small flow speeds. As such, the paper also extends our previous study on purely elastic Landau–Levich flow (Dixit & Homsy J. Fluid Mech., vol. 732, 2013, pp. 5–28) to include the effect of surface tension. The elasticity of the interface is described by the Helfrich model and surface tension is modelled in the usual way. We define an elastocapillary number, $\epsilon $, which represents the relative strength of elasticity to surface tension. Based on the size of $\epsilon $, we can define three different regimes of interest. In each of these regimes, we carry out asymptotic expansions in the small capillary (or elasticity) numbers, which represents the balance of viscous forces to surface tension (or elasticity).

In the weak elasticity regime, the film thickness is a small correction to the classical Landau–Levich law and can be written as $$\begin{eqnarray*}{\tilde {h} }_{\infty , c} = (0. 9458- 0. 0839~\mathscr{E}){l}_{c} C{a}^{2/ 3} , \quad \epsilon \ll 1,\end{eqnarray*}$$ where ${l}_{c} $ is the capillary length, $Ca$ is the capillary number and $\mathscr{E}= \epsilon / C{a}^{2/ 3} $. In the elastocapillary regime, the film thickness is a function of $\epsilon $ through the power-law relationship $$\begin{eqnarray*}{\tilde {h} }_{\infty , ec} = {\bar {h} }_{\infty , e} L\hspace{0.167em} f(\epsilon )C{a}^{4/ 7} , \quad \epsilon \sim O(1),\end{eqnarray*}$$ where ${\bar {h} }_{\infty , e} $ is a numerical coefficient obtained in our previous study, $L$ is the elastocapillary length, and $f(\epsilon )$ represents the functional dependence of film thickness on the elastocapillary parameter.
Damn You, Little h! (Or, Real-World Applications of the Hubble Constant Using Observed and Simulated Data)
Authors: Croton Darren J.
Published: October 2013

The Hubble constant, H0, or its dimensionless equivalent, “little h”, is a fundamental cosmological property that is now known to an accuracy better than a few per cent. Despite its cosmological nature, little h commonly appears in the measured properties of individual galaxies. This can pose unique challenges for users of such data, particularly with survey data. In this paper we show how little h arises in the measurement of galaxies, how to compare like-properties from different datasets that have assumed different little h cosmologies, and how to fairly compare theoretical data with observed data, where little h can manifest in vastly different ways. This last point is particularly important when observations are used to calibrate galaxy formation models, as calibrating with the wrong (or no) little h can lead to disastrous results when the model is later converted to the correct h cosmology. We argue that in this modern age little h is an anachronism, being one of least uncertain parameters in astrophysics, and we propose that observers and theorists instead treat this uncertainty like any other. We conclude with a ‘cheat sheet’ of nine points that should be followed when dealing with little h in data analysis.
Impaired Cerebrovascular Hemodynamics are Associated with Cerebral White Matter Damage
Authors: Purkayastha Sushmita , Fadar Otite , Mehregan Aujan , Salat David H , Moscufo Nicola , Meier Dominik S , Guttmann Charles RG , Fisher Naomi DL , Lipsitz Lewis A , Sorond Farzaneh A
Published: October 2013

White matter hyperintensities (WMH) in elderly individuals with vascular diseases are presumed to be due to ischemic small vessel diseases; however, their etiology is unknown. We examined the cross-sectional relationship between cerebrovascular hemodynamics and white matter structural integrity in elderly individuals with vascular risk factors. White matter hyperintensity volumes, fractional anisotropy (FA), and mean diffusivity (MD) were obtained from MRI in 48 subjects (75±7years). Pulsatility index (PI) and dynamic cerebral autoregulation (dCA) was assessed using transcranial Doppler ultrasound of the middle cerebral artery. Dynamic cerebral autoregulation was calculated from transfer function analysis (phase and gain) of spontaneous blood pressure and flow velocity oscillations in the low (LF, 0.03 to 0.15 Hz) and high (HF, 0.16 to 0.5 Hz) frequency ranges. Higher PI was associated with greater WMH ( P<0.005). Higher phase across all frequency ranges was associated with greater FA and lower MD ( P<0.005). Lower gain was associated with higher FA in the LF range ( P=0.001). These relationships between phase and FA were significant in the territories limited to the middle cerebral artery as well as across the entire brain. Our results show a strong relationship between impaired cerebrovascular hemodynamics (PI and dCA) and loss of cerebral white matter structural integrity (WMH and DTI metrics) in elderly individuals.
Nanostructured light-absorbing crystalline CuIn(1–x)GaxSe2 thin films grown through high flux, low energy ion irradiation
Authors: Hall Allen J. , Hebert Damon , Shah Amish B. , Bettge Martin , Rockett Angus A.
Published: October 2013

A hybrid effusion/sputtering vacuum system was modified with an inductively coupled plasma (ICP) coil enabling ion assisted physical vapor deposition of CuIn1−xGaxSe2 thin films on GaAs single crystals and stainless steel foils. With <80 W rf power to the ICP coil at 620–740  °C, film morphologies were unchanged compared to those grown without the ICP. At low temperature (600–670  °C) and high rf power (80–400 W), a light absorbing nanostructured highly anisotropic platelet morphology was produced with surface planes dominated by {112}T facets. At 80–400 W rf power and 640–740  °C, both interconnected void and small platelet morphologies were observed while at >270 W and above >715  °C nanostructured pillars with large inter-pillar voids were produced. The latter appeared black and exhibited a strong {112}T texture with interpillar twist angles of ±8°. Application of a negative dc bias of 0–50 V to the film during growth was not found to alter the film morphology or stoichiometry. The results are interpreted as resulting from the plasma causing strong etching favoring formation of {112}T planes and preferential nucleation of new grains, balanced against conventional thermal diffusion and normal growth mechanisms at higher temperatures. The absence of effects due to applied substrate bias suggests that physical sputtering or ion bombardment effects were minimal. The nanostructured platelet and pillar films were found to exhibit less than one percent reflectivity at angles up to 75° from the surface normal.
Detecting invariant manifolds as stationary Lagrangian coherent structures in autonomous dynamical systems
Authors: Teramoto Hiroshi , Haller George , Komatsuzaki Tamiki
Published: October 2013

Normally hyperbolic invariant manifolds (NHIMs) are well-known organizing centers of the dynamics in the phase space of a nonlinear system. Locating such manifolds in systems far from symmetric or integrable, however, has been an outstanding challenge. Here, we develop an automated detection method for codimension-one NHIMs in autonomous dynamical systems. Our method utilizes Stationary Lagrangian Coherent Structures (SLCSs), which are hypersurfaces satisfying one of the necessary conditions of a hyperbolic LCS, and are also quasi-invariant in a well-defined sense. Computing SLCSs provides a quick way to uncover NHIMs with high accuracy. As an illustration, we use SLCSs to locate two-dimensional stable and unstable manifolds of hyperbolic periodic orbits in the classic ABC flow, a three-dimensional solution of the steady Euler equations.
Thermodynamic properties of supercritical n-m Lennard-Jones fluids and isochoric and isobaric heat capacity maxima and minima
Authors: Mairhofer Jonas , Sadus Richard J.
Published: October 2013

Molecular dynamics simulations are reported for the thermodynamic properties of n-m Lennard-Jones fluids, where n = 10 and 12, and m = 5 and 6. Results are reported for the thermal expansion coefficient, isothermal and adiabatic compressibilities, isobaric and isochoric heat capacities, Joule-Thomson coefficient, and speed of sound at supercritical conditions covering a wide range of fluid densities. The thermodynamic criteria for maxima/minima in the isochoric and isobaric heat capacities are identified and the simulation results are also compared with calculations from Lennard-Jones equations of state. The Johnson et al. [Mol. Phys. 78, 591 (1993)] equation of state can be used to reproduce all heat capacity phenomena reported [T. M. Yigzawe and R. J. Sadus, J. Chem. Phys. 138, 194502 (2013)] from molecular dynamics simulations for the 12-6 Lennard-Jones potential. Significantly, these calculations and molecular dynamics results for other n-m Lennard-Jones potentials support the existence of Cp minima at supercritical conditions. The values of n and m also have a significant influence on many other thermodynamic properties.
Boron ion beam generation using a self-sputtering planar magnetron
Authors: Vizir Aleksey , Nikolaev Aleksey , Oks Efim , Savkin Konstantin , Shandrikov Maxim , Yushkov Georgy
Published: October 2013

A boron ion source based on planar magnetron discharge with solid boron target has been developed. To obtain a sufficient conductivity of the boron target for high current discharge ignition, the target was heated to the temperature more than 350 °C. To reach this temperature, thermally isolated target was heated by low-current high-voltage magnetron DC discharge. Applying a high-current pulse (100 μs range) provides a self-sputtering mode of the discharge, which generates the boron plasma. Boron ion beam with current more than 150 mA was extracted from the plasma by applying an accelerating voltage of 20 kV. The boron ion fraction in the beam reached 95%, averaged over the pulse length, and the rest ions were working gas (Kr+). It was shown that “keeping alive” DC discharge completely eliminates a time delay of pulsed discharge current onset, and reduces the pulsed discharge minimal working pressure.
EBIS charge breeder for CARIBU
Authors: Kondrashev S. , Barcikowski A. , Dickerson C. , Fischer R. , Ostroumov P. N. , Vondrasek R. , Pikin A.
Published: October 2013

A high-efficiency charge breeder based on an Electron Beam Ion Source (EBIS) is being developed by the ANL Physics Division to increase the intensity and improve the purity of accelerated radioactive ion beams. A wide variety of low-energy neutron-rich ion beams are produced by the Californium Rare Isotope Breeder Upgrade (CARIBU) for the Argonne Tandem Linac Accelerator System (ATLAS). These beams will be charge-bred by an EBIS charge breeder to a charge-to-mass ratio (q/A) ≥ 1/7 and accelerated by ATLAS to energies of about 10 MeV/u. The assembly of the CARIBU EBIS charge breeder except the injection/extraction beam lines has been completed. This summer we started electron beam commissioning of the EBIS. The first results on electron beam extraction, transport from the electron gun to a high power electron collector are presented and discussed.
A turnstile mechanism for fronts propagating in fluid flows
Authors: Mahoney John R. , Mitchell Kevin A.
Published: October 2013

We consider the propagation of fronts in a periodically driven flowing medium. It is shown that the progress of fronts in these systems may be mediated by a turnstile mechanism akin to that found in chaotic advection. We first define the modified (“active”) turnstile lobes according to the evolution of point sources across a transport boundary. We then show that the lobe boundaries may be constructed from stable and unstable burning invariant manifolds (BIMs)—one-way barriers to front propagation analogous to traditional invariant manifolds for passive advection. Because the BIMs are one-dimensional curves in a three-dimensional (xyθ) phase space, their projection into xy-space exhibits several key differences from their advective counterparts: (lobe) areas are not preserved, BIMs may self-intersect, and an intersection between stable and unstable BIMs does not map to another such intersection. These differences must be accommodated in the correct construction of the new turnstile. As an application, we consider a lobe-based treatment protocol for protecting an ocean bay from an invading algae bloom.
On symmetries and conserved quantities in Nambu mechanics
Authors: Fecko M.
Published: October 2013

In Hamiltonian mechanics, a (continuous) symmetry leads to conserved quantity, which is a function on (extended) phase space. In Nambu mechanics, a straightforward consequence of symmetry is just a relative integral invariant, a differential form which only upon integration over a cycle provides a conserved real number. The origin of the difference may be traced back to a shift in degrees of relevant forms present in equations of motion, or, alternatively, to a corresponding shift in degrees of relevant objects in action integral for Nambu mechanics.
Suppression of zero-crossing distortion for single-phase grid-connected photovoltaic inverters with unipolar modulation
Authors: Zeng Bin , Xu Hong-bing , Chen Kai , Chen Jian-guo
Published: October 2013

For single-phase grid-connected photovoltaic inverters, current-control with unipolar modulation can reduce the losses of power tubes and improve the efficiency compared with using the bipolar modulation. However, it suffers inherent zero-crossing distortion which is related to the grid current and voltage. In this paper, the reason for zero-crossing distortion is analyzed and simulated, also a novel current-control approach with commutating in advance is proposed to resolve this problem. This approach obtains a leading angle of the grid current by using the feedback of proportional-integral controller of the unipolar inverter, and then set the working mode of power tubes according to this angle through commutation.
Hybrid approach combining dissipative particle dynamics and finite-difference diffusion model: Simulation of reactive polymer coupling and interfacial polymerization
Authors: Berezkin Anatoly V. , Kudryavtsev Yaroslav V.
Published: October 2013

A novel hybrid approach combining dissipative particle dynamics (DPD) and finite difference (FD) solution of partial differential equations is proposed to simulate complex reaction-diffusion phenomena in heterogeneous systems. DPD is used for the detailed molecular modeling of mass transfer, chemical reactions, and phase separation near the liquid/liquid interface, while FD approach is applied to describe the large-scale diffusion of reactants outside the reaction zone. A smooth, self-consistent procedure of matching the solute concentration is performed in the buffer region between the DPD and FD domains. The new model is tested on a simple model system admitting an analytical solution for the diffusion controlled regime and then applied to simulate practically important heterogeneous processes of (i) reactive coupling between immiscible end-functionalized polymers and (ii) interfacial polymerization of two monomers dissolved in immiscible solvents. The results obtained due to extending the space and time scales accessible to modeling provide new insights into the kinetics and mechanism of those processes and demonstrate high robustness and accuracy of the novel technique.
Highly bent (110) Ge crystals for efficient steering of ultrarelativistic beams
Authors: De Salvador D. , Maggioni G. , Carturan S. , Bazzan M. , Argiolas N. , Carnera A. , Dalla Palma M. , Della Mea G. , Bagli E. , Mazzolari A. , Bandiera L. , Guidi V. , Lietti D. , Berra A. , Guffanti G. , Prest M. , Vallazza E.
Published: October 2013

Thanks to the effective electrostatic potential generated by the ordered atomic structure, bent crystals can efficiently deflect ultra relativistic charged beams by means of planar and axial channeling phenomena as well as of the recently discovered volume reflection effect. Most of the experimental knowledge about these phenomena has been gathered with Si crystals, but it has been recently demonstrated that the steering performance can be improved by using high quality Ge materials which have a larger atomic number. In this paper, we investigate channeling and volume reflection of 400 GeV protons from (110) lattice planes in highly bent Ge strips crystals. Both production and characterization of the strips are presented. Herein, the experimental results on deflection are compared with theoretical predictions, with previous published data and with the expected performances of Si crystals in similar experimental conditions.
Filament velocity scaling laws for warm ions
Authors: Manz P. , Carralero D. , Birkenmeier G. , Müller H. W. , Müller S. H. , Fuchert G. , Scott B. D. , Stroth U.
Published: October 2013

The dynamics of filaments or blobs in the scrape-off layer of magnetic fusion devices are studied by magnitude estimates of a comprehensive drift-interchange-Alfvén fluid model. The standard blob models are reproduced in the cold ion case. Even though usually neglected, in the scrape-off layer, the ion temperature can exceed the electron temperature by an order of magnitude. The ion pressure affects the dynamics of filaments amongst others by adding up to the interchange drive and the polarisation current. It is shown how both effects modify the scaling laws for filament velocity in dependence of its size. Simplifications for experimentally relevant limit regimes are given. These are the sheath dissipation, collisional, and electromagnetic regime.
A high-performance dielectric elastomer consisting of bio-based polyester elastomer and titanium dioxide powder
Authors: Yang Dan , Tian Ming , Dong Yingchao , Kang Hailan , Gong Daolin , Zhang Liqun
Published: October 2013

A bio-based polyester elastomer containing many polar groups was combined with high-dielectric-constant titanium dioxide (TiO2) powder to form a dielectric elastomer composite for the first time. The effects of the titanium dioxide filler on the elastic modulus, dielectric properties, and electromechanical responses of the polyester dielectric elastomer were studied. We found that the dielectric constant of composites increased with increasing content of TiO2. Nevertheless, the elastic modulus of the composites did not increase with increasing content of TiO2, and the polyester elastomer filled with 6 vol. % of TiO2 exhibited the lowest elastic modulus, which led to a high prestrain-free actuated strain of 11.8% at a low electric field of just 9.8 kV/mm. The actuated strain is better than other dielectric elastomers reported in the literature. The high electromechanical performance was attributed to the increase in dielectric constant and decrease in elastic modulus of the composite from those of the pure polyester elastomer. The decrease in elastic modulus was explained in detail by the competing effects of crosslink density and filler network. In addition, a dramatic increase in dielectric constant of the composite was observed and discussed through several dielectric mixing rules. Finally, the polyester elastomer and titanium dioxide are both environment-friendly, making possible the composite to be used in biological and medical devices.
Theoretical study of energy deposition in ionization chambers for tritium measurements
Authors: Chen Zhilin , Peng Shuming , Meng Dan , He Yuehong , Wang Heyi
Published: October 2013

Energy deposition in ionization chambers has been theoretically studied for tritium measurements in gaseous form. A one-dimension model is introduced to establish the quantitative relationship between energy deposition rate and many factors, including carrier gas, gas pressure, wall material, chamber size, and gas temperature. Energy deposition rate has been calculated at pressure varying from 5 kPa to 500 kPa based on some approximations. It is found that energy deposition rate varies greatly for different parameters, especially at low gas pressure. For the same chamber, energy deposition rate in argon is much higher than in deuterium, as much as 70.7% higher at 5 kPa. Gold plated chamber gives highest energy deposition rate in the calculations while aluminum chamber results in the lowest. As chamber size gets smaller, β ray emitted by tritium will deposit less energy in the sensitive region of the chamber. For chambers flowing through with the same gas, energy deposition rate in a 10 L chamber is 23.9% higher than in a 0.05 L chamber at 5 kPa. Gas temperature also places slight influence on energy deposition rate, and 373 K will lead to 6.7% lower deposition rate than 233 K at 5 kPa. In addition, experiments have been performed to obtain energy deposition rate in a gold plated chamber, which show good accordance with theoretical calculations.
Low dark current silicon-on-insulator waveguide metal-semiconductor-metal-photodetector based on internal photoemissions at 1550 nm
Authors: Casalino M. , Iodice M. , Sirleto L. , Rao S. , Rendina I. , Coppola G.
Published: October 2013

We report on the fabrication and characterization of a metal-semiconductor-metal photodetector operating at 1550 nm and integrated into a silicon-on-insulator waveguide. Detection uses internal photoemissions through a metal/Si interface. In particular, a small metal/Si contact layer directly deposited on the vertical output facet of the waveguide absorbs the incoming radiation confined into a rib waveguide. The device parameters for responsivity, dark current, and bandwidth take values 3.5 mA, 3.5 nA, and 1 GHz, respectively. The results obtained indicate device suitability in power monitoring and telecommunications applications.
The effects of plasma shape control on the edge collisionless ion orbit loss
Authors: Wu G. J. , Zhang X. D. , Li Y. D. , Sun P. J. , Cao G. M.
Published: October 2013

Double null magnetic configurations with different elongation κ and triangularity δ are constructed by using an analytical solution of the Grad–Shafranov equation. The ion orbit losses in plasma edge region are calculated by solving the ion guiding center orbit equation for different values of κ and δ. It is found that the ion orbit loss is larger for a smaller value of κ or δ. The variation of the ion orbit loss fraction on the magnetic surface is also studied.
Enhanced non-radiative recombination in the vicinity of plasma-etched side walls of luminescing Si/Ge-quantum dot structures
Authors: Schilling J. , Talalaev V. , Tonkikh A. , Fuhrmann B. , Heyroth F. , Otto M.
Published: October 2013

The photoluminescence from plasma etched, wedge shaped Ge-quantum dot arrays is investigated locally. The wedge geometry allows a convenient measurement of the luminescence intensity within a well defined distance from the etched side facets. A zone of reduced photoluminescence with a thickness of several hundred nanometers is detected adjacent to the etched facets due to the strong non-radiative surface recombination. Covering the surface with thin layers of aluminium oxide passivates part of the surface states leading to a reduction of the luminescence quenching zone.
Microstructural origin for the piezoelectricity evolution in (K0.5Na0.5)NbO3-based lead-free ceramics
Authors: Guo Hanzheng , Zhang Shujun , Beckman Scott P. , Tan Xiaoli
Published: October 2013

Chemically modified (K0.5Na0.5)NbO3 compositions with finely tuned polymorphic phase boundaries (PPBs) have shown excellent piezoelectric properties. The evolution of the domain morphology and crystal structure under applied electric fields of a model material, 0.948(K0.5Na0.5)NbO3–0.052LiSbO3, was directly visualized using in situ transmission electron microscopy. The in situ observations correlate extremely well with measurements of the electromechanical response on bulk samples. It is found that the origin of the excellent piezoelectric performance in this lead-free composition is due to a tilted monoclinic phase that emerges from the PPB when poling fields greater than 14 kV/cm are applied.
In situ study of the role of substrate temperature during atomic layer deposition of HfO2 on InP
Authors: Dong H. , K.C. Santosh, , Qin X. , Brennan B. , McDonnell S. , Zhernokletov D. , Hinkle C. L. , Kim J. , Cho K. , Wallace R. M.
Published: October 2013

The dependence of the “self cleaning” effect of the substrate oxides on substrate temperature during atomic layer deposition (ALD) of HfO2 on various chemically treated and native oxide InP (100) substrates is investigated using in situ X-ray photoelectron spectroscopy. The removal of In-oxide is found to be more efficient at higher ALD temperatures. The P oxidation states on native oxide and acid etched samples are seen to change, with the total P-oxide concentration remaining constant, after 10 cycles of ALD HfO2 at different temperatures. An (NH4)2 S treatment is seen to effectively remove native oxides and passivate the InP surfaces independent of substrate temperature studied (200 °C, 250 °C and 300 °C) before and after the ALD process. Density functional theory modeling provides insight into the mechanism of the changes in the P-oxide chemical states.
A generalized lumped element modeling of electrically and magnetically dual-tunable coupled microstrip filters
Authors: Zhou Hao-Miao , Zhu Feng-Jie
Published: October 2013

A generalized lumped element modeling for electrically and magnetically dual-tunable coupled microstrip filters is established through the introduction of the coupling factor which stands for coupling between magnetoelectric layered structure and the input/output microstrip. Then, the lumped element modeling for an existing filter is established and used to predict the electric and magnetic tunability of the filter that manifests as a shift in pass-band. The results have a good consistency with the experimental data and the electromagnetic simulation results in quality and quantity. Then the effects of applied electric field, microstrip's size, substrate's size, and the ferrite-piezoelectric layered structure's size on the filter performance are analyzed by the lumped element modeling. The predicted results show that the performance of the filter can be effectively improved through the increase of microstrip's length and the structure's thickness in a certain range, or the decrease of structure's width and length and the distance between the microstrip and the structure appropriately.
Polarization independent blue phase liquid crystal gratings based on periodic polymer slices structure
Authors: Yan Jing , Li Qing , Hu Kai
Published: October 2013

A polarization independent switchable phase grating based on polymer stabilized blue phase liquid crystal is proposed. A high efficiency of the phase grating has been achieved because of the sharp rectangular phase profile which shows good agreement with the simulation results. The diffraction efficiency of the 1st order is 38%, the response time is in the submillisecond range, and the phase grating is independent of the polarization of the incident light. The voltage-induced hysteresis characteristics are also investigated.
Giant magnetothermopower in charge ordered Nd0.75Na0.25MnO3
Authors: Maheswar Repaka D. V. , Mahendiran R.
Published: October 2013

We report magnetization, resistivity, and thermopower in the charge-orbital ordered antiferromagnet Nd0.75Na0.25MnO3. Magnetic-field induced collapse of antiferromagnetism is found to be accompanied by a giant negative magnetothermopower (=80%–100% for a field change of 5 T) over a wide temperature (T = 60–225 K) and giant magnetoresistance. While the field-induced metamagnetic transition in magnetization is reversible upon field-cycling at T > 40 K, it is irreversible at lower temperatures and this has impact on magnetoresistance, magnetothermopower as well as change in the temperature of the sample. Our results indicate high sensitivity of thermopower to changes in the magnetic state of the sample.
Neutron irradiation effects on gallium nitride-based Schottky diodes
Authors: Lin Chung-Han , Katz Evan J. , Qiu Jie , Zhang Zhichun , Mishra Umesh K. , Cao Lei , Brillson Leonard J.
Published: October 2013

Depth-resolved cathodoluminescence spectroscopy (DRCLS), time-resolved surface photovoltage spectroscopy, X-ray photoemission spectroscopy (XPS), and current-voltage measurements together show that fast versus thermal neutrons differ strongly in their electronic and morphological effects on metal-GaN Schottky diodes. Fast and thermal neutrons introduce GaN displacement damage and native point defects, while thermal neutrons also drive metallurgical reactions at metal/GaN interfaces. Defect densities exhibit a threshold neutron fluence below which thermal neutrons preferentially heal versus create new native point defects. Scanning XPS and DRCLS reveal strong fluence- and metal-dependent electronic and chemical changes near the free surface and metal interfaces that impact diode properties.
Enhanced surface mobility and quantum oscillations in topological insulator Bi1.5Sb0.5Te1.7Se1.3 nanoflakes
Authors: Hsiung Te-Chih , Chen Ding-Yuan , Zhao Li , Lin Yi-Hsin , Mou Chung-Yu , Lee Ting-Kuo , Wu Maw-Kuen , Chen Yang-Yuan
Published: October 2013

In this study, a series of Bi1.5Sb0.5Te1.7Se1.3 (BSTS) flakes 80-nm to 140-μm in thickness was fabricated to investigate their metallic surface states. We report the observation of surface-dominated transport in these topological insulator BSTS nanoflakes. The achievement of surface-dominated transport can be attributed to high surface mobility (∼3000 cm2/V s) and low bulk mobility (12 cm2/V s). Up to 90% of the total conductance, the surface channel was estimated based on the thickness dependence of electrical conductance and the result of the Shubnikov-de Hass oscillations in a 200-nm BSTS. The nature of nontrivial Dirac surface states was also confirmed by the weak anti-localization effect.
Degradation in AlGaN/GaN heterojunction field effect transistors upon electrical stress: Effects of field and temperature
Authors: Zhu C. Y. , Zhang F. , Ferreyra R. A. , Avrutin V. , Özgür Ü. , Morkoç H.
Published: October 2013

AlGaN/GaN heterojunction field effect transistors (HFETs) with 2 μm gate length were subjected to on-state-high-field (high drain bias and drain current) and reverse-gate-bias (no drain current and reverse gate bias) stress at room and elevated temperatures for up to 10 h. The resulting degradation of the HFETs was studied by direct current and uniquely phase noise before and after stress. A series of drain and gate voltages was applied during the on-state-high-field and reverse-gate-bias stress conditions, respectively, to examine the effect of electric field on degradation of the HFET devices passivated with SiNx. The degradation behaviors under these two types of stress conditions were analyzed and compared. In order to isolate the effect of self-heating/temperature on device degradation, stress experiments were conducted at base plate temperatures up to 150 °C. It was found that the electric field induced by reverse-gate-bias mainly generated trap(s), most likely in the AlGaN barrier, which initially were manifested as generation-recombination (G-R) peak(s) in the phase noise spectra near 103 Hz. Meanwhile electric field induced by on-state-high-field stress mainly generated hot-electron and hot-phonon effects, which result in a nearly frequency independent increase of noise spectra. The external base plate temperatures promote trap generation as evidenced by increased G-R peak intensities.
Benzonitrile Oxide Cycloadditions with Exocyclic Methylene Benzothiazepine Dioxides
Authors: Ryan Sarah J. , Francis Craig L. , Savage G. Paul
Published: October 2013

N-substituted 5-methylene-2,3,4,5-tetrahydrobenzo[f][1,2]thiazepine 1,1-dioxides underwent 1,3-dipolar cycloaddition with benzonitrile oxide, generated in situ, to give isoxazoline spiro adducts. The cycloadditions were completely regioselective to give the hitherto unreported 3,4-dihydro-2H,4′H-spiro[benzo[f][1,2]thiazepine-5,5′-isoxazole] 1,1-dioxide cycloadduct. Where the N-substituent on the sulfonamide cycloaddition precursor was a 2-substituted arene, the resulting atropisomerism along the N-aryl bond led to facial selectivity in the cycloaddition reaction, with greater than 90 % diastereoselectivity.
Attitudes of rangeland holders towards sustainable range management in Iran: a case study of the Semnan rangelands
Authors: Abolhassani Leili , Oesten Gerhard , Rajmis Sandra , Azadi Hossein
Published: October 2013

Rangeland depletion is a persistent problem in many developing countries and is often a result of inappropriate management activities such as overstocking, particularly in the regions of West Asia and North Africa (WANA). To convert to a sustainable system of range management, programs aimed at improving rangeland condition, such as range management or livestock development plans, which are mainly based on the range succession model, have been developed and implemented by several governments. A primary objective of these programs is to maintain stocking rates at a sustainable level. However, in many cases, rangeland users’ ignorance of socioeconomic factors has caused ineffectual implementation and thus a reduction in the effectiveness of these programs overall.
In this study, a survey was conducted on rangeland communities in central northern Iran where the livestock population is 15% above the proposed carrying capacity 20 years after the inception of the Range Management Plan (RMP). The focus of this study was to investigate reasons that the RMP has not been successful, from the perspective of the rangeland holders. The data were collected using open-ended interviews.
The data analysis indicated that the primary barriers to the successful implementation of the RMP are quite well matched with the description of the ‘diffusion of innovations’ theory. The three characteristics of the RMP innovation, including the lack of high relative advantages, incompatible structure of the RMP with the traditional rules, and lack of observability of short-term benefits from the RMP, were realised as the main barriers to the success of the RMP adoption. An additional concern for the rangeland holders was drought, which they felt was not adequately addressed or dealt with in the RMP. Lastly, the government’s failure to fulfil the initial commitments of the RMP, for instance financial supports, has resulted in a loss of confidence of rangeland holders in the enforcement agency and governmental policies.
The G20 development consensus: an African perspective
Authors: Zondi Siphamandla
Published: October 2013

In critical theoretical paradigms, serious commitment to the concept of development as a tool for social change epitomises or intimates an alternative to the dominant ideologies and paradigms born out of economic liberalism, blamed for the existence of affluent centres and poverty-stricken peripheries in the world system. In development policy, these paradigms are also known as the Washington Consensus, which is a bone of contention with liberals proclaiming its triumph after the collapse of the Communist bloc, and critical theorists declaring that the world is ripe for an alternative to the neoliberal consensus. For this reason many, especially in the developing world and in Africa, have been anticipating the birth of a post-Washington consensus. The announcement in November 2010 of the Seoul Development Consensus by the G20, a group of 20 significant economies bridging the North–South divide, has raised hopes that this influential network has begun to think about an alternative policy consensus and paradigm. This article assesses, on the basis of a critical analysis of available documents, whether indeed the Seoul Consensus is a post- Washington consensus.
Recent Developments In Mental Health Courts: What Have We Learned?
Authors: Sarteschi Christine , Vaughn Michael G.
Published: October 2013

Mental health courts (MHCs) are problem-solving courts that attempt to redirect individuals with mental illness into treatment rather than incarceration (Wolff, 2003). The primary purpose of this article is to provide a narrative review of recent evidence on the empirical status of MHCs and suggest directions for future social work research. Such a review is critical given the existence of 300 MHCs in the United States (Council of State Governments Justice Center, 2011) with more in development. Four major questions guided our review: (a) How do they work? (b) Does a theoretical basis exist to explain how they work? (c) What is the nature of the evidence? and (d) What are the characteristics of the mentally ill who choose not to participate in MHC programs and of those who are negatively terminated? Though studies have shown reductions in assessed outcomes, a lack of methodologically strong evaluations significantly limits the strength of those results. There exists a need for additional, methodologically rigorous studies to better understand the effectiveness of MHCs.
Attrition in Drug Court Research: Examining Participant Characteristics and Recommendations for Follow-Up
Authors: Mendoza Natasha , Linley Jessica V. , Nochajski Thmoas H. , Farrell Mark G.
Published: October 2013

Drug court research is often challenged by study attrition. In this study, researchers attempted to predict study completion using variables traditionally associated with treatment attrition. Findings showed that participants who reported a need for additional help to resolve legal problems and who reported accessing outpatient treatments were more likely to complete the study at the 3-month follow-up. The study also demonstrated a relationship between trauma-related symptoms and study attrition. Although sample size was a limitation with these pilot data, researchers are urged to examine attrition and increase efforts to engage drug court enrollees in research studies, especially those with trauma-related symptoms.
SOAPfusion: a robust and effective computational fusion discovery tool for RNA-seq reads
Authors: Wu Jikun , Zhang Wenqian , Huang Songbo , He Zengquan , Cheng Yanbing , Wang Jun , Lam Tak-Wah , Peng Zhiyu , Yiu Siu-Ming
Published: October 2013

Motivation: RNA-Seq provides a powerful approach to carry out ab initio investigation of fusion transcripts representing critical translocation and post-transcriptional events that recode hereditary information. Most of the existing computational fusion detection tools are challenged by the issues of accuracy and how to handle multiple mappings.

Results: We present a novel tool SOAPfusion for fusion discovery with paired-end RNA-Seq reads. SOAPfusion is accurate and efficient for fusion discovery with high sensitivity (≥93%), low false-positive rate (≤1.36%), even the coverage is as low as 10×, highlighting its ability to detect fusions efficiently at low sequencing cost. From real data of Universal Human Reference RNA (UHRR) samples, SOAPfusion detected 7 novel fusion genes, more than other existing tools and all genes have been validated through reverse transcription-polymerase chain reaction followed by Sanger sequencing. SOAPfusion thus proves to be an effective method with precise applicability in search of fusion transcripts, which is advantageous to accelerate pathological and therapeutic cancer studies.

Availability:  http://soap.genomics.org.cn/SOAPfusion.html

Contact:  smyiu@cs.hku.hk

Supplementary information:  Supplementary data are available at Bioinformatics online.
PLIDA: cross-platform gene expression normalization using perturbed topic models
Authors: Deshwar Amit G. , Morris Quaid
Published: October 2013

Motivation: Gene expression data are currently collected on a wide range of platforms. Differences between platforms make it challenging to combine and compare data collected on different platforms. We propose a new method of cross-platform normalization that uses topic models to summarize the expression patterns in each dataset before normalizing the topics learned from each dataset using per-gene multiplicative weights.

Results: This method allows for cross-platform normalization even when samples profiled on different platforms have systematic differences, allows the simultaneous normalization of data from an arbitrary number of platforms and, after suitable training, allows for online normalization of expression data collected individually or in small batches. In addition, our method outperforms existing state-of-the-art platform normalization tools.

Availability and implementation: MATLAB code is available at http://morrislab.med.utoronto.ca/plida/.

Contact:  Amit.Deshwar@utoronto.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
GIIRA—RNA-Seq driven gene finding incorporating ambiguous reads
Authors: Zickmann Franziska , Lindner Martin S. , Renard Bernhard Y.
Published: October 2013

Motivation: The reliable identification of genes is a major challenge in genome research, as further analysis depends on the correctness of this initial step. With high-throughput RNA-Seq data reflecting currently expressed genes, a particularly meaningful source of information has become commonly available for gene finding. However, practical application in automated gene identification is still not the standard case. A particular challenge in including RNA-Seq data is the difficult handling of ambiguously mapped reads.

Results: We present GIIRA (Gene Identification Incorporating RNA-Seq data and Ambiguous reads), a novel prokaryotic and eukaryotic gene finder that is exclusively based on a RNA-Seq mapping and inherently includes ambiguously mapped reads. GIIRA extracts candidate regions supported by a sufficient number of mappings and reassigns ambiguous reads to their most likely origin using a maximum-flow approach. This avoids the exclusion of genes that are predominantly supported by ambiguous mappings. Evaluation on simulated and real data and comparison with existing methods incorporating RNA-Seq information highlight the accuracy of GIIRA in identifying the expressed genes.

Availability and implementation: GIIRA is implemented in Java and is available from https://sourceforge.net/projects/giira/.

Contact: renardB@rki.de

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Two novel pathway analysis methods based on a hierarchical model
Authors: Evangelou Marina , Dudbridge Frank , Wernisch Lorenz
Published: October 2013

Motivation: Over the past few years several pathway analysis methods have been proposed for exploring and enhancing the analysis of genome-wide association data. Hierarchical models have been advocated as a way to integrate SNP and pathway effects in the same model, but their computational complexity has prevented them being applied on a genome-wide scale to date.

Methods: We present two novel methods for identifying associated pathways. In the proposed hierarchical model, the SNP effects are analytically integrated out of the analysis, allowing computationally tractable model fitting to genome-wide data. The first method uses Bayes factors for calculating the effect of the pathways, whereas the second method uses a machine learning algorithm and adaptive lasso for finding a sparse solution of associated pathways.

Results: The performance of the proposed methods was explored on both simulated and real data. The results of the simulation study showed that the methods outperformed some well-established association methods: the commonly used Fisher’s method for combining P-values and also the recently published BGSA. The methods were applied to two genome-wide association study datasets that aimed to find the genetic structure of platelet function and body mass index, respectively. The results of the analyses replicated the results of previously published pathway analysis of these phenotypes but also identified novel pathways that are potentially involved.

Availability: An R package is under preparation. In the meantime, the scripts of the methods are available on request from the authors.

Contact: marina.evangelou@cimr.cam.ac.uk

Supplementary Information: Supplementary data are available at Bioinformatics online.
Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets
Authors: Rodriguez-R Luis M. , Konstantinidis Konstantinos T.
Published: October 2013

Motivation: Determining the fraction of the diversity within a microbial community sampled and the amount of sequencing required to cover the total diversity represent challenging issues for metagenomics studies. Owing to these limitations, central ecological questions with respect to the global distribution of microbes and the functional diversity of their communities cannot be robustly assessed.

Results: We introduce Nonpareil, a method to estimate and project coverage in metagenomes. Nonpareil does not rely on high-quality assemblies, operational taxonomic unit calling or comprehensive reference databases; thus, it is broadly applicable to metagenomic studies. Application of Nonpareil on available metagenomic datasets provided estimates on the relative complexity of soil, freshwater and human microbiome communities, and suggested that ∼200 Gb of sequencing data are required for 95% abundance-weighted average coverage of the soil communities analyzed.

Availability and implementation: Nonpareil is available at https://github.com/lmrodriguezr/nonpareil/ under the Artistic License 2.0.

Contact:  kostas@ce.gatech.edu.

Supplementary information:  Supplementary data are available at Bioinformatics online.