bluuebunny/crossref_metadata_2025 huggingface dataset:
Heating of thermal non-equilibrium ions by Alfvén wave via nonresonant interaction
Authors: Liu Hai-Feng , Wang Shi-Qing , Li Ke-Hua
Published: October 2013

Pickup of thermal non-equilibrium ions by Alfvén wave via nonresonant wave-particle interaction is investigated by means of analytical test-particle theory. Some interesting and new results are found. No matter what the initial velocity distribution is, if the background magnetic field, the Alfvén speed, and the Alfvén magnetic field are fixed, the average parallel velocity never changes when t→∞. Heating effects in the perpendicular and parallel direction just depend on the initial temperature, and the perpendicular temperature increase is more prominent. It is noted that the heating effect of thermal non-equilibrium ions (Kappa ions) is weaker than that of the Maxwellian. This phenomenon may be relative to the heating of ions in the solar corona as well as in some toroidal confinement fusion devices.
Intense terahertz generation at low frequencies using an interdigitated ZnSe large aperture photoconductive antenna
Authors: Ropagnol X. , Blanchard F. , Ozaki T. , Reid M.
Published: October 2013

We demonstrate the generation of intense THz pulses at low frequencies, and THz pulse shaping, using a ZnSe interdigitated large aperture photoconductive antenna. We have experimentally measured a THz pulse energy of 3.6 ±0.8 μJ, corresponding to a calculated peak THz electric field of 143 ± 17 kV/cm. We also used a binary phase mask instead of a traditional shadow mask with our interdigitated photoconductive antenna, which allows us to generate THz field profiles that range from a symmetric single-cycle THz pulse to an asymmetric half-cycle THz pulse.
First-principles study of temperature-dependent diffusion coefficients for helium in α-Ti
Authors: Lu Yong , Zheng Fawei , Zhang Ping
Published: October 2013

The temperature-dependent diffusion coefficients of interstitial helium atom in α-Ti are predicted using the transition state theory. The microscopic parameters in the pre-factor and activation energy of the impurity diffusion coefficients are obtained from first-principles total energy and phonon calculations including the full coupling between the vibrational modes of the diffusing atom and the host lattice. The climbing image nudged elastic band method is used to search for the minimum energy pathways and associated saddle point structures. It is demonstrated that the diffusion coefficients within the xy plane (Dxy) is always higher than that along the z axis (Dz), showing remarkable anisotropy. Also, it is found that the formation of helium dimer centered at the octahedral site reduces the total energy and confines the diffusion of helium atoms.
Large magneto-elastic anisotropy enhancement with temperature in composition-graded FeCoTa thin films
Authors: Phuoc Nguyen N. , Chapon Patrick , Acher Olivier , Ong C. K.
Published: October 2013

Static and dynamic magnetic properties of composition-graded FeCoTa thin films were systematically studied with respect to temperature and the deposition power of Ta target. The magnetic anisotropy field and ferromagnetic resonance frequency were found to be increased with the increasing of deposition power of Ta target due to the enhancement of stress when Ta concentration is increased. Thermal stability of the films shows a very interesting behavior with a peculiar and large increasing of magnetic anisotropy with temperature when the deposition power for Ta is moderate while it exhibits normal decreasing with temperature when the deposition power is low or high. The results are discussed and explained in terms of the magneto-elastic anisotropy contribution when the stress of the films is varied.
Many-body enhancement of the tunable gap in biased bilayer graphene
Authors: Stroucken T. , Grönqvist J. H. , Koch S. W.
Published: October 2013

A self-consistent microscopic theory is applied to analyze the influence of many-body effects on the energy spectrum of biased bilayer graphene. The results show a monotonic increase of the quasiparticle gap with the applied external field and a significant enhancement of the gap due to the many-body interactions.
Al2O3/TiO2 stack layers for effective surface passivation of crystalline silicon
Authors: Suh Dongchul , Choi Duk-Yong , Weber Klaus J.
Published: October 2013

For silicon surface passivation, we investigate stack layers consisting of a thin Al2O3 layer and a TiO2 capping layer deposited by means of thermal atomic layer deposition (ALD). In this work, we studied the influence of different thermal post-deposition treatments and film thickness for the activation of passivating ALD Al2O3 single layers and Al2O3/TiO2 stack layers. Our experiments show a substantial improvement of the passivation for the Al2O3/TiO2 stack layers compared to a thin single Al2O3 layer. For the stacks, especially with less than 10 nm Al2O3, a TiO2 capping layer results in a remarkably lower surface recombination. Effective fixed charge density of Al2O3/TiO2 stack layers increases after TiO2 deposition and O2 annealing. It is also demonstrated that the enhanced surface passivation can be mainly related to a remarkably low interface defect density of 1.1 × 1010 eV−1 cm−2, whereas post-TiO2 heat treatment in O2 ambience is not beneficial for the passivation of silicon, which is attributed to increasing interface defect density of stack layers.
Combined effects of diffuse phase transition and microstructure on the electrocaloric effect in Ba1−xSrxTiO3 ceramics
Authors: Bai Yang , Han Xi , Ding Kai , Qiao Li-Jie
Published: October 2013

This paper demonstrates the combined effects of diffuse phase transition and microstructure on the electrocaloric effect (ECE) in Ba1−xSrxTiO3 (x = 0.2–0.4) ferroelectric ceramics. The ECE was characterized by direct heat flow measurement and an indirect thermodynamic method, which both provided consistent results. With increasing amount of Sr, the phase transition diffused and the grains grew larger. Since larger grains favor a high ΔTmax while a diffuse phase transition does not, the combination of these two effects induced nonmonotonic variation of the ECE. The x = 0.35 sample showed the best performance, with an ECE strength of 0.23 K·m/MV near room temperature.
Vector vortex beam emission from organic semiconductor microlasers
Authors: Qian H. , Markman B. D. , Giebink N. C.
Published: October 2013

High order Bessel beams (HOBBs) carrying discrete orbital angular momentum (OAM) are currently being explored for use in applications ranging from optical trapping to high-speed communication, all of which would benefit from the availability of compact semiconductor lasers with direct HOBB output. Here, we use an organic semiconductor gain medium to demonstrate a bilayer microdisk laser architecture that yields cylindrical vector HOBB emission with OAM quanta per photon >400ℏ. These devices feature azimuthally polarized, few-mode lasing with optical pumping thresholds <100 μJ/cm2 and emission wavelengths that can be tuned over a range of ∼40 nm by varying the organic microdisk thickness. Our approach is generally applicable to organic and inorganic semiconductors alike and may therefore serve as a practical route for integrating HOBB functionality into a range of optoelectronic and photonic applications throughout the visible and near-infrared spectrum.
Complex structural dynamics of bismuth under laser-driven compression
Authors: Hu Jianbo , Ichiyanagi Kouhei , Doki Tomoaki , Goto Arihiro , Eda Takayuki , Norimatsu Katsura , Harada Shinichi , Horiuchi Dai , Kabasawa Yuki , Hayashi Shingo , Uozumi Shin-ichi , Kawai Nobuaki , Nozawa Shunsuke , Sato Tokushi , Adachi Shin-ichi , Nakamura Kazutaka G.
Published: October 2013

With the aid of nanosecond time-resolved X-ray diffraction techniques, we have explored the complex structural dynamics of bismuth under laser-driven compression. The results demonstrate that shocked bismuth undergoes a series of structural transformations involving four solid structures: the Bi-I, Bi-II, Bi-III, and Bi-V phases. The transformation from the Bi-I phase to the Bi-V phase occurs within 4 ns under shock compression at ∼11 GPa, showing no transient phases with the available experimental conditions. Successive phase transitions (Bi-V → Bi-III → Bi-II → Bi-I) during the shock release within 30 ns have also been resolved, which were inaccessible using other dynamic techniques.
Reinforcement of metal with liquid-exfoliated inorganic nano-platelets
Authors: May Peter , Khan Umar , Coleman Jonathan N.
Published: October 2013

We have prepared metal matrix composites of a pewter alloy filled with liquid-exfoliated Molybdenum Telluride (MoTe2) nano-platelets. The combination of MoTe2 and pewter was chosen due to their near-identical densities, thus reducing the scope for buoyancy-induced separation during melt mixing. The addition of nanofiller results in a doubling of the Young's modulus, Y, for a volume fraction, Vf, of <1% MoTe2, corresponding to a reinforcement of dY/dVf = 110 GPa. We find that this degree of reinforcement to be reasonably consistent with that predicted by a simplified version of Halpin-Tsai theory.
Phononic band gap structures based on compacted nanoceramics
Authors: Salamatov E. , Taranov A. , Khazanov E.
Published: October 2013

It is shown both theoretically and experimentally that the compacted ceramics can exhibit the properties of a phononic lattice, i.e., a forbidden gap may arise in the phonon spectrum. The position and width of the gap in such systems are determined by the average grain size of ceramics, as well as by the thickness and elastic properties of the grain boundaries. In the case of composites, a dominant role in the gap formation is played by the most fine-grained phase.
Focusing of spoof surface-acoustic-waves by a gradient-index structure
Authors: Ye Yangtao , Ke Manzhu , Li Yixiang , Wang Tian , Liu Zhengyou
Published: October 2013

We have investigated the focusing of the spoof surface acoustic waves (SSAWs) on a rigid surface engraved with array of cylindrical holes. To focus the SSAWs launched along x direction, the holes array, with a shape of rectangle as a whole, is fabricated to possess gradient index of refraction along both the +y and −y directions, which is achieved by varying linearly the radii of the holes along the corresponding directions. Good focusing performance has been demonstrated experimentally, which is in good agreement with the numerical simulations. This acoustic system is believed to have potential applications in acoustic field such as high resolution detecting.
Photoluminescence characterization of a high-efficiency Cu2ZnSnS4 device
Authors: Gershon Talia , Shin Byungha , Bojarczuk Nestor , Gokmen Tayfun , Lu Siyuan , Guha Supratik
Published: October 2013

We report on low-temperature (4 K) photoluminescence of an 8.3% efficient Cu2ZnSnS4 photovoltaic device. Measurements were recorded as a function of excitation intensity, and the evolution of the resulting spectra is discussed. The spectra indicate that the radiative recombination is characteristic of heavily compensated material with a high quasi donor-acceptor pair density, as determined by the relationship between peak height, peak position, and excitation intensity, as well as the carrier lifetimes at different wavelengths. The blue-shift of the defect-derived peak position is used to estimate the quasi donor-acceptor pair spacing and density. The data indicate an average pair spacing of roughly 3.3 nm, yielding an overall total radiative-defect density of ∼1.3 × 1019 cm−3.
Epitaxial films of Heusler compound Co2FeAl0.5Si0.5 with high crystalline quality grown by off-axis sputtering
Authors: Peters B. , Alfonsov A. , Blum C. G. F. , Hageman Stephen J. , Woodward P. M. , Wurmehl S. , Büchner B. , Yang F. Y.
Published: October 2013

Co2FeAl0.5Si0.5 films with a surface roughness of 0.12 nm have been grown epitaxially on lattice-matched MgAl2O4 (001) substrates by off-axis sputtering. X-ray diffraction shows pronounced Laue oscillations, rocking curves as narrow as 0.0043°, and clear Co2FeAl0.5Si0.5 (111) peaks indicating L21 ordering. Magnetic characterizations show a clear magnetocrystalline anisotropy comprising cubic and epitaxy-induced uniaxial terms. Nuclear magnetic resonance measurements reveal L21 order of 81% in the Co2FeAl0.5Si0.5 films. Magnetotransport measurements show a distinct separation of anisotropic magnetoresistance and ordinary magnetoresistance. These results demonstrate the state-of-the-art crystalline quality and magnetic uniformity of the Co2FeAl0.5Si0.5 films.
Note: A 1-m Foucault pendulum rolling on a ball
Authors: Salva H. R. , Benavides R. E. , Venturino J. A. , Cuscueta D. J. , Ghilarducci A. A.
Published: October 2013

We have built a short Foucault pendulum of 1-m length. The aim of this work was to increase the sensitivity to elliptical trajectories from other longer pendula. The design was a semi-rigid pendulum that rolls over a small ball. The measurements of the movements (azimuth and elliptical trajectory) were done by an optical method. The resulting pendulum works in a medium satisfactory way due to problems of the correct choice of the mass of the bob together with the diameter of the supporting ball. It is also important to keep the rolling surface very clean.
Optimally enhanced optical emission in laser-induced air plasma by femtosecond double-pulse
Authors: Chen Anmin , Li Suyu , Li Shuchang , Jiang Yuanfei , Shao Junfeng , Wang Tingfeng , Huang Xuri , Jin Mingxing , Ding Dajun
Published: October 2013

In laser-induced breakdown spectroscopy, a femtosecond double-pulse laser was used to induce air plasma. The plasma spectroscopy was observed to lead to significant increase of the intensity and reproducibility of the optical emission signal compared to femtosecond single-pulse laser. In particular, the optical emission intensity can be optimized by adjusting the delay time of femtosecond double-pulse. An appropriate pulse-to-pulse delay was selected, that was typically about 50 ps. This effect can be especially advantageous in the context of femtosecond laser-induced breakdown spectroscopy, plasma channel, and so on.
Observation of bubble-involving spontaneous gas dissolution in superheated Al alloy melt
Authors: Zhang S. G. , Zhang L. , Lu W. Q. , Zhang W. , Yu J. D. , Fu Y. N. , Li J. G.
Published: October 2013

We present a direct visualization of spontaneous gas dissolution in Al-7.7 mass% Ca eutectic alloy melt during superheating using high-brilliance synchrotron X-ray imaging. A bubble-involving gas dissolution process was observed, which can be understood within the framework of adsorption-diffusion-dissolution mechanism. The heterogenous nucleation and combined effect of hydrogen diffusivity and solubility results in the growth of individual bubbles in a stochastic way with Gaussian distribution. This also applies to the behavior of group bubbles in early stage, while which in final stage can be treated as reverse Ostwald ripening dominated by Lifshitz-Slyozov-Wagner diffusion mechanism when pure diffusive condition is satisfied.
Enhanced Seebeck coefficient of bismuth telluride compounds with graded doping profiles
Authors: Huang Hung-Hsien , Lu Meng-Pei , Chiu Chien-Hao , Su Lin-Chieh , Liao Chien-Neng , Huang Jing-Yi , Hsieh Huey-Lin
Published: October 2013

Thermoelectric properties of Bi-Sb-Te and Bi-Se-Te compounds with graded Ag doping profiles are reported. A junction structure with graded doping is formed in the Bi-Te based compounds through thermally driven Ag diffusion, which has demonstrated a greatly enhanced Seebeck coefficient when a thermal gradient is applied in the same direction of carrier concentration gradient. A mechanism based on the spatial variation of bandgap narrowing induced by heavy-doping effect is proposed to explain the anomalous thermoelectric property of Bi-Te based compounds with graded doping profiles.
A study of flow induced by laser induced breakdown-enhanced dielectric barrier discharges in air
Authors: Im S. , Bak M. S. , Cappelli M. A.
Published: October 2013

The flow induced by an asymmetric dielectric barrier discharge (DBD) actuator in air together with laser induced breakdown (LIB) near the exposed electrode is investigated using particle image velocimetry. In this approach, the electrodes, driven by alternating current (8 kHz, 14 kVp-p) serve primarily to accelerate the ions generated by the laser pulse (532 nm, 15 mJ per pulse, and 2 Hz). The mean velocity fields suggest that this hybrid scheme leads to a significant enhancement in the wall-jet velocity and momentum flux generated by actuation.
Leakage current in atomic-size surface interconnects
Authors: Kepenekian Mikaël , Robles Roberto , Joachim Christian , Lorente Nicolás
Published: October 2013

The current lost into a doped silicon substrate from a surface-supported nanowire is evaluated using transport calculations based on density functional theory. The calculations are performed for an infinite non-periodic wire for various types of dopants. Two concentration limits are explored: the single-dopant and the massively doped limits. Our calculations permit us to conclude that n-doped Si will be less leaky than p-doped Si. For the low bias at which these nanodevices will operate, leakage currents will be less than 10% for n-doped Si substrates and 20% for p-doped ones.
Microfluidic immunomagnetic cell separation using integrated permanent micromagnets
Authors: Osman O. , Toru S. , Dumas-Bouchiat F. , Dempsey N. M. , Haddour N. , Zanini L.-F. , Buret F. , Reyne G. , Frénéa-Robin M.
Published: October 2013

In this paper, we demonstrate the possibility to trap and sort labeled cells under flow conditions using a microfluidic device with an integrated flat micro-patterned hard magnetic film. The proposed technique is illustrated using a cell suspension containing a mixture of Jurkat cells and HEK (Human Embryonic Kidney) 293 cells. Prior to sorting experiments, the Jurkat cells were specifically labeled with immunomagnetic nanoparticles, while the HEK 293 cells were unlabeled. Droplet-based experiments demonstrated that the Jurkat cells were attracted to regions of maximum stray field flux density while the HEK 293 cells settled in random positions. When the mixture was passed through a polydimethylsiloxane (PDMS) microfluidic channel containing integrated micromagnets, the labeled Jurkat cells were selectively trapped under fluid flow, while the HEK cells were eluted towards the device outlet. Increasing the flow rate produced a second eluate much enriched in Jurkat cells, as revealed by flow cytometry. The separation efficiency of this biocompatible, compact micro-fluidic separation chamber was compared with that obtained using two commercial magnetic cell separation kits.
Communication: A tractable design for a thermal transistor
Authors: Murad Sohail , Puri Ishwar K.
Published: October 2013

We propose a conceptual design for a logic device that is the thermal analog of a transistor. It has fixed hot (emitter) and cold (collector) temperatures, and a gate controls the heat current. Thermal logic could be applied for thermal digital computing, enhance energy conservation, facilitate thermal rheostats, and enable the transport of phononic data. We demonstrate such a device using molecular dynamics simulations that consider thermal transport across hot and cold solid Si regions that seal water within them. Changes in the hot side, or emitter, heat current are linear with respect to varying gate temperature but the corresponding variation in the collector current is nonlinear. This nonlinear variation in collector current defines the ON and OFF states of the device. In its OFF state, the thermal conductivity of the device is positive. In the ON state, however, more heat is extracted through the cold terminal than is provided at the hot terminal due to the intervention of the base terminal. This makes it possible to alter the transport factor by varying the gate conditions. When the device is ON, the transport factor is greater than unity, i.e., more heat is rejected at the collector than is supplied to the emitter.
Improved photovoltaic performance of crystalline-Si/organic Schottky junction solar cells using ferroelectric polymers
Authors: Liu Q. , Khatri I. , Ishikawa R. , Fujimori A. , Ueno K. , Manabe K. , Nishino H. , Shirai H.
Published: October 2013

The effect of inserting an ultrathin layer of ferroelectric (FE) poly(vinylidene fluoride-tetrafluoroethylene) P(VDF-TeFE) at the crystalline (c-)Si/poly(3,4-ethylenedioxythiophene): poly(styrenesulfonate) (PEDOT:PSS) interface of a c-Si/PEDOT:PSS Schottky junction solar cell is demonstrated. P(VDF-TeFE) is a highly resistive material that exhibits a large, permanent, internal polarization electric field by poling of molecular dipole among the polymer chains. Because of these properties, performance can be enhanced by adjusting the thickness of the FE layer and subsequent poling process. Inserting a 3-nm-thick FE layer increases the power conversion efficiency η from 10.2% to 11.4% with a short-circuit current density Jsc of 28.85 mA/cm2, an open-circuit voltage Voc of 0.57 V, and a fill factor FF of 0.692. Subsequent poling of the FE layer under a reverse DC bias stress increased η up to 12.3% with a Jsc of 29.7 mA/cm2, a Voc of 0.58 V, and an FF of 0.71. The obtained results confirm that the spontaneous polarization of the FE layers is responsible for the enhancement of η, and that the polarization-based enhancement works if the FE layer is highly crystalline. These findings originate from efficient charge extraction to the electrodes and a suppression of non-radiative recombination at the c-Si/PEDOT:PSS interface.
Improved Mechanical Properties of Graphene Oxide/Poly(ethylene oxide) Nanocomposites by Dynamic Interfacial Interaction of Coordination
Authors: Lin Chen , Liu Yi-Tao , Xie Xu-Ming
Published: October 2013

A simple and cost-effective strategy to create a strong interfacial interaction of coordination bonds in graphene oxide/poly(ethylene oxide) (GO/PEO) nanocomposites by divalent metal ions are demonstrated in this study. The strong interfacial interaction realizes efficient load transfer during the tensile process to significantly improve the mechanical properties of PEO. In addition, the dynamic interfacial interaction of coordination bonds minimizes the elongation loss. This strategy is applicable to a variety of polymer matrices containing coordination atoms, thus opens up a new opportunity for high-performance GO/polymer nanocomposites with significantly improved mechanical properties.
Using protein backbone mutagenesis to dissect the link between ion occupancy and C-type inactivation in K
+
channels
Authors: Matulef Kimberly , Komarov Alexander G. , Costantino Corey A. , Valiyaveetil Francis I.
Published: October 2013

Significance

C-type inactivation is a gating process that takes place at the selectivity filter of K
+
channels. C-type inactivation is important in regulating cellular excitability. A defining characteristic of C-type inactivation is a dependence on the permeant ion, but the underlying mechanism is not known. We use protein backbone mutagenesis to alter ion binding at specific sites in the selectivity filter and determine the effect on inactivation. We show that C-type inactivation is linked to ion occupancy at a specific site in the selectivity filter. This study underscores the utility of unnatural mutagenesis for investigating the mechanisms of channel function. Furthermore, permeant ions modulate function in many channel families; therefore, the approaches used in this study are generally applicable.
The pains of democratisation: the uneasy interface between elections and power-sharing arrangements in Africa
Authors: Matlosa Khabele , Shale Victor
Published: October 2013

The recent and increasingly prevalent phenomenon of power-sharing in Africa raises questions about its value for state legitimacy, especially as far as elections are concerned. While there are various circumstances that may give rise to power-sharing, comparative insights from the case studies in this article highlight two trends: first, power-sharing following protracted violent conflicts that have been resolved through negotiated settlement; and second, power-sharing following electoral contests that went awry. In both cases, power-sharing has been employed as an instrument for conflict management. The article explores power-sharing experiments in both scenarios, investigating its utility as an instrument of democratisation. However, the results of power-sharing experiments are not uniform: the record is a mixed bag. Also, the context of, and peculiar circumstances in, each country have determined power-sharing outcomes. In post-war situations such as in Burundi and South Africa, power-sharing experiments have bolstered prospects for consociational democracy, institutionalised politics, and nation-building. Conversely, in post-election crisis experiments such as in Kenya and Zimbabwe, power-sharing arrangements have not really served the ideal of consociational democracy but, rather, the interests of political elites, especially their appetite for state power.
Continuity and change in the foreign policies of South Africa’s De Klerk and Mandela governments, 1989–1999
Authors: Landsberg Chris
Published: October 2013

The issue of continuity and change in foreign-policy analysis is one that receives scant scholarly attention, and South Africa is no exception. Even though the country is now almost two decades past the transitional period, and a good 14 years since Nelson Mandela stepped down as the first democratically elected President of South Africa, important lessons could still be drawn from the foreign-policy trends of this era. The foreign policies of South Africa’s two governments during the transition, from 1989 to 1999, show features of both continuity and change, protestations to the contrary notwithstanding. Continuity and change often co-exist as a mixture or as dialectical opposites, making prediction of the future very uncertain. Continuity is often at play when it is least expected; and change can occur in the most unexpected of contexts.
Utilization of the Massachusetts Youth Screening Instrument-2 (MAYSI-2) with a Southern, African American Adolescent Male Population
Authors: Jaggers Jeremiah , Young Sarah R. , McKinney Robert , Bolland Kathleen , Church II Wesley T.
Published: October 2013

The Massachusetts Youth Screening Instrument-2 (MAYSI-2) is a widely accepted instrument for screening adolescents in detention facilities for mental health problems. However, African Americans often experience mental illness differently from other racial groups. The purpose of this study is to examine the usefulness of the MAYSI-2 with Southern African American adolescents. Results indicate that the MAYSI-2 factor structure as originally conceived does not accurately represent mental illness as experienced by this group. Instead, findings suggest that African American adolescents do indeed experience mental illness in a way different from youth for whom the MAYSI-2 was designed. Furthermore, the MAYS-2’s ability to detect psychotic illness in this group is called into question by these findings.
GGS-groups: Order of congruence quotients and Hausdorff dimension
Authors: Fernández-Alcober Gustavo , Zugadi-Reizabal Amaia
Published: October 2013

If

G
G

is a GGS-group defined over a

p
p

-adic tree, where

p
p

is an odd prime, we calculate the order of the congruence quotients

G
n

=
G

/

S
t
a
b

G

(
n
)

G_n=G/\mathrm {Stab}_G(n)

for every

n
n

. If

G
G

is defined by the vector

e

=
(

e
1

,
…
,

e

p
−
1

)
∈

F

p

p
−
1

\mathbf {e}=(e_1,\ldots ,e_{p-1})\in \mathbb {F}_p^{p-1}

, the determination of the order of

G
n

G_n

is split into three cases, according to whether

e

\mathbf {e}

is non-symmetric, non-constant symmetric, or constant. The formulas that we obtain only depend on

p
p

,

n
n

, and the rank of the circulant matrix whose first row is

e

\mathbf {e}

. As a consequence of these formulas, we also obtain the Hausdorff dimension of the closures of all GGS-groups over the

p
p

-adic tree.
SecStAnT: secondary structure analysis tool for data selection, statistics and models building
Authors: Maccari Giuseppe , Spampinato Giulia L.B. , Tozzini Valentina
Published: October 2013

Motivation: Atomistic or coarse grained (CG) potentials derived from statistical distributions of internal variables have recently become popular due to the need of simplified interactions for reaching larger scales in simulations or more efficient conformational space sampling. However, the process of parameterization of accurate and predictive statistics-based force fields requires a huge amount of work and is prone to the introduction of bias and errors.

Results: This article introduces SecStAnT, a software for the creation and analysis of protein structural datasets with user-defined primary/secondary structure composition, with a particular focus on the CG representation. In addition, the possibility of managing different resolutions and the primary/secondary structure selectivity allow addressing the mapping-backmapping of atomistic to CG representation and study the secondary to primary structure relations. Sample datasets and distributions are reported, including interpretation of structural features.

Availability and implementation: SecStAnT is available free of charge at secstant.sourceforge.net/. Source code is freely available on request, implemented in Java and supported on Linux, MS Windows and OSX.

Contact: giuseppe.maccari@iit.it

Supplementary information:  Supplementary data are available at Bioinformatics online.
ORMAN: Optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms
Authors: Dao Phuong , Numanagić Ibrahim , Lin Yen-Yi , Hach Faraz , Karakoc Emre , Donmez Nilgun , Collins Colin , Eichler Evan E. , Sahinalp S. Cenk
Published: October 2013

Motivation: RNA-Seq technology is promising to uncover many novel alternative splicing events, gene fusions and other variations in RNA transcripts. For an accurate detection and quantification of transcripts, it is important to resolve the mapping ambiguity for those RNA-Seq reads that can be mapped to multiple loci: >17% of the reads from mouse RNA-Seq data and 50% of the reads from some plant RNA-Seq data have multiple mapping loci.

In this study, we show how to resolve the mapping ambiguity in the presence of novel transcriptomic events such as exon skipping and novel indels towards accurate downstream analysis. We introduce ORMAN (Optimal Resolution of Multimapping Ambiguity of RNA-Seq Reads), which aims to compute the minimum number of potential transcript products for each gene and to assign each multimapping read to one of these transcripts based on the estimated distribution of the region covering the read. ORMAN achieves this objective through a combinatorial optimization formulation, which is solved through well-known approximation algorithms, integer linear programs and heuristics.

Results: On a simulated RNA-Seq dataset including a random subset of transcripts from the UCSC database, the performance of several state-of-the-art methods for identifying and quantifying novel transcripts, such as Cufflinks, IsoLasso and CLIIQ, is significantly improved through the use of ORMAN. Furthermore, in an experiment using real RNA-Seq reads, we show that ORMAN is able to resolve multimapping to produce coverage values that are similar to the original distribution, even in genes with highly non-uniform coverage.

Availability: ORMAN is available at http://orman.sf.net

Contact: cenk@cs.sfu.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
Bullying and ADHD: Which Came First and Does it Matter?
Authors: Keder Robert , Sege Robert , Raffalli Peter C. , Augustyn Marilyn
Published: October 2013

CASE: Aiden, a 13-year-old boy in the sixth grade who is relatively new to your practice, is seen for follow-up after his routine physical last month when you noted concerns for possible attention-deficit hyperactivity disorder (ADHD) and gave the family Vanderbilt Scales to complete. Aiden has a family history of ADHD, specific learning disabilities, and mood disorder.

His mother reports that she is concerned about how Aiden is doing at school; his teachers are complaining that he is not doing his work, and she is worried that he may be kept back in school. Aiden first began having trouble in the third grade. He was retained in the fourth grade for academic and behavioral reasons. Now his mother has been receiving calls about him not paying attention, distracting others, and staring at his paper. At home, he does not want to do homework and gets very frustrated. In fifth grade, he had a psychoeducational evaluation and was found not eligible for services. His achievement testing showed average scores in reading, math, and writing. Cognitive testing demonstrated average scores for verbal and nonverbal abilities and memory but was significantly below average for processing speed. Aiden continues to have problems now in into the sixth grade.

You speak with Aiden in the office and ask him about school. He says, “It's bad. I'm failing.” He believes his major problems at school are that he is not doing his homework, he easily becomes frustrated, and he argues with the teachers. He has supportive relationships with his family and friends at school. He gets along well with some of his teachers, noting that he loves his science teacher even though she is tough and “gives hard homework.” He describes his history teacher as “annoying.” When you ask what he means he states this teacher “Can be not nice and says mean things. She picks on me a lot.” His description is consistent with the use of shaming as a behavior he experiences at school.

You review the completed parent and teacher Vanderbilt forms; both are consistent and concerning for combined type ADHD. You discuss the diagnosis of ADHD with his mother and both agree to revisit pharmacotherapy in September when the school year resumes. You give her resources on ADHD and classroom accommodations and discuss requesting a 504 plan at school. You also discuss behavioral therapy to better address his self-regulation skills.

A week later, you receive a telephone call from Aiden's mother. “Aiden got home today and he is more upset than I have ever seen him! His teacher told him in front of the class that he would probably stay back a year and now he is saying there is no point in going to school.” She is not aware if retention has been recommended for Aiden.

What would you say to Aiden's mother? What would you do next?
Imprinted green beards: a little less than kin and more than kind
Authors: Haig David
Published: October 2013

RNA is complementary to the DNA sequence from which it is transcribed. Therefore, interactions between DNA and RNA provide a simple mechanism of genetic self-detection within nuclei. Imprinted RNAs could enable alleles of maternal and paternal origin to detect whether they are the same (homozygous) or different (heterozygous), and thereby provide strategic information about expected relatedness to siblings.
Dissecting ant recognition systems in the age of genomics
Authors: Tsutsui Neil D.
Published: October 2013

Hamilton is probably best known for his seminal work demonstrating the role of kin selection in social evolution. His work made it clear that, for individuals to direct their altruistic behaviours towards appropriate recipients (kin), mechanisms must exist for kin recognition. In the social insects, colonies are typically comprised of kin, and colony recognition cues are used as proxies for kinship cues. Recent years have brought rapid advances in our understanding of the genetic and molecular mechanisms that are used for this process. Here, I review some of the most notable advances, particularly the contributions from recent ant genome sequences and molecular biology.
Kinship and the evolution of social behaviours in the sea
Authors: Kamel Stephanie J. , Grosberg Richard K.
Published: October 2013

Until recently, little attention has been paid to the existence of kin structure in the sea, despite the fact that many marine organisms are sessile or sedentary. This lack of attention to kin structure, and its impacts on social evolution, historically stems from the pervasive assumption that the dispersal of gametes and larvae is almost always sufficient to prevent any persistent associations of closely related offspring or adults. However, growing evidence, both theoretical and empirical, casts doubt on the generality of this assumption, not only in species with limited dispersal, but also in species with long dispersive phases. Moreover, many marine organisms either internally brood their progeny or package them in nurseries, both of which provide ample opportunities for kinship to influence the nature and outcomes of social interactions among family members. As the evidence for kin structure within marine populations mounts, it follows that kin selection may play a far greater role in the evolution of both behaviours and life histories of marine organisms than is presently appreciated.
Quantifying Waddington landscapes and paths of non-adiabatic cell fate decisions for differentiation, reprogramming and transdifferentiation
Authors: Li Chunhe , Wang Jin
Published: October 2013

Cellular differentiation, reprogramming and transdifferentiation are determined by underlying gene regulatory networks. Non-adiabatic regulation via slow binding/unbinding to the gene can be important in these cell fate decision-making processes. Based on a stem cell core gene network, we uncovered the stem cell developmental landscape. As the binding/unbinding speed decreases, the landscape topography changes from bistable attractors of stem and differentiated states to more attractors of stem and other different cell states as well as substates. Non-adiabaticity leads to more differentiated cell types and provides a natural explanation for the heterogeneity observed in the experiments. We quantified Waddington landscapes with two possible cell fate decision mechanisms by changing the regulation strength or regulation timescale (non-adiabaticity). Transition rates correlate with landscape topography through barrier heights between different states and quantitatively determine global stability. We found the optimal speeds of these cell fate decision-making processes. We quantified biological paths and predict that differentiation and reprogramming go through an intermediate state (IM1), whereas transdifferentiation goes through another intermediate state (IM2). Some predictions are confirmed by recent experimental studies.
A new sphenodontian (Lepidosauria: Rhynchocephalia) from the Late Triassic of Argentina and the early origin of the herbivore opisthodontians
Authors: Martínez Ricardo N. , Apaldetti Cecilia , Colombi Carina E. , Praderio Angel , Fernandez Eliana , Malnis Paula Santi , Correa Gustavo A. , Abelin Diego , Alcober Oscar
Published: October 2013

Sphenodontians were a successful group of rhynchocephalian reptiles that dominated the fossil record of Lepidosauria during the Triassic and Jurassic. Although evidence of extinction is seen at the end of the Laurasian Early Cretaceous, they appeared to remain numerically abundant in South America until the end of the period. Most of the known Late Cretaceous record in South America is composed of opisthodontians, the herbivorous branch of Sphenodontia, whose oldest members were until recently reported to be from the Kimmeridgian–Tithonian (Late Jurassic). Here, we report a new sphenodontian,Sphenotitan leyesigen. et sp. nov., collected from the Upper Triassic Quebrada del Barro Formation of northwestern Argentina. Phylogenetic analysis identifiesSphenotitanas a basal member of Opisthodontia, extending the known record of opisthodontians and the origin of herbivory in this group by 50 Myr.
A novel B/C inter-genotype recombinant of hepatitis B virus identified in north-west China
Authors: Chen Xiaoming , Dai Bangyao , Liu Zhengcai , Gao Jie , Ji Zhaohua , Guo Jutao , Chen Gang , Deng Zhongrong , Shao Zhongjun
Published: October 2013

The characteristics of life-long persistent infection of hepatitis B virus (HBV) and the prevalence of different genotypes of HBV in China may cause new recombinants. In north-west China, HBV inter-genotype recombinants have been reported frequently over the last decade. Here, we report a B/C inter-genotype recombinant HBV with a novel genome mosaic structure from Lanzhou, a city in north-west China.
Rice WRKY13 Regulates Cross Talk between Abiotic and Biotic Stress Signaling Pathways by Selective Binding to Different cis-Elements
Authors: Xiao Jun , Cheng Hongtao , Li Xianghua , Xiao Jinghua , Xu Caiguo , Wang Shiping
Published: October 2013

Plants use a complex signal transduction network to regulate their adaptation to the ever-changing environment. Rice (Oryza sativa) WRKY13 plays a vital role in the cross talk between abiotic and biotic stress signaling pathways by suppressing abiotic stress resistance and activating disease resistance. However, it is not clear how WRKY13 directly regulates this cross talk. Here, we show that WRKY13 is a transcriptional repressor. During the rice responses to drought stress and bacterial infection, WRKY13 selectively bound to certain site- and sequence-specific cis-elements on the promoters of SNAC1 (for STRESS RESPONSIVE NO APICAL MERISTEM, ARABIDOPSIS TRANSCRIPTION ACTIVATION FACTOR1/2, CUP-SHAPED COTYLEDON), the overexpression of which increases drought resistance, and WRKY45-1, the knockout of which increases both bacterial disease and drought resistance. WRKY13 also bound to two cis-elements of its native promoter to autoregulate the balance of its gene expression in different physiological activities. WRKY13 was induced in leaf vascular tissue, where bacteria proliferate, during infection, and in guard cells, where the transcriptional factor SNAC1 enhances drought resistance, during both bacterial infection and drought stress. These results suggest that WRKY13 regulates the antagonistic cross talk between drought and disease resistance pathways by directly suppressing SNAC1 and WRKY45-1 and autoregulating its own expression via site- and sequence-specific cis-elements on the promoters of these genes in vascular tissue where bacteria proliferate and guard cells where the transcriptional factor SNAC1 mediates drought resistance by promoting stomatal closure.
Pustulotic arthro‐osteitis associated with palmoplantar pustulosis
Authors: Yamamoto Toshiyuki
Published: October 2013

Palmoplantar pustulosis (PPP) is a chronic inflammatory disorder characterized by sterile pustules predominantly involving the palms and soles of middle‐aged women. PPP frequently develops or exacerbates following focal infections, such as tonsillitis, odontogenic infection and sinusitis, either with or without arthralgia and/or extra‐palmoplantar lesions. Pustulotic arthro‐osteitis (PAO) is a joint comorbidity of PPP, most often affecting the anterior chest wall. PAO is sometimes regarded as the same entity as synovitis, acne, pustulosis, hyperostosis and osteitis (SAPHO) syndrome, and may be a subtype or incomplete type of SAPHO syndrome; however, there are several differences. In Japanese patients, PPP with PAO is frequently seen, whereas SAPHO syndrome in the true meaning is rare. A difference of incidence depending on race suggests that different genetic backgrounds may be responsible for susceptibility to these disorders. Bacterial infection, especially Propionibacterium acnes, is suggested to play an important role in the pathogenesis of SAPHO syndrome. P. acnes is responsible for acne, however, bacterium is unassociated with PPP skin lesions which are characterized by sterile pustules. On the other hand, PAO is frequently triggered by focal infection, and treatment of focal infection results in dramatic effects on the release of joint pain. This paper reviews current insights into the clinicopathophysiology of PAO, and discusses its possible mechanisms in comparison with SAPHO syndrome.
Four mild but refractory cases of pemphigus foliaceus successfully treated with intravenous immunoglobulin
Authors: Kawakami Tamihiro , Koga Hiroshi , Saruta Hiroshi , Ueda Akihiro , Inoue Yoshihiko , Soma Yoshinao , Ishii Norito , Hashimoto Takashi
Published: October 2013

Intravenous immunoglobulin (IVIG) is a potential second line of therapy for pemphigus, with increasing evidence of its effectiveness and safety, although oral corticosteroids remain the first treatment for pemphigus. IVIG is usually applied in severe cases of pemphigus, particularly pemphigus vulgaris (PV). Pemphigus foliaceus (PF) caused by immunoglobulin PF autoantibodies to desmoglein 1 (Dsg1) is usually milder than PV. However, PF cases are occasionally resistant to corticosteroids and require long‐term treatment to control the disease, leading to various adverse effects. IVIG was used in patients with relatively mild PF, who were resistant to therapies with corticosteroids and dapsone. We assessed the disease severity by Pemphigus Disease Area Index (PDAI) and measured anti‐Dsg1 antibody indices by enzyme‐linked immunosorbent assay, before and 4 months after IVIG. Four Japanese female PF patients (57.3 ± 8.6 years) were treated with a single cycle of IVIG (400 mg/kg per day for five consecutive days) in combination with the previous therapies. Within 1–2 months of addition of IVIG, all PF cases showed remarkable improvement of skin lesions, and PDAI also markedly decreased. For 2 years after IVIG, no apparent exacerbation was observed. Anti‐Dsg1 antibody indices decreased in all cases during the 2 years. IVIG could be a potential treatment for not only severe cases of PV but also mild and refractory cases of PF. IVIG may trigger the shift from intractable condition to remission via non‐pathogenic anti‐Dsg1 antibodies or some mechanisms excluding anti‐Dsg1 antibody.