bluuebunny/crossref_metadata_2025 huggingface dataset:
Stability and electronic properties of small boron nitride nanotubes
Authors: Zhang Zhuhua , Guo Wanlin , Dai Yitao
Published: April 2009

We report the stability and electronic structures of the boron nitride nanotubes (BNNTs) with diameters below 4 Å by semiempirical quantum mechanical molecular dynamics simulations and ab initio calculations. Among them (3,0), (3,1), (2,2), (4,0), (4,1), and (3,2) BNNTs can be stable well over room temperature. These small BNNTs become globally stable when encapsulated in a larger BNNT. It is found that the energy gaps and work functions of these small BNNTs are strongly dependent on their chirality and diameters. The small zigzag BNNTs become desirable semiconductors and have peculiar distribution of nearly free electron (NFE) states due to strong hybridization effect. When such a small BNNT is inserted in a larger one, the energy gap of the formed double-walled BNNT can be even much reduced due to the coupled effect of wall buckling difference and interwall NFE-π∗ hybridization.
Franz–Keldysh effect in the interband optical absorption of semiconducting nanostructures
Authors: Xia Congxin , Spector Harold N.
Published: April 2009

We present a theoretical calculation of the effect of an electric field applied either parallel or perpendicular to the direction of confinement on the interband optical absorption of semiconducting nanostructures such as quantum wells, quantum wires, and quantum boxes. We find that the application of the electric field decreases the optical absorption coefficient for both the parallel and perpendicular to the direction of carrier confinement. The absorption is greater when the electric field is along the direction of carrier confinement than when it is perpendicular to the direction of carrier confinement. Our work differs from that of others in that we present detailed theoretical calculations of the effect of the electric field on the optical absorption coefficient and obtain analytical expressions for the absorption coefficient. We find that there are additional oscillations in the absorption above the effective band gap in addition to the structure in the absence of the electric field, which are due to the Franz–Keldysh effect for the electric field parallel to the axis of the wire and the plane of the well. Numerical results also show that there is a smaller threshold for the optical absorption of cylindrical wires than for rectangular wires with the same cross sectional area.
Local and nonlocal magnetic behavior of dilute manganese-doped nickel alloys
Authors: Podolak K. R. , Willis R. F. , Wilson M. J. , Schiffer P. E. , Norman T. A. , Altmann K. N.
Published: April 2009

We report magnetic behavior of a dilute ferromagnetic alloy Ni1−xMnx, 0<x<25%. Magnetic circular dichroism (MCD) is used to examine the local magnetic moment on each element, and superconducting quantum interference device magnetometry is used to evaluate the magnetization of the alloy as a whole. Both MCD and hysteresis loops show a collapse in moment at x≈15% measured at 100 K. The Mn doping appears to disturb the long-range ordering of the host nickel spins which, in the concentration range studied, is a precursor disordered ferromagnet prior to a spin-glass phase.
Temperature dependence of excitonic transitions in a-plane AlN epitaxial layers
Authors: Murotani Hideaki , Kuronaka Takahiro , Yamada Yoichi , Taguchi Tsunemasa , Okada Narihito , Amano Hiroshi
Published: April 2009

The excitonic optical properties of a-plane AlN epitaxial layers have been studied by means of temperature-dependent photoluminescence (PL) and optical reflectance (OR) spectroscopy. An exciton resonance and free-exciton luminescence were clearly observed up to room temperature in the OR and PL measurements, respectively. Analysis of the low temperature OR spectrum enabled us to obtain a splitting energy of 7.3 meV between longitudinal and transverse-exciton resonances for AlN, which was approximately one order of magnitude larger than that for GaN. An emission from the upper branch of the excitonic polariton was also observed at temperatures above 100 K, reflecting thermal repopulation of excitonic polaritons from the lower to the upper branch. In addition, the temperature dependence of the transverse-exciton resonance could be well described using an empirical equation based on Bose–Einstein statistics, in which the Einstein characteristic temperature was estimated to be 455 K.
Selective growth of Co islands on ion beam induced nucleation centers in a native SiO2 film
Authors: Čechal Jan , Tomanec Ondřej , Škoda David , Koňáková Kateřina , Hrnčíř Tomáš , Mach Jindřich , Kolíbal Miroslav , Šikola Tomáš
Published: April 2009

We present a straightforward method for fabrication of patterns of metallic nanostructures. The focused ion beam (FIB) lithography has been used to locally modify a native SiO2 layer on a silicon substrate. On the modified areas preferential nucleation of cobalt islands is observed. The cobalt islands formed upon deposition at 400–430 °C combined with an intermediate annealing at 550 °C have a uniform size distribution and their size can be controlled by the distance between the nucleation sites and the amount of deposited material. It is proposed that the island formation at patterned sites is due to reduced surface diffusion of Co atoms in the vicinity of FIB modified areas. The intermediate annealing improves the island morphology since the kinetic diffusion limits are lowered and system reconfigures toward its equilibrium state.
Ultraviolet-light-emitting AlN:Gd thin-film electroluminescence device using an energy transfer from Gd3+ ions to N2 molecules
Authors: Toyama Toshihiko , Ota Jun , Adachi Daisuke , Niioka Yasumasa , Lee Dong-Hun , Okamoto Hiroaki
Published: April 2009

An ultraviolet (UV)-light-emitting AlN:Gd thin-film electroluminescence device (TFELD) was demonstrated for application to flat-panel lighting. AlN:Gd thin films were deposited by rf magnetron sputtering at 200 °C and applied to an ac-voltage-driven TFELD with a double-insulating structure as an emission layer. UV-light emission was observed over a threshold voltage of 270 V for a 5 kHz sinusoidal ac voltage. Electroluminescence (EL) spectra were compared with photoluminescence and cathodoluminescence spectra of AlN:Gd originating from Gd3+ P6j→S87/2 transitions and with an emission spectrum of the second positive system (C3Πu→B3Πg) of N2 molecules. As a result, an energy transfer from Gd3+ P6j→S87/2 to N2 C3Πu→B3Πg is discussed as a likely mechanism for the UV EL. Finally, a preliminary result, associated with the conversion from UV light into blue-green light via a phosphor, is demonstrated for the color tunability of the TFELD.
Neutron structural studies on the superconducting (Nd1−xCax)(Ba1.6La0.4)Cu3Oz system
Authors: Joshi Amish G. , Kulkarni R. G. , Yelon W. B. , Prasad Ram , Gonal M. R.
Published: April 2009

We have investigated the influence of Ca ion substitution on the structural and superconducting properties of (Nd1−xCax)(Ba1.6La0.4)Cu3Oz system. Magnetization, x-ray diffraction, and neutron diffraction studies have been carried out on a series of compounds with x=0.0–0.6. The superconducting transition temperature Tc, determined from magnetization measurements, increases with increasing Ca2+ substitution. Neutron diffraction studies reveal that these compounds crystallize in a tetragonal structure (space group P4∕mmm). A detailed analysis of the neutron diffraction data reveals that Ca and La ions are intermixed at the nominal Ba and Nd sites. While a major fraction of Ca ions occupy the usual Nd site, a small fraction occupies the Ba site. Consequently, the corresponding amount of La substitutes at the nominal Nd site. The intermixing of Ca and La sites randomizes the chain site oxygens leading to a tetragonal structure despite an oxygen content close to 7.0 for all the Ca doped samples. Further increase in Ca content leads to change in its coordination from sixfold to eightfold at x⩾0.4.
A theoretical design of half-metallic compounds by a long range of doping Mn for Heusler-type Cr3Al
Authors: Li Jia , Chen Hongjian , Li Yangxian , Xiao Yu , Li Zhiqing
Published: April 2009

The electronic structure and magnetic properties of Mn-doped Heusler-type compounds (Cr1−xMnx)3Al (x=n/12, n=0,2,4,6,8,10,12) were investigated using the plane-wave pseudopotential method. The results show that the compounds of x=2/12,4/12,6/12,8/12,1 exhibit the half-metallic character with 100% spin polarization, and their total moments are all negative values, in well agreement with the Slater–Pauling rule. The compound of x=0 shows a nearly half-metallicity since the Fermi level slightly touches the valence bands, leading to a high but not 100% spin polarization. Because the Mn atom has more 3d electrons than the Cr atom, the preferable occupation of Mn atom for all the doped compounds is the (A,C) sites and not the B site. The more symmetric surroundings of atom coordination in the B site in contrast to the (A,C) sites lead to a typical 3d electronic splitting. The Cr(A,C) and Cr(B) moments show an antiferromagnetic coupling character, and the Mn(A,C) moments show a ferromagnetic coupling with the Cr(A,C) moments.
Effect of knotting on polymer shapes and their enveloping ellipsoids
Authors: Millett Kenneth C. , Plunkett Patrick , Piatek Michael , Rawdon Eric J. , Stasiak Andrzej
Published: April 2009

We simulate freely jointed chains to investigate how knotting affects the overall shapes of freely fluctuating circular polymeric chains. To characterize the shapes of knotted polygons, we construct enveloping ellipsoids that minimize volume while containing the entire polygon. The lengths of the three principal axes of the enveloping ellipsoids are used to define universal size and shape descriptors analogous to the squared radius of gyration and the inertial asphericity and prolateness. We observe that polymeric chains forming more complex knots are more spherical and also more prolate than chains forming less complex knots with the same number of edges. We compare the shape measures, determined by the enveloping ellipsoids, with those based on constructing inertial ellipsoids and explain the differences between these two measures of polymer shape.
Equilibrium polymerization models of re-entrant self-assembly
Authors: Dudowicz Jacek , Douglas Jack F. , Freed Karl F.
Published: April 2009

As is well known, liquid-liquid phase separation can occur either upon heating or cooling, corresponding to lower and upper critical solution phase boundaries, respectively. Likewise, self-assembly transitions from a monomeric state to an organized polymeric state can proceed either upon increasing or decreasing temperature, and the concentration dependent ordering temperature is correspondingly called the “floor” or “ceiling” temperature. Motivated by the fact that some phase separating systems exhibit closed loop phase boundaries with two critical points, the present paper analyzes self-assembly analogs of re-entrant phase separation, i.e., re-entrant self-assembly. In particular, re-entrant self-assembly transitions are demonstrated to arise in thermally activated equilibrium self-assembling systems, when thermal activation is more favorable than chain propagation, and in equilibrium self-assembly near an adsorbing boundary where strong competition exists between adsorption and self-assembly. Apparently, the competition between interactions or equilibria generally underlies re-entrant behavior in both liquid-liquid phase separation and self-assembly transitions.
Absolute FKBP binding affinities obtained via nonequilibrium unbinding simulations
Authors: Ytreberg F. Marty
Published: April 2009

We compute the absolute binding affinities for two ligands bound to the FKBP protein using nonequilibrium unbinding simulations. The methodology is straightforward requiring little or no modification to many modern molecular simulation packages. The approach makes use of a physical pathway, eliminating the need for complicated alchemical decoupling schemes. We compare our nonequilibrium results to those obtained via a fully equilibrium approach and to experiment. The results of this study suggest that to obtain accurate results using nonequilibrium approaches one should use the stiff-spring approximation with the second cumulant expansion. From this study we conclude that nonequilibrium simulation could provide a simple means to estimate protein-ligand binding affinities.
R
-matrix calculation of low-energy electron collisions with uracil
Authors: Dora Amar , Tennyson Jonathan , Bryjko Lilianna , van Mourik Tanja
Published: April 2009

R -matrix calculations on electron-uracil collisions are presented within the static exchange, static exchange plus polarization, and close-coupling approximations. Particularly as input for the close-coupling calculations, a series of target calculations is performed which considers low-lying singlet and triplet excited states of the uracil target. The scattering calculations find three low-lying shape resonances of A2″ symmetry and three higher-energy Feshbach resonances of A2′ symmetry. In both symmetries the precise resonance parameters are found to be sensitive to the treatment of polarization effects employed. Cross sections are presented for both elastic scattering and electronic excitation. Comparisons are made with energy-dependent, differential cross section measurements at 90° angle and good agreement is found for scattering energies above 0.5 eV.
Effect of thermal annealing on charge exchange between oxygen interstitial defects within HfO2 and oxygen-deficient silicon centers within the SiO2/Si interface
Authors: Lauer J. L. , Shohet J. L. , Nishi Y.
Published: April 2009

We compare the charging response of rapid thermally annealed (800 and 1000 °C) 4 nm thick HfO2 to as-deposited HfO2 on Si by measuring the surface potential of the HfO2 layers after vacuum ultraviolet (VUV) irradiation with 11.6 eV photons. From VUV spectroscopy, we determined all HfO2 layers show the presence of oxygen-interstitial defects (OIDs). The electronic states of OID in HfO2 line up in energy with oxygen-deficient Si centers within the SiO2 interfacial layer. This implies charge exchange between OIDs within HfO2 and the O-deficient silicon centers within the SiO2 interfacial layer are very important for controlling the radiation-induced trapped charge in HfO2 dielectric stacks.
Frequency dependent capacitance and plasmon excitations in a coherent parallel-plate capacitor
Authors: Quan Jun , Yu Yabin , Au Yeung T. C.
Published: April 2009

We report the theoretical investigations of frequency-dependent capacitance in a coherent parallel-plate capacitor. It is found that the capacitance strongly depends on frequency and is complex at finite frequency. An interesting result is that in the frequency dependence of capacitance, a peak in the imaginary part of capacitance corresponds to the minimum of the real part and is related to a plasmonlike excitation, which is of damping and has a short lifetime. We also discussed the size effect of the capacitor and find that the capacitance approaches geometric capacitance when the distance between two plates of the capacitor is very large.
Photoadsorption and photodesorption for GaN
Authors: Foussekis M. , Baski A. A. , Reshchikov M. A.
Published: April 2009

The effect of an ambient environment on the surface photovoltage and photoluminescence observed for GaN is studied. In air ambient the upward band bending gradually increases under UV illumination and is explained by the photoinduced chemisorption of surface adsorbates. Specifically, the increase in negative surface charge is consistent with the transfer of electrons from surface states or bulk to oxygen species physisorbed at the GaN surface. In contrast, the upward band bending gradually decreases in vacuum under UV illumination and can be explained by the photoinduced desorption of these species. The photoadsorption and photodesorption of negatively charged species cause the surface depletion region to increase and decrease, respectively. This change in depletion region width is consistent with the observed decrease in photoluminescence intensity in air ambient and its significant increase in vacuum for a sample with low free electron concentration.
Pfirsch–Schlüter electric field in a tokamak
Authors: Catto Peter J. , Simakov Andrei N.
Published: April 2009

A concise and complete differential equation determining the Pfirsch–Schlüter radial electric field in an up-down symmetric tokamak is presented in the limit of weak poloidal magnetic field.
Optofluidic evanescent dye laser based on a distributed feedback circular grating
Authors: Song Wuzhou , Vasdekis Andreas E. , Li Zhenyu , Psaltis Demetri
Published: April 2009

We demonstrate an optofluidic evanescent laser based on a solid circular distributed feedback grating with the dye solution acting as the cladding layer. The laser mode is confined within the grating and experiences optical gain via the interaction between its evanescent component with the dye solution. Above a pump energy of 9.5 μJ/pulse, the laser exhibited single mode operation at 571 nm. Stable, narrow-linewidth emission was observed for a wide range of fluid refractive indices, even for those lower than of polydimethylsiloxane. We attribute this property to the evanescent coupling of the laser mode with the fluidic gain.
Photoinduced electron paramagnetic resonance study of electron traps in TiO2 crystals: Oxygen vacancies and Ti3+ ions
Authors: Yang Shan , Halliburton L. E. , Manivannan A. , Bunton P. H. , Baker D. B. , Klemm M. , Horn S. , Fujishima A.
Published: April 2009

Electron paramagnetic resonance (EPR) is used to identify photoinduced titanium-associated electron traps in TiO2 crystals (rutile). Defect production occurs at low temperature with 442 nm laser light. Spectra with S=1/2 and S=1 are assigned to singly ionized and neutral oxygen vacancies, respectively. These oxygen vacancies have their unpaired spins localized on the two neighboring titanium ions aligned along the c axis. A Ti3+ ion next to a Si4+ ion, a Ti3+ self-trapped electron, and a self-trapped hole shared by two adjacent oxygen ions are also observed. Isolated substitutional Fe3+ and Cr3+ ions serve as hole traps.
Retrieval of satellite pulses of single isolated attosecond pulses
Authors: Chini Michael , Wang He , Khan Sabih D. , Chen Shouyuan , Chang Zenghu
Published: April 2009

When isolated attosecond pulses are reconstructed from an ideal streaked photoelectron spectrogram, the relative amplitude of accompanying satellite pulses can be identified from their interference. However, the interference pattern in the spectrogram can be smeared by variation of the streaking laser intensity in the focal volume and by interpolation when using large delay steps acquiring the spectrogram, making accurate measurement of the relative intensity of the satellite pulses difficult. We investigate these effects on the reconstruction of satellite pulses with full- and half-cycle separations. Our simulations show that satellite pulses with full-cycle separation are largely unaffected by these issues.
A metallic graphene layer adsorbed with lithium
Authors: Yang Chih-Kai
Published: April 2009

We found, by density functional calculation, that lithium atoms can be bonded to a graphene layer alternately on both sides by distorting the relative positions of the carbon atoms in the honeycomb lattice. Compared to the recently synthesized graphane by hydrogenation in which each carbon is pulled out of the plane by hydrogen, the carbon is pushed off instead by the attached lithium. And, surprisingly, the counterintuitive structure is a conductor. This should give consequences to its application in lithium storage.
Quantum confinement and coherence in a two-dimensional electron gas in a carbon-face 3C-SiC/6H-SiC polytype heterostructure
Authors: Lu Jie , Chandrashekhar M. V. S. , Parks J. J. , Ralph D. C. , Spencer Michael G.
Published: April 2009

We report the observation of the quantum coherence in a two-dimensional electron gas (2DEG) at a C-face 3C-/6H-SiC polytype heterostructure. Electronic confinement and coherence were observed at 1.5 K and high magnetic fields, indicating the presence and confinement of a 2DEG. The measured mobility of the 2DEG is 2000 cm2/V s and the electron sheet density is 2.7×1012/cm2.
Discourse, Power, and Energy Conflicts: Understanding Welsh Renewable Energy Planning Policy
Authors: Stevenson Ruth
Published: April 2009

The Welsh Assembly updated their planning policy for renewables in the form of Technical Advice Note 8 (TAN 8) on renewable energy in 2005. The policy-making process was in line with the Assembly's commitment to participative and stakeholder policy-led development. I explore the policymaking process through a Foucauldian understanding of power, discourses, and policy rationalities, identifing four primary rationalities within the TAN 8 policy: spatial planning, energy targets, reliance on large-scale wind power, and the rationale that the traditional planning paradigm can resolve deep-seated conflicts over renewable energy. I explore how these rationalities emerged and were reinforced through the powerful discourse coalitions that emerged within the TAN 8 stakeholder group. As a result, I suggest that ‘consensus' should not necessarily be the aim of participative policy making and that the participatory process should not be relied upon to deliver ‘rational’ planning policies, leading to sustainable development. Instead, we must embrace the notion of pluralism with an understanding of the discursive powers at work within the policy-making process.
Host–pathogen time series data in wildlife support a transmission function between density and frequency dependence
Authors: Smith Matthew J. , Telfer Sandra , Kallio Eva R. , Burthe Sarah , Cook Alex R. , Lambin Xavier , Begon Michael
Published: April 2009

A key aim in epidemiology is to understand how pathogens spread within their host populations. Central to this is an elucidation of a pathogen's transmission dynamics. Mathematical models have generally assumed that either contact rate between hosts is linearly related to host density (density-dependent) or that contact rate is independent of density (frequency-dependent), but attempts to confirm either these or alternative transmission functions have been rare. Here, we fit infection equations to 6 years of data on cowpox virus infection (a zoonotic pathogen) for 4 natural populations to investigate which of these transmission functions is best supported by the data. We utilize a simple reformulation of the traditional transmission equations that greatly aids the estimation of the relationship between density and host contact rate. Our results provide support for an infection rate that is a saturating function of host density. Moreover, we find strong support for seasonality in both the transmission coefficient and the relationship between host contact rate and host density, probably reflecting seasonal variations in social behavior and/or host susceptibility to infection. We find, too, that the identification of an appropriate loss term is a key component in inferring the transmission mechanism. Our study illustrates how time series data of the host–pathogen dynamics, especially of the number of susceptible individuals, can greatly facilitate the fitting of mechanistic disease models.
Schizosaccharomyces pombe
Rtf2 mediates site-specific replication termination by inhibiting replication restart
Authors: Inagawa Takabumi , Yamada-Inagawa Tomoko , Eydmann Trevor , Mian I. Saira , Wang Teresa S. , Dalgaard Jacob Z.
Published: April 2009

Here, we identify a phylogenetically conserved
Schizosaccharomyces pombe
factor, named Rtf2, as a key requirement for efficient replication termination at the site-specific replication barrier
RTS1
. We show that Rtf2, a proliferating cell nuclear antigen-interacting protein, promotes termination at
RTS1
by preventing replication restart; in the absence of Rtf2, we observe the establishment of “slow-moving” Srs2-dependent replication forks. Analysis of the
pmt3
(SUMO) and
rtf2
mutants establishes that
pmt3
causes a reduction in
RTS1
barrier activity, that
rtf2
and
pmt3
are nonadditive, and that
pmt3
(SUMO) partly suppresses the
rtf2
-dependent replication restart. Our results are consistent with a model in which Rtf2 stabilizes the replication fork stalled at
RTS1
until completion of DNA synthesis by a converging replication fork initiated at a flanking origin.
Thermodynamic mechanism for solution phase chiral amplification via a lattice model
Authors: Lombardo Thomas G. , Stillinger Frank H. , Debenedetti Pablo G.
Published: April 2009

We formulate a two-dimensional lattice model to study the equilibrium phase behavior of a ternary mixture composed of two enantiomeric forms of a chiral molecule and a nonchiral liquid solvent. Numerical solution of the model invoking the mean-field approximation of statistical mechanics allows the calculation of a ternary phase diagram. A prominent feature of the phase diagram is the appearance of a mirror-image pair of triple points involving coexistence of a liquid phase enriched in one of the enantiomers with two solid phases: a racemic and an enantiopure crystal. Thus, over broad ranges of initial composition, including liquid mixtures containing almost equal amounts of the two enantiomers, the equilibrium state of the system produces liquid-phase chiral amplification. The calculations predict that chiral amplification is favored at low temperatures, and by strengthening those molecular interactions that stabilize the racemic crystal. The phase behavior that we obtain is qualitatively identical to that reported in a recent experimental study of solutions of amino acids, aimed at probing the liquid-phase control of asymmetric catalysis. Those results, and the present calculations that provide molecular-level insight into their underlying causes, suggest a possible thermodynamic scenario for the liquid-phase emergence of chiral imbalance in a prebiotic and presumably nearly racemic world.
Membrane-tethered ligands are effective probes for exploring class B1 G protein-coupled receptor function
Authors: Fortin Jean-Philippe , Zhu Yuantee , Choi Charles , Beinborn Martin , Nitabach Michael N. , Kopin Alan S.
Published: April 2009

Class B1 (secretin family) G protein-coupled receptors (GPCRs) modulate a wide range of physiological functions, including glucose homeostasis, feeding behavior, fat deposition, bone remodeling, and vascular contractility. Endogenous peptide ligands for these GPCRs are of intermediate length (27–44 aa) and include receptor affinity (C-terminal) as well as receptor activation (N-terminal) domains. We have developed a technology in which a peptide ligand tethered to the cell membrane selectively modulates corresponding class B1 GPCR-mediated signaling. The engineered cDNA constructs encode a single protein composed of (i) a transmembrane domain (TMD) with an intracellular C terminus, (ii) a poly(asparagine-glycine) linker extending from the TMD into the extracellular space, and (iii) a class B1 receptor ligand positioned at the N terminus. We demonstrate that membrane-tethered peptides, like corresponding soluble ligands, trigger dose-dependent receptor activation. The broad applicability of this approach is illustrated by experiments using tethered versions of 7 mammalian endogenous class B1 GPCR agonists. In parallel, we carried out mutational studies focused primarily on incretin ligands of the glucagon-like peptide-1 receptor. These experiments suggest that tethered ligand activity is conferred in large part by the N-terminal domain of the peptide hormone. Follow-up studies revealed that interconversion of tethered agonists and antagonists can be achieved with the introduction of selected point mutations. Such complementary receptor modulators provide important new tools for probing receptor structure–function relationships as well as for future studies aimed at dissecting the tissue-specific biological role of a GPCR in vivo (e.g., in the brain vs. in the periphery).
Protein function annotation from sequence: prediction of residues interacting with RNA
Authors: Spriggs R. V. , Murakami Y. , Nakamura H. , Jones S.
Published: April 2009

Motivation: All eukaryotic proteomes are characterized by a significant percentage of proteins of unknown function. Comp-utational function prediction methods are therefore essential as initial steps in the function annotation process. This article describes an annotation method (PiRaNhA) for the prediction of RNA-binding residues (RBRs) from protein sequence information. A series of sequence properties (position specific scoring matrices, interface propensities, predicted accessibility and hydrophobicity) are used to train a support vector machine. This method is then evaluated for its potential to be applied to RNA-binding function prediction at the level of the complete protein.

Results: The 5-fold cross-validation of PiRaNhA on a dataset of 81 RNA-binding proteins achieves a Matthews Correlation Coefficient (MCC) of 0.50 and accuracy of 87.2%. When used to predict RBRs in 42 proteins not used in training, PiRaNhA achieves an MCC of 0.41 and accuracy of 84.5%. Decision values from the PiRaNhA predictions were used in a second SVM to make predictions of RNA-binding function at the protein level, achieving an MCC of 0.53 and accuracy of 76.1%. The PiRaNhA RBR predictions allow experimentalists to perform more targeted experiments for function annotation; and the prediction of RNA-binding function at the protein level shows promise for proteome-wide annotations.

Availability and Implementation: Freely available on the web at www.bioinformatics.sussex.ac.uk/PIRANHA or http://piranha.protein.osaka-u.ac.jp.

Contact:  s.jones@sussex.ac.uk.

Supplementary Information:  Supplementary data are available at the Bioinformatics online.
A Bayesian segmentation approach to ascertain copy number variations at the population level
Authors: Wu Long Yang , Chipman Hugh A. , Bull Shelley B. , Briollais Laurent , Wang Kesheng
Published: April 2009

Motivation: Efficient and accurate ascertainment of copy number variations (CNVs) at the population level is essential to understand the evolutionary process and population genetics, and to apply CNVs in population-based genome-wide association studies for complex human diseases. We propose a novel Bayesian segmentation approach to identify CNVs in a defined population of any size. It is computationally efficient and provides statistical evidence for the detected CNVs through the Bayes factor. This approach has the unique feature of carrying out segmentation and assigning copy number status simultaneously—a desirable property that current segmentation methods do not share.

Results: In comparisons with popular two-step segmentation methods for a single individual using benchmark simulation studies, we find the new approach to perform competitively with respect to false discovery rate and sensitivity in breakpoint detection. In a simulation study of multiple samples with recurrent copy numbers, the new approach outperforms two leading single sample methods. We further demonstrate the effectiveness of our approach in population-level analysis of previously published HapMap data. We also apply our approach in studying population genetics of CNVs.

Availability: R programs are available at http://www.mshri.on.ca/mitacs/software/SOFTWARE.HTML

Contact:  lwu@math.uwaterloo.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
MetaTISA: Metagenomic Translation Initiation Site Annotator for improving gene start prediction
Authors: Hu Gang-Qing , Guo Jiang-Tao , Liu Yong-Chu , Zhu Huaiqiu
Published: April 2009

Summary: We proposed a tool named MetaTISA with an aim to improve TIS prediction of current gene-finders for metagenomes. The method employs a two-step strategy to predict translation initiation sites (TISs) by first clustering metagenomic fragments into phylogenetic groups and then predicting TISs independently for each group in an unsupervised manner. As evaluated on experimentally verified TISs, MetaTISA greatly improves the accuracies of TIS prediction of current gene-finders.

Availability: The C++ source code is freely available under the GNU GPL license viahttp://mech.ctb.pku.edu.cn/MetaTISA/.

Contact:  hqzhu@pku.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
Literature-based priors for gene regulatory networks
Authors: Steele E. , Tucker A. , Hoen P.A.C. 't , Schuemie M.J.
Published: April 2009

Motivation: The use of prior knowledge to improve gene regulatory network modelling has often been proposed. In this article we present the first research on the massive incorporation of prior knowledge from literature for Bayesian network learning of gene networks. As the publication rate of scientific papers grows, updating online databases, which have been proposed as potential prior knowledge in past research, becomes increasingly challenging. The novelty of our approach lies in the use of gene-pair association scores that describe the overlap in the contexts in which the genes are mentioned, generated from a large database of scientific literature, harnessing the information contained in a huge number of documents into a simple, clear format.

Results: We present a method to transform such literature-based gene association scores to network prior probabilities, and apply it to learn gene sub-networks for yeast, Escherichia coli and Human organisms. We also investigate the effect of weighting the influence of the prior knowledge. Our findings show that literature-based priors can improve both the number of true regulatory interactions present in the network and the accuracy of expression value prediction on genes, in comparison to a network learnt solely from expression data. Networks learnt with priors also show an improved biological interpretation, with identified subnetworks that coincide with known biological pathways.

Contact:  emma.steele@brunel.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
KIRMES: kernel-based identification of regulatory modules in euchromatic sequences
Authors: Schultheiss Sebastian J. , Busch Wolfgang , Lohmann Jan U. , Kohlbacher Oliver , Rätsch Gunnar
Published: April 2009

Motivation: Understanding transcriptional regulation is one of the main challenges in computational biology. An important problem is the identification of transcription factor (TF) binding sites in promoter regions of potential TF target genes. It is typically approached by position weight matrix-based motif identification algorithms using Gibbs sampling, or heuristics to extend seed oligos. Such algorithms succeed in identifying single, relatively well-conserved binding sites, but tend to fail when it comes to the identification of combinations of several degenerate binding sites, as those often found in cis-regulatory modules.

Results: We propose a new algorithm that combines the benefits of existing motif finding with the ones of support vector machines (SVMs) to find degenerate motifs in order to improve the modeling of regulatory modules. In experiments on microarray data from Arabidopsis thaliana, we were able to show that the newly developed strategy significantly improves the recognition of TF targets.

Availability: The python source code (open source-licensed under GPL), the data for the experiments and a Galaxy-based web service are available at http://www.fml.mpg.de/raetsch/suppl/kirmes/

Contact:  sebi@tuebingen.mpg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Differential roles of the fan-shaped body and the ellipsoid body in Drosophila visual pattern memory
Authors: Pan Yufeng , Zhou Yanqiong , Guo Chao , Gong Haiyun , Gong Zhefeng , Liu Li
Published: April 2009

The central complex is a prominent structure in the Drosophila brain. Visual learning experiments in the flight simulator, with flies with genetically altered brains, revealed that two groups of horizontal neurons in one of its substructures, the fan-shaped body, were required for Drosophila visual pattern memory. However, little is known about the role of other components of the central complex for visual pattern memory. Here we show that a small set of neurons in the ellipsoid body, which is another substructure of the central complex and connected to the fan-shaped body, is also required for visual pattern memory. Localized expression of rutabaga adenylyl cyclase in either the fan-shaped body or the ellipsoid body is sufficient to rescue the memory defect of the rut2080 mutant. We then performed RNA interference of rutabaga in either structure and found that they both were required for visual pattern memory. Additionally, we tested the above rescued flies under several visual pattern parameters, such as size, contour orientation, and vertical compactness, and revealed differential roles of the fan-shaped body and the ellipsoid body for visual pattern memory. Our study defines a complex neural circuit in the central complex for Drosophila visual pattern memory.
What the nucleolus says to a tumour pathologist
Authors: Derenzini Massimo , Montanaro Lorenzo , Treré Davide
Published: April 2009

The importance of nucleolar changes in cancer cells is underestimated in tumour pathology. There is evidence that the nucleolus is the mirror of a series of metabolic changes that characterize cancer cells. Cell entry into the cell cycle is always associated with up‐regulation of the nucleolar function and increased nucleolar size, which are also directly dependent on the rapidity of cell cycle progression. Furthermore, alterations of the major tumour suppressor retinoblastoma (Rb) and p53 pathways also contribute to the stimulation of nucleolar function and to nucleolar enlargement. High cell growth fraction, high cell growth rate and disruption of the Rb and p53 pathways are responsible for greater aggressiveness of cancer tissues. Therefore, the evaluation of nucleolar size allows one to obtain reliable information on the clinical outcome of the cancer: the greater the nucleolar size, the worse the tumour prognosis. Indeed, a series of studies carried out on numerous human tumours has shown that nucleolar hypertrophy (prominent nucleolus) was an independent predictive and prognostic parameter of a fatal clinical outcome.
HAb18G (CD147), a cancer‐associated biomarker and its role in cancer detection
Authors: Li Yu , Xu Jing , Chen Li , Zhong Wei‐De , Zhang Zheng , Mi Li , Zhang Yang , Liao Cheng‐Gong , Bian Hui‐Jie , Jiang Jian‐Li , Yang Xiang‐Min , Li Xiao‐Yan , Fan Chun‐Mei , Zhu Ping , Fu Li , Chen Zhi‐Nan
Published: April 2009

Aims:  To evaluate HAb18G/CD147 as a cancer‐associated biomarker using its monoclonal antibody HAb18.

Methods and results:  On immunohistochemical analysis of 28 tissue microarrays and pathological sections of 1117 breast tissue samples, HAb18G/CD147 was expressed in carcinoma with an overall positivity rate of 67.76%, which was significantly higher than that in sarcomas (27.34%, P < 0.0001) and normal epithelial (5.18%, P < 0.0001) and fetal (2.67%, P < 0.0001) tissues. In epithelial tissues from 14 organs, the difference in HAb18G/CD147 expression between normal epithelium and the corresponding carcinoma was also significant (P < 0.05 for each pair). This expression in carcinoma was also found at the mRNA level, suggesting transcriptional level regulation of HAb18G/CD147 expression. In a retrospective study of 106 patients with infiltrating ductal carcinoma of the breast, the level of HAb18G/CD147 expression was positively correlated with tumour recurrence/metastasis (P = 0.0003) and negatively correlated with survival of breast cancer patients (P = 0.002). Multivariable Cox regression analysis showed that HAb18G/CD147 was an independent prognostic factor.

Conclusions:  HAb18G/CD147 is significantly expressed in various cancers and appears to have prognostic significance, rendering it a possible cancer‐associated biomarker for pathological diagnosis, prognostic evaluation, targeted therapy and radioimmunoimaging of a broad range of cancer types.
Barrett’s dysplasia and the Vienna classification: reproducibility, prediction of progression and impact of consensus reporting and p53 immunohistochemistry
Authors: Kaye Philip V , Haider Syeda A , Ilyas Mohammed , James Peter D , Soomro Irshad , Faisal Wasek , Catton James , Parsons Simon L , Ragunath Krish
Published: April 2009

Aims:  The Vienna classification is used to classify dysplasia in Barrett’s oesophagus (BO), but reproducibility and value of diagnosis of lower grades in particular are often questioned. The aim was to test the diagnostic variability and correlation with patient outcome and to attempt to define histological features causing discrepant diagnoses, as well as to test the impact of adding p53 immunohistochemistry on reproducibility and prediction of outcome.

Methods and results:  One hundred and forty‐three patients with 154 sets of biopsy specimens originally diagnosed with Barrett’s dysplasia were retrieved from the pathology records of Nottingham University Hospital. Thirty‐two Barrett’s patients without dysplasia were added. Anonymized slides were graded independently by five pathologists without and with p53‐stained slides. Interobserver variation, correlation with outcome and diagnostic accuracy were determined. Weighted κ scores between pairs of pathologists showed substantial agreement and improved after p53 immunohistochemistry. Agreement with the original diagnosis was substantially lower. Fourteen of 34 low‐grade dysplasias (LGD) and 27 of 30 high‐grade dysplasias on consensus progressed within 10 years compared with 18/94 and 28/39 of original diagnoses. Progression correlated with p53 positivity.

Conclusion:  The Vienna classification is useful and reproducible in BO. Consensus diagnosis by gastrointestinal pathologists produces high specificity and predictive value, even for LGD. p53 immunohistochemistry assists in diagnosis in difficult cases and predicts progression.
Increased expression of SDF‐1/CXCR4 is associated with lymph node metastasis of invasive micropapillary carcinoma of the breast
Authors: Liu Fangfang , Lang Ronggang , Wei Jia , Fan Yu , Cui Lifang , Gu Feng , Guo Xiaojing , Pringle Gordon A , Zhang Xinmin , Fu Li
Published: April 2009

Aims:  Stromal cell‐derived factor‐1 (SDF‐1) and its receptor CXCR4 are implicated in tumour chemotaxis and metastasis. The aim was to examine their roles in the metastasis of invasive micropapillary carcinoma (IMPC) of the breast, a tumour with a high propensity for nodal spread.

Methods and results:  We compared the expression of SDF‐1 and CXCR4 in 103 cases of breast cancer containing IMPC components with a control group of 96 cases of invasive ductal carcinoma (IDC), not otherwise specified type by immunohistochemistry and chemical in situ hybridization (CISH). The results showed that the predominant cytoplasmic expression of both SDF‐1 and CXCR4 was greater in tumour cells of the IMPC components than in those of the non‐IMPC components and the control IDC cases, and was correlated significantly with the number of positive lymph nodes (P < 0.05). SDF‐1 expression on cell membranes was less frequently identified in IMPC than IDC (P = 0.021). Immunohistochemical detection of SDF‐1 in endothelial cells of lymphatic vessels was more common in IMPC (P = 0.007) and correlated significantly with lymph node status (P = 0.002), although SDF‐1 mRNA was rarely detected by CISH.

Conclusions:  This study suggests that up‐regulation of cytoplasmic expression of SDF‐1/CXCR4 might be one of the molecular mechanisms facilitating lymph node metastasis of IMPC.
Histone deacetylase 1, 2, 6 and acetylated histone H4 in B‐ and T‐cell lymphomas
Authors: Marquard Lena , Poulsen Christian B , Gjerdrum Lise Mette , De Nully Brown Peter , Christensen Ib J , Jensen Peter B , Sehested Maxwell , Johansen Preben , Ralfkiær Elisabeth
Published: April 2009

Aims:  Histone deacetylase (HDAC) inhibitors are novel therapeutics in the treatment of peripheral T‐cell lymphoma, unspecified (PTCL) and diffuse large B‐cell lymphoma (DLBCL), where, for unknown reasons, T‐cell malignancies appear to be more sensitive than B‐cell malignancies. The aim was to determine HDAC expression in DLBCL and PTCL which has not previously been investigated.

Methods and results:  The expression of HDAC1, HDAC2, HDAC6 and acetylated histone H4 was examined immunohistochemically in 31 DLBCL and 45 PTCL. All four markers showed high expression in both DLBCL and PTCL compared with normal lymphoid tissue. HDAC1 was more abundantly expressed in PTCL than in DLBCL (P = 0.0046), whereas acetylated H4 was more frequent in DLBCL (P < 0.0001), the latter suggesting a mechanism for T‐cell lymphoma sensitivity to HDAC inhibitors. Moderate to strong HDAC6 expression was significantly correlated with favourable outcome (P = 0.016) in DLBCL patients, whereas the opposite effect was observed in PTCL patients (P < 0.0001). The other markers did not correlate with survival (P > 0.05).

Conclusions:  HDAC1, HDAC2, HDAC6 and acetylated H4 are overexpressed in DLBCL and PTCL relative to normal lymphoid tissue. Furthermore, HDAC6 may be an important prognostic marker associated with favourable outcome in DLBCL and a more aggressive course in PTCL.
Expression of multidrug resistance‐associated protein 1 in invasive ovarian carcinoma: implication for prognosis
Authors: Faggad Areeg , Darb‐Esfahani Silvia , Wirtz Ralph , Sinn Bruno , Sehouli Jalid , Könsgen Dominique , Lage Hermann , Noske Aurelia , Weichert Wilko , Buckendahl Ann‐Christin , Budczies Jan , Müller Berit M , Elwali Nasr E , Dietel Manfred , Denkert Carsten
Published: April 2009

Aims:  Multidrug resistance is a major impediment in chemotherapeutic treatment of ovarian carcinoma patients. The aim of this study was to investigate the expression of multidrug resistance‐associated protein 1 (MRP1) and to assess the possible associations with clinicopathological variables and patient outcome in primary ovarian carcinoma.

Methods and results:  Tumour specimens from 129 patients were obtained before chemotherapy and analysed by immunohistochemistry on tissue microarrays, and by real‐time reverse transcriptase‐polymerase chain reaction on RNA extracted from formalin‐fixed paraffin‐embedded tissue specimens using a new technique. Significantly increased MRP1 protein expression was observed in high‐grade tumours (P = 0.005) and advanced International Federation of Gynaecology and Obstetrics stages (P = 0.036). On univariate Kaplan–Meier analysis, patients with higher expression of MRP1 protein had significantly decreased overall survival (P = 0.006). On multivariate Cox regression analysis, MRP1 protein expression retained its significance as an independent negative prognostic marker for overall survival (hazard ratio = 6.52, P = 0.003). Furthermore, MRP1 expression correlated with topoisomerase IIα expression both at mRNA and protein level (P < 0.001 and P = 0.023, respectively).

Conclusion:  In summary, in patients with primary ovarian cancer, overexpression of MRP1 is an adverse marker for patient outcome and cancer aggressiveness. Our data provide a translational basis for further clinical studies on the predictive value of MRP1 expression for response to chemotherapy.