bluuebunny/crossref_metadata_2025 huggingface dataset:
Temperature dependence of magnetic behaviour in very fine grained, spark plasma sintered NiCuZn ferrites
Authors: Ahmadi Behzad , Zehani Karim , LoBue Martino , Loyau Vincent , Mazaleyrat Frederic
Published: February 2012

Recently, using spark plasma sintering technique, a family of very fine grained, fully dense NiCuZn ferrites have been produced, which show constant permeability up to several 10 MHz. These ferrites can be used for filtering purposes in high frequency applications where a wide frequency band is required. In this paper, we study the magnetization processes taking place in these nano grained materials, in the frequency interval of 100 kHz to 5 MHz. Using a fluxmetric hysteresis graph, permeability, loss, and BH loops are measured at different temperatures, from −5 °C to 110 °C. Results are compared to the behavior of micrometric grain size ferrites, which are commonly used for power electronic and high frequency applications.
Evolution of crystallographic texture and magnetic properties of polycrystalline barium ferrite thick films with Bi2O3 additive
Authors: Chen Daming , Liu Yingli , Li Yuanxun , Yang Kai , Zhang Huaiwu
Published: February 2012

In this study, polycrystalline barium ferrite (BaM) thick films with and without additives were prepared by tape casting. It was found that Bi2O3 was effective for fabricating highly oriented and dense polycrystalline barium ferrite thick films, and in turn, the magnetic properties were improved. The degree of crystallographic orientation (F) of the sample was increased from 0.55 without Bi2O3 to 0.82 containing 2 wt. % Bi2O3, meanwhile, the relative density varied from 81% to 96%. In addition, the SEM and XRD results showed that polycrystalline thick film had hexagonal morphology with crystal texture of c-axis grains perpendicular to film plane. It was also observed that the magnetic properties of polycrystalline barium ferrites were strongly influenced by their crystallographic texture. With increasing the F from 0.55 to 0.82, remanent magnetization and squareness ratio (Mr/Ms) were enhanced 39% and 21%, respectively. The barium ferrite containing 2 wt. % Bi2O3 had excellent magnetic properties with remanent magnetization of 3213.33 G, squareness ratio (Mr/Ms) of 0.82, and coercivity of 611.3 Oe. These results indicated that the specimens exhibited highly oriented and self-biased properties, which ensure that they are suitable for possible use in self-biased millimeter wave devices.
The effect of MgO(111) interlayer on the interface phase stability and structure of BaFe12O19/SiC(0001)
Authors: Lazarov V. K. , Hasnip P. J. , Cai Z. , Yoshida K. , Ziemer K. S.
Published: February 2012

We present a study on the effect of an interlayer of thin MgO(111) film on SiC(0001) on the interface phase stability and structure of the BaFe12O19 (BaM). The 10 nm MgO(111) interlayer followed by the BaM film were grown by molecular beam epitaxy on 6H-SiC. Cross-sectional transmission electron microscopy shows the formation of a magnesium ferrite spinel phase at the interface, and after 25 nm, a well structured BaM film was observed. In addition to the two main phases (Mg-ferrite and BaM), a thin layer of SiOx (2–3 nm) is formed at the SiC interface. In spite of the formation of this amorphous layer, the diffraction studies show that the BaM film is epitaxially grown and it has a single crystal structure. The energy dispersive x-ray analysis from the interface region shows that the MgO layer prevents significant outdiffusion of the Si into the film. Total energy calculations by density functional theory were used to investigate the stability of the various phases and to explain the observed interfacial phases in the studied system.
Magnetostrictive properties of directional solidification Fe82Ga9Al9 alloy
Authors: Zhou Y. , Wang X. L. , Wang B. W. , Liu Y. , Du Y. , Niu Y. C. , Liu L. Q.
Published: February 2012

Fe82Ga9Al9 alloy rod was prepared by the directional solidification (DS) method. The effects of uniaxial compressive stress on magnetostriction of the alloy and the temperature dependence of magnetostriction were investigated. The results show that the magnetostriction increases from 135 × 10−6 at 2.3 MPa to 221 × 10−6 at 53 MPa and then remains at this value between 53 MPa and 90 MPa. This enhancement results from domain rotation under the compressive stress. The temperature dependence results show that the saturated magnetostriction decreases by 11% (25 °C–120 °C) and 13% (25 °C–100 °C) for samples with 0 MPa and 15 MPa compressive stress applied, respectively. This decrease is due to reduced magnetic crystalline anisotropy as the temperature increases. Under the compressive stress conditions, the magnetostriction decreases more notably.
Low core loss of non-Si quaternary Fe83.3B8P8Cu0.7 nanocrystalline alloy with high Bs of 1.7 T
Authors: Urata Akiri , Yamaki Makoto , Takahashi Masahiko , Okamoto Koichi , Matsumoto Hiroyuki , Yoshida Shigeyoshi , Makino Akihiro
Published: February 2012

The effect of replacement Si by P on the soft magnetic and structural properties of nanocrystalline Fe-Si-B-P-Cu alloys has been investigated. The nanocrystalline Fe83.3SiXB8P8−XCu0.7 (X = 0, 2, 4, 6) alloy ribbons consist of precipitated α-Fe phase and residual amorphous phase, and initial permeability of these alloy ribbons are enhanced with decreasing Si content. In particular, the nanocrystalline Fe83.3B8P8Cu0.7 (X = 0) alloy has both low core loss of 1.4 W/kg at 1.0 T – 50 Hz and high saturation magnetic flux density of 1.70 T. In addition, this alloy exhibits the most favorable nanocrystalline structure containing the homogeneously precipitated α-Fe grains with 14 nm in mean diameter. Therefore, it can be concluded that the soft magnetic properties and nanostructure of Fe-Si-B-P-Cu alloys are strongly affected by Si and P content. The Fe83.3B8P8Cu0.7 alloy with low core loss and high saturation magnetic flux density compared with a Fe amorphous alloy is suitable for a magnetic core material in electronic devices such as transformers, inductors and motors.
High frequency magnetic properties and microstructure of NiZn/Co2Z composite ferrite material
Authors: Zheng Zongliang , Zhang Huaiwu , Xiao John Q. , Yang Qinghui , Wang Liguo , Su Hua
Published: February 2012

The NiZn(Ni0.4Zn0.6Fe2O4) spinel ferrite and Co2Z(Ba3Co2Fe24O41) hexagonal ferrite composite materials with the various Co2Z contents have been synthesized by the solid-state reaction method. The phases and microstructures of the sintered ceramics have been analyzed. The results show that Co2Z grains exist as a secondary phase in composites and remarkably affect the grain size and the static and high-frequency magnetic properties. With the addition ratio of Co2Z varying from 0 wt. % to 30 wt. %, the saturation magnetization only changes slightly and is closely related to the density of sintered composites. Meanwhile, the initial permeability decreases and the cut-off frequency expands from 7 MHz to 300 MHz. In addition, the product (μi − 1)fr of composites is much larger than that of the pure NiZn spinel ferrite.
Small amplitude ion-acoustic solitary waves in an adiabatic multi-component plasma
Authors: Bencheriet F. , Alifedila D. , Djebli M.
Published: February 2012

Adiabatic multi-ions species containing positive and negative ions in the presence of nonthermal electrons are considered. The properties of small, but finite, ion acoustic waves are investigated taking into account the pressure effect of positive/negative ions in the fluid equations with a polytropic (γ) coefficient ranging from 1 to 3. The reductive perturbation method has been employed to derive the Korteweg-de Vries equation for small amplitude ion-acoustic waves. The effect of ion pressure is found important, particularly for higher values of γ. The results of the present investigation may be applicable to some plasma environments, such as the Earth’s ionosphere region.
Nonlocal symmetries of Riccati and Abel chains and their similarity reductions
Authors: Bruzon M. S. , Gandarias M. L. , Senthilvelan M.
Published: February 2012

We study nonlocal symmetries and their similarity reductions of Riccati and Abel chains. Our results show that all the equations in Riccati chain share the same form of nonlocal symmetry. The similarity reduced Nth order ordinary differential equation (ODE), N = 2, 3, 4, …, in this chain yields (N − 1)th order ODE in the same chain. All the equations in the Abel chain also share the same form of nonlocal symmetry (which is different from the one that exist in Riccati chain) but the similarity reduced Nth order ODE, N = 2, 3, 4, …, in the Abel chain always ends at the (N − 1)th order ODE in the Riccati chain. We describe the method of finding general solution of all the equations that appear in these chains from the nonlocal symmetry.
Linear theory of magnetized ion-channel free-electron laser
Authors: Sadegzadeh S. , Hasanbeigi A. , Mehdian H. , Alimohamadi M.
Published: February 2012

A theory of wiggler pumped ion-channel free-electron laser (WPIC-FEL) and an axial magnetic field is presented. The motion of a relativistic electron is analyzed in the field configuration consisting of a helical wiggler magnetic field, a uniform axial magnetic field, and an electrostatic electric field produced by an ion-channel. An equation for the function Φ, which determines the rate of change of axial velocity with energy, is derived. Numerical calculations are made to illustrate the effects of two electron beam guiding devices on the trajectories. By means of linear fluid theory, the sixth-degree polynomial dispersion equation for electromagnetic and space-charge waves is derived. The dependence of growth rate-frequency curves on the ion-channel frequency and axial magnetic field is studied numerically.
Dynamics of thin metal foils irradiated by moderate-contrast high-intensity laser beams
Authors: Povarnitsyn M. E. , Andreev N. E. , Levashov P. R. , Khishchenko K. V. , Rosmej O. N.
Published: February 2012

Laser contrast is a crucial parameter in experiments with high-intensity high-energy pulses. For relativistic intensities of the main pulse ≳1019W/cm2, even high-contrast beams can produce plasma on the target surface due to a long nanosecond prepulse action which results in an undesirable early smearing of the target. In particular, dynamics of thin foils under the prepulse action is especially important for the laser ion acceleration technique and x-rays generation. To avoid the influence of the long laser prepulse, a thin foil can be arranged in front of the target. The analysis of the multi-stage foil dynamics is performed using a wide-range two-temperature hydrodynamic model, which correctly describes the foil expansion starting from the normal solid density at room temperature. Simulations show that varying the foil thickness, one can diminish the prepulse transmission through the foil material in many orders of magnitude and at the same time provide the total transparency of the foil plasma by the moment of the main high-intensity ultra-short pulse arrival. Modeling of shielded and unshielded target dynamics demonstrates the effectiveness of this technique. However, the prepulse energy re-emission by the shielding foil plasma can be sizable producing an undesirable early heating of the target placed behind the foil.
Energy harvesting in the super-harmonic frequency region of a twin-well oscillator
Authors: Masana R. , Daqaq M. F.
Published: February 2012

Nonlinear dynamical systems exhibit super-harmonic resonances that can activate large-amplitude motions at fraction integers of the fundamental frequency of the system. Such resonances offer a unique and untapped opportunity for harnessing vibratory energy from excitation sources with low-frequency components. To that end, this paper exploits the super-harmonic frequency bands of a nonlinear twin-well (bi-stable) oscillator for harvesting energy from low-frequency excitations. Theoretical and experimental studies are performed on an axially loaded clamped-clamped piezoelectric beam harvester with bi-stable potential characteristics. Voltage- and power-frequency bifurcation maps are generated near the super-harmonic resonance of order two. It is shown that, for certain base acceleration levels, the harvester can exhibit responses that are favorable for energy harvesting. These include a unique branch of large-orbit periodic inter-well oscillations, coexisting branches of large-orbit solutions, and a bandwidth of frequencies where a unique chaotic attractor exists. In these frequency regions, the harvester can produce power levels at half its fundamental frequency that are comparable to those obtained near the fundamental frequency.
Sub-TeV proton beam generation by ultra-intense laser irradiation of foil-and-gas target
Authors: Zheng F. L. , Wang H. Y. , Yan X. Q. , Tajima T. , Yu M. Y. , He X. T.
Published: February 2012

A two-phase proton acceleration scheme using an ultra-intense laser pulse irradiating a proton foil with a tenuous heavier-ion plasma behind it is presented. The foil electrons are compressed and pushed out as a thin dense layer by the radiation pressure and propagate in the plasma behind at near the light speed. The protons are in turn accelerated by the resulting space-charge field and also enter the backside plasma, but without the formation of a quasistationary double layer. The electron layer is rapidly weakened by the space-charge field. However, the laser pulse originally behind it now snowplows the backside-plasma electrons and creates an intense electrostatic wakefield. The latter can stably trap and accelerate the pre-accelerated proton layer there for a very long distance and thus to very high energies. The two-phase scheme is verified by particle-in-cell simulations and analytical modeling, which also suggests that a 0.54 TeV proton beam can be obtained with a 1023 W/cm2 laser pulse.
Three-dimensional electromagnetic strong turbulence: Dependence of the statistics and dynamics of strong turbulence on the electron to ion temperature ratio
Authors: Graham D. B. , Cairns Iver H. , Skjaeraasen O. , Robinson P. A.
Published: February 2012

The temperature ratio Ti/Te of ions to electrons affects both the ion-damping rate and the ion-acoustic speed in plasmas. The effects of changing the ion-damping rate and ion-acoustic speed are investigated for electrostatic strong turbulence and electromagnetic strong turbulence in three dimensions. When ion damping is strong, density wells relax in place and act as nucleation sites for the formation of new wave packets. In this case, the density perturbations are primarily density wells supported by the ponderomotive force. For weak ion damping, corresponding to low Ti/Te, ion-acoustic waves are launched radially outwards when wave packets dissipate at burnout, thereby increasing the level of density perturbations in the system and thus raising the level of scattering of Langmuir waves off density perturbations. Density wells no longer relax in place so renucleation at recent collapse sites no longer occurs, instead wave packets form in background low density regions, such as superpositions of troughs of propagating ion-acoustic waves. This transition is found to occur at Ti/Te ≈ 0.1. The change in behavior with Ti/Te is shown to change the bulk statistical properties, scaling behavior, spectra, and field statistics of strong turbulence. For Ti/Te>rsim0.1, the electrostatic results approach the predictions of the two-component model of Robinson and Newman, and good agreement is found for Ti/Te>rsim0.15.
59Co nuclear magnetic resonance study of the local distribution of atoms in the Heusler compound Co2FeAl0.5Si0.5
Authors: Wurmehl Sabine , Kohlhepp Jürgen T. , Swagten Henk J. M. , Koopmans Bert
Published: February 2012

In this work, the spin-echo nuclear magnetic resonance (NMR) technique is used to probe the local structure of Co2FeAl0.5Si0.5 bulk samples. The 59Co NMR spectrum of the Heusler compound Co2FeAl0.5Si0.5 consists of four main resonance lines with an underlying sub-structure. The splitting into the main resonance lines is explained by contributions of the B2 type structure. The sub-lines are attributed to a random distribution of Al and Si. By comparing the experimental results with an appropriate multinomial distribution, the fraction of the Al/Si intermixing and the ratio between the contributing structure types is assigned. The main structural contribution of as-cast bulk samples is of B2 type with 38% of L21 contributions. The L21 contribution can be enhanced to 59% by an appropriate annealing process. However, B2 contributions are still present after annealing. Additional foreign phases such as fcc-Co and Co-Al, with relative contributions of less than one percent, are also found in both as-cast and annealed samples. Resonance lines related to slight amounts of the ternary, parental Heusler compounds Co2FeAl and Co2FeSi are also observed.
Effects of bending and torsion rigidity on deformation and breakage of flexible fibers: A direct simulation study
Authors: Kabanemi Kalonji K. , Hétu Jean-François
Published: February 2012

To understand the various mechanisms of fiber deformation of flexible fiber suspensions, we carry out a direct simulation study to analyze the effect of fiber rigidity on fiber motion in simple shear flow. Such a study may be used to investigate the critical parameters controlling the breakage of flexible fibers during processing. We model the fiber as a series of rigid spheres connected by stiff springs. The stretching, bending, and torsional rigidities are determined by Young's modulus and shear modulus to realistically model the fiber rigidity. The model correctly predicts the orbit period of fiber rotation, $T\dot \gamma$Tγ̇, as well as the trend of critical flow strength, $\eta \dot \gamma /E$ηγ̇/E, versus fiber aspect ratio, rp, at which breakage occurs in simple shear flow.
Molecular beam epitaxy of InAlN lattice-matched to GaN with homogeneous composition using ammonia as nitrogen source
Authors: Hoi Wong Man , Wu Feng , Hurni Christophe A. , Choi Soojeong , Speck James S. , Mishra Umesh K.
Published: February 2012

InAlN lattice-matched to GaN was grown by molecular beam epitaxy (MBE) using ammonia as the nitrogen source. The alloy composition, growth conditions, and strain coherence of the InAlN were verified by high resolution x-ray diffraction ω-2θ scans and reciprocal space maps. Scanning transmission electron microscopy and energy-dispersive x-ray spectroscopy of the InAlN revealed the absence of lateral composition modulation that was observed in the films grown by plasma-assisted MBE. InAlN/AlN/GaN high electron mobility transistors with smooth surfaces were fabricated with electron mobilities exceeding 1600 cm2/Vs and sheet resistances below 244 Ω/sq.
Chirality switching and propagation control of a vortex domain wall in ferromagnetic nanotubes
Authors: Otálora J. A. , López-López J. A. , Vargas P. , Landeros P.
Published: February 2012

We propose a procedure to manipulate the chirality and propagation of a vortex domain wall in ferromagnetic nanotubes by applying magnetic field pulses. It is found that the chiral state of the vortex wall can be switched, provided that (1) the field amplitude is between two critical values, the so-called chiral field and the well-known Walker field, and (2) the pulse length is longer than a critical time, which is the time needed by the wall to overcome a local energy barrier. These key parameters are estimated for Permalloy nanotubes and range between a few miliTesla and some nanoseconds.
Thermal properties of the hybrid graphene-metal nano-micro-composites: Applications in thermal interface materials
Authors: Goyal Vivek , Balandin Alexander A.
Published: February 2012

The authors report on synthesis and thermal properties of the electrically conductive thermal interface materials with the hybrid graphene-metal particle fillers. The thermal conductivity of resulting composites was increased by ∼500% in a temperature range from 300 K to 400 K at a small graphene loading fraction of 5-vol.-%. The unusually strong enhancement of thermal properties was attributed to the high intrinsic thermal conductivity of graphene, strong graphene coupling to matrix materials, and the large range of the length-scale—from nanometers to micrometers—of the graphene and silver particle fillers. The obtained results are important for the thermal management of advanced electronics and optoelectronics.
Realization of a mesoscopic reprogrammable magnetic logic based on a nanoscale reconfigurable magnonic crystal
Authors: Ding J. , Kostylev M. , Adeyeye A. O.
Published: February 2012

We demonstrate functionality of magnetic logic based on a reconfigurable magnonic crystal in the form of a meander-type ferromagnetic nanowire. A ferromagnetic resonance method employing a microscopic coplanar waveguide has been used to detect the logic state of the structure coded in its magnetic ground state. Ferromagnetic resonance responses of anti-ferromagnetic and multi-cluster (mix of anti-ferromagnetic and ferromagnetic) ground states can be switched by applying a DC current in the signal line of the coplanar waveguide. Experimental demonstrations of device functionality as XOR and NOT logic gates are supported by the magnetic force microscopy images and micromagnetic simulations.
Multi-dimensional laser spectroscopy of exciton polaritons with spatial light modulators
Authors: Mai P. , Pressl B. , Sassermann M. , Vörös Z. , Weihs G. , Schneider C. , Löffler A. , Höfling S. , Forchel A.
Published: February 2012

We describe an experimental system that allows one to easily access the dispersion curve of exciton-polaritons in a microcavity. Our approach is based on two spatial light modulators, one for changing the excitation angles (momenta), and the other for tuning the excitation wavelength. We show that with this setup, an arbitrary number of states can be excited accurately and that re-configuration of the excitation scheme can be done at high speed.
Influence of fertiliser application on the occurrence and colonisation of arbuscular mycorrhizal fungi (AMF) under maize/Centrosema and sole maize systems
Authors: Emmanuel Bukola , Fagbola Olajire , Osonubi Oluwole
Published: February 2012

Soil fertility management practices can influence colonisation of crops by arbuscular mycorrhizal fungi (AMF) and their abundance. The effects of different rates of nitrogen-phosphorus-potassium (NPK) fertiliser on AMF occurrence and colonisation were studied in maize/Centrosema pascuorum and sole maize systems. The NPK treatments were at rates (kg/ha): 0-10-30, 45-10-30, and 0-0-0 (control). The AMF spore populations were enumerated by direct counting under a microscope. Nutrient uptake was calculated as the product of nutrient concentration and shoot dry weight, and maize yield was estimated per ha. In the maize/Centrosema system, spore count, AMF colonisation, and nutrient uptake (except N) decreased with NPK 45-10-30 compared with 0-10-30, although maize yields were comparable at the two fertiliser levels. In the sole maize system, fertiliser application did not influence AMF spore abundance, but colonisation, nutrient uptake, and crop yield increased significantly (P < 0.05) with NPK 45-10-30. Maize yield increased by 1200% under the maize/Centrosema system compared with sole maize at NPK 0-10-30. The lowest values for all parameters were obtained under the control treatments. Colonisation of AMF, nutrient uptake, and maize yield were positively correlated. The maize/Centrosema system can maximise AMF benefits to increase yield and also reduce fertiliser input into agricultural soils, while application of N fertiliser is important to increase yield in the sole maize system.
Evaporation-induced cavitation in nanofluidic channels
Authors: Duan Chuanhua , Karnik Rohit , Lu Ming-Chang , Majumdar Arun
Published: February 2012

Cavitation, known as the formation of vapor bubbles when liquids are under tension, is of great interest both in condensed matter science as well as in diverse applications such as botany, hydraulic engineering, and medicine. Although widely studied in bulk and microscale-confined liquids, cavitation in the nanoscale is generally believed to be energetically unfavorable and has never been experimentally demonstrated. Here we report evaporation-induced cavitation in water-filled hydrophilic nanochannels under enormous negative pressures up to -7 MPa. As opposed to receding menisci observed in microchannel evaporation, the menisci in nanochannels are pinned at the entrance while vapor bubbles form and expand inside. Evaporation in the channels is found to be aided by advective liquid transport, which leads to an evaporation rate that is an order of magnitude higher than that governed by Fickian vapor diffusion in macro- and microscale evaporation. The vapor bubbles also exhibit unusual motion as well as translational stability and symmetry, which occur because of a balance between two competing mass fluxes driven by thermocapillarity and evaporation. Our studies expand our understanding of cavitation and provide new insights for phase-change phenomena at the nanoscale.
A high-affinity, dimeric inhibitor of PSD-95 bivalently interacts with PDZ1-2 and protects against ischemic brain damage
Authors: Bach Anders , Clausen Bettina H. , Møller Magda , Vestergaard Bente , Chi Celestine N. , Round Adam , Sørensen Pernille L. , Nissen Klaus B. , Kastrup Jette S. , Gajhede Michael , Jemth Per , Kristensen Anders S. , Lundström Patrik , Lambertsen Kate L. , Strømgaard Kristian
Published: February 2012

Inhibition of the ternary protein complex of the synaptic scaffolding protein postsynaptic density protein-95 (PSD-95), neuronal nitric oxide synthase (nNOS), and the
N
-methyl-
d
-aspartate (NMDA) receptor is a potential strategy for treating ischemic brain damage, but high-affinity inhibitors are lacking. Here we report the design and synthesis of a novel dimeric inhibitor, Tat-
N
PEG4(IETDV)
2
(Tat-
N
-dimer), which binds the tandem PDZ1-2 domain of PSD-95 with an unprecedented high affinity of 4.6 nM, and displays extensive protease-resistance as evaluated in vitro by stability-measurements in human blood plasma. X-ray crystallography, NMR, and small-angle X-ray scattering (SAXS) deduced a true bivalent interaction between dimeric inhibitor and PDZ1-2, and also provided a dynamic model of the conformational changes of PDZ1-2 induced by the dimeric inhibitor. A single intravenous injection of Tat-
N
-dimer (3 nmol/g) to mice subjected to focal cerebral ischemia reduces infarct volume with 40% and restores motor functions. Thus, Tat-
N
-dimer is a highly efficacious neuroprotective agent with therapeutic potential in stroke.
Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing
Authors: Lohr Jens G. , Stojanov Petar , Lawrence Michael S. , Auclair Daniel , Chapuy Bjoern , Sougnez Carrie , Cruz-Gordillo Peter , Knoechel Birgit , Asmann Yan W. , Slager Susan L. , Novak Anne J. , Dogan Ahmet , Ansell Stephen M. , Link Brian K. , Zou Lihua , Gould Joshua , Saksena Gordon , Stransky Nicolas , Rangel-Escareño Claudia , Fernandez-Lopez Juan Carlos , Hidalgo-Miranda Alfredo , Melendez-Zajgla Jorge , Hernández-Lemus Enrique , Schwarz-Cruz y Celis Angela , Imaz-Rosshandler Ivan , Ojesina Akinyemi I. , Jung Joonil , Pedamallu Chandra S. , Lander Eric S. , Habermann Thomas M. , Cerhan James R. , Shipp Margaret A. , Getz Gad , Golub Todd R.
Published: February 2012

To gain insight into the genomic basis of diffuse large B-cell lymphoma (DLBCL), we performed massively parallel whole-exome sequencing of 55 primary tumor samples from patients with DLBCL and matched normal tissue. We identified recurrent mutations in genes that are well known to be functionally relevant in DLBCL, including
MYD88
,
CARD11
,
EZH2
, and
CREBBP
. We also identified somatic mutations in genes for which a functional role in DLBCL has not been previously suspected. These genes include
MEF2B
,
MLL2
,
BTG1
,
GNA13
,
ACTB
,
P2RY8
,
PCLO
, and
TNFRSF14
. Further, we show that
BCL2
mutations commonly occur in patients with
BCL2
/
IgH
rearrangements as a result of somatic hypermutation normally occurring at the
IgH
locus. The
BCL2
point mutations are primarily synonymous, and likely caused by activation-induced cytidine deaminase–mediated somatic hypermutation, as shown by comprehensive analysis of enrichment of mutations in WRCY target motifs. Those nonsynonymous mutations that are observed tend to be found outside of the functionally important BH domains of the protein, suggesting that strong negative selection against
BCL2
loss-of-function mutations is at play. Last, by using an algorithm designed to identify likely functionally relevant but infrequent mutations, we identify
KRAS
,
BRAF
, and
NOTCH1
as likely drivers of DLBCL pathogenesis in some patients. Our data provide an unbiased view of the landscape of mutations in DLBCL, and this in turn may point toward new therapeutic strategies for the disease.
RNA-Seq Atlas—a reference database for gene expression profiling in normal tissue by next-generation sequencing
Authors: Krupp Markus , Marquardt Jens U. , Sahin Ugur , Galle Peter R. , Castle John , Teufel Andreas
Published: February 2012

Motivation: Next-generation sequencing technology enables an entirely new perspective for clinical research and will speed up personalized medicine. In contrast to microarray-based approaches, RNA-Seq analysis provides a much more comprehensive and unbiased view of gene expression. Although the perspective is clear and the long-term success of this new technology obvious, bioinformatics resources making these data easily available especially to the biomedical research community are still evolving.

Results: We have generated RNA-Seq Atlas, a web-based repository of RNA-Seq gene expression profiles and query tools. The website offers open and easy access to RNA-Seq gene expression profiles and tools to both compare tissues and find genes with specific expression patterns. To enlarge the scope of the RNA-Seq Atlas, the data were linked to common functional and genetic databases, in particular offering information on the respective gene, signaling pathway analysis and evaluation of biological functions by means of gene ontologies. Additionally, data were linked to several microarray gene profiles, including BioGPS normal tissue profiles and NCI60 cancer cell line expression data. Our data search interface allows an integrative detailed comparison between our RNA-Seq data and the microarray information. This is the first database providing data mining tools and open access to large scale RNA-Seq expression profiles. Its applications will be versatile, as it will be beneficial in identifying tissue specific genes and expression profiles, comparison of gene expression profiles among diverse tissues, but also systems biology approaches linking tissue function to gene expression changes.

Availability and implementation:  http://medicalgenomics.org/rna_seq_atlas

Contact:  kruppm@uni-mainz.de; teufel@uni-mainz.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Signal analysis for genome-wide maps of histone modifications measured by ChIP-seq
Authors: Beck Dominik , Brandl Miriam B. , Boelen Lies , Unnikrishnan Ashwin , Pimanda John E. , Wong Jason W. H.
Published: February 2012

Motivation: Chromatin structure, including post-translational modifications of histones, regulates gene expression, alternative splicing and cell identity. ChIP-seq is an increasingly used assay to study chromatin function. However, tools for downstream bioinformatics analysis are limited and are only based on the evaluation of signal intensities. We reasoned that new methods taking into account other signal characteristics such as peak shape, location and frequencies might reveal new insights into chromatin function, particularly in situation where differences in read intensities are subtle.

Results: We introduced an analysis pipeline, based on linear predictive coding (LPC), which allows the capture and comparison of ChIP-seq histone profiles. First, we show that the modeled signal profiles distinguish differentially expressed genes with comparable accuracy to signal intensities. The method was robust against parameter variations and performed well up to a signal-to-noise ratio of 0.55. Additionally, we show that LPC profiles of activating and repressive histone marks cluster into distinct groups and can be used to predict their function.

Availability and implementation:  http://www.cancerresearch.unsw.edu.au/crcweb.nsf/page/LPCHP A Matlab implementation along with usage instructions and an example input file are available from: http://www.cancerresearch.unsw.edu.au/crcweb.nsf/page/LPCHP

Contact:  d.beck@student.unsw.edu.au; jpimanda@unsw.edu.au; jason.wong@unsw.edu.au

Supplementary information:  Supplementary data are available at Bioinformatics online.
Alcoholic Liver Disease
Authors: Cave Anna , Barnardo Adrian
Published: February 2012

Mortality rates from liver disease in the UK are increasing and alcohol is a major contributor to this trend. Over the last decade, there has been a 5-fold increase in young patients aged 35–55 years developing alcoholic cirrhosis. Patients drinking harmful levels of alcohol, with evidence of organ damage, are known to consult their GPs twice as often as the average patient; however, only 2–5% are known to primary care as harmful drinkers. This article aims to describe the epidemiology of alcoholic liver disease and its management within primary care including indications for referral to secondary care
Nocardioides szechwanensis sp. nov. and Nocardioides psychrotolerans sp. nov., isolated from a glacier
Authors: Liu Qing , Xin Yu-hua , Liu Hong-can , Zhou Yu-guang , Wen Ying
Published: February 2012

Two Gram-positive, rod-shaped, non-spore-forming bacteria (strains RHLT1-17T and RHLT2-1T) were isolated from Hailuogou glacier in Szechwan province, PR China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strains belonged to the genus

Nocardioides

and shared 97.8 % sequence similarity with each other and 97.6 and 98.4 % sequence similarity, respectively, with

Nocardioides kribbensis

KSL-2T. Strain RHLT1-17T grew at 0–35 °C and strain RHLT2-1T grew at 0–25 °C. The major cellular fatty acids of strain RHLT1-17T were C17 : 1ω8c (32.69 %) and iso-C16 : 0 (21.74 %). The major cellular fatty acids of strain RHLT2-1T were C18 : 1ω9c (28.72 %), summed feature 3 (17.14 %; comprising C16 : 1ω7c and/or C16 : 1ω6c), iso-C16 : 0 (14.35 %), C16 : 0 (9.96 %) and iso-C14 : 0 (8.34 %). Both strains contained ll-2,6-diaminopimelic acid in the cell-wall peptidoglycan and MK-8(H4) as the predominant menaquinone. On the basis of data obtained using a polyphasic approach, two novel species, Nocardioides szechwanensis sp. nov. (type strain RHLT1-17T  = CGMCC 1.11147T  = NBRC 108562T) and Nocardioides psychrotolerans sp. nov. (type strain RHLT2-1T  = CGMCC 1.11156T  = NBRC 108563T), are proposed.
Phylogenetic multilocus sequence analysis identifies seven novel

Ensifer

genospecies isolated from a less-well-explored biogeographical region in East Africa
Authors: Degefu Tulu , Wolde-meskel Endalkachew , Frostegård Åsa
Published: February 2012

The diversity of 71 rhizobial strains belonging to the genus

Ensifer

, isolated from root nodules of woody legumes growing in southern Ethiopia, was studied using multilocus sequence analysis (MLSA) and phenotypic approaches. Phylogenetic analyses based on core genes revealed that 43 strains were clustered in seven distinct and consistent positions (genospecies I–VII), while another 25 strains were also distinct but were discrepant in their placement on the different gene trees. The remaining three strains occupied the same phylogenetic branches as defined

Ensifer

species and thus were not distinct. Irrespective of their chromosomal background, the majority of the test strains were highly related with respect to their nifH and nodC gene sequences, suggesting that these symbionts might have acquired these genes recently from a common origin. On the nifH phylogenetic tree, the branch containing the test strains and reference species isolated from woody legumes in Africa was clearly separate from those isolated outside the continent, suggesting that these symbionts have a long history of separate evolution within

Ensifer

for this gene. A cross-inoculation study showed that our strains were capable of eliciting effective nodulation on the homologous host and on other host species. This suggests a potential to improve nitrogen fixation by selecting for broad-host-range inoculants. Our study confirms the presence of a wide diversity of

Ensifer

in East Africa and, while contributing to the general knowledge of the biodiversity within the genus, also highlights the need to focus on previously less-well-explored biogeographical regions to unravel as-yet-unidentified rhizobial resources.
Recycling of Methylthioadenosine Is Essential for Normal Vascular Development and Reproduction in Arabidopsis
Authors: Waduwara-Jayabahu Ishari , Oppermann Yasmin , Wirtz Markus , Hull Zachary T. , Schoor Sarah , Plotnikov Alexander N. , Hell Rüdiger , Sauter Margret , Moffatt Barbara A.
Published: February 2012

5′-Methylthioadenosine (MTA) is the common by-product of polyamine (PA), nicotianamine (NA), and ethylene biosynthesis in Arabidopsis (Arabidopsis thaliana). The methylthiol moiety of MTA is salvaged by 5′-methylthioadenosine nucleosidase (MTN) in a reaction producing methylthioribose (MTR) and adenine. The MTN double mutant, mtn1-1mtn2-1, retains approximately 14% of the MTN enzyme activity present in the wild type and displays a pleiotropic phenotype that includes altered vasculature and impaired fertility. These abnormal traits were associated with increased MTA levels, altered PA profiles, and reduced NA content. Exogenous feeding of PAs partially recovered fertility, whereas NA supplementation improved fertility and also reversed interveinal chlorosis. The analysis of PA synthase crystal structures containing bound MTA suggests that the corresponding enzyme activities are sensitive to available MTA. Mutant plants that expressed either MTN or human methylthioadenosine phosphorylase (which metabolizes MTA without producing MTR) appeared wild type, proving that the abnormal traits of the mutant are due to MTA accumulation rather than reduced MTR. Based on our results, we propose that the key targets affected by increased MTA content are thermospermine synthase activity and spermidine-dependent posttranslational modification of eukaryotic initiation factor 5A.
ANAP: An Integrated Knowledge Base for Arabidopsis Protein Interaction Network Analysis
Authors: Wang Congmao , Marshall Alex , Zhang Dabing , Wilson Zoe A.
Published: February 2012

Protein interactions are fundamental to the molecular processes occurring within an organism and can be utilized in network biology to help organize, simplify, and understand biological complexity. Currently, there are more than 10 publicly available Arabidopsis (Arabidopsis thaliana) protein interaction databases. However, there are limitations with these databases, including different types of interaction evidence, a lack of defined standards for protein identifiers, differing levels of information, and, critically, a lack of integration between them. In this paper, we present an interactive bioinformatics Web tool, ANAP (Arabidopsis Network Analysis Pipeline), which serves to effectively integrate the different data sets and maximize access to available data. ANAP has been developed for Arabidopsis protein interaction integration and network-based study to facilitate functional protein network analysis. ANAP integrates 11 Arabidopsis protein interaction databases, comprising 201,699 unique protein interaction pairs, 15,208 identifiers (including 11,931 The Arabidopsis Information Resource Arabidopsis Genome Initiative codes), 89 interaction detection methods, 73 species that interact with Arabidopsis, and 6,161 references. ANAP can be used as a knowledge base for constructing protein interaction networks based on user input and supports both direct and indirect interaction analysis. It has an intuitive graphical interface allowing easy network visualization and provides extensive detailed evidence for each interaction. In addition, ANAP displays the gene and protein annotation in the generated interactive network with links to The Arabidopsis Information Resource, the AtGenExpress Visualization Tool, the Arabidopsis 1,001 Genomes GBrowse, the Protein Knowledgebase, the Kyoto Encyclopedia of Genes and Genomes, and the Ensembl Genome Browser to significantly aid functional network analysis. The tool is available open access at http://gmdd.shgmo.org/Computational-Biology/ANAP.
SR1, a Calmodulin-Binding Transcription Factor, Modulates Plant Defense and Ethylene-Induced Senescence by Directly Regulating NDR1 and EIN3
Authors: Nie Haozhen , Zhao Chunzhao , Wu Guangheng , Wu Yingying , Chen Yongfang , Tang Dingzhong
Published: February 2012

Plant defense responses are tightly controlled by many positive and negative regulators to cope with attacks from various pathogens. Arabidopsis (Arabidopsis thaliana) ENHANCED DISEASE RESISTANCE2 (EDR2) is a negative regulator of powdery mildew resistance, and edr2 mutants display enhanced resistance to powdery mildew (Golovinomyces cichoracearum). To identify components acting in the EDR2 pathway, we screened for edr2 suppressors and identified a gain-of-function mutation in SIGNAL RESPONSIVE1 (SR1), which encodes a calmodulin-binding transcription activator. The sr1-4D gain-of-function mutation suppresses all edr2-associated phenotypes, including powdery mildew resistance, mildew-induced cell death, and ethylene-induced senescence. The sr1-4D single mutant is more susceptible to a Pseudomonas syringae pv tomato DC3000 virulent strain and to avirulent strains carrying avrRpt2 or avrRPS4 than the wild type. We show that SR1 directly binds to the promoter region of NON-RACE-SPECIFIC DISEASE RESISTANCE1 (NDR1), a key component in RESISTANCE TO PSEUDOMONAS SYRINGAE2-mediated plant immunity. Also, the ndr1 mutation suppresses the sr1-1 null allele, which shows enhanced resistance to both P. syringae pv tomato DC3000 avrRpt2 and G. cichoracearum. In addition, we show that SR1 regulates ethylene-induced senescence by directly binding to the ETHYLENE INSENSITIVE3 (EIN3) promoter region in vivo. Enhanced ethylene-induced senescence in sr1-1 is suppressed by ein3. Our data indicate that SR1 plays an important role in plant immunity and ethylene signaling by directly regulating NDR1 and EIN3.
Nucleotide and RNA Metabolism Prime Translational Initiation in the Earliest Events of Mitochondrial Biogenesis during Arabidopsis Germination
Authors: Law Simon R. , Narsai Reena , Taylor Nicolas L. , Delannoy Etienne , Carrie Chris , Giraud Estelle , Millar A. Harvey , Small Ian , Whelan James
Published: February 2012

Mitochondria play a crucial role in germination and early seedling growth in Arabidopsis (Arabidopsis thaliana). Morphological observations of mitochondria revealed that mitochondrial numbers, typical size, and oval morphology were evident after 12 h of imbibition in continuous light (following 48 h of stratification). The transition from a dormant to an active metabolic state was punctuated by an early molecular switch, characterized by a transient burst in the expression of genes encoding mitochondrial proteins. Factors involved in mitochondrial transcription and RNA processing were overrepresented among these early-expressed genes. This was closely followed by an increase in the transcript abundance of genes encoding proteins involved in mitochondrial DNA replication and translation. This burst in the expression of factors implicated in mitochondrial RNA and DNA metabolism was accompanied by an increase in transcripts encoding components required for nucleotide biosynthesis in the cytosol and increases in transcript abundance of specific members of the mitochondrial carrier protein family that have previously been associated with nucleotide transport into mitochondria. Only after these genes peaked in expression and largely declined were typical mitochondrial numbers and morphology observed. Subsequently, there was an increase in transcript abundance for various bioenergetic and metabolic functions of mitochondria. The coordination of nucleus- and organelle-encoded gene expression was also examined by quantitative reverse transcription-polymerase chain reaction, specifically for components of the mitochondrial electron transport chain and the chloroplastic photosynthetic machinery. Analysis of protein abundance using western-blot analysis and mass spectrometry revealed that for many proteins, patterns of protein and transcript abundance changes displayed significant positive correlations. A model for mitochondrial biogenesis during germination is proposed, in which an early increase in the abundance of transcripts encoding biogenesis functions (RNA metabolism and import components) precedes a later cascade of gene expression encoding the bioenergetic and metabolic functions of mitochondria.
Aspects regarding the application of the quality principles in the university library
Authors: Albu Cristina , Cristian Adriana , Pistol Nicoleta
Published: February 2012

Purpose

Providing a wealth of documents and appropriate information in support of the university curriculum and research syllabus represents the ultimate goal of all the efforts made by university libraries. The paper aims to study the quality of services as an indicator of quality improvement in the educational process.

Design/methodology/approach

The users should be permanently consulted and their satisfaction should be a permanent concern. The periodical evaluation of the services offered by the academic library, by means of questionnaires is done in order to monitor the difficulties encountered by users. The analysis of the strong and weak points of the services provided leads to improvements in the quality of service.

Findings

The paper reveals that assessment criteria, within the excellence models, provide a basis for the organization to compare its own performances against the performances of other similar organizations

Practical implications

Practical implications are a better use of the information resources.

Originality/value

The paper will help librarians to improve their library services by increasing quality and user satisfaction.
Focusing on the human resources in academic librarianship:an outlook from Serbia
Authors: Župan Vesna
Published: February 2012

Purpose

This article aims to overcome the attitude that information is most important for social development. It also aims to stress the ways of human resources development in the academic librarianship of Serbia.

Design/methodology/approach

An empirical method is implemented in this paper.

Findings

This article shows how librarians in Serbia follow world positive practice and adjust themselves in order to achieve higher levels of professional competence.

Research limitations/implications

The bibliography of researchers is pointed out as an achievement in the Serbian academic environment which is very important for the development of collaboration between readers in a professional field and researchers.

Practical implications

Human resources managers in academic libraries may rely on the experience of Serbian librarians and implement those solutions they would estimate the most useful for their academic practice.

Social implications

Some results of librarians' work are to be found in free access. These are the results of cataloguing and subject indexing through which librarians also contribute to global knowledge. Generally speaking librarians instruct users in the information society; therefore, the professional environment should create conditions for permanent improvement of human resources quality in academic libraries.

Originality/value

This article provides librarians with an alternative method to achieving stronger professional skills from information literacy tutorials and to produce reporting without the need for conventional learning management systems (LMS).