bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural anomalies, spin transitions, and charge disproportionation in LnCoO3
Authors: Knížek Karel , Jirák Zdeněk , Hejtmánek Jiří , Henry Paul , André Gilles
Published: January 2008

The diamagnetic-paramagnetic and insulator-metal transitions in LnCoO3 perovskites (Ln=La,Y, rare earths) are reinterpreted and modeled as a two-level excitation process. In distinction to previous models, the present approach can be characterized as a low-high-intermediate spin LS-HS-IS scenario. The first level is the local excitation of HS Co3+ species in the LS ground state. The second excitation is based on the interatomic electron transfer between the LS/HS pairs, leading finally to a stabilization of the metallic phase based on IS Co3+. The model parameters have been quantified for Ln=La, Pr, and Nd samples using the powder neutron diffraction on the thermal expansion of Co–O bonds that is associated with the two successive spin transitions. The same model is applied to interpret the magnetic susceptibility of LaCoO3 and YCoO3.
Hydrostatic pressure study of single-crystalline UNi0.5Sb2
Authors: Davis B. K. , Torikachvili M. S. , Mun E. D. , Frederick J. C. , Miller G. J. , Thimmaiah S. , Bud’ko S. L. , Canfield P. C.
Published: January 2008

We studied single crystals of the antiferromagnetic compound UNi0.5Sb2 (TN≈161K) by means of measurements of magnetic susceptibility (χ), specific heat (Cp), and electrical resistivity (ρ) at ambient pressure, and resistivity under hydrostatic pressures up to 20kbars, in the temperature range from 1.9to300K. The thermal coefficient of the electrical resistivity (dρ∕dT) changes drastically from positive below TN to negative above, reflecting the loss of spin-disorder scattering in the ordered phase. Two small features in the ρ versus T data centered near 40 and 85K correlate well in temperature with features in the magnetic susceptibility and are consistent with other data in the literature. These features are quite hysteretic in temperature, i.e., the difference between the warming and cooling cycles are about 10 and 6K, respectively. The effect of pressure is to raise TN at the approximate rate of 0.76K∕kbar, while progressively suppressing the amplitude of the small features in ρ versus T at lower temperatures and increasing the thermal hysteresis.
Current-perpendicular-to-plane giant magnetoresistance in half-metallic pseudo-spin-valve structures
Authors: Tripathy D. , Adeyeye A. O.
Published: January 2008

We have investigated the giant magnetoresistance (GMR) effect in Fe3O4∕Cu∕Ni80Fe20 pseudo-spin-valve (PSV) structures for the current-perpendicular-to-plane (CPP) configuration. We observed drastic changes in the CPP GMR as the thickness of the Cu spacer layer, tCu, was varied. The GMR ratio decreases monotonically with increasing tCu, in good agreement with the Valet-Fert model in the long spin diffusion length limit. It was also observed that for a fixed tCu, GMR ratio increases with increasing Fe3O4 layer thickness due to enhanced contributions from bulk scattering to the overall spin dependent scattering in the PSV structure. The CPP GMR ratio has strong temperature dependence and decreases monotonically with increasing temperature.
Novel nanophysics in antiferromagnetic Heisenberg chains
Authors: Brown G.
Published: January 2008

Recently, thermoinduced magnetization (TiM) has been predicted to lead to ferromagnetic properties in nanoparticles of antiferromagnetic materials below the ordering temperature. Specifically, the susceptibility is found to increase linearly as the temperature is increased. Here, the magnetic properties of linear chains of three-dimensional classical Heisenberg spins are calculated both analytically and using Monte Carlo techniques. TiM is shown to be associated with the ordering of the spins induced by a single-site uniaxial anisotropy, and the per-spin susceptibility is found to be approximately independent of the number of spins in the chain. For large anisotropies, TiM is shown analytically to be associated with the thermal fluctuations of individual spins, in contrast to current theories.
Detection of pinholes in magnetic tunnel junctions by magnetic coupling
Authors: Pong Philip W. T. , Dennis Cindi L. , Castillo Audie , Chen Andrew , Egelhoff William F.
Published: January 2008

Pinholes in tunnel barriers are detrimental to the performance of magnetic tunnel junctions (MTJs) since they create direct magnetic exchange coupling between the free and pinned magnetic films and may act as current short circuits. A simple and straightforward technique which enables observation of pinholes and distinguishes pinhole coupling from orange-peel coupling would aid greatly in optimizing the performance of MTJs. However, the existing methods for this determination are quite complex and destructive and do not work on complete structures. We have developed a simpler, nondestructive method that works on full MTJ structures which is able to identify whether an observed coupling arises primarily from magnetic exchange coupling through pinholes or from orange-peel coupling. The method is based on the shift in the free layer hysteresis loop at low temperatures. It is well known that the shift in the pinned layer loop at low temperatures is due to the sharp increase of the IrMn pinning strength. If pinholes exist, the free layer loop will also exhibit a shift due to direct exchange coupling. If there are no pinholes, no shift will be observed since orange-peel coupling is magnetostatic and cobalt has essentially no increase in magnetization below 300K. In this way, a quick diagnosis can be made of whether or not pinholes exist in the MTJ.
Anomalous low temperature spin reorientation in carbon substituted Pr–Co–B–C alloys
Authors: Zhao X. G. , Cui W. B. , Lv X. K. , Ren W. J. , Li D. , Liu W. , Zhang Z. D.
Published: January 2008

We studied the effects of C substitution for B on structural and magnetic properties of Pr16Co76B8−xCx (0⩽x⩽8) alloys, prepared by mechanical alloying and subsequent annealing. An attempt to synthesize Pr2Co14C compound has been carried out by a gradual C substitution of B in Pr16Co76B8. The x-ray diffraction results show that after annealed at 1073K for 30min, Pr2Co14(B,C) phase with tetragonal Nd2Fe14B-type structure is formed as the main phase for 0⩽x⩽7. The Pr2Co14C phase has not been observed in mechanical alloyed B-free powders (x=8). The lattice parameter c of the Pr2Co14(B,C) phase decreases with increasing the carbon content. The highest coercivity of 21.9kOe has been obtained in Pr16Co76B6C2 alloys. The spin-reorientation temperature TSR1 increases with increasing the carbon content from 663K for x=0 to 685K for x=7. However, the spin reorientation is observed at 40K for Pr16Co76B6C2 and then the spin-reorientation temperature TSR2 is nearly unchanged at 125K for Pr16Co76B8−xCx alloys with x=4, 6, and 7, which may be caused by the solubility of carbon atoms. The anomaly of the spin reorientation observed at low temperatures in C-substituted Pr16Co76B8−xCx (x=2, 4, 6, and 7) alloys may be related to the Pr3+ instability.
de Haas–van Alphen oscillations close to a quantum critical point
Authors: Schlottmann P.
Published: January 2008

The amplitudes of de Haas–van Alphen oscillations are calculated for a system of heavy fermions close to a quantum critical point (QCP). The Lifshitz-Kosevich expression is modified by the quasiparticle self-energy, which has been evaluated previously. The model consists of nested Fermi surfaces of an electron pocket and a hole pocket separated by a wave vector Q, which give rise to itinerant antiferromagnetism for a repulsive interaction between the particles. The order is gradually suppressed by mismatching the nesting and a QCP is obtained as TN tends to zero.
Enhancing domain wall speed in nanowires with transverse magnetic fields
Authors: Kunz Andrew , Reiff Sarah C.
Published: January 2008

Dynamic micromagnetic simulation studies have been completed to observe the motion of a domain wall in a magnetic nanowire in an effort to increase the field-driven domain wall speed. Previous studies have shown that the wire dimensions place a cap on the maximum speed attainable by a domain wall when driven by a magnetic field placed along the direction of the nanowire. Here we present data showing a significant increase in the maximum speed of a domain wall due to the addition of a magnetic field placed perpendicular to the longitudinal driving field. The results are expressed in terms of the relative alignment of the transverse field direction with respect to the direction of the magnetic moments within the domain wall. In particular, when the transverse field is parallel to the magnetic moments within the domain wall, the velocity of the wall varies linearly with the strength of the transverse field increasing by up to 20%. Further examination of the domain wall structure shows that the length of the domain wall also depends linearly on the strength of the transverse field. We present a simple model to correlate the effects.
Studies of magnetic entropy change and phase transitions in SrRu1−xMnxO3 perovskite
Authors: Zhang Xiao-Yu , Chen Yajie , Li Zhen-Ya
Published: January 2008

This paper reports a systematical investigation on the role of magnetic phase transitions on magnetocaloric effect in polycrystalline SrRu1−xMnxO3 (0⩽x⩽0.72), combining with the temperature dependent magnetization measurement by a superconducting quantum interference device. Mn substitution drives the magnetic phase transition from ferromagnetic state to antiferromagnetic state via a short-range magnetic order. The magnetic entropy change (ΔSM) presents negative values and a maximum at Curie temperature TC and/or spin freezing temperature Tf for 0⩽x⩽0.27, which is due to the contribution of the spin ordering induced by magnetic field. In addition, we also observe positive magnetic entropy changes (ΔSP) at Néel temperature TN for high Mn concentration (x⩾0.41) as the charge ordering is negligible. Since the magnetization is insensitive to external field in the vicinity of TN, the positive magnetic entropy change is considered to stem from the dramatic temperature dependence of the magnetization.
Tunable surface plasma resonance frequency in Ag core/Au shell nanoparticles system prepared by laser ablation
Authors: Han Huifeng , Fang Yan , Li Zhipeng , Xu Hongxing
Published: January 2008

A method for preparation of Ag core/Au shell nanoparticles with tunable surface plasma resonance (SPR) band was presented and studied. It was found that the tunable SPR band could be significantly conducted and achieved by laser ablation to Au plate in Ag colloidal solution, leading to the formation of Ag core/Au shell structure by the deposition of Au atoms on the surface of Ag nanoparticles. Dependence of the tunable shift of SPR bands on Ag core/Au shell structure was further illustrated by simulation of absorption spectra based on Mie theory, and consistent with the experimental results.
Reversal of single-domain magnetic nanoparticles induced by pulsed magnetic fields
Authors: Xi Haiwen , Gao Kai-Zhong , Xue Song
Published: January 2008

The magnetization dynamics of a magnetic nanoparticle in the presence of pulsed magnetic fields is described by the Landau-Lifshitz-Gilbert equation. In the circumstance where a reversal magnetic field pulse follows a transverse magnetic field pulse with a subnanosecond length, fast magnetization switching can be achieved when the field strength of the transverse field pulse is less than half of the uniaxial anisotropy field of the nanoparticle. The total field for the magnetization switching can be significantly lower than the Stoner-Wohlfarth limit. The magnetization switching is faster for larger damping constant. When the field strength of the transverse field pulse is greater than half of the uniaxial anisotropy field of the nanoparticle, the magnetization of the nanoparticle may not switch, depending on the condition and the properties of the nanoparticle. The magnetization dynamics becomes chaotic and switching of the magnetization can no longer be well controlled.
Magnetic characterization of exchange-coupled composite media
Authors: Deakin T. , O’Grady K.
Published: January 2008

In this work we compare the magnetization reversal processes in a set of exchange-coupled composite (ECC) media and a similar set of continuous granular coupled (CGC) media. We have studied the reversal processes in both systems as a function of the thickness (ts) of the soft overlayer. We find that the soft overlayer contributes a reversible contribution to the magnetization in both types of media, lowering the coercivity in both cases but that there is an optimum value of ts in terms of the resulting squareness. This has important implications for the output signal in both cases. We have also studied the activation volume of reversal which will ultimately determine the limit to the data density achievable in both types of media. We find that in each case the activation volume increases monotonically with the thickness of the soft layer, indicating that nucleation of reversal in the soft layer will determine the ultimate data density achievable. Although absolute values for the activation volume cannot be determined due to the uncertainty in the value of Ms, our data indicate unexpectedly that an exchange-coupled soft layer, i.e., the ECC media, has smaller activation volumes than is the case for CGC media. However, we cannot discount the possibility that increased anisotropy from the hard layer may contribute to this effect.
Magnetocaloric effect in Co-rich Er(Co1−xFex)2 Laves phase
Authors: Liu X. B. , Altounian Z.
Published: January 2008

Magnetic properties and magnetocaloric effect (MCE) in Co rich Er(Co1−xFex)2 have been studied by magnetic measurements and electronic structure calculations. With increasing x from 0 to 0.2, TC increases from 32to360K and the magnetization decreases from 6.8μB to 5.3μB per formula unit (5K), respectively. The peak value of the magnetic entropy change decreases rapidly from 23.0to4.5J∕kgK (under an external field change of 5T) with increasing x from 0 to 0.1. The addition of a small amount of Fe in ErCo2 drives the order of magnetic transition from first order to second order, as evidenced by the magnetothermal curves around TC, which is responsible for the decrease in MCE. The magnetic moment dependence of total energy Et(m) is studied by a fixed spin moment band structure calculation. Et(m) for x=0 has two minima at a low and a high Co magnetic moment, which correspond to a metastable and a stable magnetic state, respectively. On the other hand, Et(m) for x=0.125 shows only one minimum at a high Co (Fe) magnetic moment. These fixed spin moment calculation results explain the observed change in the order of magnetic transition by the addition of Fe in ErCo2.
256-channel magnetic imaging system
Authors: da Silva F. C. S. , Halloran S. T. , Kos A. B. , Pappas D. P.
Published: January 2008

We present the design and fabrication of a magnetoresistive imaging system capable of scanning 256 channels simultaneously along linear ranges of either 4 or 13mm. High speed electronics read the channels and transfer the data to a computer that builds and displays the images. The system was successfully used to image magnetic tapes for real-time forensic validation purposes and can also be applied in other noninvasive imaging applications.
Electron counting at room temperature in an avalanche bipolar transistor
Authors: Lany Marc , Boero Giovanni , Popovic Radivoje
Published: January 2008

We report on real-time detection of single electrons inside a n-p-n bipolar junction transistor at room temperature. Single electrons injected through the base-emitter junction trigger with a high probability the avalanche breakdown of the strongly reverse-biased collector-base junction. The breakdown, rapidly stopped by an avalanche quenching circuit, produces a voltage pulse at the collector which corresponds to the detection of a single electron. Pulse rates corresponding to currents down to the attoampere range are measured with an integration time of about 10s.
Arbitrary amplitude dust ion acoustic solitary waves in dense Fermi plasmas
Authors: Mahmood S.
Published: January 2008

The arbitrary amplitude dust ion acoustic solitary waves are investigated in unmagnetized quantum plasmas. The quantum hydrodynamic model is employed with the Sagdeev potential approach to describe the nonlinear dust ion acoustic waves in dense Fermi plasmas. It is found that electron density dip structures are formed in the subsonic as well as in the supersonic regions in such dense dusty plasmas. The range of wave Mach number is increased with the increase in the static dust density in quantum plasmas. Both the wave amplitude and width of the nonlinear structure are affected by static dust density. The quantum parameter effects only the width of the nonlinear structure. The amplitude of dust ion acoustic solitary wave is reduced with the increase in the wave Mach number.
Electron vacuum acceleration by a tightly focused laser pulse
Authors: Popov K. I. , Bychenkov V. Yu. , Rozmus W. , Sydora R. D.
Published: January 2008

Interaction of a tightly focused relativistic short laser pulse with electrons beyond the paraxial approximation is studied by using the test particle approach and the Stratton–Chu integrals for the laser fields. The investigation addresses the regime where the focal spot size may be comparable to the laser wavelength. The mapping of near focal positions of the electrons to energy space allows for the study of important features of electron vacuum acceleration by a tightly focused laser pulse and to choose optimal parameters for acceleration. Two acceleration mechanisms have been observed and discussed. Directional properties of the accelerated electrons have been analyzed.
Magnetic order in geometrically constrained domain walls
Authors: Czerner Michael , Yavorsky Bogdan Yu. , Mertig Ingrid
Published: January 2008

The magnetic structure and the electronic transport properties of domain walls in magnetic transition metal nanocontacts (Ni, Co, and Fe) are investigated from first principles. In particular, the shape of the domain wall pinned in a monatomic nanowire, which is suspended between two semi-infinite leads, and the effect on the magnetotransport are discussed in detail. For the calculation, a modification of the Korringa-Kohn-Rostoker method is used to treat noncollinear magnetic systems fully self-consistently. It is shown that the domain wall profile differs from the known Bloch and Néel walls.
High temperature ferromagnetism and perpendicular magnetic anisotropy in Fe-doped In2O3 films
Authors: Xing P. F. , Chen Y. X. , Yan Shi-Shen , Liu G. L. , Mei L. M. , Wang K. , Han X. D. , Zhang Z.
Published: January 2008

High temperature ferromagnetism and perpendicular magnetic anisotropy were observed in Fe-doped In2O3 magnetic semiconductor films deposited on R-cut sapphire by pulse laser deposition. The films show a Curie temperature as high as 927K. Strong perpendicular magnetic anisotropy with a remnant magnetization ratio of 0.77 and a coercivity of 680Oe is demonstrated. Extensive microstructure, composition, and magnetic studies indicate that Fe element incorporates into the indium oxide lattice by substituting the position of indium atoms, which suggests the observed ferromagnetism is intrinsic rather than from Fe clusters or any other magnetic impurity phases.
An improved time-of-flight method for cluster deposition and ion-scattering experiments
Authors: Turra M. , Waldschmidt B. , Kaiser B. , Schäfer R.
Published: January 2008

A molecular beam apparatus has been developed for deposition and scattering experiments of size-selected clusters. The new setup combines a bimetallic laser ablation cluster source with a collinear time-of-flight mass spectrometer. Mass selection is achieved with a pulsed electrostatic mirror. A significantly improved transmission in combination with a reduction of the kinetic energy distribution of the mass selected clusters has been obtained. Without further modification of the apparatus, surface-induced dissociation of mass selected tin clusters has been investigated, demonstrating the possibility to combine cluster beam deposition and scattering experiments.
Compact cryogenic system with mechanical cryocoolers for antihydrogen synthesis
Authors: Shibata M. , Mohri A. , Kanai Y. , Enomoto Y. , Yamazaki Y.
Published: January 2008

We have developed a compact cryogenic system which cools a vacuum chamber housing multi-ring trap electrodes (MRTs) of an antihydrogen synthesis trap using mechanical cryocoolers to achieve background pressure less than 10−12Torr. The vacuum chamber and the cryocoolers are thermally connected by copper strips of 99.9999% in purity. All components are installed within a diametric gap between the MRT of ϕ108mm and a magnet bore of ϕ160mm. An adjusting mechanism is prepared to align the MRT axis to the magnet axis. The vacuum chamber was successfully cooled down to 4.0K after 14h of cooling with heat load of 0.8W.
Electrical control of magnon propagation in multiferroic BiFeO3 films
Authors: de Sousa Rogerio , Moore Joel E.
Published: January 2008

The spin wave spectra of multiferroic BiFeO3 films is calculated using a phenomenological Landau theory that includes magnetostatic effects. The lowest frequency magnon dispersion is shown to be quite sensitive to the angle between spin wave propagation vector and the Néel moment. Since electrical switching of the Néel moment has recently been demonstrated in this material, the sensitivity of the magnon dispersion permits direct electrical switching of spin wave propagation. This effect can be used to construct spin wave logical gates without current pulses, potentially allowing reduced power dissipation per logical operation.
Modeling of nitrogen profile effects on direct tunneling probability in ultrathin nitrided oxides
Authors: Liu Po-Tsun , Huang Chen-Shuo , Lee D. Y. , Lim P. S. , Lin S. W. , Chen C. C. , Tao H. J. , Mii Y. J.
Published: January 2008

The dependence of the gate tunneling current (Jg) on nitrogen profile (N profile) within an ultrathin silicon oxynitride film is reported. It was found that gate tunneling current is dependent on N profile, even with equal oxide thickness and nitrogen dosage. Gate tunneling current increased with steeper N profile, and it had higher sensitivity for p-type metal-oxide-semiconductor field-effect transistor (MOSFET) than n-type MOSFET. A direct tunneling model based on Wentzel-Kramers-Brillouin approximation has been proposed. The model described the influence of N profiles on gate tunneling current through local change of dielectric constant, band bending, and effective mass. Also, it reasonably explained the different Jg sensitivity in n-∕p-MOSFETs, a phenomenon that has not been addressed in earlier publications.
Nanowelding of a multiwalled carbon nanotube to metal surface and its electron field emission properties
Authors: Asaka Koji , Nakahara Hitoshi , Saito Yahachi
Published: January 2008

Multiwalled carbon nanotubes (MWNTs) were manipulated inside a high-resolution transmission electron microscope combined with a nano manipulator, and a single MWNT emitter freestanding on a platinum surface was fabricated by nanowelding. The electron field emission properties of the single MWNT were in situ measured at various gap distances in a range from 27to442nm with simultaneous imaging by transmission electron microscopy. Field enhancement factors varying with the gap distance and the thermally enhanced electron emission were observed.
Spin-orbit interaction in Au structures of various dimensionalities
Authors: Yang Xiaoping , Zhou Jian , Weng Hongming , Dong Jinming
Published: January 2008

Variation of the geometrical and electronic properties of the gold materials in different dimensions has been investigated by ab initio method, taking into account the spin-orbit interaction. It is found that spin-orbit effects in different dimensional Au materials depend greatly on fundamental symmetry and dimensionality. For single-walled gold nanotubes, spin-orbit interaction decreases significantly the conducting channel number of achiral tube (4,0) and leads to spin splitting at Fermi level of chiral tube, indicating that quasi-one-dimensional gold tube can be a good candidate for the spin-electron devices. Furthermore, our results suggest that cage cluster might be synthesizable experimentally by taking gold tube structure as parent material.
Linear optical protocol for preparation of N-photon Greenberger–Horne–Zeilinger state with conventional photon detectors
Authors: Xia Yan , Song Jie , Song He-Shan
Published: January 2008

We propose a linear optical protocol to generate Greenberger–Horne–Zeilinger (GHZ) state of N distant photons with the certain success probability. The proposed setup involves simple linear optical elements, N pairs of the two-photon polarization entangled states, and the conventional photon detectors that only distinguish the vacuum and nonvacuum Fock number states. This makes the protocol more realizable in experiments.
Origin of high piezoelectric response of Pb(ZrxTi1−x)O3 at the morphotropic phase boundary: Role of elastic instability
Authors: Singh Akhilesh Kumar , Mishra Sunil Kumar , Ragini  , Pandey Dhananjai , Yoon Songhak , Baik Sunggi , Shin Namsoo
Published: January 2008

Temperature dependent structural changes in a nearly pure monoclinic phase composition (x=0.525) of Pb(ZrxTi1−x)O3 (PZT) have been investigated using Rietveld analysis of high-resolution synchrotron powder x-ray diffraction data and correlated with changes in the dielectric constant and planar electromechanical coupling coefficient. Our results show that the intrinsic piezoelectric response of the tetragonal phase of PZT is higher than that of the monoclinic phase. It is also shown that the high piezoelectric response of PZT may be linked with an anomalous softening of the elastic modulus (1∕S11E) of the tetragonal compositions closest to the morphotropic phase boundary.
Ag
–
Ba
0.75
Sr
0.25
Ti
O
3
composites with excellent dielectric properties
Authors: Huang Jiquan , Cao Yongge , Hong Maochun , Du Piyi
Published: January 2008

The percolative ceramic composites of Ba0.75Sr0.25TiO3∕Ag (BST/Ag) with dense microstructure were sintered at a low temperature of 960°C. Excellent dielectric properties, such as high dielectric constant (εr∼24000), low dielectric loss, and high dielectric tunability, were reported. The dielectric constant is found to be nearly temperature and frequency independent. It is essential to introduce the low-melting-point metal of silver into BST ceramics for significantly enhancing the dielectric properties of the composites. The superproperties make it potential to be used for electronic devices such as high charge-storage capacitors and tunable filters.
BiP mutants that are unable to interact with endoplasmic reticulum DnaJ proteins provide insights into interdomain interactions in BiP
Authors: Awad Walid , Estrada Isaac , Shen Ying , Hendershot Linda M.
Published: January 2008

The heat shock protein (Hsp)70 family of molecular chaperones interacts with unfolded proteins through a C-terminal substrate-binding domain (SBD) that is controlled by nucleotide binding to the N-terminal domain. The ATPase cycle is regulated by cochaperones, including DnaJ proteins that accelerate ATP hydrolysis to stabilize the Hsp70–substrate complex. We found that R197 in hamster BiP, which resides at the surface of the nucleotide-binding domain, is critical for both association with endoplasmic reticulum DnaJ proteins and interaction with the SBD. Decreasing the positive charge at this residue enhanced basal ATPase activity, destabilized interaction with the SBD, and reduced substrate release both
in vitro
and
in vivo
. Mutation of three glutamic acids in the SBD mimicked many of these effects. Our data provide insights into communications between the two domains and suggest a mechanism by which DnaJ proteins increase ATP hydrolysis.
B-cell receptor activation inhibits AID expression through calmodulin inhibition of E-proteins
Authors: Hauser Jannek , Sveshnikova Natalia , Wallenius Anders , Baradaran Sanna , Saarikettu Juha , Grundström Thomas
Published: January 2008

Upon encountering antigens, B-lymphocytes can adapt to produce a highly specific and potent antibody response. Somatic hypermutation, which introduces point mutations in the variable regions of antibody genes, can increase the affinity for antigen, and antibody effector functions can be altered by class switch recombination (CSR), which changes the expressed constant region exons. Activation-induced cytidine deaminase (AID) is the mutagenic antibody diversification enzyme that is essential for both somatic hypermutation and CSR. The mutagenic AID enzyme has to be tightly controlled. Here, we show that engagement of the membrane-bound antibodies of the B-cell receptor (BCR), which signals that good antibody affinity has been reached, inhibits AID gene expression and that calcium (Ca
2+
) signaling is essential for this inhibition. Moreover, we show that overexpression of the Ca
2+
sensor protein calmodulin inhibits AID gene expression, and that the transcription factor E2A is required for regulation of the AID gene by the BCR. E2A mutated in the binding site for calmodulin, and thus showing calmodulin-resistant DNA binding, makes AID expression resistant to the inhibition through BCR activation. Thus, BCR activation inhibits AID gene expression through Ca
2+
/calmodulin inhibition of E2A.
A machine-learning approach to combined evidence validation of genome assemblies
Authors: Choi Jeong-Hyeon , Kim Sun , Tang Haixu , Andrews Justen , Gilbert Don G. , Colbourne John K.
Published: January 2008

Motivation: While it is common to refer to ‘the genome sequence’ as if it were a single, complete and contiguous DNA string, it is in fact an assembly of millions of small, partially overlapping DNA fragments. Sophisticated computer algorithms (assemblers and scaffolders) merge these DNA fragments into contigs, and place these contigs into sequence scaffolds using the paired-end sequences derived from large-insert DNA libraries. Each step in this automated process is susceptible to producing errors; hence, the resulting draft assembly represents (in practice) only a likely assembly that requires further validation. Knowing which parts of the draft assembly are likely free of errors is critical if researchers are to draw reliable conclusions from the assembled sequence data.

Results: We develop a machine-learning method to detect assembly errors in sequence assemblies. Several in silico measures for assembly validation have been proposed by various researchers. Using three benchmarking Drosophila draft genomes, we evaluate these techniques along with some new measures that we propose, including the good-minus-bad coverage (GMB), the good-to-bad-ratio (RGB), the average Z-score (AZ) and the average absolute Z-score (ASZ). Our results show that the GMB measure performs better than the others in both its sensitivity and its specificity for assembly error detection. Nevertheless, no single method performs sufficiently well to reliably detect genomic regions requiring attention for further experimental verification. To utilize the advantages of all these measures, we develop a novel machine learning approach that combines these individual measures to achieve a higher prediction accuracy (i.e. greater than 90%). Our combined evidence approach avoids the difficult and often ad hoc selection of many parameters the individual measures require, and significantly improves the overall precisions on the benchmarking data sets.

Availability:  http://people.cgb.indiana.edu/jeochoi/gav/

Contact:  jeochoi@indiana.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments
Authors: Hong Fangxin , Breitling Rainer
Published: January 2008

Motivation: The proliferation of public data repositories creates a need for meta-analysis methods to efficiently evaluate, integrate and validate related datasets produced by independent groups. A t-based approach has been proposed to integrate effect size from multiple studies by modeling both intra- and between-study variation. Recently, a non-parametric ‘rank product’ method, which is derived based on biological reasoning of fold-change criteria, has been applied to directly combine multiple datasets into one meta study. Fisher's Inverse χ2 method, which only depends on P-values from individual analyses of each dataset, has been used in a couple of medical studies. While these methods address the question from different angles, it is not clear how they compare with each other.

Results: We comparatively evaluate the three methods; t-based hierarchical modeling, rank products and Fisher's Inverse χ2 test with P-values from either the t-based or the rank product method. A simulation study shows that the rank product method, in general, has higher sensitivity and selectivity than the t-based method in both individual and meta-analysis, especially in the setting of small sample size and/or large between-study variation. Not surprisingly, Fisher's χ2 method highly depends on the method used in the individual analysis. Application to real datasets demonstrates that meta-analysis achieves more reliable identification than an individual analysis, and rank products are more robust in gene ranking, which leads to a much higher reproducibility among independent studies. Though t-based meta-analysis greatly improves over the individual analysis, it suffers from a potentially large amount of false positives when P-values serve as threshold. We conclude that careful meta-analysis is a powerful tool for integrating multiple array studies.

Contact:  fxhong@jimmy.harvard.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Reconstruction of genetic association networks from microarray data: a partial least squares approach
Authors: Pihur Vasyl , Datta Somnath , Datta Susmita
Published: January 2008

Motivation: Gene association/interaction networks provide vast amounts of information about essential processes inside the cell. A complete picture of gene–gene associations/interactions would open new horizons for biologists, ranging from pure appreciation to successful manipulation of biological pathways for therapeutic purposes. Therefore, identification of important biological complexes whose members (genes and their products proteins) interact with each other is of prime importance. Numerous experimental methods exist but, for the most part, they are costly and labor intensive. Computational techniques, such as the one proposed in this work, provide a quick ‘budget’ solution that can be used as a screening tool before more expensive techniques are attempted. Here, we introduce a novel computational method based on the partial least squares (PLS) regression technique for reconstruction of genetic networks from microarray data.

Results: The proposed PLS method is shown to be an effective screening procedure for the detection of gene–gene interactions from microarray data. Both simulated and real microarray experiments show that the PLS-based approach is superior to its competitors both in terms of performance and applicability.

Availability: R code is available from the supplementary web-site whose URL is given below.

Contact: susmita.datta@louisville.edu

Supplementary information: Supplementary information are available at http://www.susmitadatta.org/Supp/GeneNet/supp.htm.
PGMapper: a web-based tool linking phenotype to genes
Authors: Xiong Qing , Qiu Yuhui , Gu Weikuan
Published: January 2008

Summary: With the availability of whole genome sequence in many species, linkage analysis, positional cloning and microarray are gradually becoming powerful tools for investigating the links between phenotype and genotype or genes. However, in these methods, causative genes underlying a quantitative trait locus, or a disease, are usually located within a large genomic region or a large set of genes. Examining the function of every gene is very time consuming and needs to retrieve and integrate the information from multiple databases or genome resources. PGMapper is a software tool for automatically matching phenotype to genes from a defined genome region or a group of given genes by combining the mapping information from the Ensembl database and gene function information from the OMIM and PubMed databases. PGMapper is currently available for candidate gene search of human, mouse, rat, zebrafish and 12 other species.

Availability: Available online at http://www.genediscovery.org/pgmapper/index.jsp

Contact:  wgu@utmem.edu; qxiong1@utmem.edu
A segmental maximum a posteriori approach to genome-wide copy number profiling
Authors: Andersson Robin , Bruder Carl E. G. , Piotrowski Arkadiusz , Menzel Uwe , Nord Helena , Sandgren Johanna , Hvidsten Torgeir R. , Diaz de Ståhl Teresita , Dumanski Jan P. , Komorowski Jan
Published: January 2008

Motivation: Copy number profiling methods aim at assigning DNA copy numbers to chromosomal regions using measurements from microarray-based comparative genomic hybridizations. Among the proposed methods to this end, Hidden Markov Model (HMM)-based approaches seem promising since DNA copy number transitions are naturally captured in the model. Current discrete-index HMM-based approaches do not, however, take into account heterogeneous information regarding the genomic overlap between clones. Moreover, the majority of existing methods are restricted to chromosome-wise analysis.

Results: We introduce a novel Segmental Maximum A Posteriori approach, SMAP, for DNA copy number profiling. Our method is based on discrete-index Hidden Markov Modeling and incorporates genomic distance and overlap between clones. We exploit a priori information through user-controllable parameterization that enables the identification of copy number deviations of various lengths and amplitudes. The model parameters may be inferred at a genome-wide scale to avoid overfitting of model parameters often resulting from chromosome-wise model inference. We report superior performances of SMAP on synthetic data when compared with two recent methods. When applied on our new experimental data, SMAP readily recognizes already known genetic aberrations including both large-scale regions with aberrant DNA copy number and changes affecting only single features on the array. We highlight the differences between the prediction of SMAP and the compared methods and show that SMAP accurately determines copy number changes and benefits from overlap consideration.

Availability: SMAP is available from Bioconductor and within the Linnaeus Centre for Bioinformatics Data Warehouse.

Contact:  Jan.Komorowski@lcb.uu.se

Supplementary information: Supplementary data are available at http://www.lcb.uu.se/papers/r_andersson/SMAP/
HCGene: a software tool to support the hierarchical classification of genes
Authors: Valentini Giorgio , Cesa-Bianchi Nicolò
Published: January 2008

Summary: The R package HCGene (Hierarchical Classification of Genes) implements methods to process and analyze the Gene Ontology and the FunCat taxonomy in order to support the functional classification of genes. HCGene allows the extraction of subgraphs and subtrees related to specific biological problems, the labeling of genes and gene products with multiple and hierarchical functional classes, and the association of different types of bio-molecular data to genes for learning to predict their functions.

Availability:  http://homes.dsi.unimi.it/~valenti/SW/hcgene/download/hcgene_1.0.tar.gz

Contact:  valentini@dsi.unimi.it

Supplementary information: Supplementary data are available at http://homes.dsi.unimi.it/~valenti/SW/hcgene
Estimation and assessment of raw copy numbers at the single locus level
Authors: Bengtsson H. , Irizarry R. , Carvalho B. , Speed T. P.
Published: January 2008

Motivation: Although copy-number aberrations are known to contribute to the diversity of the human DNA and cause various diseases, many aberrations and their phenotypes are still to be explored. The recent development of single-nucleotide polymorphism (SNP) arrays provides researchers with tools for calling genotypes and identifying chromosomal aberrations at an order-of-magnitude greater resolution than possible a few years ago. The fundamental problem in array-based copy-number (CN) analysis is to obtain CN estimates at a single-locus resolution with high accuracy and precision such that downstream segmentation methods are more likely to succeed.

Results: We propose a preprocessing method for estimating raw CNs from Affymetrix SNP arrays. Its core utilizes a multichip probe-level model analogous to that for high-density oligonucleotide expression arrays. We extend this model by adding an adjustment for sequence-specific allelic imbalances such as cross-hybridization between allele A and allele B probes. We focus on total CN estimates, which allows us to further constrain the probe-level model to increase the signal-to-noise ratio of CN estimates. Further improvement is obtained by controlling for PCR effects. Each part of the model is fitted robustly. The performance is assessed by quantifying how well raw CNs alone differentiate between one and two copies on Chromosome X (ChrX) at a single-locus resolution (27kb) up to a 200kb resolution. The evaluation is done with publicly available HapMap data.

Availability: The proposed method is available as part of an open-source R package named aroma.affymetrix. Because it is a bounded-memory algorithm, any number of arrays can be analyzed.

Contact:  hb@stat.berkeley.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Using repeated measurements to validate hierarchical gene clusters
Authors: Bréhélin Laurent , Gascuel Olivier , Martin Olivier
Published: January 2008

Motivation: Hierarchical clustering is a common approach to study protein and gene expression data. This unsupervised technique is used to find clusters of genes or proteins which are expressed in a coordinated manner across a set of conditions. Because of both the biological and technical variability, experimental repetitions are generally performed. In this work, we propose an approach to evaluate the stability of clusters derived from hierarchical clustering by taking repeated measurements into account.

Results: The method is based on the bootstrap technique that is used to obtain pseudo-hierarchies of genes from resampled datasets. Based on a fast dynamic programming algorithm, we compare the original hierarchy to the pseudo-hierarchies and assess the stability of the original gene clusters. Then a shuffling procedure can be used to assess the significance of the cluster stabilities. Our approach is illustrated on simulated data and on two microarray datasets. Compared to the standard hierarchical clustering methodology, it allows to point out the dubious and stable clusters, and thus avoids misleading interpretations.

Availability: The programs were developed in C and R languages.

Contact:  brehelin@lirmm.fr

Supplementary information: Supplementary Material and source code are available at address http://www.lirmm.fr/~brehelin/Stability/
DiMoVo: a Voronoi tessellation-based method for discriminating crystallographic and biological protein–protein interactions
Authors: Bernauer Julie , Bahadur Ranjit Prasad , Rodier Francis , Janin Joël , Poupon Anne
Published: January 2008

Motivation: Knowledge of the oligomeric state of a protein is often essential for understanding its function and mechanism. Within a protein crystal, each protein monomer is in contact with many others, forming many small interfaces and a few larger ones that are biologically significant if the protein is a homodimer in solution, but not if the protein is monomeric. Telling such ‘crystal dimers’ from real ones remains a difficult task.

Results: It has already been demonstrated that the interfaces of native and non-native protein–protein complexes can be distinguished using a combination of parameters computed with a method on the Voronoi tessellation. We show in this article that the same parameters highlight significant differences between the interfaces of biological and crystal dimers. Using these parameters as descriptors in machine learning methods leads to accurate classification of specific and non-specific protein–protein interfaces.

Availability: Software is available at http://fifi.ibbmc.u-psud.fr/DiMoVo

Contact:  anne@rezo.net
GENESIS: genome evolution scenarios
Authors: Gog Simon , Bader Martin , Ohlebusch Enno
Published: January 2008

Summary: We implemented a software tool called GENESIS for three different genome rearrangement problems: Sorting a unichromosomal genome by weighted reversals and transpositions (SwRT), sorting a multichromosomal genome by reversals, translocations, fusions and fissions (SRTl), and sorting a multichromosomal genome by weighted reversals, translocations, fusions, fissions and transpositions (SwRTTl).

Availability: Source code can be obtained by the authors, or use the web interface http://www.uni-ulm.de/in/theo/research/genesis.html

Contact:  simon.gog@uni-ulm.de
TreeMos: a high-throughput phylogenomic approach to find and visualize phylogenetic mosaicism
Authors: Moore J. D. , Allaby R. G.
Published: January 2008

Summary: TreeMos is a novel high-throughput graphical analysis application that allows the user to search for phylogenetic mosaicism among one or more DNA or protein sequence multiple alignments and additional unaligned sequences. TreeMos uses a sliding window and local alignment algorithm to identify the nearest neighbour of each sequence segment, and visualizes instances of sequence segments whose nearest neighbour is anomalous to that identified using the global alignment. Data sets can include whole genome sequences allowing phylogenomic analyses in which mosaicism may be attributed to recombination between any two points in the genome. TreeMos can be run from the command line, or within a web browser allowing the relationships between taxa to be explored by drill-through.

Availability:  http://www2.warwick.ac.uk/fac/sci/whri/research/archaeobotany

Contact:  jonathan.moore@warwick.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.
Light Induces Peroxisome Proliferation in Arabidopsis Seedlings through the Photoreceptor Phytochrome A, the Transcription Factor HY5 HOMOLOG, and the Peroxisomal Protein PEROXIN11b
Authors: Desai Mintu , Hu Jianping
Published: January 2008

Peroxisomes are single membrane-delimited subcellular organelles that carry out numerous vital metabolic reactions in nearly all eukaryotes. Peroxisomes alter their morphology, abundance, and enzymatic constituents in response to environmental cues, yet little is known about the underlying mechanisms. In this work, we investigated the regulatory role of light in peroxisome proliferation in Arabidopsis (Arabidopsis thaliana). We provide evidence that light induces proliferation of peroxisomes in Arabidopsis seedlings and that the peroxisomal protein PEX11b plays an important role in mediating this process. The far-red light receptor phytochrome A (phyA) and the bZIP transcription factor HY5 HOMOLOG (HYH) are both required for the up-regulation of PEX11b in the light. We further demonstrate that the phyA and hyh mutants exhibit reduced peroxisome abundance, a phenotype that can be rescued by overexpressing PEX11b in these plants. The HYH protein is able to bind to the promoter of PEX11b, suggesting that the PEX11b gene is a direct target of HYH. We conclude that HYH and PEX11b constitute a novel branch of the phyA-mediated light signaling cascade, which promotes peroxisome proliferation during seedling photomorphogenesis.