bluuebunny/crossref_metadata_2025 huggingface dataset:
Ion-pairing dynamics of Li+ and SCN− in dimethylformamide solution: Chemical exchange two-dimensional infrared spectroscopy
Authors: Lee Kyung-Koo , Park Kwang-Hee , Kwon Donghyun , Choi Jun-Ho , Son Hyewon , Park Sungnam , Cho Minhaeng
Published: February 2011

Ultrafast two-dimensional infrared (2DIR) spectroscopy has been proven to be an exceptionally useful method to study chemical exchange processes between different vibrational chromophores under thermal equilibria. Here, we present experimental results on the thermal equilibrium ion pairing dynamics of Li+ and SCN− ions in N,N-dimethylformamide. Li+ and SCN− ions can form a contact ion pair (CIP). Varying the relative concentration of Li+ in solution, we could control the equilibrium CIP and free SCN− concentrations. Since the CN stretch frequency of Li–SCN CIP is blue-shifted by about 16 cm−1 from that of free SCN− ion, the CN stretch IR spectrum is a doublet. The temperature-dependent IR absorption spectra reveal that the CIP formation is an endothermic (0.57 kJ/mol) process and the CIP state has larger entropy by 3.12 J/(K mol) than the free ion states. Since the two ionic configurations are spectrally distinguishable, this salt solution is ideally suited for nonlinear IR spectroscopic investigations to study ion pair association and dissociation dynamics. Using polarization-controlled IR pump–probe methods, we first measured the lifetimes and orientational relaxation times of these two forms of ionic configurations. The vibrational population relaxation times of both the free ion and CIP are about 32 ps. However, the orientational relaxation time of the CIP, which is ∼47 ps, is significantly longer than that of the free SCN−, which is ∼7.7 ps. This clearly indicates that the effective moment of inertia of the CIP is much larger than that of the free SCN−. Then, using chemical exchange 2DIR spectroscopy and analyzing the diagonal peak and cross-peak amplitude changes with increasing the waiting time, we determined the contact ion pair association and dissociation time constants that are found to be 165 and 190 ps, respectively. The results presented and discussed in this paper are believed to be important, not only because the ion-pairing dynamics is one of the most fundamental physical chemistry problems but also because such molecular ion–ion interactions are of critical importance in understanding Hofmeister effects on protein stability.
Terahertz/optical sum and difference frequency generation in liquids
Authors: Feil Thomas , Allen S. J.
Published: February 2011

A high-sensitivity setup for the observation of χ(2)-based, terahertz/optical, sum and difference frequency generation in liquids is presented. It relies on launching wavefront modulated terahertz radiation into a liquid traversed by an optical beam. Phase matching and polarization selection rules can be tuned to support three wave mixing via either chiral allowed electric dipole processes or higher order quadrupole/magnetic dipole processes. Under nonresonant excitation, hyperpolarizabilities from quadrupole/magnetic dipole processes are measured. Since this approach does not require terahertz transmission through macroscopic thicknesses of water, it has the potential to open a new window on the terahertz dynamics of water solvated molecules.
Comparison of scrape-off layer turbulence simulations with experiments using a synthetic gas puff imaging diagnostic
Authors: Russell D. A. , Myra J. R. , D’Ippolito D. A. , Munsat T. L. , Sechrest Y. , Maqueda R. J. , Stotler D. P. , Zweben S. J. ,   The NSTX Team
Published: February 2011

A synthetic gas puff imaging (GPI) diagnostic has been added to the scrape-off layer turbulence (SOLT) simulation code, enabling comparisons with GPI data from the National Spherical Torus Experiment (NSTX) [M. Ono et al., Nucl. Fusion 40, 557 (2000)]. The edge and scrape-off layer are modeled in the radial and poloidal (bidirectional) dimensions of the outboard midplane region of NSTX. A low-confinement mode discharge is simulated by choosing reference parameters, including radial density and temperature profiles, to be consistent with those of the shot (no. 112825). NSTX and simulation GPI data are submitted to identical analyses. It is demonstrated that the level of turbulent fluctuations in the simulation may be adjusted to give synthetic GPI radial intensity profiles similar to those of the experiment; for a “best-case” simulation, SOLT and NSTX probability distribution functions of blob radial locations, widths, and GPI image velocities are compared. For the simulation, synthetic GPI image velocity and fluid convection (E×B) velocity are compared and contrasted.
Extended hydrodynamic approach to quantum-classical nonequilibrium evolution. I. Theory
Authors: Bousquet David , Hughes Keith H. , Micha David A. , Burghardt Irene
Published: February 2011

A mixed quantum-classical formulation is developed for a quantum subsystem in strong interaction with an N-particle environment, to be treated as classical in the framework of a hydrodynamic representation. Starting from the quantum Liouville equation for the N-particle distribution and the corresponding reduced single-particle distribution, exact quantum hydrodynamic equations are obtained for the momentum moments of the single-particle distribution coupled to a discretized quantum subsystem. The quantum-classical limit is subsequently taken and the resulting hierarchy of equations is further approximated by various closure schemes. These include, in particular, (i) a Grad–Hermite-type closure, (ii) a Gaussian closure at the level of a quantum-classical local Maxwellian distribution, and (iii) a dynamical density functional theory approximation by which the hydrodynamic pressure term is replaced by a free energy functional derivative. The latter limit yields a mixed quantum-classical formulation which has previously been introduced by I. Burghardt and B. Bagchi, Chem. Phys. 134, 343 (2006).
Effectiveness of active flow control for turbulent skin friction drag reduction
Authors: Chung Yongmann M. , Talha Tariq
Published: February 2011

The effectiveness of the opposition control method proposed by Choi et al. [J. Fluid Mech. 262, 75 (1994)] has been studied using direct numerical simulations. In this study, the effects of the amplitude and the phase of wall blowing and suction control input were considered separately. It is found that the amplitude of wall blowing and suction as well as the detection plane location played an important role in active control for skin-friction drag reduction. By changing the amplitude, a substantial drag reduction was achieved for all detection plane locations considered, and the efficiency of the opposition control was also improved. When the control was effective, the drag reduction was proportional to the wall blowing and suction strength. There existed a maximum wall blowing and suction strength, beyond which the opposition control became less effective or even unstable. Turbulence characteristics affected by various wall blowing and suction parameters were analyzed to understand the underlying mechanisms for drag reduction. The wall-normal velocity and vorticity fluctuations showed a strong correlation with drag reduction.
Is Stokes number an appropriate indicator for turbulence modulation by particles of Taylor-length-scale size?
Authors: Lucci Francesco , Ferrante Antonino , Elghobashi Said
Published: February 2011

It has been established both numerically and experimentally [see, e.g., A. Ferrante and S. E. Elghobashi, “On the physical mechanisms of two-way coupling in particle-laden isotropic turbulence,” Phys. Fluids 15, 315 (2003); T. S. Yang and S. S. Shy, “Two-way interaction between solid particles and homogeneous air turbulence: Particle settling rate and turbulence modification measurements,” J. Fluid Mech. 526, 171 (2005)] that the Stokes number, τp/τk, can be used as an indicator to determine the extent to which small particles (dp<η) modify the turbulence structure for fixed values of their volume fraction and mass fraction, where dp, τp, η, and τk are the particle diameter, the response time, the Kolmogorov length, and time scales, respectively. The objective of the present study is to investigate whether the Stokes number can also be used as an indicator for the modulation of turbulence by particles of the Taylor-length-scale size, i.e., dp∼λ⪢η. We employ direct numerical simulation with an immersed boundary method to fully resolve the flow around 4800 freely moving particles of Taylor-length-scale size (dp∼λ) in decaying isotropic turbulence with initial Taylor-microscale Reynolds number, Reλ=110, using a computational mesh of 5123 grid points. Our results show that particles whose diameter dp∼λ⪢η and have identical τp (but different dp and/or ρp) can have different effects on isotropic turbulence. Thus, τp/τk should not be used as an indicator of turbulence modulation by these “large” particles.
Two-dimensional electromagnetic Child–Langmuir law of a short-pulse electron flow
Authors: Chen S. H. , Tai L. C. , Liu Y. L. , Ang L. K. , Koh W. S.
Published: February 2011

Two-dimensional electromagnetic particle-in-cell simulations were performed to study the effect of the displacement current and the self-magnetic field on the space charge limited current density or the Child–Langmuir law of a short-pulse electron flow with a propagation distance of ζ and an emitting width of W from the classical regime to the relativistic regime. Numerical scaling of the two-dimensional electromagnetic Child–Langmuir law was constructed and it scales with (ζ/W) and (ζ/W)2 at the classical and relativistic regimes, respectively. Our findings reveal that the displacement current can considerably enhance the space charge limited current density as compared to the well-known two-dimensional electrostatic Child–Langmuir law even at the classical regime.
Nonlinear dependence of complex plasma parameters on applied electric field
Authors: Sodha M. S. , Mishra S. K. , Misra Shikha
Published: February 2011

This paper presents an analysis of the effect of an applied static or alternating electric field on the electron density and temperature, charge on the particles, the electron collision frequency, the electronic conductivity, and the coefficient of electron diffusion in a complex plasma (i) when not illuminated by light, which can cause photoelectric emission from the particles, and (ii) when so illuminated. A parametric analysis based on computations for some typical sets of parameters has also been made. The significance of this work to (i) the disappearance of a polar mesospheric summer echoes structure by radio wave and (ii) magneto-hydrodynamic (MHD) power generation has also been indicated. The time dependence of the various parameters after the application of the electric field has also been discussed.
Observation of tunneling of slow and fast electromagnetic modes in coupled periodic waveguides
Authors: Ha Sangwoo , Sukhorukov Andrey A. , Lavrinenko Andrei V. , Shadrivov Ilya V. , Powell David A. , Kivshar Yuri S.
Published: February 2011

We report the experimental observation of tunneling of slow and fast electromagnetic modes in coupled periodic waveguides shifted longitudinally by half of modulation period. According to the symmetry analysis, such a coupler supports two electromagnetic modes with exactly matched slow or fast group velocities but different phase velocities for frequencies close to the edge of the photonic band. We confirm the predicted properties of the modes by directly extracting their dispersion and group velocities from the near-field measurements using specialized Bloch-wave spectral analysis method.
Hyperspherical slow variable discretization method for weakly bound triatomic molecules
Authors: Suno Hiroya
Published: February 2011

We develop a method for calculating the bound state energies and the wave functions of weakly bound triatomic molecular systems. The method is based on the use of hyperspherical coordinates, combined with the slow variable discretization approach. The finite-element methods-discrete variable representation scheme provides an efficient means to solve the coupled-channel hyper-radial equations. Our method is applied to searching for bound states of the 20Ne2H and 4He20NeH triatomic molecules, using the best empirical pairwise interaction potentials. We consider not only zero total nuclear orbital momentum, J = 0, states but also J > 0 states. The 20Ne2H system has been found to possess one bound state each for the \documentclass[12pt]{minimal}\begin{document}$J^\Pi =0^+,1^-$\end{document}JΠ=0+,1−, and 2+ symmetries, while there exist only one bound state for the 4He20NeH system in the 0+ symmetry. We shall calculate the bound state energies and analyze the molecular structures of these species in detail.
Pair correlation function of soft-sphere fluids
Authors: Brańka A. C. , Heyes D. M.
Published: February 2011

A closed-form analytic formula for the radial distribution function (RDF) or g(r) of inverse power fluids is proposed. The RDF is expressed as a sum of separate component functions, one monotonic and a series of exponentially damped oscillatory functions. Unlike previous treatments in the literature, this formula does not rely on patching different functional forms at arbitrary crossover distances. This expression, which we refer to as gM(r), yields the expected asymptotic behavior at large distance and reproduces the main features of the RDF generated by molecular dynamics (MD) simulations. The gM is applied to the soft n = 4 inverse power fluid, and it is shown that in this case seven or fewer terms are sufficient to represent accurately the MD-generated RDF over the entire fluid domain. The relative contributions of the separate terms of the gM as a function of density are analyzed and discussed. The key role played by the monotonic component function and two oscillatory terms is demonstrated. The origin of the crossover from the oscillatory to the monotonic behavior is shown to be the same as that recently proposed by Evans and Henderson [R. Evans and J. R. Henderson, J. Phys.: Condens. Matter 21, 474220 (2009)] for the dispersion interactions.
Selective control of polarized emission from patterned GaN/AlN quantum dot ensembles on Si(111)
Authors: Moshe O. , Rich D. H. , Damilano B. , Massies J.
Published: February 2011

GaN/AlN quantum dots (QDs) were grown by the Stranski–Krastanov method on Si(111). The thermal expansion coefficient mismatch between the Si substrate and GaN/AlN film leads to an additional biaxial tensile stress of 20–30 kbar in the III-nitride film, which we have selectively modified by etching a cross-hatched pattern into the as-grown sample. The results show that a suitable choice of stripe orientation and width from ∼2 to 10 μm can create regions of in-plane uniaxial stress that enable a selective and local control of the polarized luminescence from ensembles of QDs which were probed with cathodoluminescence.
Metamagnetic phase transformation in Mn50Ni37In10Co3 polycrystalline alloy
Authors: Wu Zhigang , Liu Zhuhong , Yang Hong , Liu Yinong , Wu Guangheng
Published: February 2011

This letter reports on an alloy design of Mn50Ni37In10Co3 based on the principle of Mn-Mn ferromagnetic coupling via Co doping. The alloy is shown to exhibit a metamagnetic martensitic transformation and a high saturation magnetization of 118 emu/g in its austenitic state. The transformation generates a large magnetization difference of 89 emu/g, more than 200% of what is reported in the literature for similar alloys. A complete magnetic field induced martensitic transformation was achieved at 170 K. Such a high magnetization difference provides a strong driving force for magnetic-field-induced transformation, making this material a promising candidate for magnetic actuation applications.
Phonon deformation potentials in wurtzite GaN and ZnO determined by uniaxial pressure dependent Raman measurements
Authors: Callsen G. , Reparaz J. S. , Wagner M. R. , Kirste R. , Nenstiel C. , Hoffmann A. , Phillips M. R.
Published: February 2011

We report the phonon deformation potentials of wurtzite GaN and ZnO for all zone center optical phonon modes determined by Raman measurements as a function of uniaxial pressure. Despite all the structural and optical similarities between these two material systems, the pressure dependency of their vibrational spectra exhibits fundamental distinctions, which is attributed to their different bond ionicities. In addition, the LO-TO splitting of the A1 and E1 phonon modes is analyzed which yields insight into the uniaxial pressure dependency of Born’s transverse effective charge eT∗.
A comparative study of photoluminescence of Zn-polar and O-polar faces in single crystal ZnO using moment analysis
Authors: Yamamoto Aishi , Moriwaki Yuta , Hattori Ken , Yanagi Hisao
Published: February 2011

We report on differences in photoluminescence (PL) spectra between Zn-polar and O-polar faces in single crystal ZnO. The PL intensity ratios of one phonon to two phonon replicas of free-excitons in the two polar faces were found to be the same. This result clearly indicates that exciton-phonon coupling strengths in both faces are the same. From moment analysis, however, the relative PL intensity of the zero-phonon free-excitons in the O-polar face was larger than that in the Zn-polar face. We propose that the opposite band bending at the two polar faces causes the difference in the PL properties.
Organic semiconductor memory devices based on a low-band gap polyfluorene derivative with isoindigo as electron-trapping moieties
Authors: Xu Xinjun , Li Lidong , Liu Bo , Zou Yingping
Published: February 2011

Polyfluorene and its derivatives are good candidates to fabricate single-component polymer memories. However, the reported polyfluorenes for use in memories all have a big band gap and exhibit an absorption peak near the ultraviolet region. We report here organic memories based on a low-band gap polyfluorene derivative with isoindigo as electron-trapping moieties to improve on/off ratios. Also, possible factors which may influence the performance of polymer memory devices are investigated and feasible approaches for improving device performance are provided.
Stability and electronic structure of bilayer graphone
Authors: Zhou J. , Wang Q. , Sun Q. , Jena P.
Published: February 2011

Stability, reconstruction, and electronic structure of a bilayer graphone have been studied, where the most stable configuration undergoes a (1×2) surface reconstruction. An energy barrier of 1.83 eV separates this structure from the nonbonded state. The stability of the reconstructed bilayer at room temperature is confirmed by both frequency calculation and molecular dynamics simulation. Unlike the graphone sheet, the bilayer graphone is nonmagnetic but remains metallic due to the existence of delocalized π orbital on the zigzag sp2 carbon chains, which are stable against Peierls instability. The metallicity is also stable under gate external electric field.
Diversity and antibacterial activity of actinomycetes from wetland soil
Authors: George Maya , George Gisha , Hatha A. A. Mohamed
Published: February 2011

Diversity of soil actinomycetes isolated from various regions of a wetland was analysed. The strains were assigned under 11 genera according to their morphological and biochemical characteristics. They are: Nocardia, Pseudonocardia, Streptomyces, Micromonospora, Rhodococcus, Actinosynnema, Nocardiodes, Kitasatospora, Gordona, Intrasporangium and Streptoalloteichus. Around 55% of the identified strains are Nocardioform actinomycetes. Screening for their antibacterial activities revealed that 96% of the isolated strains showed different degrees of inhibition potential against 12
test pathogenic bacteria (including various serotypes of Salmonella, Vibrio cholerae, Bacillus subtilis and Escherichia coli). Of these about 41% of strains showed antagonism towards Bacillus subtilis. The Nocardioform actinomycetes
exhibited antibacterial activity against 9 out of 12 test organisms. The least antibacterial potential was exhibited by Gordona, Rhodococcus, Micromonospora and Kitasatospora. The isolated strains differed among themselves in their ability to decompose proteins and amino acids and also in enzyme production potential.
Calculation of the cross-plane thermal conductivity of a quantum cascade laser active region
Authors: Szymański M
Published: February 2011

The key problem in thermal modelling of a quantum cascade laser (QCL) is determining the thermal conductivity λ of its active region. The parameter is highly anisotropic. In particular, the cross-plane value λ⊥ is significantly reduced, which may be attributed to the presence of a large number of interfaces between epitaxial layers. In this work, two relatively simple models of phonon scattering at solid–solid boundary are used to calculate λ⊥ for the terahertz QCL. The theoretical results are in good agreement with measurements.
Nano-impact testing of TiFeN and TiFeMoN films for dynamic toughness evaluation
Authors: Beake B D , Vishnyakov V M , Colligon J S
Published: February 2011

TiFeN and TiFeMoN films were deposited on silicon wafers by ion-beam-assisted deposition. Their mechanical properties were measured by nanoindentation (quasi-static) and nano-impact (dynamic) techniques. Nano-impact testing enabled assessment of their toughness and resistance to fatigue fracture under repetitive loading. At low impact forces, films with a higher resistance to plastic deformation (H
3/E
2) were much more resistant to the formation of cracks throughout the test. At higher impact forces, these films initially show impact resistance but with continued impacts they are unable to protect the Si substrate, performing as poorly as films with lower H
3/E
2 and suffer delamination from the Si substrate over a large area.
Transport properties of a Fe0.04Si0.96 film at low temperatures
Authors: Su W F , Wang J L , Zhu H , Fan Y L , Jiang Z M
Published: February 2011

The transport properties of a Fe0.04Si0.96 film are studied. From the relationship between the resistivity of the film and the temperature, two activation energies, 40 and 2.5 meV, are obtained in two low-temperature regions below 50 K. Temperature-dependent magnetoresistance (MR) shows a peak feature with the largest value of 935% at 30 K. MR values are also measured under different configurations of field direction with respect to the current direction and the film plane, and their relationship in magnitude is discussed in terms of curving of carrier trajectories and shrinkage of wave function of localized states in a magnetic field.
Structural deformations and current oscillations in armchair-carbon nanotube cross devices: a theoretical study
Authors: Naieni A Kashefian , Yaghoobi P , Woodsworth D J , Nojeh A
Published: February 2011

A carbon nanotube (CNT) cross is a structure consisting of two CNTs with one draped over the other at an angle. Because of the localized mechanical deformation induced at the intersection point, the electronic properties of the nanotubes in a cross could vary significantly compared with those of intact nanotubes, potentially leading to the formation of nanoscale quantum dots.

Using classical molecular dynamics, we determined the relaxed nanotube structures and the induced mechanical deformations in a CNT cross. We found that the final relaxed shape of the cross structure is relatively insensitive to the starting shape. We then calculated the electronic transport properties of this device using a first-principles, non-equilibrium Green's function approach. We obtained current oscillations that can be attributed to the formation of a nanoscale quantum dot in the top nanotube at the intersection region.
Effect of Li3+ heavy ion irradiation on the Mo doped In2O3 thin films prepared by spray pyrolysis technique
Authors: Parthiban S , Elangovan E , Ramamurthi K , Kanjilal D , Asokan K , Martins R , Fortunato E
Published: February 2011

The high visible–near infrared transparent and high carrier mobility (μ) Mo doped (0.5 at%) indium oxide (IMO) films were deposited by the spray pyrolysis technique. The deposited films were irradiated by 50 MeV Li3+ ions with different fluences of 1 × 1011, 1 × 1012 and 1 × 1013 ions cm−2. X-ray diffraction analysis confirmed the cubic bixbyite structure of indium oxide. A fascinating feature is that the ion irradiation process has introduced a fraction of the molybdenum oxide phase. The μ of as-deposited IMO films is decreased from ∼122.4 to 93.3 cm2 V−1 s−1, following the ion irradiation. The theoretically calculated μ and carrier density values were correlated with those measured experimentally. The transport mechanism has been analysed based on the ionized and neutral impurity scattering centres. The average transmittance (400–2500 nm) of the as-deposited IMO films is decreased from 83% to 60% following irradiation.
Orthonormal dilations of non-tight frames
Authors: Bownik Marcin , Jasper John , Speegle Darrin
Published: February 2011

We establish dilation theorems for non-tight frames with additional structure, i.e., frames generated by unitary groups of operators and projective unitary representations. This generalizes previous dilation results for Parseval frames due to Han and Larson, and Gabardo and Han. We also extend the dilation theorem for Parseval wavelets due to Dutkay, Han, Picioroaga, and Sun by identifying the optimal class of frame wavelets for which dilation into an orthonormal wavelet is possible.
The posttranslational modification of tubulin undergoes a switch from detyrosination to acetylation as epithelial cells become polarized
Authors: Quinones Geraldine B. , Danowski Barbara A. , Devaraj Anjan , Singh Vimla , Ligon Lee A.
Published: February 2011

Tubulin posttranslational modifications (PTMs) have been suggested to provide navigational cues for molecular motors to deliver cargo to spatially segregated subcellular domains, but the molecular details of this process remain unclear. Here we show that in Madin-Darby Canine Kidney (MDCK) epithelial cells, microtubules express several tubulin PTMs. These modifications, however, are not coordinated, and cells have multiple subpopulations of microtubules that are marked by different combinations of PTMs. Furthermore these subpopulations show differential sensitivity to both drug- and cold-induced depolymerization, suggesting that they are functionally different as well. The composition and distribution of modified microtubules change as cells undergo the morphogenesis associated with polarization. Two-dimensionally polarized spreading cells have more detyrosinated microtubules that are oriented toward the leading edge, but three-dimensionally polarized cells have more acetylated microtubules that are oriented toward the apical domain. These data suggest that the transition from 2D polarity to 3D polarity involves both a reorganization of the microtubule cytoskeleton and a change in tubulin PTMs. However, in both 2D polarized and 3D polarized cells, the modified microtubules are oriented to support vectorial cargo transport to areas of high need.
SBML-PET-MPI: a parallel parameter estimation tool for Systems Biology Markup Language based models
Authors: Zi Zhike
Published: February 2011

Summary: Parameter estimation is crucial for the modeling and dynamic analysis of biological systems. However, implementing parameter estimation is time consuming and computationally demanding. Here, we introduced a parallel parameter estimation tool for Systems Biology Markup Language (SBML)-based models (SBML-PET-MPI). SBML-PET-MPI allows the user to perform parameter estimation and parameter uncertainty analysis by collectively fitting multiple experimental datasets. The tool is developed and parallelized using the message passing interface (MPI) protocol, which provides good scalability with the number of processors.

Availability: SBML-PET-MPI is freely available for non-commercial use at http://www.bioss.uni-freiburg.de/cms/sbml-pet-mpi.html or http://sites.google.com/site/sbmlpetmpi/.

Contact:  zhike.zi@bioss.uni-freiburg.de
GeneTUKit: a software for document-level gene normalization
Authors: Huang Minlie , Liu Jingchen , Zhu Xiaoyan
Published: February 2011

Motivation: Linking gene mentions in an article to entries of biological databases can facilitate indexing and querying biological literature greatly. Due to the high ambiguity of gene names, this task is particularly challenging. Manual annotation for this task is cost expensive, time consuming and labor intensive. Therefore, providing assistive tools to facilitate the task is of high value.

Results: We developed GeneTUKit, a document-level gene normalization software for full-text articles. This software employs both local context surrounding gene mentions and global context from the whole full-text document. It can normalize genes of different species simultaneously. When participating in BioCreAtIvE III, the system obtained good results among 37 runs: the system was ranked first, fourth and seventh in terms of TAP-20, TAP-10 and TAP-5, respectively on the 507 full-text test articles.

Availability and implementation: The software is available at http://www.qanswers.net/GeneTUKit/.

Contact:  aihuang@tsinghua.edu.cn
French Direct Investments in the Ottoman Empire Before World War I
Authors: Geyikdagi V. Necla
Published: February 2011

Foreign direct investment entered into the Ottoman Empire to support and develop foreign trade. Europeans who wanted to sell their manufactured products and acquire raw materials were instrumental in the construction of trade-related infrastructure in this country. Therefore, the first French investments, like those of other countries, were made for constructing railways and ports. The growth of raw material production in primary commodities, finally led to an increase in the number of foreign service companies such as banks and insurance providers that served these transport and production facilities. The initial motivations of French investors were mainly economic as they tried to find new markets and secure a viable share in these markets before their international competitors. Motives gradually became political as the opinion about the disintegration of the Ottoman Empire got stronger by the end of the nineteenth century. The French government assisted its investors in obtaining important concessions for investments in Anatolia, the Balkans, and the Arab provinces of the Empire.
Teenage Pregnancy
Authors: Mason Katy
Published: February 2011

The need for teenage contraceptive services is highlighted by the relatively poor sexual health of adolescents in the UK. Young people are currently disproportionately affected by sexually transmitted diseases, and although the teenage pregnancy rate is falling, it is still not at the level experienced by other Western European countries.
Colour-producing β-keratin nanofibres in blue penguin (Eudyptula minor) feathers
Authors: D'Alba Liliana , Saranathan Vinodkumar , Clarke Julia A. , Vinther Jakob A. , Prum Richard O. , Shawkey Matthew D.
Published: February 2011

The colours of living organisms are produced by the differential absorption of light by pigments (e.g. carotenoids, melanins) and/or by the physical interactions of light with biological nanostructures, referred to as structural colours. Only two fundamental morphologies of non-iridescent nanostructures are known in feathers, and recent work has proposed that they self-assemble by intracellular phase separation processes. Here, we report a new biophotonic nanostructure in the non-iridescent blue feather barbs of blue penguins (Eudyptula minor) composed of parallel β-keratin nanofibres organized into densely packed bundles. Synchrotron small angle X-ray scattering and two-dimensional Fourier analysis of electron micrographs of the barb nanostructure revealed short-range order in the organization of fibres at the appropriate size scale needed to produce the observed colour by coherent scattering. These two-dimensional quasi-ordered penguin nanostructures are convergent with similar arrays of parallel collagen fibres in avian and mammalian skin, but constitute a novel morphology for feathers. The identification of a new class of β-keratin nanostructures adds significantly to the known mechanisms of colour production in birds and suggests additional complexity in their self-assembly.
The initial stages of bioglass dissolution: a Car–Parrinello molecular-dynamics study of the glass–water interface
Authors: Tilocca Antonio , Cormack Alastair N.
Published: February 2011

The initial dissolution stages following implantation of a biomaterial in a physiological environment are critical for its bioactive properties. Car–Parrinello molecular-dynamics (CPMD) simulations of the interface between the 45S5 bioglass surface and liquid water have been carried out to investigate these processes. The analysis of a 40 ps CPMD trajectory has highlighted the potential mechanism of Na
+
/H
+
exchange, leading to formation of surface silanols through water dissociation. Moreover, by comparing the properties of water layers arranged at different distances from the glass surface, we discuss the way in which the particular structure and composition of the bioglass surface affects the hydrogen-bond network and orientation of water in its close proximity.
Bats are able to maintain long-term social relationships despite the high fission–fusion dynamics of their groups
Authors: Kerth Gerald , Perony Nicolas , Schweitzer Frank
Published: February 2011

Elephants, dolphins, as well as some carnivores and primates maintain social links despite their frequent splitting and merging in groups of variable composition, a phenomenon known as fission–fusion. Information on the dynamics of social links and interactions among individuals is of high importance to the understanding of the evolution of animal sociality, including that of humans. However, detailed long-term data on such dynamics in wild mammals with fully known demography and kin structures are scarce. Applying a weighted network analysis on 20 500 individual roosting observations over 5 years, we show that in two wild Bechstein's bat colonies with high fission–fusion dynamics, individuals of different age, size, reproductive status and relatedness maintain long-term social relationships. In the larger colony, we detected two stable subunits, each comprising bats from several family lineages. Links between these subunits were mainly maintained by older bats and persisted over all years. Moreover, we show that the full details of the social structure become apparent only when large datasets are used. The stable multi-level social structures in Bechstein's bat colonies resemble that of elephants, dolphins and some primates. Our findings thus may shed new light on the link between social complexity and social cognition in mammals.
Acoustic facilitation of object movement detection during self-motion
Authors: Calabro F. J. , Soto-Faraco S. , Vaina L. M.
Published: February 2011

In humans, as well as most animal species, perception of object motion is critical to successful interaction with the surrounding environment. Yet, as the observer also moves, the retinal projections of the various motion components add to each other and extracting accurate object motion becomes computationally challenging. Recent psychophysical studies have demonstrated that observers use a flow-parsing mechanism to estimate and subtract self-motion from the optic flow field. We investigated whether concurrent acoustic cues for motion can facilitate visual flow parsing, thereby enhancing the detection of moving objects during simulated self-motion. Participants identified an object (the target) that moved either forward or backward within a visual scene containing nine identical textured objects simulating forward observer translation. We found that spatially co-localized, directionally congruent, moving auditory stimuli enhanced object motion detection. Interestingly, subjects who performed poorly on the visual-only task benefited more from the addition of moving auditory stimuli. When auditory stimuli were not co-localized to the visual target, improvements in detection rates were weak. Taken together, these results suggest that parsing object motion from self-motion-induced optic flow can operate on multisensory object representations.
Natural variation in
Pristionchus pacificus
dauer formation reveals cross-preference rather than self-preference of nematode dauer pheromones
Authors: Mayer Melanie G. , Sommer Ralf J.
Published: February 2011

Many free-living nematodes, including the laboratory model organisms
Caenorhabditis elegans
and
Pristionchus pacificus
, have a choice between direct and indirect development, representing an important case of phenotypic plasticity. Under harsh environmental conditions, these nematodes form dauer larvae, which arrest development, show high resistance to environmental stress and constitute a dispersal stage.
Pristionchus pacificus
occurs in a strong association with scarab beetles in the wild and remains in the dauer stage on the living beetle. Here, we explored the circumstances under which
P. pacificus
enters and exits the dauer stage by using a natural variation approach. The analysis of survival, recovery and fitness after dauer exit of eight
P. pacificus
strains revealed that dauer larvae can survive for up to 1 year under experimental conditions. In a second experiment, we isolated dauer pheromones from 16
P. pacificus
strains, and tested for natural variation in pheromone production and sensitivity in cross-reactivity assays. Surprisingly, 13 of the 16 strains produce a pheromone that induces the highest dauer formation in individuals of other genotypes. These results argue against a simple adaptation model for natural variation in dauer formation and suggest that strains may have evolved to induce dauer formation precociously in other strains in order to reduce the fitness of these strains. We therefore discuss intraspecific competition among genotypes as a previously unconsidered aspect of dauer formation.
Host–parasite local adaptation after experimental coevolution of
Caenorhabditis elegans
and its microparasite
Bacillus thuringiensis
Authors: Schulte Rebecca D. , Makus Carsten , Hasert Barbara , Michiels Nico K. , Schulenburg Hinrich
Published: February 2011

Coevolving hosts and parasites can adapt to their local antagonist. In studies on natural populations, the observation of local adaptation patterns is thus often taken as indirect evidence for coevolution. Based on this approach, coevolution was previously inferred from an overall pattern of either parasite or host local adaptation. Many studies, however, failed to detect such a pattern. One explanation is that the studied system was not subject to coevolution. Alternatively, coevolution occurred, but remained undetected because it took different routes in different populations. In some populations, it is the host that is locally adapted, whereas in others it is the parasite, leading to the absence of an overall local adaptation pattern. Here, we test for overall as well as population-specific patterns of local adaptation using experimentally coevolved populations of the nematode
Caenorhabditis elegans
and its bacterial microparasite
Bacillus thuringiensis
. Furthermore, we assessed the importance of random interaction effects using control populations that evolved in the absence of the respective antagonist. Our results demonstrate that experimental coevolution produces distinct local adaptation patterns in different replicate populations, including host, parasite or absence of local adaptation. Our study thus provides experimental evidence of the predictions of the geographical mosaic theory of coevolution, i.e. that the interaction between parasite and host varies across populations.
Lysine Acetylation Is a Widespread Protein Modification for Diverse Proteins in Arabidopsis
Authors: Wu Xia , Oh Man-Ho , Schwarz Eliezer M. , Larue Clayton T. , Sivaguru Mayandi , Imai Brian S. , Yau Peter M. , Ort Donald R. , Huber Steven C.
Published: February 2011

Lysine acetylation (LysAc), a form of reversible protein posttranslational modification previously known only for histone regulation in plants, is shown to be widespread in Arabidopsis (Arabidopsis thaliana). Sixty-four Lys modification sites were identified on 57 proteins, which operate in a wide variety of pathways/processes and are located in various cellular compartments. A number of photosynthesis-related proteins are among this group of LysAc proteins, including photosystem II (PSII) subunits, light-harvesting chlorophyll a/b-binding proteins (LHCb), Rubisco large and small subunits, and chloroplastic ATP synthase (β-subunit). Using two-dimensional native green/sodium dodecyl sulfate gels, the loosely PSII-bound LHCb was separated from the LHCb that is tightly bound to PSII and shown to have substantially higher level of LysAc, implying that LysAc may play a role in distributing the LHCb complexes. Several potential LysAc sites were identified on eukaryotic elongation factor-1A (eEF-1A) by liquid chromatography/mass spectrometry and using sequence- and modification-specific antibodies the acetylation of Lys-227 and Lys-306 was established. Lys-306 is contained within a predicted calmodulin-binding sequence and acetylation of Lys-306 strongly inhibited the interactions of eEF-1A synthetic peptides with calmodulin recombinant proteins in vitro. These results suggest that LysAc of eEF-1A may directly affect regulatory properties and localization of the protein within the cell. Overall, these findings reveal the possibility that reversible LysAc may be an important and previously unknown regulatory mechanism of a large number of nonhistone proteins affecting a wide range of pathways and processes in Arabidopsis and likely in all plants.
Detailed Quantitative Analysis of Architectural Traits of Basal Roots of Young Seedlings of Bean in Response to Auxin and Ethylene
Authors: Basu Paramita , Brown Kathleen M. , Pal Anupam
Published: February 2011

Vertical placement of roots within the soil determines their efficiency of acquisition of heterogeneous belowground resources. This study quantifies the architectural traits of seedling basal roots of bean (Phaseolus vulgaris), and shows that the distribution of root tips at different depths results from a combined effect of both basal root growth angle (BRGA) and root length. Based on emergence locations, the basal roots are classified in three zones, upper, middle, and lower, with each zone having distinct architectural traits. The genotypes characterized as shallow on BRGA alone produced basal roots with higher BRGA, greater length, and more vertically distributed roots than deep genotypes, thereby establishing root depth as a robust measure of root architecture. Although endogenous indole-3-acetic acid (IAA) levels were similar in all genotypes, IAA and 1-N-naphthylphthalamic acid treatments showed different root growth responses to auxin because shallow and deep genotypes tended to have optimal and supraoptimal auxin levels, respectively, for root growth in controls. While IAA increased ethylene production, ethylene also increased IAA content. Although differences in acropetal IAA transport to roots of different zones can account for some of the differences in auxin responsiveness among roots of different emergence positions, this study shows that mutually dependent ethylene-auxin interplay regulates BRGA and root growth differently in different genotypes. Root length inhibition by auxin was reversed by an ethylene synthesis inhibitor. However, IAA caused smaller BRGA in deep genotypes, but not in shallow genotypes, which only responded to IAA in the presence of an ethylene inhibitor.
The DPP‐4 inhibitor linagliptin does not prolong the QT interval at therapeutic and supratherapeutic doses
Authors: Ring Arne , Port Andreas , Graefe‐Mody E. Ulrike , Revollo Ivette , Iovino Mario , Dugi Klaus A.
Published: February 2011

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• Linagliptin (BI 1356) is an oral, highly selective dipeptidyl peptidase‐4 inhibitor which is under development for the treatment of type 2 diabetes mellitus and for which the pivotal phase III programme has recently been completed.

• There have been no observed electrocardiogram changes in a linagliptin single rising dose study with up to 600 mg, and no preclinical signals for QT liability.

WHAT THIS STUDY ADDS

• This manuscript describes the findings of a thorough QT study for linagliptin conducted according to the ICH E14 guideline, with a therapeutic dose (5 mg) and a 20‐fold therapeutic dose (100 mg).

• Linagliptin does not cause clinically relevant changes of the corrected QT interval with a therapeutic dose and a 20‐fold therapeutic dose.

• The 20‐fold therapeutic dose of linagliptin was safe and well tolerated.

AIM To evaluate the potential effects of therapeutic and supratherapeutic doses of linagliptin (BI 1356) on the QT/QTc interval in healthy subjects.

METHODS The study was a randomized, double‐blind, placebo‐controlled, four‐period crossover study using single oral doses of linagliptin (5 mg and 100 mg), moxifloxacin (400 mg) and placebo. Electrocardiogram (ECG) profiles using triplicates of 12‐lead 10‐s ECGs were digitally recorded pre‐dose and after drug administration. The mean change from baseline (MCfB) of the individually heart rate corrected QT interval (QTcI) between 1 and 4 h postdrug administration was the primary end point. Blood samples to measure plasma concentrations of linagliptin and its main metabolite were also obtained.

RESULTS Forty‐four Caucasian subjects (26 male) entered the study and 43 subjects completed the study as planned in the protocol. Linagliptin was not associated with an increase in the baseline‐adjusted mean QTcI, at any time point. The placebo‐corrected MCfB of QTcI was −1.1 (90% CI −2.7, 0.5) ms and −2.5 (–4.1, –0.9) ms for linagliptin 5 mg and 100 mg, respectively, thus within the non‐inferiority margin of 10 ms according to ICH E14. Linagliptin was well tolerated; the assessment of ECGs and other safety parameters gave no clinically relevant findings at either dose tested. Maximum plasma concentrations after administration of 100‐mg linagliptin were ∼24‐fold higher than those observed previously for chronic treatment with the therapeutic 5‐mg dose. Assay sensitivity was confirmed by a placebo‐corrected MCfB of QTcI with moxifloxacin of 6.9 (90% CI 5.4, 8.5) ms.

CONCLUSIONS Therapeutic and significantly supratherapeutic exposure to linagliptin is not associated with QT interval prolongation.
B‐cell receptor, clinical course and prognosis in chronic lymphocytic leukaemia: the growing saga of the IGHV3 subgroup gene usage
Authors: Dal‐Bo Michele , Del Giudice Ilaria , Bomben Riccardo , Capello Daniela , Bertoni Francesco , Forconi Francesco , Laurenti Luca , Rossi Davide , Zucchetto Antonella , Pozzato Gabriele , Marasca Roberto , Efremov Dimitar G. , Guarini Anna , Del Poeta Giovanni , Foà Robin , Gaidano Gianluca , Gattei Valter
Published: February 2011

The immunoglobulin heavy chain variable gene (IGHV) mutational status has been recognized as an important predictor of prognosis in chronic lymphocytic leukaemia (CLL) since 1999. More recently, other features of the B‐cell receptor, such as stereotypy, have been identified as capable of refining the prognostic potential of IGHV status in the clinical assessment of CLL patients. In this context, different genes belonging to the IGHV3 subgroup, the most frequently used subgroup in CLL, have been shown to denote disease subsets that either display a bad prognosis (i.e. IGHV3‐21, IGHV3‐23) or are associated with particularly good clinical outcomes, including a highly stable/indolent clinical course, even prone to spontaneous regression (i.e. IGHV3‐72, IGHV3‐30). The present review focuses on the molecular and biological features of CLL‐expressing specific genes belonging to the IGHV3 subgroup that are known to mark disease subsets with completely different clinical courses, and may be possibly related to CLL pathogenesis via antigen and/or superantigen involvement.