bluuebunny/crossref_metadata_2025 huggingface dataset:
Self-assembled monolayer of alkanephosphoric acid on nanotextured Ti
Authors: Clair Sylvain , Variola Fabio , Kondratenko Mykola , Jedrzejowski Pawel , Nanci Antonio , Rosei Federico , Perepichka Dmitrii F.
Published: April 2008

Surface modification of titanium and its alloys is of great importance for their practical application as biomedical implants. We have studied and compared assembly of dodecylphosphoric acid on commercial polished and on nanostructured titanium disks. The latter were produced by chemical etching that created nanoscale pits of typical size of about 20nm. Enhanced hydrophobicity and high molecular density were obtained after functionalization of the nanotextured substrate. Aging tests showed a lifetime of the organic films of about one month in phosphate buffer. The samples were characterized by means of infrared spectroscopy, contact angle measurements, ellipsometry, and atomic force and scanning tunneling microscopies.
Theoretical and numerical study of the phase diagram of patchy colloids: Ordered and disordered patch arrangements
Authors: Bianchi Emanuela , Tartaglia Piero , Zaccarelli Emanuela , Sciortino Francesco
Published: April 2008

We report theoretical and numerical evaluations of the phase diagram for a model of patchy particles. Specifically, we study hard spheres whose surface is decorated by a small number f of identical sites (“sticky spots”) interacting via a short-ranged square-well attraction. We theoretically evaluate, solving the Wertheim theory, the location of the critical point and the gas-liquid coexistence line for several values of f and compare them to the results of Gibbs and grand canonical Monte Carlo simulations. We study both ordered and disordered arrangements of the sites on the hard-sphere surface and confirm that patchiness has a strong effect on the phase diagram: the gas-liquid coexistence region in the temperature-density plane is significantly reduced as f decreases. We also theoretically evaluate the locus of specific heat maxima and the percolation line.
Conformational behavior of polymers adsorbed on nanotubes
Authors: Gurevitch Inna , Srebnik Simcha
Published: April 2008

The importance of hydrophobic interactions in determining polymer adsorption and wrapping of carbon nanotubes is still under debate. In this work, we concentrate on the effect of short-ranged weakly attractive hydrophobic interactions between polymers and nanotubes (modeled as an infinitely long and smooth cylindrical surface), neglecting all other interactions apart for chain flexibility. Using coarse-grained Monte Carlo simulation of such simplified systems, we find that uniform adsorption and wrapping of the nanotube occur for all degrees of chain flexibility for tubes with sufficiently large outer radii. However, the adsorbed conformations depend on chain stiffness, ranging from randomly adsorbed conformations of the flexible chain to perfect helical or multihelical conformations (in the case of more concentrated solutions) of the rigid chains. Adsorption appears to occur in a sequential manner, wrapping the nanotube nearly one monomer at a time from the point of contact. Once adsorbed, the chains travel on the surface of the cylinder, retaining their helical conformations for the semiflexible and rigid chains. Our findings may provide additional insight to experimentally observed ordered polymer wrapping of carbon nanotubes.
Cavitation phenomena occurring due to interaction of shear layer vortices with the trailing corner of a two-dimensional open cavity
Authors: Liu Xiaofeng , Katz Joseph
Published: April 2008

The onset of cavitation in a high Reynolds number, two-dimensional open cavity shear flow occurs on top of the cavity trailing edge, well before it appears in the shear layer. However, the cavitation there disappears periodically, even at pressures that are much lower than inception level and when cavitation expands to the shear layer upstream. The primary cause for this phenomenon is periodic elimination of the pressure minimum on top of the corner due to flow induced by shear layer vortices arriving to the trailing edge of the cavity. Both the location of and conditions for cavitation inception agree with measured mean and fluctuating pressures performed using a novel technique for determining instantaneous spatial pressure distributions.
A hybrid explicit/implicit solvation method for first-principle molecular dynamics simulations
Authors: Brancato Giuseppe , Rega Nadia , Barone Vincenzo
Published: April 2008

In this work, we present a hybrid explicit/implicit solvation model, well suited for first-principles molecular dynamics simulations of solute-solvent systems. An effective procedure is presented that allows to reliably model a solute with a few explicit solvation shells, ensuring solvent bulk behavior at the boundary with the continuum. Such an approach is integrated with high-level ab initio methods using localized basis functions to perform first-principles or mixed quantum mechanics/molecular mechanics simulations within the extended-Lagrangian formalism. A careful validation of the model along with illustrative applications to solutions of acetone and glycine radical are presented, considering two solvents of different polarity, namely, water and chloroform. Results show that the present model describes dynamical and solvent effects with an accuracy at least comparable to that of conventional approaches based on periodic boundary conditions.
Structures of MAu16− (M=Ag, Li, Na, and K): How far is the endohedral doping?
Authors: Fa Wei , Dong Jinming
Published: April 2008

The structural and electronic properties of MAu16− (M=Ag, Li, Na, and K) have been studied by the scalar relativistic all-electron density-functional calculations, in which particular attention is paid to the stability of the endohedral Au16− cage doped by different dopant atoms. It is found that only the smaller atoms, such as Cu, Li, and Na, can be stably encapsulated in the Au16− cage, while the addition of the larger Ag or K atom prefers to locate in the surface or outside of the cage, which is inconsistent with the previous hypothesis that the Au16− cage could act as a container to hold an arbitrary heterometal atom. The stable endohedral Li@Au16− and Na@Au16− have a large energy gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital gap, indicating that they are chemically stable and may be used as potential building blocks for designing cluster-assembled materials.
Syntheses and thermoelectric properties of Bi2Te3∕Sb2Te3 bulk nanocomposites with laminated nanostructure
Authors: Cao Y. Q. , Zhao X. B. , Zhu T. J. , Zhang X. B. , Tu J. P.
Published: April 2008

Nanocomposites with constituent sizes of <50nm are considered as a promising approach to enhance the figure of merit of bulk thermoelectric materials. A simple route involving hydrothermal synthesis and hot pressing was used in this work to prepare Bi2Te3∕Sb2Te3 bulk nanocomposites. It is shown that the composites have a laminated structure composed of Bi2Te3 and Sb2Te3 nanolayers with the thickness varying alternately between 5 and 50nm. The transport measurements indicate that the nanoscale laminated structure improves the thermoelectric performance with the maximal dimensionless figure of merit of 1.47 for the nanocomposite hot pressed from Bi2Te3 and Sb2Te3 nanopowders.
Optical band gap of BiFeO3 grown by molecular-beam epitaxy
Authors: Ihlefeld J. F. , Podraza N. J. , Liu Z. K. , Rai R. C. , Xu X. , Heeg T. , Chen Y. B. , Li J. , Collins R. W. , Musfeldt J. L. , Pan X. Q. , Schubert J. , Ramesh R. , Schlom D. G.
Published: April 2008

Bi Fe O 3 thin films have been deposited on (001) SrTiO3 substrates by adsorption-controlled reactive molecular-beam epitaxy. For a given bismuth overpressure and oxygen activity, single-phase BiFeO3 films can be grown over a range of deposition temperatures in accordance with thermodynamic calculations. Four-circle x-ray diffraction reveals phase-pure, epitaxial films with ω rocking curve full width at half maximum values as narrow as 29arcsec (0.008°). Multiple-angle spectroscopic ellipsometry reveals a direct optical band gap at 2.74eV for stoichiometric as well as 5% bismuth-deficient single-phase BiFeO3 films.
Kilovolt Blumlein pulse generator with variable pulse duration and polarity
Authors: de Angelis Andrea , Kolb Juergen F. , Zeni Luigi , Schoenbach Karl H.
Published: April 2008

A Blumlein pulse generator which utilizes the superposition of electrical pulses launched from two individually switched pulse forming lines has been designed and tested. By using a power metal-oxide-semiconductor field-effect transistor as a switch on each end of the Blumlein line, we were able to generate pulses with amplitudes of 1kV across a 100Ω load. Pulse duration and polarity can be controlled by the temporal delay in the triggering of the two switches. Using this technique, we have demonstrated the generation of pulses with durations between 8 and 60ns. The lower limit in pulse duration was determined by the switch closing time and the upper limit by the length of the pulse forming line. A further advantage of the concept is that pulse distortions caused by the non-negligible on-resistance of a line with a single switch can be eliminated by using switches with identical characteristics.
On a three-dimensional symmetric Ising tetrahedron and contributions to the theory of the dilogarithm and Clausen functions
Authors: Coffey Mark W.
Published: April 2008

Perturbative quantum field theory for the Ising model at the three-loop level yields a tetrahedral Feynman diagram C(a,b) with masses a and b and four other lines with unit mass. The completely symmetric tetrahedron CTet≡C(1,1) has been of interest from many points of view, with several representations and conjectures having been given in the literature. We prove a conjectured exponentially fast convergent sum for C(1,1), as well as a previously empirical relation for C(1,1) as a remarkable difference of Clausen function values. Our presentation includes propositions extending the theory of the dilogarithm Li2 and Clausen Cl2 functions, as well as their relation to other special functions of mathematical physics. The results strengthen connections between Feynman diagram integrals, volumes in hyperbolic space, number theory, and special functions and numbers, specifically including dilogarithms, Clausen function values, and harmonic numbers.
Polarization-dependent below band-gap optical absorption of aluminum nitride bulk crystals
Authors: Bickermann Matthias , Münch Andreas , Epelbaum Boris M. , Filip Octavian , Heimann Paul , Nagata Shunro , Winnacker Albrecht
Published: April 2008

The polarization dependence of the below band-gap optical absorption of aluminum nitride (AlN) is investigated in detail using cuts of bulk single crystals grown by physical vapor transport. We show that optical absorption at 445nm (2.8eV) features a polarization-dependent transition which is strongest for P⊥c, while optical absorption in the range of 250–320nm (4–5eV) features a transition which is strongest for P∥c. Such information may aid in understanding the nature of the underlying electronic transitions and subsequently decreasing unwanted blue/UV optical absorption in AlN.
New surface forces apparatus using two-beam interferometry
Authors: Kawai Hiroshi , Sakuma Hiroshi , Mizukami Masashi , Abe Takashi , Fukao Yasuhiro , Tajima Haruo , Kurihara Kazue
Published: April 2008

We designed a new surface forces apparatus for measuring the interactions between two nontransparent substrates and/or in nontransparent liquids. The small displacement of a surface, the bottom one in this study, was measured by the two-beam (twin path) interferometry technique using the phase difference between the laser light reflected by the fixed mirror and that by the mirror on the back of the bottom surface unit. It is possible to determine the distance with a resolution of 1nm in the working range of 5μm. This apparatus was successfully applied to measure the forces between mica surfaces in pure water and aqueous KBr solutions.
Effect of sulfurization conditions on structural and electrical properties of copper sulfide films
Authors: Kundu Manisha , Hasegawa Tsuyoshi , Terabe Kazuya , Aono Masakazu
Published: April 2008

We examined the structural and electrical properties of copper sulfide films as a function of the sulfurization time of 70-nm-thick Cu films. Copper sulfide films with various phases such as mixed metallic Cu-chalcocite, chalcocite, roxbyite, and mixed roxbyite-covellite phases were formed with increasing sulfurization time. The Cu∕S atomic percentage ratio of the films decreased with increasing sulfurization time, and films with various compositions such as Cu-rich and stoichiometric copper sulfide with underlying unreacted Cu as well as pure stoichiometric and S-rich copper sulfide were obtained. The surface morphology and the electrical resistivity of the films depended on the chemical phase and composition of the films. The resistivity decreased with increasing Cu deficiency in the films. Distinct switching of the resistance from high to low-state, and vice versa, with the reversal of the bias polarity of the film was observed only for the mixed metallic Cu-chalcocite phased film with underlying Cu. However, the chalcocite film with underlying Cu exhibited a semiconducting behavior. This indicated that excess Cu within the chalcocite film is required for the observation of the switching behavior of the resistance.
Supersymmetry versus ghosts
Authors: Robert D. , Smilga A. V.
Published: April 2008

We consider the simplest nontrivial supersymmetric quantum mechanical system involving higher derivatives. We unravel the existence of additional bosonic and fermionic integrals of motion forming a nontrivial algebra. This allows one to obtain the exact solution both in the classical and quantum cases. The supercharges Q and Q¯ are not Hermitially conjugate to each other anymore, which allows for the presence of negative energies in the spectrum. We show that the spectrum of the Hamiltonian is unbounded from below. It is discrete and infinitely degenerate in the free oscillatorlike case and becomes continuous running from −∞ to ∞ when interactions are added. Notwithstanding the absence of the ground state, there is no collapse, which suggests that a unitary evolution operator may be defined.
Determination of the intrinsic parameters of SnBi4Se7 via the characterization of electrical properties
Authors: Ahmed S. A. , Diab A. K. , Abdel Hakeem A. M.
Published: April 2008

I – V measurements and temperature dependence of electrical conductivity on polycrystalline samples of Bi2Se3 and SnBi4Se7 have been performed. From the analysis of the temperature dependence of electron concentration in the activation regime above room temperature, the effective mass me* has been determined. Some intrinsic and contact properties such as barrier heights, ideality factors, and carrier concentrations have been investigated by using I–V characteristics. It has been found that all samples exhibit Ohmic and space charge limited conduction at low and high fields, respectively.
The influence of nitrogen plasma treatment on the lattice vibrational properties of hydrothermally grown ZnO nanorods
Authors: Le H. Q. , Tripathy S. , Chua S. J.
Published: April 2008

In this study, the authors have investigated the optical properties of hydrothermally grown ZnO nanorods subjected to the combination of thermal annealing and nitrogen plasma treatments. In particular, ultraviolet-visible micro-Raman scattering has been used to study the influence of nitrogen incorporation in ZnO nanorods grown on GaN/sapphire templates. The band-edge photoluminescence spectra show significant changes due to nitrogen plasma treatment. In addition, visible Raman spectra show intensity enhancement of the disorder-activated vibrational modes from plasma-treated ZnO nanorods. Multiple longitudinal optical (LO) phonons are observed under ultraviolet resonant Raman excitation from these nanorods. The first-order resonant LO phonon line shape fitting is correlated to the nitrogen-induced lattice disorder.
Strong coercivity reduction in perpendicular FePt∕Fe bilayers due to hard/soft coupling
Authors: Casoli F. , Albertini F. , Nasi L. , Fabbrici S. , Cabassi R. , Bolzoni F. , Bocchi C.
Published: April 2008

We have prepared perpendicular hard/soft bilayers made of a 10nm L10-FePt layer, which has been epitaxially grown on MgO(100) and a Fe layer with thicknesses of 2 and 3.5nm. The control of the interface morphology allows to modify the magnetic regime at fixed Fe thickness (from rigid magnet to exchange-spring magnet), due to the nanoscale structure effect on the hard/soft coupling and to tailor the hysteresis loop characteristics. Despite the small thickness of the soft layer, the coercivity is strongly reduced compared to the hard layer value, indicating that high anisotropy perpendicular systems with moderate coercivity can be easily obtained.
Ring closure of rolled-up Si∕Cr nanoribbons
Authors: Zhang Li , Dong Lixin , Nelson Bradley J.
Published: April 2008

Nanobelts formed by the ring closure of rolled-up Si∕Cr nanoribbons are fabricated on a Si (001) substrate. Interlayer bonding strengths are investigated by tangential unrolling and radial stretching using nanorobotic manipulation. Experimental results confirm that the multiwalled Si∕Cr nanobelts can be considered physically closed structures and have strong interlayer bonding. The load versus deformation curve of nanobelts of varying ribbon widths reveals that the radial stiffness fulfills Hooke’s law for small deformations. The measured radial stiffness of the nanobelts is also comparable to that of ideal seamless rings.
First principles assessment of metal/oxide interface adhesion
Authors: Jiang Yong , Smith John R. , Evans Anthony G.
Published: April 2008

Adhesion at the interface between metals and oxides is strongly affected by the presence of impurities and dopants. We report a strategy for characterizing the influence of such species on adhesion through systematic first principles calculations. This is demonstrated for a technologically important interface that between a γ-Ni(Al) alloy and α-Al2O3. The effects on adhesion of stoichiometry, Al activity, impurities, and dopants are thoroughly examined, both in the bulk and at the interface. A surprising discovery is that doping with Hf provides several concurrent benefits, including an increase in the work of separation of the clean stoichiometric interface by a factor of 3.
Fluorine containing C60 derivatives for high-performance electron transporting field-effect transistors and integrated circuits
Authors: Wöbkenberg Paul H. , Ball James , Bradley Donal D. C. , Anthopoulos Thomas D. , Kooistra Floris , Hummelen Jan C. , de Leeuw Dago M.
Published: April 2008

We report on electron transporting organic transistors and integrated ring oscillators based on four different solution processible fluorine containing C60 derivatives. Electron mobilities up to 0.15cm2∕Vs are obtained from as-prepared bottom-gate, bottom-contact transistors utilizing gold source-drain electrodes. Despite the high mobility, no long-range structural order could be identified with the semiconductor films exhibiting amorphouslike characteristics. The good electron transport is attributed to the structural symmetry of the fullerene derivatives and the enhanced π-π interactions between C60 units even in the case of amorphouslike films. These advantageous characteristics make fluorine containing C60 derivatives attractive for application in high-performance, large-area organic electronics.
Velocity distribution of neutral species during magnetron sputtering by Fabry–Perot interferometry
Authors: Britun N. , Han J. G. , Oh S.-G.
Published: April 2008

The velocity distribution of a metallic neutral species sputtered in a dc magnetron discharge was measured using a planar Fabry–Perot interferometer and a hollow cathode lamp as a reference source. The measurement was performed under different angles of view relative to the target surface. The velocity distribution function in the direction perpendicular to the target becomes asymmetrical as the Ar pressure decreases, whereas it remains nearly symmetrical when the line of sight is parallel to the target surface. The average velocity of the sputtered Ti atoms was measured to be about 2km∕s.
Highly efficient organic solar cells with printable low-cost transparent contacts
Authors: Ahlswede Erik , Mühleisen Wolfgang , bin Moh Wahi Mohd Wahinuddin , Hanisch Jonas , Powalla Michael
Published: April 2008

Highly efficient organic solar cells with all-solution-processed low-cost transparent front contacts based on highly conductive formulations of poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) are reported, demonstrating the feasibility of replacing the costly conventional vacuum-deposited indium-tin-oxide contacts by means of simple printing techniques. For small cell areas, the relatively high sheet resistances were found to be less detrimental to the photovoltaic performance than the deficiencies in the transparency of the contact layer.
Optical behaviors of ZnO-porphyrin conjugates and their potential applications for cancer treatment
Authors: Liu Yuanfang , Zhang Yongbin , Wang Shaopeng , Pope Carey , Chen Wei
Published: April 2008

ZnO nanoparticles were synthesized and conjugated to the porphyrin derivative, meso-tetra (o-amino phenyl) porphyrin (MTAP). Energy transfer from the ZnO nanoparticles to MTAP was investigated and the energy transfer rate was measured to be as high as 83%. Compared with MTAP and ZnO alone, ZnO-MTAP conjugates have low toxicity under dark conditions but high phototoxicity in the human ovarian carcinoma cell line NIH:OVCAR-3. The results indicate that ZnO-MTAP conjugates may be useful in photodynamic therapy for deep cancer treatment.
In vitro maturation of porcine oocytes with retinoids improves embryonic development
Authors: Almiñana C. , Gil M. A. , Cuello C. , Caballero I. , Roca J. , Vazquez J. M. , Gomez E. , Martinez E. A.
Published: April 2008

In the present study, the effects of retinoid metabolite administration during in vitro maturation (IVM) on oocyte maturation, parameters of in vitro fertilisation (IVF) and embryo development were examined. Varying concentrations of 9-cis retinoic acid (RA; 0, 5, 50 and 500 nm; Experiment 1) and all-trans retinol (ROH; 0, 125, 1250 and 12 500 nm; Experiment 2) were included in the maturation medium. Cumulus–oocyte complexes were matured in vitro and inseminated with frozen–thawed spermatozoa. Presumptive zygotes were cultured for 16 h to assess IVF parameters or for 7 days to assess embryo development and quality. In Experiment 1, the oocyte maturation rate to metaphase II was significantly decreased (P < 0.001), with values below 5%, in the presence of the highest concentration of RA (500 nm). However, 5 and 50 nm RA had no effect compared with control. Treatment with 5 nm RA improved the blastocyst development rate (P < 0.001). In Experiment 2, the oocyte maturation rate did not differ between 125 and 1250 nm ROH treatment groups and control. However, treatment with 12 500 nm ROH was deleterious because no matured oocytes were observed following the treatment. The penetration rate was lower in the group treated with 1250 nm ROH compared with the 125 nm ROH-treated and control groups, but the blastocyst formation rate did not differ among the three groups. In conclusion, 5 nm RA in the IVM medium significantly increased the blastocyst formation rate, suggesting that RA may play an important role during IVM.
Normal developmental competence to the blastocyst stage is preserved in rabbit ovarian tissue following cryopreservation and autografting to the mesometrium
Authors: Chao Lan , Deng Xiaohui , Wang Xiao , Fu Qingzhao , Xu Anran , Hao Chunyan , Yu Hongling , Yu Xuan
Published: April 2008

The aim of the present study was to evaluate mesometrial autotransplantation of frozen–thawed ovarian tissue in the adult rabbit and investigate the developmental competence of oocytes retrieved from grafts by in vitro maturation, fertilisation and blastocyst formation. Twenty-five rabbits were divided into control, fresh tissue transplantation and frozen–thawed tissue transplantation groups. Rabbits were stimulated with follicle-stimulating hormone (FSH) and oocytes were retrieved 3 months after transplantation. Oocytes matured in vivo or in vitro were then fertilised by conventional in vitro fertilisation (IVF) or intracytoplasmic sperm injection (ICSI), followed by observation and evaluation of fertilisation and blastocyst formation rates. No significant differences were found in the percentage of oocytes, maturation, fertilisation, cleavage and blastocyst formation among the three groups. Significantly higher fertilisation rates of in vitro-matured (IVM) oocytes were observed with ICSI compared with IVF in each group (81.1% v. 58.5%, 79.2% v. 59.6% and 80.4% v. 56.0% in the control, fresh tissue transplantation and frozen–thawed tissue transplantation groups, respectively). The blastocyst formation rate of IVM oocytes was significantly lower than that of in vivo-matured oocytes in each group (25.5% v. 65.7%, 22.4% v. 61.8% and 28.9% v. 63.0% in the control, fresh tissue transplantation and frozen–thawed tissue transplantation groups, respectively). In concusion, the mesometrium is a promising site for ovarian autografts in the rabbit. Oocytes retrieved from mesometrial grafts can develop to the blastocyst stage.
Cross-Talk between Fibroblast Growth Factor and Bone Morphogenetic Proteins Regulates Gap Junction-mediated Intercellular Communication in Lens Cells
Authors: Boswell Bruce A. , Lein Pamela J. , Musil Linda S.
Published: April 2008

Homeostasis in the lens is dependent on an extensive network of cell-to-cell gap junctional channels. Gap junction-mediated intercellular coupling (GJIC) is higher in the equatorial region of the lens than at either pole, an asymmetry believed essential for lens transparency. Primary cultures of embryonic chick lens epithelial cells up-regulate GJIC in response to purified fibroblast growth factor (FGF)1/2 or to medium conditioned by vitreous bodies, the major reservoir of factors (including FGF) for the lens equator. We show that purified bone morphogenetic protein (BMP)2, -4, and -7 also up-regulate GJIC in these cultures. BMP2, -4, or both are present in vitreous body conditioned medium, and BMP4 and -7 are endogenously expressed by lens cells. Remarkably, lens-derived BMP signaling is required for up-regulation of GJIC by purified FGF, and sufficient for up-regulation by vitreous humor. This is the first demonstration of an obligatory interaction between FGF and BMPs in postplacode lens cells, and of a role for FGF/BMP cross-talk in regulating GJIC in any cell type. Our results support a model in which the angular gradient in GJIC in the lens, and thus proper lens function, is dependent on signaling between the FGF and BMP pathways.
MedEvi: Retrieving textual evidence of relations between biomedical concepts from Medline
Authors: Kim Jung-jae , Pezik Piotr , Rebholz-Schuhmann Dietrich
Published: April 2008

Summary: Search engines running on MEDLINE abstracts have been widely used by biologists to find publications that are related to their research. The existing search engines such as PubMed, however, have limitations when applied for the task of seeking textual evidence of relations between given concepts. The limitations are mainly due to the problem that the search engines do not effectively deal with multi-term queries which may imply semantic relations between the terms. To address this problem, we present MedEvi, a novel search engine that imposes positional restriction on occurrences matching multi-term queries, based on the observation that terms with semantic relations which are explicitly stated in text are not found too far from each other. MedEvi further identifies additional keywords of biological and statistical significance from local context of matching occurrences in order to help users reformulate their queries for better results.

Availability:  http://www.ebi.ac.uk/tc-test/textmining/medevi/

Contact:  kim@ebi.ac.uk
EPO-KB: a searchable knowledge base of biomarker to protein links
Authors: Lustgarten Jonathan L. , Kimmel Chad , Ryberg Henrik , Hogan William
Published: April 2008

Summary: The knowledge base EPO-KB (Empirical Proteomic Ontology Knowledge Base) is based on an OWL ontology that represents current knowledge linking mass-to-charge (m/z) ratios to proteins on multiple platforms including Matrix Assisted Laser/Desorption Ionization (MALDI) and Surface Enhanced Laser/Desorption Ionization (SELDI) – Time of Flight (TOF). At present, it contains information on m/z ratio to protein links that were extracted from 120 published research papers. It has a web interface that allows researchers to query and retrieve putative proteins that correspond to a user-specified m/z ratio. EPO-KB also allows automated entry of additional m/z ratio to protein links and is expandable to the addition of gene to protein and protein to disease links.

Availability: http://www.dbmi.pitt.edu/EPO-KB

Contact:  JLL47@pitt.edu
Fast network component analysis (FastNCA) for gene regulatory network reconstruction from microarray data
Authors: Chang Chunqi , Ding Zhi , Hung Yeung Sam , Fung Peter Chin Wan
Published: April 2008

Motivation: Recently developed network component analysis (NCA) approach is promising for gene regulatory network reconstruction from microarray data. The existing NCA algorithm is an iterative method which has two potential limitations: computational instability and multiple local solutions. The subsequently developed NCA-r algorithm with Tikhonov regularization can help solve the first issue but cannot completely handle the second one. Here we develop a novel Fast Network Component Analysis (FastNCA) algorithm which has an analytical solution that is much faster and does not have the above limitations.

Results: Firstly FastNCA is compared to NCA and NCA-r using synthetic data. The reconstruction of FastNCA is more accurate than that of NCA-r and comparable to that of properly converged NCA. FastNCA is not sensitive to the correlation among the input signals, while its performance does degrade a little but not as dramatically as that of NCA. Like NCA, FastNCA is not very sensitive to small inaccuracies in a priori information on the network topology. FastNCA is about several tens times faster than NCA and several hundreds times faster than NCA-r. Then, the method is applied to real yeast cell-cycle microarray data. The activities of the estimated cell-cycle regulators by FastNCA and NCA-r are compared to the semi-quantitative results obtained independently by Lee et al. (2002). It is shown here that there is a greater agreement between the results of FastNCA and Lee's, which is represented by the ratio 23/33, than that between the results of NCA-r and Lee's, which is 14/33.

Availability: Software and supplementary materials are available from http://www.eee.hku.hk/~cqchang/FastNCA.htm

Contact:  cqchang@eee.hku.hk
The Pentratricopeptide Repeat Protein DELAYED GREENING1 Is Involved in the Regulation of Early Chloroplast Development and Chloroplast Gene Expression in Arabidopsis
Authors: Chi Wei , Ma Jinfang , Zhang Dongyuan , Guo Jinkui , Chen Fan , Lu Congming , Zhang Lixin
Published: April 2008

An Arabidopsis (Arabidopsis thaliana) mutant that exhibited a delayed greening phenotype (dg1) was isolated from a population of activation-tagged Arabidopsis lines. Young, inner leaves of dg1 mutants were initially very pale, but gradually greened and mature outer leaves, more than 3 weeks old, appeared similar to those of wild-type plants. Sequence and transcription analyses showed that DG1 encodes a chloroplast protein consisting of eight pentratricopeptide repeat domains and that its expression depends on both light and developmental status. In addition, analysis of the transcript profiles of chloroplast genes revealed that plastid-encoded polymerase-dependent transcript levels were markedly reduced, while nucleus-encoded polymerase-dependent transcript levels were increased, in dg1 mutants. Thus, DG1 is probably involved in the regulation of plastid-encoded polymerase-dependent chloroplast gene expression during early stages of chloroplast development.
Role of Swollenin, an Expansin-Like Protein fromTrichoderma, in Plant Root Colonization
Authors: Brotman Yariv , Briff Eden , Viterbo Ada , Chet Ilan
Published: April 2008

Swollenin, a protein first characterized in the saprophytic fungus Trichoderma reesei, contains an N-terminal carbohydrate-binding module family 1 domain (CBD) with cellulose-binding function and a C-terminal expansin-like domain. This protein was identified by liquid chromatography-mass spectrometry among many other cellulolytic proteins secreted in the coculture hydroponics medium of cucumber (Cucumis sativus) seedlings and Trichoderma asperellum, a well-known biocontrol agent and inducer of plant defense responses. The swollenin gene was isolated and its coding region was overexpressed in the same strain under the control of the constitutive pki1 promoter. Trichoderma transformants showed a remarkably increased ability to colonize cucumber roots within 6 h after inoculation. On the other hand, overexpressors of a truncated swollenin sequence bearing a 36-amino acid deletion of the CBD did not differ from the wild type, showing in vivo that this domain is necessary for full protein activity. Root colonization rates were reduced in transformants silenced in swollenin gene expression. A synthetic 36-mer swollenin CBD peptide was shown to be capable of stimulating local defense responses in cucumber roots and leaves and to afford local protection toward Botrytis cinerea and Pseudomonas syringae pv lachrymans infection. This indicates that the CBD domain might be recognized by the plant as a microbe-associated molecular pattern in the Trichoderma-plant interaction.
Effects of density on above and below ground biomass of the native alpine grass Poa fawcettiae and the environmental weed Achillea millefolium
Authors: Johnston Frances M. , Pickering Catherine M.
Published: April 2008

Competition between Poa fawcettiae Vickery, the dominant native snowgrass, and the invasive herbaceous Achillea millefolium L., was examined in three glasshouse experiments. The first experiment investigated the potential for intra‐specific competition in plants by growing them in pots with low and high density. The second experiment examined the potential for inter‐specific competition at low, medium and high density. In the third experiment plants in pots where either roots or shoots of the species could not compete were compared to those where root and shoot competition was possible.

Achillea millefolium plants produced more than four times the biomass of P. fawcettiae plants. As a result the two species responded differently. In the A. millefolium monocultures both root and shoot biomass per plant declined at high density. By contrast, P. fawcettiae biomass was not affected. In mixed species pots, P. fawcettiae had no effect on the biomass of A. millefolium plants, while P. fawcettiae shoot and root biomass per plant decreased when grown with A. millefolium at all densities tested. Root competition from A. millefolium appears to be the main cause of the decrease in biomass of P. fawcettiae. The results imply that A. millefolium may have a competitive advantage over P. fawcettiae in the Australian Alps.
Spore morphology of some Brachytheciaceae Schimp. species (Bryophyta) from Turkey
Authors: Potoglu Erkara Ismuhan , Savaroglu Filiz
Published: April 2008

The spores ofHomalothecium sericeum(Hedw.) Schimp.,Brachythecium populeum(Hedw.) Schimp.,B. velutinum(Hedw.) Schimp. var.salicinum(Schimp.) Mönk.,B. velutinum(Hedw.) Schimp. var.validumC. Jens. andEurhynchium hians(Hedw.) Sande Lac. were studied by light and scanning electron microscopy for the first time. The apertural region consists of a leptoma in all spores. Two spore types, characterized by their surface ornamentation, are established, reflecting the species taxonomic relationships. While the surface ornamentation is of the insuloid type inEurhynchium hians,it consists of a granuloid type inHomalothecium sericeum,Brachythecium populeum,B. velutinum. var.salicinum, B. velutinumvar.validum.The spore wall of the family Brachyteciaceae includes sclerine (the dinstinction between exine and perine may be difficult to define) and intine. The taxonomy of the generaBrachyteciumand are discussed on the basis of their spore morphology.
Metapopulation pollination in the deceptive orchidAnacamptis pyramidalis
Authors: Lind Henrik , Franzén Markus , Pettersson† Börge , Anders Nilsson L.
Published: April 2008

Pollen dispersal between local plant populations within a range of 6 km in a geographically defined metapopulation of the lepidopteran‐pollinated deceptive orchidAnacamptis pyramidaliswas studied on the island Öland in the Baltic Sea. LocalA. pyramidalispopulations were examined for pollinators, flowering individuals, and fruit set. Population sizes of pollen vector species were estimated using a mark–release–recapture technique. As pollen vectors, the burnet mothZygaena minosand the butterflyAporia crataegidominated. 205 out of 745 marked lepidopterans were pollinarium carriers. The proportion carriers of the total was considerably higher inZ. minos(50.3%), than inA. crataegi(21.5%) and nymphalidae (8.2%). Furthermore,Z. minosmoved much shorter distances thanA. crataegidid, while no difference in potential pollen dispersal distances were found between males and females. The number of individual vectors recaptured in another local population ofA. pyramidaliswas low:A. crataegi(8) andZ. minos(1). The ratio of pollinaria transferred to another localA. pyramidalispopulation compared to pollinaria remaining within the same local population was 1:41. This study highlights that pollen dispersal distances vary between pollen vector species.
Genetic structure of Euclea schimperi (Ebenaceae) populations in monsoonal fog oases of the southern Arabian Peninsula
Authors: Meister Jörg , Kilian Norbert , Oberprieler Christoph
Published: April 2008

Euclea schimperi, a widespread Afromontane shrub or tree, occurs in the Arabian Peninsula in fragmented, semi‐evergreen or evergreen woodland refugia in wet escarpment localities of the western and southern mountain chains. In the southern coastal mountains, the (semi‐) evergreen woodland with E. schimperi is close to its ecological limit and consequently today very rare, with the exception of the monsoonal fog oases of east Yemen and south Oman in the central south coast of the Arabian Peninsula. Due to the steep precipitation gradient from the centre to the western edge in this monsoon affected area, E. schimperi is found in two different habitat types: in continuous woodland belts in the Hawf and Dhofar mountains, and in isolated, scattered woodland patches in the Fartak Mountains. Ten populations (138 individuals) from across the southern Arabian distribution area of the species were analysed using chloroplast microsatellites and AFLP fingerprinting to a) reconstruct the phylogeographical pattern of E. schimperi on the southern Arabian Peninsula and b) to evaluate the consequences of population fragmentation on the genetic diversity harboured in isolated patches vs cohering stands. Phylogeographical reconstructions show that the distribution area of E. schimperi in the southern Arabian Peninsula is characterised by a geographical split that separates the southwestern populations (representated by material from Jabal Eraf and Jabal Uthmar), from the southcentral populations, which themselves are split from each other into a western (Ras Fartak) and an eastern refugium (Hawf/Dhofar). The analysis of the within‐population genetic diversity in E. schimperi populations resulted in a slightly, but not significantly higher genetic variation in small and isolated woodland patches (HS=0.302) compared to larger, cohering stands (HS=0.291).
Contribution of the M3 muscarinic receptors to the vasodilator response to acetylcholine in the human forearm vascular bed
Authors: Attinà Teresa M. , Oliver James J. , Malatino Lorenzo S. , Webb David J.
Published: April 2008

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• Available evidence suggests that the M3 receptor on endothelial cells is responsible for acetylcholine (Ach)‐dependent vasodilatation.

• Data from human studies only provide indirect evidence for this, and results are more difficult to interpret.

WHAT THIS STUDY ADDS

• This study used the new M3 receptor antagonist darifenacin as a pharmacological ‘tool’ to investigate the role of M3 receptor in the human forearm circulation.

• It provides evidence for a major role for the M3 receptors in ACh‐dependent vasodilatation in the forearm vascular bed.

AIMS

Acetylcholine (ACh) is a muscarinic agonist that causes receptor‐mediated, endothelium‐dependent vasodilatation in the forearm vasculature. Previous indirect evidence suggests this effect may be mediated by muscarinic M3 receptors. Darifenacin is a recently developed antimuscarinic drug with greater M3 selectivity, and our main objective was to investigate whether darifenacin affects dose‐dependent vasodilatation to ACh in the forearm circulation.

METHODS

Healthy subjects were enrolled in two studies designed to assess the effects of atropine and darifenacin on the forearm blood flow (FBF) response to ACh.

RESULTS

In both studies ACh caused similar dose‐dependent vasoditation in the forearm vasculature. In study I (5 subjects), the FBF response to ACh was largely attenuated by pretreatment with the nonselective muscarinic antagonist atropine. In study II (10 subjects), oral administration of darifenacin 15 mg for 1 week significantly reduced the FBF dose‐dependent response to ACh 20 µg min−1 {mean difference from placebo 5.8 [95% confidence interval (CI) 3.1, 8.7] ml min−1 per 100 ml of forearm volume, P < 0.001} and to ACh 60 µg min−1[mean difference from placebo 5.9 (95% CI 3.1, 8.7) ml min−1 per 100 ml of forearm volume, P < 0.001]. After darifenacin, the AUC of change in FBF from baseline was reduced by almost 50% compared with placebo.

CONCLUSIONS

These results suggest that, in the forearm vasculature, muscarinic M3 receptors play a major role in ACh‐induced endothelium‐mediated vasodilatation.
Undergraduate preparation for prescribing: the views of 2413 UK medical students and recent graduates
Authors: Heaton Amy , Webb David J. , Maxwell Simon R. J.
Published: April 2008

WHAT IS ALREADY KNOWN ON THIS SUBJECT

• Adverse drug events are common in National Health Service (NHS) hospitals where junior doctors take responsibility for most of the prescribing.

• Safe and effective prescribing of drugs is a core competency expected of all medical graduates.

• There is a perception from some of those who supervise the prescribing of drugs in the NHS that undergraduate teaching in this area may be deficient, although this view is contested.

WHAT THIS STUDY ADDS

• Our study suggests that a large proportion of medical students and recent graduates from UK medical schools who responded also believe that their teaching and assessment in this area was inadequate.

• This result implies that those responsible for overseeing undergraduate education should urgently review teaching and assessment of competency in relation to prescribing in all UK medical schools.

AIMS

To gather opinions from UK medical students and recent graduates about their undergraduate training to prescribe and their confidence about meeting the relevant competencies identified by the General Medical Council (GMC).

METHODS

We designed a web‐based survey that was distributed to UK medical students and first year Foundation doctors (graduation years 2006–2008) via medical schools and postgraduate networks.

RESULTS

Analysis was restricted to 2413 responses from students graduating in 2006–2008 from the 25 UK medical schools (mean 96.5 per school) with a complete undergraduate curriculum. Distinct courses and assessments in ‘clinical pharmacology & therapeutics (or equivalent)’ were identified by 17% and 13%, respectively, with mode of learning described most commonly as ‘opportunistic learning during clinical attachments’ (41%). Only 38% felt ‘confident’ about prescription writing and only a minority (35%) had filled in a hospital prescription chart more than three times during training. The majority (74%) felt that the amount of teaching in this area was ‘too little’ or ‘far too little’, and most tended to disagree or disagreed that their assessment ‘thoroughly tested knowledge and skills’ (56%). When asked if they were confident that they would be able to achieve the prescribing competencies set out by the GMC, 42% disagreed or tended to disagree, whereas only 29% agreed or tended to agree.

CONCLUSIONS

Many respondents clearly perceived a lack of learning opportunities and assessment related to the safe and effective use of drugs and had little confidence that they would meet the competencies identified by the GMC. There is an urgent need to review undergraduate training in this area.
Maraviroc:in vitroassessment of drug–drug interaction potential
Authors: Hyland Ruth , Dickins Maurice , Collins Claire , Jones Hannah , Jones Barry
Published: April 2008

WHAT IS ALREADY KNOWN ABOUT THE SUBJECT

• Maraviroc is known to undergo oxidative metabolismin vivoand is a substrate for cytochrome P450 (CYP).

• Simcyp™ has recently become more widely used for the prediction of CYP‐mediated drug–drug interactions (DDIs) usingin vitrometabolism data.

WHAT THIS STUDY ADDS

• Maraviroc has been identified as a CYP3A4 substrate and the kinetic constants characterized.

• The predicted DDIs associated with maraviroc as a CYP3A4 substrate using Simcyp™ have been compared against the clinical data.

• This study demonstrates the value of a reliable Simcyp™ model for prediction of DDIs.

AIMS

To characterize the cytochrome P450 enzyme(s) responsible for the N‐dealkylation of maravirocin vitro, and predict the extent of clinical drug–drug interactions (DDIs).

METHODS

Human liver and recombinant CYP microsomes were used to identify the CYP enzyme responsible for maraviroc N‐dealkylation. Studies comprised enzyme kinetics and evaluation of the effects of specific CYP inhibitors.In vitrodata were then used as inputs for simulation of DDIs with ketoconazole, ritonavir, saquinavir and atazanvir, using the Simcyp™ population‐based absorption, distribution, metabolism and elimination (ADME) simulator. Study designs for simulations mirrored those actually used in the clinic.

RESULTS

Maraviroc was metabolized to its N‐dealkylated product via a single CYP enzyme characterized by aKmof 21 µM andVmaxof 0.45 pmol pmol−1 min−1in human liver microsomes and was inhibited by ketoconazole (CYP3A4 inhibitor). In a panel of recombinant CYP enzymes, CYP3A4 was identified as the major CYP responsible for maraviroc metabolism. Using recombinant CYP3A4, N‐dealkylation was characterized by aKmof 13 µM and aVmaxof 3 pmol pmol−1CYP min−1. Simulations therefore focused on the effect of CYP3A4 inhibitors on maraviroc pharmacokinetics. The simulated median AUC ratios were in good agreement with observed clinical changes (within twofold in all cases), although, in general, there was a trend for overprediction in the magnitude of the DDI.

CONCLUSION

Maraviroc is a substrate for CYP3A4, and exposure will therefore be modulated by CYP3A4 inhibitors. Simcyp™ has successfully simulated the extent of clinical interactions with CYP3A4 inhibitors, further validating this software as a good predictor of CYP‐based DDIs.