bluuebunny/crossref_metadata_2025 huggingface dataset:
Global ab initio potential energy surfaces for the O2(Σ3g−)+O2(Σ3g−) interaction
Authors: Bartolomei Massimiliano , Carmona-Novillo Estela , Hernández Marta I. , Campos-Martínez José , Hernández-Lamoneda Ramón
Published: September 2010

Completely ab initio global potential energy surfaces (PESs) for the singlet and triplet spin multiplicities of rigid O2(Σ3g−)+O2(Σ3g−) are reported for the first time. They have been obtained by combining an accurate restricted coupled cluster theory with singles, doubles, and perturbative triple excitations [RCCSD(T)] quintet potential [Bartolomei et al.,J. Chem. Phys. 128, 214304 (2008)] with complete active space second order perturbation theory (CASPT2) or, alternatively, multireference configuration interaction (MRCI) calculations of the singlet-quintet and triplet-quintet splittings. Spherical harmonic expansions, containing a large number of terms due to the high anisotropy of the interaction, have been built from the ab initio data. The radial coefficients of these expansions are matched at long range distances with analytical functions based on recent ab initio calculations of the electric properties of the monomers [M. Bartolomei, E. Carmona-Novillo, M. I. Hernández, J. Campos-Martínez, and R. Hernández-Lamoneda, J. Comput. Chem. (2010) (in press)]. The singlet and triplet PESs obtained from either RCCSD(T)-CASPT2 or RCCSD(T)-MRCI calculations are quite similar, although quantitative differences appear in specific terms of the expansion. CASPT2 calculations are the ones giving rise to larger splittings and more attractive interactions, particularly in the region of the absolute minima (in the rectangular D2h geometry). The new singlet, triplet, and quintet PESs are tested against second virial coefficient B(T) data and, their spherically averaged components, against integral cross sections measured with rotationally hot effusive beams. Both types of multiconfigurational approaches provide quite similar results, which, in turn, are in good agreement with the measurements. It is found that discrepancies with the experiments could be removed if the PESs were slightly more attractive. In this regard, the most attractive RCCSD(T)-CASPT2 PESs perform slightly better than the RCCSD(T)-MRCI counterpart.
Correlation of nonexponentiality with dynamic heterogeneity from four-point dynamic susceptibility χ4(t) and its approximation χT(t)
Authors: Roland C. M. , Fragiadakis D. , Coslovich D. , Capaccioli S. , Ngai K. L.
Published: September 2010

Various properties of vitrifying liquids are correlated with the dispersity of the dynamics, the latter reflected in the magnitude of the nonexponentiality parameter, βK, describing the distribution of relaxation times. These properties include the mean relaxation time, τα, the fragility, and the dynamic crossover. The correlations with βK are observed in both experimental data and the results from molecular dynamics simulations on Lennard-Jones (LJ) type systems. Another, rather obvious property to correlate with βK is the dynamic heterogeneity, which can be quantified from the number of molecules, Nc, dynamically correlated over a time span τα. For a given LJ system, Nc can be rigorously calculated and we find that it does indeed correlate with βK over a range of thermodynamic conditions. However, the analysis of experimental data for a broad range of real materials, wherein an approximation is required to obtain Nc, reveals the absence of any relationship between Nc and βK among different materials.
Fabrication of fluoropolymer piezoelectrets by using rigid template: Structure and thermal stability
Authors: Zhang Xiaoqing , Cao Gongxun , Sun Zhuanlan , Xia Zhongfu
Published: September 2010

Fluorocarbon films with regular void structure, made of compact fluoroethylenepropylene (FEP), or skived polytetrafluoroethylene (PTFE), and patterned porous PTFE layers, are successfully fabricated by using a rigid template and fusion bonding process. A corona charging technique is used to make the films piezoelectric, i.e., to be piezoelectrets. The results show that the typical Young’s moduli of the films are in the range of 0.45–0.80 MPa. A maximum quasistatic piezoelectric d33 coefficient up to 500 pC/N is achieved. Compared to the laminated FEP/porous PTFE piezoelectrets without regular void structure, the presently fabricated films show significantly improved thermal stability. Furthermore, when the films are designed, fabricated, and corona charged such that positive charges are deposited in the porous PTFE layers, the thermal stability of d33 coefficients can be further improved. For example, after annealing at 90 °C for 4500 min, these samples have a remaining d33 value of 86% compared with 77% for samples where positive charges are deposited in both, the porous PTFE and the compact FEP layers.
Guided ion beam and theoretical study of the reactions of Hf+ with H2, D2, and HD
Authors: Hinton Christopher S. , Armentrout P. B.
Published: September 2010

The kinetic energy dependences of reactions of the third-row transition metal cation Hf+ with H2, D2, and HD were determined using a guided ion beam tandem mass spectrometer. A flow tube ion source produces Hf+ in its D2 (6s25d1) electronic ground state level. Corresponding state-specific reaction cross sections are obtained. The kinetic energy dependences of the cross sections for the endothermic formation of HfH+ and HfD+ are analyzed to give a 0 K bond dissociation energy of D0(Hf+–H)=2.11±0.08 eV. Quantum chemical calculations at several levels of theory performed here generally overestimate the experimental bond energy but results obtained using the Becke-half-and-half-LYP functional show good agreement. Theory also provides the electronic structures of these species and the reactive potential energy surfaces. Results from the reactions with HD provide insight into the reaction mechanisms and indicates that Hf+ reacts via a statistical mechanism. We also compare this third-row transition metal system with the first-row and second-row congeners, Ti+ and Zr+, and find that Hf+ has a weaker M+–H bond. As most third-row transition metal hydride cation bonds exceed their lighter congeners, this trend is unusual but can be understood using promotion energy arguments.
Chaotic electron trajectories in an electromagnetic wiggler free-electron laser with ion-channel guiding
Authors: Taghavi Amin , Esmaeilzadeh Mahdi , Fallah Mohammad S.
Published: September 2010

Chaotic behavior of an electron motion in combined backward propagating electromagnetic wiggler and ion-channel electrostatic fields is studied. The Poincaré surface-of-sections are employed to investigate chaotic behavior of electron motion. It is shown that the electron motion can exhibit chaotic behavior when the ion-channel density is low or medium, while for sufficiently high ion-channel density, the electron motion becomes regular (nonchaotic). Also, the chaotic trajectories decrease when the effects of self-fields of electron beam are taken into account and under Budker condition all trajectories become regular. The above result is in contrast with magnetostatic helical wiggler with axial magnetic field in which chaotic motion is produced by self-fields of electron beam. The chaotic and nonchaotic electron trajectories are confirmed by calculating Liapunov exponents.
An exactly solvable Schrödinger equation with finite positive position-dependent effective mass
Authors: Lévai G. , Özer O.
Published: September 2010

The solution of the one-dimensional Schrödinger equation is discussed in the case of position-dependent mass. The general formalism is specified for potentials that are solvable in terms of generalized Laguerre polynomials and mass functions that are positive and bounded on the whole real x axis. The resulting four-parameter potential is shown to belong to the class of “implicit” potentials. Closed expressions are obtained for the bound-state energies and the corresponding wave functions, including their normalization constants. The constant mass case is obtained by a specific choice of the parameters. It is shown that this potential contains both the harmonic oscillator and the Morse potentials as two distinct limiting cases and that the original potential carries several characteristics of these two potentials. Possible generalizations of the method are outlined.
Microwave assisted switching In bit patterned media: Accessing multiple states
Authors: Fal T. J. , Camley R. E.
Published: September 2010

Using a micromagnetics calculation, we explore the properties of a submicron magnetic square with microwave assisted switching. For a 10×160×160 nm3 structure of Fe–Ti–N, there are three particular stable magnetic states for reversal fields up to −320 Oe. One can switch between these different states by adding a microwave field. The strength and the frequency of the microwave field determine the final state. A microwave field of up to 30 Oe does not change the magnetization. Fields of 50 to 75 Oe result in an intermediate state, while larger microwave fields produce a reversed ground state.
Transient chaos measurements using finite-time Lyapunov exponents
Authors: Stefański K. , Buszko K. , Piecyk K.
Published: September 2010

The notion of finite-time Lyapunov exponent averaged over initial conditions is used for characterizing transient chaos observed in one-dimensional maps. A model of its dependence on time is verified by comparing theoretically predicted values with those obtained numerically. Finally, the same model is used for estimating duration of transient chaos (rambling time) for some maps from the logistic family.
Experimental studies on the plasma bullet propagation and its inhibition
Authors: Karakas Erdinc , Laroussi Mounir
Published: September 2010

Plasma bullets generated by atmospheric pressure low temperature plasma jets have recently been an active research topic due to their unique properties and their enhanced plasma chemistry. In this paper, experimental insights into the plasma bullet lifetime and its velocity are reported. Data obtained from intensified charge-coupled device camera and time-resolved optical emission spectroscopy (OES) elucidated the existence of a weakly ionized channel between the plasma bullet and its source (such as the plasma pencil). Factors responsible for the inhibition of the propagation of the bullet, such as low helium mole fraction, the magnitude of the applied voltage, and the secondary discharge ignition time, are also revealed. A new technique is discussed to accurately measure the plasma bullet velocity, using time-resolved OES. This new technique shows that during its lifetime the plasma bullet goes through launching, propagation, and ending phases. In addition, it is noted that the plasma bullet exhibits an unstable behavior at the early beginning and late ending of the propagation.
Microwave magnetoelectric effects in bilayers of piezoelectrics and ferrites with cubic magnetocrystalline anisotropy
Authors: Tatarenko A. S. , Ustinov A. B. , Srinivasan G. , Petrov V. M. , Bichurin M. I.
Published: September 2010

The strain mediated microwave magnetoelectric coupling is studied in bilayers of ferrites with cubic anisotropy and piezoelectrics. The strength of magnetoelectric coupling is determined from data on ferromagnetic resonance frequency shift Δf versus applied electric field E. Studies at 6–10 GHz on samples of nickel zinc ferrite and polycrystalline lead zirconium titanate, lead magnesium niobate–lead titanate or lead zinc niobate-lead titanate (PZN–PT) show shifts Δf on the order of 30–150 MHz for E=10 kV/cm. Bilayers of nickel zinc ferrite and PZN-PT demonstrated the highest magnetoelectric coefficient of 5.3 Oe cm/kV. Theoretical estimates of the frequency shifts are in very good agreement with the data.
Multicolor fluorescence enhancement from a photonics crystal surface
Authors: Pokhriyal A. , Lu M. , Huang C. S. , Schulz S. , Cunningham B. T.
Published: September 2010

A photonic crystal substrate exhibiting resonant enhancement of multiple fluorophores has been demonstrated. The device, fabricated uniformly from plastic materials over a ∼3×5 in.2 surface area by nanoreplica molding, utilizes two distinct resonant modes to enhance electric field stimulation of a dye excited by a λ=632.8 nm laser (cyanine-5) and a dye excited by a λ=532 nm laser (cyanine-3). Resonant coupling of the laser excitation to the photonic crystal surface is obtained for each wavelength at a distinct incident angle. Compared to detection of a dye-labeled protein on an ordinary glass surface, the photonic crystal surface exhibited a 32× increase in fluorescent signal intensity for cyanine-5 conjugated streptavidin labeling, while a 25× increase was obtained for cyanine-3 conjugated streptavidin labeling. The photonic crystal is capable of amplifying the output of any fluorescent dye with an excitation wavelength in the 532 nm<λ<633 nm range by selection of an appropriate incident angle. The device is designed for biological assays that utilize multiple fluorescent dyes within a single imaged area, such as gene expression microarrays.
On the fold-Hopf bifurcation for continuous piecewise linear differential systems with symmetry
Authors: Llibre Jaume , Ponce Enrique , Ros Javier , Torres Francisco
Published: September 2010

In this paper a partial unfolding for an analog to the fold-Hopf bifurcation in three-dimensional symmetric piecewise linear differential systems is obtained. A particular biparametric family of such systems is studied starting from a very degenerate configuration of nonhyperbolic periodic orbits and looking for the possible bifurcation of limit cycles. It is proved that four limit cycles can coexist after perturbation of the original configuration, and other two limit cycles are conjectured. It is shown that the described bifurcation scenario appears for appropriate values of parameters in the celebrated Chua’s oscillator.
A new perspective on in vitro assessment method for evaluating quantum dot toxicity by using microfluidics technology
Authors: Mahto Sanjeev Kumar , Yoon Tae Hyun , Rhee Seog Woo
Published: September 2010

In this study, we demonstrate a new perspective on in vitro assessment method for evaluating quantum dot (QD) toxicity by using microfluidics technology. A new biomimetic approach, based on the flow exposure condition, was applied in order to characterize the cytotoxic potential of QD. In addition, the outcomes obtained from the flow exposure condition were compared to those of the static exposure condition. An in vitro cell array system was established that used an integrated multicompartmented microfluidic device to develop a sensitive flow exposure condition. QDs modified with cetyltrimethyl ammonium bromide/trioctylphosphine oxide were used for the cytotoxicity assessment. The results suggested noticeable differences in the number of detached and deformed cells and the viability percentages between two different exposure conditions. The intracellular production of reactive oxygen species and release of cadmium were found to be the possible causes of QD-induced cytotoxicity, irrespective of the types of exposure condition. In contrast to the static exposure, the flow exposure apparently avoided the gravitational settling of particles and probably assisted in the homogeneous distribution of nanoparticles in the culture medium during exposure time. Moreover, the flow exposure condition resembled in vivo physiological conditions very closely, and thus, the flow exposure condition can offer potential advantages for nanotoxicity research.
Ionization energy of the phosphorus donor in 3C–SiC from the donor-acceptor pair emission
Authors: Ivanov I. G. , Henry A. , Yan Fei , Choyke W. J. , Janzén E.
Published: September 2010

Donor-acceptor pair luminescence of P–Al and N–Al pairs in 3C–SiC is analyzed. The structures in the spectra corresponding to recombination of pairs at intermediate distances are fitted with theoretical spectra of type I (P–Al pairs) and type II (N–Al pairs). It is shown that in the regions chosen for fitting the line positions obey the equation ℏω(R)=EG−ED−EA+e2/εR, where ℏω(R) is the energy of the photon emitted by recombination of a pair at a distance R, e is the electron charge, ε is the static dielectric constant, and EG, ED, and EA are the electronic band gap and the donor and acceptor ionization energies, respectively. The fits yield the values EG−ED−EA for the N–Al (2094 meV) and P–Al (2100.1 meV) cases. Using the known value of the nitrogen ionization energy, 54.2 meV, phosphorus ionization energy of 48.1 meV is obtained. Identification of the sharp lines corresponding to recombination of close pairs in the P–Al spectrum is suggested.
Size-driven magnetic transitions in La1/3Ca2/3MnO3 nanoparticles
Authors: Markovich V. , Fita I. , Wisniewski A. , Mogilyansky D. , Puzniak R. , Titelman L. , Gorodetsky G.
Published: September 2010

Magnetic properties of electron-doped La1/3Ca2/3MnO3 manganite nanoparticles with average particle size ranging from 12 to 42 nm, prepared by the glycine-nitrate method, have been investigated in temperature range 5–300 K and in magnetic fields up to 90 kOe. Reduction in the particle size suppresses antiferromagnetism and decreases the Néel temperature. In contrast to bulk crystals, the charge ordering does not occur in all studied nanoparticles, while a weak ferromagnetism appears above 200 K. Low temperature magnetic hysteresis loops indicate upon exchange bias effect displayed by horizontal and vertical shifts in field cooled processes. The spontaneous and remanent magnetization at low temperature shows a relatively complex variation with particle size. The size-induced structural/magnetic disorder drives the La1/3Ca2/3MnO3 nanoparticles to a pronounced glassy behavior for the smallest 12 nm particles, as evidenced by large difference between zero field cooled and field cooled magnetization, frequency dependent ac-susceptibility, as well as characteristic slowing down in the spin dynamics. Time evolution of magnetization recorded in magnetic fields after field cooling to low temperatures exhibits pronounced relaxation and a very noisy behavior that may be caused by formation of some collective states. Magnetic properties of the nanoparticle samples are compared with those of La0.2Ca0.8MnO3 nanoparticles. These results shed some light on the coupling between charges and spin degrees of freedom in antiferromagnetic manganite nanoparticles.
Three-dimensional magnetization evolution and the role of anisotropies in thin Fe/MgO films: Static and dynamic measurements
Authors: Carpene E. , Mancini E. , Dallera C. , Puppin E. , De Silvestri S.
Published: September 2010

We have quantitatively characterized the real-space components of the magnetization vector M in thin epitaxial Fe(001)/MgO(001) films through an experimental set-up based on the magneto-optical Kerr effect. The capabilities of the method permit to investigate the magnetization reversal under the effect of an applied field directly on the real-space trajectories of M, providing a straightforward interpretation of the magnetization switching mechanisms in terms of magnetic anisotropies and domains formation. Using the pump-probe technique we also studied the three-dimensional precession dynamics of the magnetization vector triggered by a femtosecond laser pulse, revealing how the anisotropy fields (magnetocrystalline and shape) affect the observed features of the precessional dynamics, i.e., the frequency and the amplitude of motion. Our quantitative approach permits a deeper understanding of the basic mechanisms underlying spin dynamics and it can be successfully applied to a large class of magnetic thin layers.
Suppression of roll-off characteristics of electroluminescence at high current densities in organic light emitting diodes by introducing reduced carrier injection barriers
Authors: Setoguchi Yousuke , Adachi Chihaya
Published: September 2010

We experimentally investigated suppression of the roll-off characteristics of the electroluminescence efficiency at high current densities in organic light emitting diodes (OLEDs). To increase exciton density, we propose a nonheterostructure OLED that consists of a single emitting layer of 4,4′-bis[(N-carbazole)styryl]biphenyl (BSB-Cz) and layers locally with doped donors/acceptors on the cathode and anode sides. The OLED exhibited suppression of the roll-off characteristics at high current densities over 100 A/cm2 with balanced bipolar injection and transport, resulting in the high exciton density of 1024 cm−3 s−1. Furthermore, amplified spontaneous emission with a relatively low threshold of Eth=24 μJ/cm2 was obtained by optically pumping the single-layer device. However, to realize electrical excitation it was necessary to reduce the lasing threshold by two orders of magnitude or to inject a 100 times higher current density.
Capillary-based liquid microdroplet deposition
Authors: Lutfurakhmanov Artur , Loken Gregory K. , Schulz Douglas L. , Akhatov Iskander S.
Published: September 2010

Liquid droplet deposition through a capillary onto a substrate is studied. The application of pressure into the capillary causes a liquid meniscus to form at the outlet. Touching the substrate with the liquid meniscus and subsequent capillary retraction gives liquid deposition on the substrate. Theoretical and experimental studies of the steady liquid bridge structure between the capillary and substrate identified the range of parameters when deposition of small droplets (no blot) can be performed. Experiments revealed that in this range of parameters the size of deposited liquid droplets is less than 10%–15% of inner diameter of the capillary.
Electronic structure and properties of isoelectronic magic clusters: Al13X (X=H,Au,Li,Na,K,Rb,Cs)
Authors: Ko Yeon Jae , Shakya Anisha , Wang Haopeng , Grubisic Andrej , Zheng Weijun , Götz Matthias , Ganteför Gerd , Bowen Kit H. , Jena Puru , Kiran Boggavarapu
Published: September 2010

The equilibrium structure, stability, and electronic properties of the Al13X (X=H,Au,Li,Na,K,Rb,Cs) clusters have been studied using a combination of photoelectron spectroscopy experiment and density functional theory. All these clusters constitute 40 electron systems with 39 electrons contributed by the 13 Al atoms and 1 electron contributed by each of the X (X=H,Au,Li,Na,K,Rb,Cs) atom. A systematic study allows us to investigate whether all electrons contributed by the X atoms are alike and whether the structure, stability, and properties of all the magic clusters are similar. Furthermore, quantitative agreement between the calculated and the measured electron affinities and vertical detachment energies enable us to identify the ground state geometries of these clusters both in neutral and anionic configurations.
Study of phase transitions in ternary lead indium niobate-lead magnesium niobate-lead titanate relaxor ferroelectric morphotropic single crystals
Authors: Finkel Peter , Robinson Harold , Stace Joseph , Amin Ahmed
Published: September 2010

In this work we report on the elastic hysteretic behavior observed in ferroelectric lead indium niobate-lead magnesium niobate-lead titanate (PIN-PMN-PT) relaxor single crystals under conditions of cooperative stress, temperature, and electric field. Room temperature elastic response displays strong and sharp discontinuity associated with stress induced phase transition. Quasistatic elastic response and ultrasonic wave propagation measurements demonstrated that this strain discontinuity in PIN-PMN-PT single crystal is associated with a ferroelectric rhombohedral (FR)—ferroelectric orthorhombic (FO) phase transition. The temperature dependent elastic response and transition strain were modeled by Devonshire theory. The crystal instability under compression is significantly improved by application of a dc bias electric field.
Importance of backdonation in [M–(CO)]p+ complexes isoelectronic to [Au–(CO)]+
Authors: Gourlaouen C. , Parisel O. , Piquemal J.-P.
Published: September 2010

In this contribution, we study several monocarbonyl-metal complexes in order to unravel the contribution of relativistic effects to the metal-ligand bond length and complexation energy. Using scalar density functional theory (DFT) constrained space orbital variation (CSOV) energy decomposition analysis supplemented by all-electron four-component DFT computations, we describe the dependency of relativistic effects on the orbitals involved in the complexation for the Au+ isoelectronic series, namely, the fully occupied 5d orbitals and the empty 6s orbitals. We retrieve the well-known sensitivity of gold toward relativity. For platinum and gold, the four-component results illustrate the simultaneous relativistic expansion of the 5d orbitals and the contraction of the 6s orbitals. The consequences of such modifications are evidenced by CSOV computations, which show the importance of both donation and backdonation within such complexes. This peculiar synergy fades away with mercury and thallium for which coordination becomes driven by the accepting 6s orbitals only, which makes the corresponding complexes less sensitive toward the relativistic effects.
An efficiently tunable microring resonator using a liquid crystal-cladded polymer waveguide
Authors: Cai Tao , Liu Qingkun , Shi Yaocheng , Chen Pengxin , He Sailing
Published: September 2010

An electrically tunable polymer microring resonator of large tunability and low applied voltage is demonstrated using active liquid crystal (LC) cladding. A large tuning range of 0.73 nm is achieved due to more homogenous LC molecular alignment and enhanced interaction of the light with the LC cladding in the simplified polymer waveguide structure. The operating voltage decreases to 10 V with a threshold of only 3 V by the utilization of interdigital electrodes.
Global effects of the small RNA biogenesis machinery on the
Arabidopsis thaliana
transcriptome
Authors: Laubinger Sascha , Zeller Georg , Henz Stefan R. , Buechel Sabine , Sachsenberg Timo , Wang Jia-Wei , Rätsch Gunnar , Weigel Detlef
Published: September 2010

In
Arabidopsis thaliana
, four different dicer-like (DCL) proteins have distinct but partially overlapping functions in the biogenesis of microRNAs (miRNAs) and siRNAs from longer, noncoding precursor RNAs. To analyze the impact of different components of the small RNA biogenesis machinery on the transcriptome, we subjected
dcl
and other mutants impaired in small RNA biogenesis to whole-genome tiling array analysis. We compared both protein-coding genes and noncoding transcripts, including most pri-miRNAs, in two tissues and several stress conditions. Our analysis revealed a surprising number of common targets in
dcl1
and
dcl2 dcl3 dcl4
triple mutants. Furthermore, our results suggest that the DCL1 is not only involved in miRNA action but also contributes to silencing of a subset of transposons, apparently through an effect on DNA methylation.
Metric learning for enzyme active-site search
Authors: Kato Tsuyoshi , Nagano Nozomi
Published: September 2010

Motivation: Finding functionally analogous enzymes based on the local structures of active sites is an important problem. Conventional methods use templates of local structures to search for analogous sites, but their performance depends on the selection of atoms for inclusion in the templates.

Results: The automatic selection of atoms so that site matches can be discriminated from mismatches. The algorithm provides not only good predictions, but also some insights into which atoms are important for the prediction. Our experimental results suggest that the metric learning automatically provides more effective templates than those whose atoms are selected manually.

Availability: Online software is available at http://www.net-machine.net/∼kato/lpmetric1/

Contact:  kato-tsuyoshi@k.u-tokyo.ac.jp

Supplementary information:  Supplementary data are available at Bioinformatics online.
Statistical considerations for digital approaches to non-invasive fetal genotyping
Authors: Chu Tianjiao , Bunce Kimberly , Hogge W. Allen , Peters David G.
Published: September 2010

Motivation: A growing body of literature has demonstrated the potential for non-invasive diagnosis of a variety of human genetic diseases using cell-free DNA extracted from maternal plasma samples in early gestation. Such methods are of great significance to the obstetrics community because of their potential use as clinical standard of care. Proof of concept for such approaches has been established for aneuploidy and paternally inherited dominant traits. Although significant progress has recently been made, the non-invasive diagnosis of monogenic diseases that segregate in a recessive mendelian fashion is more problematic. Recent developments in microfluidic digital PCR and DNA sequencing have resulted in a number of recent advances in this field. These have largely, although not exclusively, been used for the development of diagnostic methods for aneuploidy. However, given their prevalence, it is likely that such methods will be utilized towards the development of non-invasive methods for diagnosing monogenetic disorders.

Results: With this in mind, we have undertaken a statistical modeling of three contemporary (digital) analytical methods in the context of prenatal diagnosis using cell free DNA for monogenic diseases that segregate in a recessive mendelian fashion. We provide an experimental framework for the future development of diagnostic methods in this context that should be considered when designing molecular assays that seek to establish proof of concept in this field.

Contact:  dgp6@pitt.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Identification of Context-Dependent Motifs by Contrasting ChIP Binding Data
Authors: Mason Mike J. , Plath Kathrin , Zhou Qing
Published: September 2010

Motivation: DNA binding proteins play crucial roles in the regulation of gene expression. Transcription factors (TFs) activate or repress genes directly while other proteins influence chromatin structure for transcription. Binding sites of a TF exhibit a similar sequence pattern called a motif. However, a one-to-one map does not exist between each TF and motif. Many TFs in a protein family may recognize the same motif with subtle nucleotide differences leading to different binding affinities. Additionally, a particular TF may bind different motifs under certain conditions, for example in the presence of different co-regulators. The availability of genome-wide binding data of multiple collaborative TFs makes it possible to detect such context-dependent motifs.

Results: We developed a contrast motif finder (CMF) for the de novo identification of motifs that are differentially enriched in two sets of sequences. Applying this method to a number of TF binding datasets from mouse embryonic stem cells, we demonstrate that CMF achieves substantially higher accuracy than several well-known motif finding methods. By contrasting sequences bound by distinct sets of TFs, CMF identified two different motifs that may be recognized by Oct4 dependent on the presence of another co-regulator and detected subtle motif signals that may be associated with potential competitive binding between Sox2 and Tcf3.

Availability: The software CMF is freely available for academic use at www.stat.ucla.edu/∼zhou/CMF

Contact:  zhou@stat.ucla.edu

Supplementary information:  Supplementary data are available at Bioinformatics online and the CMF website.
The cardiac renin–angiotensin system is responsible for high‐salt diet‐induced left ventricular hypertrophy in mice
Authors: Le Corvoisier Philippe , Adamy Christophe , Sambin Lucien , Crozatier Bertrand , Berdeaux Alain , Michel Jean‐Baptiste , Hittinger Luc , Su JinBo
Published: September 2010

Aims

This study aimed to determine the role of the renin–angiotensin system (RAS) in high‐salt (HS) diet‐induced left ventricular hypertrophy (LVH).

Methods and results

Swiss mice were subjected to regular salt (RS) diet (0.6% NaCl), HS diet (4% NaCl), and HS plus irbesartan (50 mg/kg/day) or ramipril (1 mg/kg/day). After 8 weeks, arterial pressure was similar in all groups and similar to baseline, whereas left ventricle/body weight ratio was higher in HS mice than in RS mice (P < 0.005). There were also significant increases in collagen density, angiotensin‐converting enzyme activity, angiotensin II type 1 receptor (AT1 receptor) density, and extracellular signal‐regulated kinase (ERK1/2) phosphorylation in the left ventricle. Interestingly, increases in wall thickness and ERK1 phosphorylation were more marked in the septum than in the rest of the left ventricle. Irbesartan or ramipril treatment prevented LVH and the increase in ERK phosphorylation and reduced collagen content and AT1 up‐regulation but up‐regulated AT2 receptors.

Conclusion

In normal mice, HS diet induces septum‐predominant LVH and fibrosis through activation of the cardiac RAS–ERK pathway, which can be blocked by irbesartan or ramipril, indicating a key role of the cardiac RAS in HS diet‐induced LVH.
Pseudoxanthomonas indica sp. nov., isolated from a hexachlorocyclohexane dumpsite
Authors: Kumari Kirti , Sharma Pooja , Tyagi Kshitiz , Lal Rup
Published: September 2010

A bacterial strain, designated P15T, was isolated from the soil of an open hexachlorocyclohexane dumpsite. Comparative sequence analysis showed that strain P15T displayed high 16S rRNA gene sequence similarities (94.4–97.2 %) with members of the genus Pseudoxanthomonas. The isolate was most closely related to Pseudoxanthomonas mexicana AMX 26BT (97.2 % 16S rRNA gene sequence similarity) and Pseudoxanthomonas japonensis 12-3T (97.2 %). DNA–DNA relatedness studies showed unambiguously that strain P15T represented a novel species that was separate from P. mexicana DSM 17121T (7.7 %) and P. japonensis DSM 17109T (9.4 %). The predominant cellular fatty acids of strain P15T were iso-C16 : 0 (21.4 %), iso-C15 : 0 (16.1 %), summed feature 9 (comprising iso-C17 : 1ω9c and/or 10-methyl C16 : 0; 14.9 %), iso-C11 : 0 3-OH (8.3 %) and iso-C14 : 0 (7.0 %). The polar lipid profile of strain P15T showed the presence of large amounts of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol in addition to unknown glycolipids, phospholipids and an amino-group-containing polar lipid. Ubiquinone 8 was found as the major quinone. The polyamine profile showed the presence of spermidine. The DNA G+C content was 62.9±2 mol%. Strain P15T is described as representing a new member of the genus Pseudoxanthomonas, for which the name Pseudoxanthomonas indica sp. nov. is proposed. The type strain is P15T ( = MTCC 8596T = CCM 7430T).
‘Candidatus Pasteuria aldrichii’, an obligate endoparasite of the bacterivorous nematode Bursilla
Authors: Giblin-Davis R. M. , Nong G. , Preston J. F. , Williams D. S. , Center B. J. , Brito J. A. , Dickson D. W.
Published: September 2010

A novel bacterium of the genusPasteuriawas discovered parasitizing bacterivorous nematodes of the genusBursilla, in selected bermudagrass (Cynodon) field plots in Davie, FL, USA. Soil containing this bacterium was sampled and supplied with bi-weekly inoculations of cultured species of the genusBursillain order to build and maintain a source of endospores for continuousin vivoconservation of the bacteria for further study and characterization. 16S rRNA gene sequence similarities supported its congeneric ranking with other members of the genusPasteuriathat have been identified from nematodes and cladocerans. There were, however, no clear sister candidates for this organism, which supported the evidence of endospore ultrastructure and host-range studies, suggesting it belonged to a novel taxon. Because members of the genusPasteuriacannot yet be isolated, definitive type strains could not be maintained; therefore, the name ‘CandidatusPasteuria aldrichii’ is proposed for this organism.
Streptomyces scopuliridis sp. nov., a bacteriocin-producing soil streptomycete
Authors: Farris M. Heath , Duffy Carol , Findlay Robert H. , Olson Julie B.
Published: September 2010

Actinomycete strain RB72T was isolated from woodland bluff soil in northern Alabama, USA, and shown to produce a broad spectrum bacteriocin. Based on morphological and chemotaxonomic characteristics, the strain was determined to belong to the genus Streptomyces. Phylogenetic analysis of the near-complete 16S rRNA gene sequence indicated that it differed from those of the described streptomycetes available in public databases. The distinctive white aerial hyphae and lack of sporulation suggest a deficiency in the whi pathway of the organism. A combination of substrate utilization patterns, morphological and chemotaxonomic characteristics and DNA–DNA hybridization results supported the affiliation of strain RB72T to the genus Streptomyces and enabled the genotypic and phenotypic differentiation of strain RB72T from closely related reference strains. Strain RB72T therefore represents a novel species of the genus Streptomyces, for which the name Streptomyces scopuliridis sp. nov. is proposed. The type strain is RB72T ( = DSM 41917T  = NRRL B-24574T).
Bacillus xiaoxiensis sp. nov., a slightly halophilic bacterium isolated from non-saline forest soil
Authors: Chen Yi-Guang , Zhang Yu-Qin , Chen Qi-Hui , Klenk Hans-Peter , He Jian-Wu , Tang Shu-Kun , Cui Xiao-Long , Li Wen-Jun
Published: September 2010

A novel Gram-stain-positive, slightly halophilic, catalase-positive, oxidase-negative, endospore-forming, motile, facultatively anaerobic, rod-shaped bacterium, designated strain JSM 081004T, was isolated from non-saline forest soil in Xiaoxi National Natural Reserve, China. Growth occurred with 0.5–20 % (w/v) NaCl (optimum 2–4 %), at pH 6.0–10.5 (optimum pH 8.0) and at 5–40 °C (optimum 25–30 °C).meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The major cellular fatty acids were iso-C15 : 0and anteiso-C15 : 0. Strain JSM 081004Tcontained MK-7 as the predominant respiratory quinone, and diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol as the major polar lipids. The genomic DNA G+C content of strain JSM 081004Twas 40.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain JSM 081004Tshould be assigned to the genusBacillusand was most closely related to the type strains ofBacillus lehensis(sequence similarity 97.8 %),Bacillus oshimensis(97.8 %) andBacillus patagoniensis(97.3 %). Phylogenetic analysis, DNA–DNA relatedness values, phenotypic characteristics and chemotaxonomic data all support the proposal of strain JSM 081004Tas a representative of a novel species of the genusBacillus, for which the nameBacillus xiaoxiensissp. nov. is proposed; the type strain is JSM 081004T( = CCTCC AA 208057T = DSM 21943T).
Gluconobacter nephelii sp. nov., an acetic acid bacterium in the class Alphaproteobacteria
Authors: Kommanee Jintana , Tanasupawat Somboon , Yukphan Pattaraporn , Malimas Taweesak , Muramatsu Yuki , Nakagawa Yasuyoshi , Yamada Yuzo
Published: September 2010

Three strains, RBY-1T, PHD-1 and PHD-2, were isolated from fruits in Thailand. The strains were Gram-negative, aerobic rods with polar flagella, produced acetic acid from ethanol and did not oxidize acetate or lactate. In phylogenetic trees based on 16S rRNA gene sequences and 16S–23S rRNA gene internal transcribed spacer (ITS) sequences, the strains formed a cluster separate from the type strains of recognized species of the genus Gluconobacter. The calculated 16S rRNA gene sequence and 16S–23S rRNA gene ITS sequence similarities were respectively 97.7–99.7 % and 77.3–98.1 %. DNA G+C contents ranged from 57.2 to 57.6 mol%. The strains showed high DNA–DNA relatedness of 100 % to one another, but low DNA–DNA relatedness of 11–34 % to the tested type strains of recognized Gluconobacter species. Q-10 was the major quinone. On the basis of the genotypic and phenotypic data obtained, the three strains clearly represent a novel species, for which the name Gluconobacter nephelii sp. nov. is proposed. The type strain is RBY-1T ( = BCC 36733T = NBRC 106061T = PCU 318T), whose DNA G+C content is 57.2 mol%.
Development of a sensitive, multiplexed immunoassay using xMAP beads for detection of serotype-specific Streptococcus pneumoniae antigen in urine samples
Authors: Sheppard Carmen L. , Harrison Timothy G. , Smith Michael D. , George Robert C.
Published: September 2010

In support of the surveillance of pneumococcal infections in the era of conjugate vaccines, a sensitive and specific multiplex immunoassay using xMAP beads has been developed for direct detection of pneumococcal serotype-specific polysaccharides in clinical samples, particularly urine. The assay was tested on panels of spiked urine specimens, clinical urine specimens and bacterial isolates. Each of the 14 serotypes in the multiplex assay can be detected to 0.1 ng purified polysaccharide ml−1, or less. Testing of a panel of urine specimens from patients with culture-confirmed pneumococcal or non-pneumococcal disease indicated that the multiplex assay is both sensitive and specific. The correct pneumococcal serotype was identified directly from urine in 46/58 (79.3 %) patients who had a contemporaneous blood culture isolate of a multiplex assay serotype. Furthermore, the specificity of the assay on this panel of samples was 99.3 % (145/146). This multiplex assay could be useful, in conjunction with the pneumococcal screening test Binax NOW, in urine for diagnosis of pneumococcal disease and the identification of the aetiological serotype, and potentially be of benefit in culture-negative patients.
Arsenic Speciation in Phloem and Xylem Exudates of Castor Bean
Authors: Ye Wen-Ling , Wood B. Alan , Stroud Jacqueline L. , Andralojc P. John , Raab Andrea , McGrath Steve P. , Feldmann Jörg , Zhao Fang-Jie
Published: September 2010

How arsenic (As) is transported in phloem remains unknown. To help answer this question, we quantified the chemical species of As in phloem and xylem exudates of castor bean (Ricinus communis) exposed to arsenate [As(V)], arsenite [As(III)], monomethylarsonic acid [MMA(V)], or dimethylarsinic acid. In the As(V)- and As(III)-exposed plants, As(V) was the main species in xylem exudate (55%–83%) whereas As(III) predominated in phloem exudate (70%–94%). The ratio of As concentrations in phloem to xylem exudate varied from 0.7 to 3.9. Analyses of phloem exudate using high-resolution inductively coupled plasma-mass spectrometry and accurate mass electrospray mass spectrometry coupled to high-performance liquid chromatography identified high concentrations of reduced and oxidized glutathione and some oxidized phytochelatin, but no As(III)-thiol complexes. It is thought that As(III)-thiol complexes would not be stable in the alkaline conditions of phloem sap. Small concentrations of oxidized glutathione and oxidized phytochelatin were found in xylem exudate, where there was also no evidence of As(III)-thiol complexes. MMA(V) was partially reduced to MMA(III) in roots, but only MMA(V) was found in xylem and phloem exudate. Despite the smallest uptake among the four As species supplied to plants, dimethylarsinic acid was most efficiently transported in both xylem and phloem, and its phloem concentration was 3.2 times that in xylem. Our results show that free inorganic As, mainly As(III), was transported in the phloem of castor bean exposed to either As(V) or As(III), and that methylated As species were more mobile than inorganic As in the phloem.
Expression of a Low CO2–Inducible Protein, LCI1, Increases Inorganic Carbon Uptake in the Green Alga Chlamydomonas reinhardtii
Authors: Ohnishi Norikazu , Mukherjee Bratati , Tsujikawa Tomoki , Yanase Mari , Nakano Hirobumi , Moroney James V. , Fukuzawa Hideya
Published: September 2010

Aquatic photosynthetic organisms can modulate their photosynthesis to acclimate to CO2-limiting stress by inducing a carbon-concentrating mechanism (CCM) that includes carbonic anhydrases and inorganic carbon (Ci) transporters. However, to date, Ci-specific transporters have not been well characterized in eukaryotic algae. Previously, a Chlamydomonas reinhardtii mutant (lcr1) was identified that was missing a Myb transcription factor. This mutant had reduced light-dependent CO2 gas exchange (LCE) activity when grown under CO2-limiting conditions and did not induce the CAH1 gene encoding a periplasmic carbonic anhydrase, as well as two as yet uncharacterized genes, LCI1 and LCI6. In this study, LCI1 was placed under the control of the nitrate reductase promoter, allowing for the induction of LCI1 expression by nitrate in the absence of other CCM components. When the expression of LCI1 was induced in the lcr1 mutant under CO2-enriched conditions, the cells showed an increase in LCE activity, internal Ci accumulation, and photosynthetic affinity for Ci. From experiments using indirect immunofluorescence, LCI1–green fluorescent protein fusions, and cell fractionation procedures, it appears that LCI1 is mainly localized to the plasma membrane. These results provide strong evidence that LCI1 may contribute to the CCM as a component of the Ci transport machinery in the plasma membrane.
Hydrogen Peroxide–Mediated Activation of MAP Kinase 6 Modulates Nitric Oxide Biosynthesis and Signal Transduction inArabidopsis
Authors: Wang Pengcheng , Du Yanyan , Li Yuan , Ren Dongtao , Song Chun-Peng
Published: September 2010

Nitric oxide (NO) is a bioactive molecule that functions in numerous physiological and developmental processes in plants, including lateral root development. In this study, we used biochemical and genetic approaches to analyze the function of Arabidopsis thaliana mitogen-activated protein kinase 6 (MPK6) in the regulation of NO synthesis in response to hydrogen peroxide (H2O2) during lateral root development. In both mpk6 mutants studied, H2O2-induced NO synthesis and nitrate reductase (NR) activity were decreased dramatically. Furthermore, one NR isoform, NIA2, was required for the MPK6-mediated production of NO induced by H2O2. Notably, NIA2 interacted physically with MPK6 in vitro and in vivo and also served as a substrate of MPK6. Phosphorylation of NIA2 by MPK6 led to an increase in NR activity, and Ser-627 was identified as the putative phosphorylation site on NIA2. Phenotypical analysis revealed that mpk6-2 and mpk6-3 seedlings produce more and longer lateral roots than wild-type plants did after application of the NO donor sodium nitroprusside or H2O2. These data support strongly a function of MPK6 in modulating NO production and signal transduction in response to H2O2 during Arabidopsis root development.
Arabidopsis ABCG Transporters, Which Are Required for Export of Diverse Cuticular Lipids, Dimerize in Different Combinations
Authors: McFarlane Heather E. , Shin John J.H. , Bird David A. , Samuels A. Lacey
Published: September 2010

ATP binding cassette (ABC) transporters play diverse roles, including lipid transport, in all kingdoms. ABCG subfamily transporters that are encoded as half-transporters require dimerization to form a functional ABC transporter. Different dimer combinations that may transport diverse substrates have been predicted from mutant phenotypes. In Arabidopsis thaliana, mutant analyses have shown that ABCG11/WBC11 and ABCG12/CER5 are required for lipid export from the epidermis to the protective cuticle. The objective of this study was to determine whether ABCG11 and ABCG12 interact with themselves or each other using bimolecular fluorescence complementation (BiFC) and protein traffic assays in vivo. With BiFC, ABCG11/ABCG12 heterodimers and ABCG11 homodimers were detected, while ABCG12 homodimers were not. Fluorescently tagged ABCG11 or ABCG12 was localized in the stem epidermal cells of abcg11 abcg12 double mutants. ABCG11 could traffic to the plasma membrane in the absence of ABCG12, suggesting that ABCG11 is capable of forming flexible dimer partnerships. By contrast, ABCG12 was retained in the endoplasmic reticulum in the absence of ABCG11, indicating that ABCG12 is only capable of forming a dimer with ABCG11 in epidermal cells. Emerging themes in ABCG transporter biology are that some ABCG proteins are promiscuous, having multiple partnerships, while other ABCG transporters form obligate heterodimers for specialized functions.