bluuebunny/crossref_metadata_2025 huggingface dataset:
MSI4/FVE interacts with CUL4–DDB1 and a PRC2-like complex to control epigenetic regulation of flowering time in
Arabidopsis
Authors: Pazhouhandeh Maghsoud , Molinier Jean , Berr Alexandre , Genschik Pascal
Published: February 2011

Flowering at the right time is crucial to ensure successful plant reproduction and seed yield and is dependent on both environmental and endogenous parameters. Among the different pathways that impinge on flowering, the autonomous pathway promotes floral transition independently of day length through the repression of the central flowering repressor
FLOWERING LOCUS C
(
FLC
). FLC blocks floral transition by repressing flowering time integrators such as
FLOWERING LOCUS T
(
FT
). MSI4/FVE is a key regulator of the autonomous pathway that reduces
FLC
expression. Here we report that the MSI4 protein is a DDB1 and CUL4-associated factor that represses
FLC
expression through its association with a CLF-Polycomb Repressive Complex 2 (PRC2) in
Arabidopsis
. Thus, the lack of MSI4 or decreased CUL4 activity reduces H3K27 trimethylation on
FLC,
but also on its downstream target
FT,
resulting in increased expression of both genes. Moreover, CUL4 interacts with
FLC
chromatin in an MSI4-dependant manner, and the interaction between MSI4 and CUL4–DDB1 is necessary for the epigenetic repression of
FLC
. Overall our work provides evidence for a unique functional interaction between the cullin-RING ubiquitin ligase (CUL4–DDB1
MSI4
) and a CLF–PRC2 complex in the regulation of flowering timing in
Arabidopsis
.
Rare copy number variations in congenital heart disease patients identify unique genes in left-right patterning
Authors: Fakhro Khalid A. , Choi Murim , Ware Stephanie M. , Belmont John W. , Towbin Jeffrey A. , Lifton Richard P. , Khokha Mustafa K. , Brueckner Martina
Published: February 2011

Dominant human genetic diseases that impair reproductive fitness and have high locus heterogeneity constitute a problem for gene discovery because the usual criterion of finding more mutations in specific genes than expected by chance may require extremely large populations. Heterotaxy (Htx), a congenital heart disease resulting from abnormalities in left-right (LR) body patterning, has features suggesting that many cases fall into this category. In this setting, appropriate model systems may provide a means to support implication of specific genes. By high-resolution genotyping of 262 Htx subjects and 991 controls, we identify a twofold excess of subjects with rare genic copy number variations in Htx (14.5% vs. 7.4%,
P
= 1.5 × 10
−4
). Although 7 of 45 Htx copy number variations were large chromosomal abnormalities, 38 smaller copy number variations altered a total of 61 genes, 22 of which had
Xenopus
orthologs. In situ hybridization identified 7 of these 22 genes with expression in the ciliated LR organizer (gastrocoel roof plate), a marked enrichment compared with 40 of 845 previously studied genes (sevenfold enrichment,
P
< 10
−6
). Morpholino knockdown in
Xenopus
of Htx candidates demonstrated that five (NEK2, ROCK2, TGFBR2, GALNT11, and NUP188) strongly disrupted both morphological LR development and expression of
pitx2
, a molecular marker of LR patterning. These effects were specific, because 0 of 13 control genes from rare Htx or control copy number variations produced significant LR abnormalities (
P
= 0.001). These findings identify genes not previously implicated in LR patterning.
Alloying effect on the magnetic properties of RFeB-type bulk magnets
Authors: Chang H W , Hsieh C C , Gan J Y , Cheng Y T , Shih M F , Chang W C
Published: January 2011

Composition dependence on the magnetic properties of directly casted cylindrical RFeBM-type magnets with diameters from 0.7 mm to 1.5 mm has been studied. In order to refine the microstructure for improving the magnetic properties of bulk magnets with various sizes, the following ways were adopted in the alloys: (1) changing the boron concentration, (2) substituting different kinds of refractory elements for Fe, (3) adding a slight carbon and finally, (4) adopting multi-component refractory elements. The experimental results showed that the Nd9.5Fe72.5Ti3B15 bulk magnets with a diameter of 0.7 mm demonstrated the optimal magnetic properties of B
r = 6.5 kG, i
H
c = 10.3 kOe and (BH)max = 8.7 MG Oe, while the highest i
H
c of 16.2 kOe was achieved for the Pr9.5Fe71.5Nb4B15 magnet. Meanwhile, the diameter of the magnets could be increased to 0.9 mm preserving the attractive magnetic properties by the substitution of 0.5 at% Zr for Ti in the Nd9.5Fe72.5Ti3B15 magnet. Finally, the directly casted Nd9.5Fe72.5−y
Ti2.5Zr0.5Cr
y
B15−x
C
x
(x = 0.25–1; y = 0–3) magnets with a larger diameter of 1.3 mm exhibited attractive magnetic properties of B
r = 5.3–6.1 kG, i
H
c = 7.2–12.5 kOe and (BH)max = 6.5–7.2 MG Oe.
Recent progress in high Bs Fe-based nanocrystalline soft magnetic alloys
Authors: Ohta M , Yoshizawa Y
Published: January 2011

High saturation magnetic flux density (high-B
s) alloy has been developed in an Fe-based nanocrystalline alloy system. A nanocrystalline phase with an average grain size of about 20 nm is obtained by annealing Cu-substituted and/or Cu-and-Si-complex-substituted Fe–B amorphous alloys. The alloy exhibits low coercivity of less than 7 A m−1 and a high B
s of more than 1.8 T. The iron loss at 50 Hz and 1.6 T for a toroidal core made of Fe80.5Cu1.5Si4B14 nanocrystalline alloy is 0.46 W kg−1, which is about 2/3 of that of grain-oriented Si steel. Moreover, the iron loss at 10 kHz and 0.2 T for a wound core made of this alloy is 7.5 W kg−1, which is about 25% of that of non-grain-oriented Si steel and about 60% of that of an Fe-based amorphous alloy. In addition, the cut cores made of the alloy show good superimposed dc-current characteristics and appear promising in applications such as power choke coils (at the high-frequency region).
Electric-field effects on magnetic anisotropy in Pd/Fe/Pd(0 0 1) surface
Authors: Haraguchi Shinya , Tsujikawa Masahito , Gotou Junpei , Oda Tatsuki
Published: January 2011

Electric-field (EF) effects have been studied on magnetic anisotropy in the metallic surfaces Pt/Fe/Pt(0 0 1) and Pd/Fe/Pd(0 0 1) by means of the first-principles electronic structure calculation which employs the generalized gradient approximation. The variation of anisotropy energy with respect to the EF is found to be opposite to each other. The modulus rate of the variation is larger by a few factors in the Pt substrate than in the Pd one. These results agree qualitatively well with the available experimental data. The electronic structures are presented and the origins in EF effects are discussed along a line of the second perturbative fashion.
Gate modulation of spin precession in a semiconductor channel
Authors: Koo Hyun Cheol , Kwon Jae Hyun , Eom Jonghwa , Chang Joonyeon , Han Suk Hee , Johnson Mark
Published: January 2011

Gate control of spin precession is experimentally presented in an InAs quantum well with ferromagnetic spin injector and detector. The gate electric field modulates the spin–orbit interaction and spin precession. As a consequence, spin dependent conductance in the InAs channel is controlled by the gate voltage. Using ballistic spin transport theory, gate modulation results are proved to fit very well with gate voltage dependence of Rashba field strength.
Switching phase diagrams of current-induced magnetization switching in asymmetric MgO-based magnetic tunnel junctions
Authors: Park Seung-Young , Han Jae-Ho , Oh Se-Chung , Lee Jang-Eun , Nam Kyung-Tae , Lee Hyun-Woo , Jo Younghun , Lee Kyung-Jin
Published: January 2011

We investigated the effect of the free-layer composition and the pattern size of magnetic cell on current-induced magnetization switching in asymmetric MgO-based magnetic tunnel junctions. We found that the normalized switching phase diagrams (SPDs) measured at low temperature are mostly determined by the material composition of ferromagnetic electrodes but are not much sensitive to the intrinsic energy barrier and the anisotropy field of the sample. This experimental result indicates that the normalized SPD can be used to study the fundamental characteristics of spin-transfer torque.
Temperature dependence of spin-dependent transport properties of Co2MnSi-based current-perpendicular-to-plane magnetoresistive devices
Authors: Sakuraba Y , Izumi K , Bosu S , Saito K , Takanashi K
Published: January 2011

The origin of magnetoresistance (MR) ratio reduction below ∼80 K in Co2MnSi (CMS)/Ag/Co2MnSi current-perpendicular-to-plane giant magnetoresistive devices was investigated. The temperature dependence of ΔRA was independent of the CMS layer thickness, indicating that the spin-diffusion length in the CMS layers is unimportant for the reduction in the MR ratio at low temperatures. A small 90° interlayer exchange coupling, which originated from inter-diffused Mn impurities in the Ag spacer, was observed only at low temperatures from 5 to ∼100 K. A possible origin for the reduction in the MR ratio below ∼80 K is the drastic reduction in the spin-diffusion length of the Ag spacer due to magnetic ordering of the Mn impurities.
Adsorbate-induced spin-polarization enhancement of Fe3O4(0 0 1)
Authors: Pratt A , Kurahashi M , Sun X , Yamauchi Y
Published: January 2011

Using a spin-polarized metastable helium beam, we have investigated the remanent spin polarization at the surface of clean, hydrogen-terminated and benzene-adsorbed Fe3O4(0 0 1) thin films prepared on MgO(0 0 1) substrates. For the clean surface, a small negative asymmetry is detected in the ejected electron yields for helium-electron spins aligned parallel and anti-parallel to the sample magnetization direction. This confirms earlier experimental results from less surface-sensitive techniques which show that the spin polarization at the surface of Fe3O4(0 0 1) is much reduced from the bulk value and, furthermore, implies that majority-spin states actually dominate at the Fermi level. However, when hydrogen-terminated, the asymmetry is considerably enhanced and positive highlighting the important role that surface adsorption and passivation will play in the development of spintronic materials. This is further demonstrated for the adsorption of the simplest π-conjugated molecule, benzene, at the clean Fe3O4(0 0 1) surface where a similar enhancement in the spin polarization is observed, an effect that could prove beneficial to the design and fabrication of organic spintronic devices.
Antiferromagnetic coupling between spinel ferrite and α-Fe layers in Fe3−δO4/MgO/Fe(0 0 1) epitaxial films
Authors: Yanagihara Hideto , Toyoda Yuta , Kita Eiji
Published: January 2011

We have investigated interlayer exchange coupling (IEC) in epitaxial films of both Fe3O4/MgO/Fe(0 0 1) and γ-Fe2O3/MgO/Fe(0 0 1). Depending on the thickness of the MgO spacer, both systems exhibit strong antiferromagnetic IEC of −1 to −2 erg cm−2. The γ-Fe2O3/MgO/Fe(0 0 1) trilayer exhibits the strongest IEC when the thickness of the MgO spacer is approximately 7 Å, whereas the Fe3O4/MgO/Fe(0 0 1) trilayer exhibits the strongest IEC when the thickness of the MgO spacer is zero. The results suggest that two different types of exchange coupling exist in the magnetic trilayers which consist of metallic iron and spinel ferrite layers.
Monte Carlo simulations of the magnetocaloric effect in magnetic Ni–Mn–X (X = Ga, In) Heusler alloys
Authors: Buchelnikov V D , Sokolovskiy V V , Taskaev S V , Khovaylo V V , Aliev A A , Khanov L N , Batdalov A B , Entel P , Miki H , Takagi T
Published: January 2011

Monte Carlo simulations were used for a detailed description of magnetic, martensitic and magnetocaloric properties of Ni2+x
Mn1−x
Ga (0.18 ⩽ x ⩽ 0.24) and Ni50Mn34In16 Heusler alloys, which undergo a first-order magnetostructural phase transition. In the simulations we made use of magnetic exchange parameters which were obtained by ab initio calculations. Results of magnetic and lattice contributions to the total specific heat as well as the change in the isothermal magnetic entropy ΔS
mag and the adiabatic temperature ΔT
ad changes around the magnetic and magnetostructural transitions in an external magnetic field agree fairly well with available experimental data.
Changes in electronic states and magnetic free energy in La1−zCez(FexSi1−x)13 magnetic refrigerants
Authors: Fujita A , Fujieda S , Fukamichi K
Published: January 2011

The influence of partial substitution of Ce on the electronic structure and magnetic free energy has been investigated for La1−z
Ce
z
(Fe
x
Si1−x
)13. From the Mössbauer spectroscopy of La0.7Ce0.3(Fe0.88Si0.12)13, the distribution of the electric field gradient is found to be scarcely changed, therefore, the volume reduction by partial substitution is regarded as isotropic. The change of the isomer shift to positive sign after the partial substitution is closely correlated with the 5d and/or 4f electrons of Ce.

The change in magnetic free energy has been examined for La0.7Ce0.3(Fe0.86Si0.14)13 having a large magnetic entropy change ΔS
m and a small hysteretic behaviour. From the results analysed by the Landau expansion theory, the large ΔS
m and the small hysteresis of this compound are attributed to the magnitude and thermal variation of the fourth-order Landau coefficient in magnetic free energy. Consequently, the combination of partial substitution and control of Fe concentration is useful for highly efficient magnetic refrigerants.
Garnet composite films with Au particles fabricated by repetitive formation for enhancement of Faraday effect
Authors: Uchida H , Mizutani Y , Nakai Y , Fedyanin A A , Inoue M
Published: January 2011

To prepare garnet (Bi : YIG) composite films with Au particles, we used a repetitive formation method to increase the number density of particles. On increasing the number of repetitions, the diameter distribution of the particles changed. After five repetitions using 5 nm Au films, the diameter distribution separated into two size groups. Shift of wavelength-excited localized surface plasmon resonance is discussed relative to the diameter distribution. In the composite films, enhancement of Faraday rotation associated with surface plasmons was observed. With six repetitions, a maximum enhanced rotation of −1.2° was obtained, which is 20 times larger than that of a single Bi : YIG film. The figures of merit for the composite films are discussed. The thickness of a Bi : YIG composite film working for enhanced Faraday rotation was examined using an ion milling method.
Magnetic-field tunable transmittance in a ferrofluid-filled silicon nitride photonic crystal slab
Authors: Lee H M , Horng L , Wu J C
Published: January 2011

A numerical simulation was performed to demonstrate the active manipulation of the transmittance spectra in a ferrofluid-filled silicon nitride (SiN) photonic crystal slab (PCS) with magnetic field applied perpendicularly to the plane. Many sharp transmittance resonances were found to be correlated with the modes extracted from band structure calculations, where they show red-shift and mutual approach as the external magnetic field increases. By changing the angle of the incident light, we found strong coupling modes because of their asymmetric electric field distributions. This in situ control of transmittance properties of ferrofluid-filled SiN PCS should open up new applications for designing filters, mirrors and displacement sensors in compact optical devices.
Evaluation of a miniature magnetostrictive actuator using Galfenol under tensile stress
Authors: Ueno Toshiyuki , Miura Hidemitsu , Yamada Sotoshi
Published: January 2011

We are, at present, developing miniature actuators using an iron–gallium alloy (Galfenol). Galfenol is an iron-based magnetostrictive material with magnetostriction exceeding 200 ppm, Young's modulus of 70 GPa and a high relative permeability (>100). The advantages of an actuator using this material are capability of miniaturization, stability against external force, low voltage driving and high power. In this study, a miniature vibrator using an E core of Galfenol under tensile stress up to 20 MPa was investigated. The vibrator did not fracture and maintained the magnetostriction even under a high tensile stress. In addition, the resonance frequency, unchanged under the tensile stress, was lower than the cutoff frequency, hence the vibrator can be driven with a low voltage even in resonance driving. The temperature rise in resonance driving was low and creep was not observed in resonance driving under tensile stress. The vibrator will be applicable in flat panel or bone conductive speakers.
Sub-nm resolution depth profiling of the magnetic structure of thin films by the depth-resolved x-ray magnetic circular dichroism technique
Authors: Amemiya K , Sakamaki M
Published: January 2011

The principle and applications of the depth-resolved x-ray magnetic circular dichroism (XMCD) technique are demonstrated, by which depth profiling of the magnetic structure of thin films is achieved with sub-nm resolution. The formation of a NiO-like layer at the surface of a Ni/Cu(1 0 0) thin film is revealed by this technique. Moreover, a small uncompensated magnetic moment in the surface layer is suggested, which shows an antiparallel coupling to that in the inner Ni layers. Development of a three-dimensional XMCD technique is also demonstrated, in which an x-ray microbeam is combined with the depth-resolved XMCD. A preliminary study on the magnetic anisotropy of Fe/Ni/Cu(1 0 0) is shown using this new technique.
Microstructure and optical band-gap of mechano-synthesized CdxZn1−xS quantum dots
Authors: Sain S , Patra S , Pradhan S K
Published: January 2011

Cd
x
Zn1−x
S (x = 0.0 to 1.0, at 0.1 interval) quantum dots (QDs) were synthesized by mechanical alloying of the stoichiometric mixture of elemental Cd, Zn and S powders at room temperature under Ar in record minimum time. The Cd0.5Zn0.5S QDs were formed after 25 min and the Cd0.1Zn0.9S QDs after 160 min of milling. The x-ray and high resolution transmission electron microscope characterizations reveal the presence of both major and minor zinc-blende and wurtzite phases and stacking faults in these QDs. Lattice parameters of both these phases decrease and the optical band-gaps increase continuously with increasing Zn concentrations. A very distinct change in colour of these QDs from blue to red is noticed with increasing Cd concentration from 0 to 1, indicating that optical band-gap varies with varying composition.
Direct and controllable nitric oxide delivery into biological media and living cells by a pin-to-hole spark discharge (PHD) plasma
Authors: Dobrynin D , Arjunan K , Fridman A , Friedman G , Clyne A Morss
Published: January 2011

Nitric oxide has great potential for improving wound healing through both inflammatory and vascularization processes. Nitric oxide can be produced in high concentrations by atmospheric pressure thermal plasmas. We measured the physical characteristics and nitric oxide production of a pin-to-hole spark discharge (PHD) plasma, as well as plasma-produced nitric oxide delivery into liquid and endothelial cells. The plasma temperature was calculated as 9030 ± 320 K by the Boltzmann method, which was adequate to produce nitric oxide, although the average gas temperature was near room temperature. The plasma produced significant UV radiation and hydrogen peroxide, but these were prevented from reaching the cells by adding a straight or curved tube extension to the plasma device. Plasma-produced nitric oxide in gas reached 2000 ppm and rapidly diffused into liquid and cells. Cells remained viable following plasma treatment and showed a linear increase in cGMP concentration with plasma treatment, indicating an intracellular functional response to PHD plasma NO. These data suggest that this plasma may provide a novel method for delivering NO locally and directly for enhanced wound healing.
Comparison of the reflection properties of a metal wire in the visible spectral and terahertz regime
Authors: He Xiaoyong , Zhong Xu
Published: January 2011

The reflection properties of terahertz waves propagating along a metal wire are investigated and compared with the results in the visible spectral regime. The effects of metal wire radii, radiation frequencies and dielectric surrounding materials on the reflection characteristics are given and discussed. The contour plots show that as radiation frequency increases, the reflection amplitude decreases, and the reflection phase increases. With an increase in metal wire radius, the reflection amplitude decreases, and the reflection phase increases. The results are very useful for the application of metal wire antennas and plasmonic resonators.
Crystal structure and luminescence properties of (Ca2.94−xLuxCe0.06)(Sc2−yMgy)Si3O12 phosphors for white LEDs with excellent colour rendering and high luminous efficiency
Authors: Liu Yongfu , Zhang Xia , Hao Zhendong , Lu Wei , Liu Xingyuan , Wang XiaoJun , Zhang Jiahua
Published: January 2011

Lu-modified (Ca2.94−x
Lu
x
Ce0.06)(Sc2−y
Mg
y
)Si3O12 (CLSMS : Ce3+) yellow emitting phosphors are prepared by a solid-state reaction. Controllable luminescent intensity and emitting colour are studied as a function of Lu and Mg contents. Fixing the Mg content to be 1, the effect of Lu content on crystal phase formation, luminescence properties and temperature characteristics is studied. It is revealed that the Lu-induced luminescent enhancement is the result of an increase in absorbance of Ce3+ rather than the internal quantum efficiency. Intense and broadband emission is realized by controlling the Lu content to obtain a pure CLSMS crystal phase. The maximum luminescence intensity is obtained at x = 0.54, which is as high as 156% of the Lu-free phosphor. The Lu-containing phosphor also exhibits better temperature characteristics for its big activation energy (0.20 eV) than the Lu-free one (0.18 eV). Combining the present phosphor with a blue light-emitting diode (LED) chip, a white LED with an excellent colour rendering index R

a
of 86 and a high luminous efficiency of 86 lm W−1 is obtained. The results of the present study demonstrate that the CLSMS : Ce3+ phosphors show a good performance and are attractive candidates for commercial applications when used in white LEDs.
NEXAFS studies of La0.8Bi0.2Fe1−xMnxO3(0.0 ⩽ x ⩽ 0.4) multiferroic system using x-ray absorption spectroscopy
Authors: Anjum G , Kumar Ravi , Mollah S , Thakur P , Gautam S , Chae K H
Published: January 2011

We report the electronic structure studies of well-characterized La0.8Bi0.2Fe1−x
Mn
x
O3 (LBFM, 0.0 ⩽ x ⩽ 0.4) multiferroic samples investigated by soft x-ray absorption spectroscopy at O K-, Mn L3,2-, Mn K-, Fe L3,2- and La M4,5-edges along with the spectra of reference compounds. The investigations are performed to find out the chemical states and crystal field symmetry of ions present in the LBFM multiferroic samples after the substitution of Mn ions at Fe sites. Studies reveal a slight shift in the peak positions of O K-edge spectra along with growth in intensities of low-energy features. An analysis of the Mn L3,2- and K-edge, in addition to the comparison with the spectra of reference compounds, indicates that the Mn ions are present in mixed valence states. It is found that the Mn ions are mainly in +3 states along with a small contribution of +2 and +4 ones. The study of Fe L3,2-edge confirms the trivalent state of Fe ion. M4,5-edges of La corroborate the +3 state of La in the system. Atomic multiplet calculations are also performed on Fe L3,2-, Mn L3,2- and La M4,5-edges to further verify the valency, symmetry and the crystal field splitting.
Surface effects on the electromechanical coupling and bending behaviours of piezoelectric nanowires
Authors: Yan Zhi , Jiang Liying
Published: January 2011

In this work, surface effects, including surface elasticity, residual surface stress and surface piezoelectricity, are considered to study the electromechanical coupling (EMC) behaviour of piezoelectric nanowires (NWs) with the Euler–Bernoulli beam theory. Using the surface-layer-based model, explicit formula for EMC coefficient is derived. It is clearly observed that this coefficient is size-dependent and can be strongly enhanced when the geometric dimensions of NWs scale down. The static bending of a cantilever piezoelectric NW is also studied. The surface effects are found to significantly influence the stiffness and electric field distribution in the NW. The results indicate that surface effects play a significant role in the EMC and bending behaviours of piezoelectric nanobeam. This work is very helpful for understanding the size-dependent properties of nanostructured piezoelectric materials and improving the performance of the piezoelectric nanobeam-based devices in energy harvesting.
Mechanism of the tonal emission from ac high voltage overhead transmission lines
Authors: Straumann Ueli
Published: January 2011

Foul weather conditions can lead to corona discharges on high voltage overhead transmission lines which are perceivable as an audible broadband crackling and hissing noise. In such situations this noise is often accompanied by a humming noise at twice the mains frequency (2f).

While the crackling and hissing noise component was widely investigated in the past, the 2f-component went largely uncommented. Only a scant amount of literature suggests mechanisms explaining the occurrence of this emission, but these suggestions are either vague or controversial.

In this paper a mechanism analogous to that of ion loudspeakers is presented, which describes the sound levels of audible 2f-emissions from high voltage model lines quantitatively in a satisfactory manner. While the broadband component of corona noise emissions has its immediate origin in the discharges themselves, the 2f-emissions arise from the drift of ions left behind by the discharges. Due to collisions with gas molecules, these ions cause in the sum a rise of heat in and a force applying on the neutral gas, thus producing the 2f-emissions. Depending on the situation, both can give rise to contributions of similar magnitude.
Simulation of the space charge near coronating conductors of ac overhead transmission lines
Authors: Straumann Ueli
Published: January 2011

In the case of ac high voltage overhead transmission lines, corona discharges may result in a broadband crackling and a humming noise at twice the mains frequency (2f). The computation of the emitted 2f-levels presupposes the knowledge of the apparent power and force passed by the ions to the gas in the surroundings of the conductors. In this paper a simulation determining these magnitudes used in a previous publication is presented. For that purpose the ideas of earlier publications by other authors to compute corona losses are followed. Their central idea is to define an onset field strength on the surface of the conductor which is not exceeded by injecting the right amount of charges in the vicinity of the conductor. This injection together with the recombination determines the amount of drifting ions. The novelty of the method applied in this work is the consideration of different onset field strengths over the conductor surface in dependence of the polar angle. Further 2f-force and 2f-power acting on the gas in the vicinity of the conductor are determined out of the resulting ion drift. The corona currents thus computed coincide fairly well with measured results.
Semi-analytic approach to diverted tokamak equilibria with incompressible toroidal and poloidal flows
Authors: Shi Bingren
Published: February 2011

Generalized Grad–Shafranov equation for tokamak equilibrium with incompressible toroidal and poloidal flows is solved to obtain a double-null diverted configuration based on an approach presented before (Shi 2008
Plasma Phys. Control. Fusion
50 085006). This solution consists of only two terms of base functions obtained from the variable-separating method and suitable for describing both the internal region within the separatrix and a scrape-off layer region. Dependences of the main equilibrium properties, such as the magnetic field, plasma pressure and the equilibrium radial electric field and the plasma current on flows are revealed. In particular, we find that the presence of poloidal flow causes a deviation of the current surface from the magnetic surface and the sheared poloidal flow produces a non-zero toroidal current component that possibly affects the peeling–ballooning stability of the pedestal.
Electrical and optical properties of indium-modified Se2Sb2Te6 films
Authors: Mahmoud S T , Qamhieh N , Ghamlouche H , Ayesh A
Published: January 2011

The electrical and optical characteristics of indium-doped Se2Sb2Te6 phase-change alloy are studied in this paper. It is found that adding indium to Se2Sb2Te6 alloy increases its amorphous–crystalline transition temperature, T
C, and reduces the electrical conduction activation energy. The capacitance–temperature measurements showed a drastic change in the capacitance of the modified film as the temperature approaches T
C and eventually the capacitance becomes negative and nonlinear. The negativity and nonlinearity in the capacitance–voltage dependence can be attributed to the growth of conductive crystalline islands with increasing temperature.
Who Participates in Household Scanning Panels?
Authors: Lusk Jayson L. , Brooks Kathleen
Published: January 2011

We compare two widely used household scanning panels maintained by the Nielsen Company and Information Resources Inc. to a random sample of the U.S. population. Results indicate that the demographic characteristics of the random sample more closely match the Census Bureau data than the household scanning panels. We also show that after controlling for demographic differences, participants in the household scanning panels are slightly more price sensitive than participants in the random sample. The two household scanning panels yield similar results in relation to one another, which suggests that the household scanning panels may suffer from sample selection and participation biases.
Modular analysis of the probabilistic genetic interaction network
Authors: Hou Lin , Wang Lin , Qian Minping , Li Dong , Tang Chao , Zhu Yunping , Deng Minghua , Li Fangting
Published: January 2011

Motivation: Epistatic Miniarray Profiles (EMAP) has enabled the mapping of large-scale genetic interaction networks; however, the quantitative information gained from EMAP cannot be fully exploited since the data are usually interpreted as a discrete network based on an arbitrary hard threshold. To address such limitations, we adopted a mixture modeling procedure to construct a probabilistic genetic interaction network and then implemented a Bayesian approach to identify densely interacting modules in the probabilistic network.

Results: Mixture modeling has been demonstrated as an effective soft-threshold technique of EMAP measures. The Bayesian approach was applied to an EMAP dataset studying the early secretory pathway in Saccharomyces cerevisiae. Twenty-seven modules were identified, and 14 of those were enriched by gold standard functional gene sets. We also conducted a detailed comparison with state-of-the-art algorithms, hierarchical cluster and Markov clustering. The experimental results show that the Bayesian approach outperforms others in efficiently recovering biologically significant modules.

Contact:  dengmh@pku.edu.cn; fangtingli@pku.edu.cn; zhuyp@hupo.org.cn

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format
Authors: Edmonson Michael N. , Zhang Jinghui , Yan Chunhua , Finney Richard P. , Meerzaman Daoud M. , Buetow Kenneth H.
Published: January 2011

Summary: Bambino is a variant detector and graphical alignment viewer for next-generation sequencing data in the SAM/BAM format, which is capable of pooling data from multiple source files. The variant detector takes advantage of SAM-specific annotations, and produces detailed output suitable for genotyping and identification of somatic mutations. The assembly viewer can display reads in the context of either a user-provided or automatically generated reference sequence, retrieve genome annotation features from a UCSC genome annotation database, display histograms of non-reference allele frequencies, and predict protein-coding changes caused by SNPs.

Availability: Bambino is written in platform-independent Java and available from https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/index.html, along with documentation and example data. Bambino may be launched online via Java Web Start or downloaded and run locally.

Contact:  edmonson@nih.gov.
Conveyor: a workflow engine for bioinformatic analyses
Authors: Linke Burkhard , Giegerich Robert , Goesmann Alexander
Published: January 2011

Motivation: The rapidly increasing amounts of data available from new high-throughput methods have made data processing without automated pipelines infeasible. As was pointed out in several publications, integration of data and analytic resources into workflow systems provides a solution to this problem, simplifying the task of data analysis. Various applications for defining and running workflows in the field of bioinformatics have been proposed and published, e.g. Galaxy, Mobyle, Taverna, Pegasus or Kepler. One of the main aims of such workflow systems is to enable scientists to focus on analysing their datasets instead of taking care for data management, job management or monitoring the execution of computational tasks. The currently available workflow systems achieve this goal, but fundamentally differ in their way of executing workflows.

Results: We have developed the Conveyor software library, a multitiered generic workflow engine for composition, execution and monitoring of complex workflows. It features an open, extensible system architecture and concurrent program execution to exploit resources available on modern multicore CPU hardware. It offers the ability to build complex workflows with branches, loops and other control structures. Two example use cases illustrate the application of the versatile Conveyor engine to common bioinformatics problems.

Availability: The Conveyor application including client and server are available at http://conveyor.cebitec.uni-bielefeld.de.

Contact:  conveyor@CeBiTec.Uni-Bielefeld.DE; blinke@ceBiTec.Uni-Bielefeld.De.

Supplementary information:  Supplementary data are available at Bioinformatics online.
PiNGO: a Cytoscape plugin to find candidate genes in biological networks
Authors: Smoot Michael , Ono Keiichiro , Ideker Trey , Maere Steven
Published: January 2011

Summary: PiNGO is a tool to screen biological networks for candidate genes, i.e. genes predicted to be involved in a biological process of interest. The user can narrow the search to genes with particular known functions or exclude genes belonging to particular functional classes. PiNGO provides support for a wide range of organisms and Gene Ontology classification schemes, and it can easily be customized for other organisms and functional classifications. PiNGO is implemented as a plugin for Cytoscape, a popular network visualization platform.

Availability: PiNGO is distributed as an open-source Java package under the GNU General Public License (http://www.gnu.org/), and can be downloaded via the Cytoscape plugin manager. A detailed user guide and tutorial are available on the PiNGO website (http://www.psb.ugent.be/esb/PiNGO.

Contact:  steven.maere@psb.vib-ugent.be
SHRiMP2: Sensitive yet Practical Short Read Mapping
Authors: David Matei , Dzamba Misko , Lister Dan , Ilie Lucian , Brudno Michael
Published: January 2011

Summary: We report on a major update (version 2) of the original SHort Read Mapping Program (SHRiMP). SHRiMP2 primarily targets mapping sensitivity, and is able to achieve high accuracy at a very reasonable speed. SHRiMP2 supports both letter space and color space (AB/SOLiD) reads, enables for direct alignment of paired reads and uses parallel computation to fully utilize multi-core architectures.

Availability: SHRiMP2 executables and source code are freely available at: http://compbio.cs.toronto.edu/shrimp/.

Contact:  shrimp@cs.toronto.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Modeling and comparing the organization of circular genomes
Authors: Shieh Grace S. , Zheng Shurong , Johnson Richard A. , Chang Yi-Feng , Shimizu Kunio , Wang Chia-Chang , Tang Sen-Lin
Published: January 2011

Motivation: Most prokaryotic genomes are circular with a single chromosome (called circular genomes), which consist of bacteria and archaea. Orthologous genes (abbreviated as orthologs) are genes directly evolved from an ancestor gene, and can be traced through different species in evolution. Shared orthologs between bacterial genomes have been used to measure their genome evolution. Here, organization of circular genomes is analyzed via distributions of shared orthologs between genomes. However, these distributions are often asymmetric and bimodal; to date, there is no joint distribution to model such data. This motivated us to develop a family of bivariate distributions with generalized von Mises marginals (BGVM) and its statistical inference.

Results: A new measure based on circular grade correlation and the fraction of shared orthologs is proposed for association between circular genomes, and a visualization tool developed to depict genome structure similarity. The proposed procedures are applied to eight pairs of prokaryotes separated from domain down to species, and 13 mycoplasma bacteria that are mammalian pathogens belonging to the same genus. We close with remarks on further applications to many features of genomic organization, e.g. shared transcription factor binding sites, between any pair of circular genomes. Thus, the proposed procedures may be applied to identifying conserved chromosome backbones, among others, for genome construction in synthetic biology.

Availability: All codes of the BGVM procedures and 1000+ prokaryotic genomes are available at http://www.stat.sinica.edu.tw/∼gshieh/bgvm.htm.

Contact:  gshieh@stat.sinica.edu.tw

Supplementary information:  Supplementary data are available at Bioinformatics online.
A Ruby API to query the Ensembl database for genomic features
Authors: Strozzi Francesco , Aerts Jan
Published: January 2011

Summary: The Ensembl database makes genomic features available via its Genome Browser. It is also possible to access the underlying data through a Perl API for advanced querying. We have developed a full-featured Ruby API to the Ensembl databases, providing the same functionality as the Perl interface with additional features. A single Ruby API is used to access different releases of the Ensembl databases and is also able to query multi-species databases.

Availability and Implementation: Most functionality of the API is provided using the ActiveRecord pattern. The library depends on introspection to make it release independent. The API is available through the Rubygem system and can be installed with the command gem install ruby-ensembl-api.

Contact:  jan.aerts@esat.kuleuven.be
How to do (or not to do) … Assessing the impact of a policy change with routine longitudinal data
Authors: Lagarde Mylene
Published: January 2011

A lack of good quality evidence on the effect of alternative social policies in low- and middle-income countries has been recently underlined and the value of randomized trials increasingly advocated. However, it is also acknowledged that randomization is not always feasible or politically acceptable. Analyses using longitudinal data series before and after an intervention can also deliver robust results and such data are often reasonably easy to access.

Using the example of evaluating the impact on utilization of a change in health financing policy, this article explains how studies in the literature have often failed to address the possible biases that can arise in a simple analysis of routine longitudinal data. It then describes two possible statistical approaches to estimate impact in a more reliable manner and illustrates in detail the more simple method. Advantages and limitations of this quasi-experimental approach to evaluating the impact of health policies are discussed.
Sensitive and Specific Detection of Xanthomonas oryzae pv. oryzae by Real-Time Bio-PCR Using Pathovar-Specific Primers Based on an rhs Family Gene
Authors: Cho Min Seok , Kang Man Jung , Kim Chang Kug , Seol Young-Joo , Hahn Jang Ho , Park Soo Chul , Hwang Duk Ju , Ahn Tae-Young , Park Duck Hwan , Lim Chun Keun , Park Dong Suk
Published: February 2011

The present study describes bio-polymerase chain reaction (PCR) assays to detect bacterial leaf blight caused by Xanthomonas oryzae pv. oryzae in rice. Successful control of X. oryzae. pv. oryzae requires a specific and reliable diagnostic tool. However, other X. oryzae pathovars are detected by currently available molecular and serological methods. In this study, SYBR Green real-time and conventional PCR primer sets were designed based on an rhs family gene of X. oryzae pv. oryzae KACC10331 because these genes are structurally diverse. The specificity of the primers was evaluated using purified DNA from 11 isolates of two X. oryzae pathovars, 21 other Xanthomonas species, and 4 other reference phytopathogenic bacteria and fungi. The assay was also able to detect at least two genome equivalents of cloned amplified target DNA using purified DNA. Thus, the SYBR Green real-time PCR-based method can be used for the rapid and specific detection of X. oryzae pv. oryzae and will potentially simplify and facilitate diagnosis and monitoring of this pathogen and guide plant disease management.
A Novel Fusarium Species Causes a Canker Disease of the Critically Endangered Conifer, Torreya taxifolia
Authors: Smith Jason A. , O'Donnell Kerry , Mount Lacey L. , Shin Keumchul , Peacock Kelly , Trulock Aaron , Spector Tova , Cruse-Sanders Jenny , Determann Ron
Published: February 2011

A canker disease of Florida torreya (Torreya taxifolia) has been implicated in the decline of this critically endangered species in its native range of northern Florida and southeastern Georgia. In surveys of eight Florida torreya sites, cankers were present on all dead trees and 71 to 100% of living trees, suggesting that a fungal pathogen might be the causal agent. To identify the causal agent, nuclear ribosomal internal transcribed spacer region (ITS rDNA) sequences were determined for 115 fungi isolated from cankers on 46 symptomatic trees sampled at three sites in northern Florida. BLASTn searches of the GenBank nucleotide database, using the ITS rDNA sequences as the query, indicated that a novel Fusarium species designated Fsp-1 might be the etiological agent. Molecular phylogenetic analyses of partial translation elongation factor 1-alpha (EF-1) and RNA polymerase second largest subunit (RPB2) gene sequences indicate that Fsp-1 represents a novel species representing one of the earliest divergences within the Gibberella clade of Fusarium. Results of pathogenicity experiments established that the four isolates of Fsp-1 tested could induce canker symptoms on cultivated Florida torreya in a growth chamber. Koch's postulates were completed by the recovery and identification of Fsp-1 from cankers of the inoculated plants.
Protein Storage Vacuoles Are Transformed into Lytic Vacuoles in Root Meristematic Cells of Germinating Seedlings by Multiple, Cell Type-Specific Mechanisms
Authors: Zheng Huiqiong , Staehelin L. Andrew
Published: January 2011

We have investigated the structural events associated with vacuole biogenesis in root tip cells of tobacco (Nicotiana tabacum) seedlings preserved by high-pressure freezing and freeze-substitution techniques. Our micrographs demonstrate that the lytic vacuoles (LVs) of root tip cells are derived from protein storage vacuoles (PSVs) by cell type-specific sets of transformation events. Analysis of the vacuole transformation pathways has been aided by the phytin-dependent black osmium staining of PSV luminal contents. In epidermal and outer cortex cells, the central LVs are formed by a process involving PSV fusion, storage protein degradation, and the gradual replacement of the PSV marker protein α-tonoplast intrinsic protein (TIP) with the LV marker protein γ-TIP. In contrast, in the inner cortex and vascular cylinder cells, the transformation events are more complex. During mobilization of the stored molecules, the PSV membranes collapse osmotically upon themselves, thereby squeezing the vacuolar contents into the remaining bulging vacuolar regions. The collapsed PSV membranes then differentiate into two domains: (1) vacuole “reinflation” domains that produce pre-LVs, and (2) multilamellar autophagosomal domains that are later engulfed by the pre-LVs. The multilamellar autophagosomal domains appear to originate from concentric sheets of PSV membranes that create compartments within which the cytoplasm begins to break down. Engulfment of the multilamellar autophagic vacuoles by the pre-LVs gives rise to the mature LVs. During pre-LV formation, the PSV marker α-TIP disappears and is replaced by the LV marker γ-TIP. These findings demonstrate that the central LVs of root cells arise from PSVs via cell type-specific transformation pathways.
Supercomplex Formation with Photosystem I Is Required for the Stabilization of the Chloroplast NADH Dehydrogenase-Like Complex in Arabidopsis
Authors: Peng Lianwei , Shikanai Toshiharu
Published: January 2011

In higher plants, the chloroplast NADH dehydrogenase-like complex (NDH) interacts with photosystem I (PSI) to form the NDH-PSI supercomplex via two minor light-harvesting complex I (LHCI) proteins, Lhca5 and Lhca6. Previously, we showed that in lhca5 and lhca6, NDH still associates with PSI to form smaller versions of the NDH-PSI supercomplex, although their molecular masses are far smaller than that of the full-size NDH-PSI supercomplex. In this study, we show that the NDH complex is present in the monomeric form in Arabidopsis (Arabidopsis thaliana) lhca5 lhca6, implying that NDH interacts with multiple copies of PSI. NDH subunit levels were slightly reduced in immature leaves and more drastically (approximately 50%) in mature leaves of the lhca5 lhca6 double mutant compared with the wild type. Chlorophyll fluorescence analyses detected NDH activity of lhca5 lhca6, suggesting that the supercomplex formation is not essential for NDH activity. However, the severe phenotypes of the lhca5 lhca6 proton gradient regulation5 triple mutant in both plant growth rate and photosynthesis suggest that the function of NDH was impaired in this mutant in vivo. Accumulation of NDH subunits was drastically reduced in lhca5 lhca6 when the light intensity was shifted from 50 to 500 μmol photons m−2 s−1. Furthermore, the half-life of NDH subunits, especially that of NDH18, was shorter in monomeric NDH than in the NDH-PSI supercomplex under the high-light conditions. We propose that NDH-PSI supercomplex formation stabilizes NDH and that the process is especially required under stress conditions.