bluuebunny/crossref_metadata_2025 huggingface dataset:
Flow dependence of interfacial thermal resistance in nanochannels
Authors: Liu Chong , Fan Hai-Bo , Zhang Kai , Yuen Matthew M. F. , Li Zhigang
Published: March 2010

In nanochannel flows, the thermal resistance at the fluid-solid interface may depend on the flow scenario. In this work, we study the interfacial thermal resistance Rth in nanoscale force-driven flows at different temperatures and fluid-wall interactions. For Ar flows in Cu and Ag channels, the fluid-wall binding energy is strong and it is found that Rth assumes a maximum value as the external force is varied. The maximum value is caused by the fluid adsorption on the solid surfaces and the temperature increase in the fluid due to viscous frictions. However, when the fluid-wall interaction is weak, the maximum value is not observed and the interfacial thermal resistance decreases monotonously with increasing external force. With the presence of fluid adsorption, it is also found that the peak in Rth is more detectable at low temperature than high temperature.
Strain-driven spin reorientation in magnetite/barium titanate heterostructures
Authors: Sterbinsky G. E. , Wessels B. W. , Kim J.-W. , Karapetrova E. , Ryan P. J. , Keavney D. J.
Published: March 2010

We report spin reorientation transitions in a Fe3O4/BaTiO3 heterostructure driven by strain at the structural phase transitions of BaTiO3. These spin reorientations result from the emergence of an in-plane uniaxial magnetic anisotropy. The magnetoelastic response of Fe3O4 to the variations in epitaxial strain that occur at the BaTiO3 phase transitions gives rise to the uniaxial anisotropy. The anisotropy energies calculated from the in-plane strain are in quantitative agreement with a change in the Zeeman energy.
Microstress relaxation effect of Pb(Zr0.52Ti0.48)O3 films with thicknesses for micro/nanopiezoelectric device
Authors: Lee Jeong Hoon , Hwang Kyo Seon , Kim Tae Song
Published: March 2010

In this study, we analyzed the microstress of Pb(Zr0.52Ti0.48)O3 (PZT) films using Raman spectrum and the macrostress using the wafer curvature method. Based on the stress analysis, we also determined the relationship between the residual stress and piezoelectric properties. We found that a thickness of 1 μm was critical since the stress relaxation starts due to surface roughening. Similarly, the film thickness dependence of the piezoelectric coefficient had saturation values around 1 μm, where the preferred orientation started to change from (111) to (110), indicating that the piezoelectric response was related to the stress relaxation with a preferred orientation change.
Prediction of RNA multiloop and pseudoknot conformations from a lattice-based, coarse-grain tertiary structure model
Authors: Jost Daniel , Everaers Ralf
Published: March 2010

We present a semiquantitative lattice model of RNA folding, which is able to reproduce complex folded structures such as multiloops and pseudoknots without relying on the frequently employed ad hoc generalization of the Jacobson–Stockmayer loop entropy. We derive the model parameters from the Turner description of simple secondary structural elements and pay particular attention to the unification of mismatch and coaxial stacking parameters as well as of border and nonlocal loop parameters, resulting in a reduced, unified parameter set for simple loops of arbitrary type and size. For elementary structures, the predictive power of the model is comparable to the standard secondary structure approaches, from which its parameters are derived. For complex structures, our approach offers a systematic treatment of generic effects of chain connectivity as well as of excluded volume or attractive interactions between and within all elements of the secondary structure. We reproduce the native structures of tRNA multiloops and of viral frameshift signal pseudoknots.
Band gap states of copper phthalocyanine thin films induced by nitrogen exposure
Authors: Sueyoshi Tomoki , Kakuta Haruya , Ono Masaki , Sakamoto Kazuyuki , Kera Satoshi , Ueno Nobuo
Published: March 2010

The impact of 1 atm N2 gas exposure on the electronic states of copper phthalocyanine thin films was investigated using ultrahigh-sensitivity ultraviolet photoelectron spectroscopy. The highest occupied molecular orbital band of the film showed a drastic reversible change in the bandwidth and band shape as well as in the energy position upon repeated cycles of N2 exposure and subsequent annealing. Furthermore, two types of gap-state densities with Gaussian and exponential distributions appeared after the exposure and disappeared due to the annealing. These changes are ascribed to a weak disorder in the molecular packing structure induced by N2 diffusion into the film.
Decentralized robust static synchronous compensator control for wind farms to augment dynamic transfer capability
Authors: Hossain M. J. , Pota H. R. , Kumble C.
Published: March 2010

This paper presents an algorithm to design a decentralized robust controller for static synchronous compensators (STATCOMs) using minimax linear quadratic output-feedback control design approach. There is an increase in the available (dynamic) transfer capability of power systems with fixed-speed wind generators due to the designed decentralized controllers. The effects of the integration of various types of wind generators into power systems based on transfer limit have also been analyzed in this paper. The effectiveness of the suggested control strategy is validated by simulations on a benchmark two area power system. The performance of the designed controller is also compared to a conventional proportional-integral-based STATCOM controller. Simulation results show that both the dynamic voltage stability and the transient stability can be improved by using the robust STATCOM control proposed in this paper.
Single-photon emission from InGaAs quantum dots grown on (111) GaAs
Authors: Stock Erik , Warming Till , Ostapenko Irina , Rodt Sven , Schliwa Andrei , Töfflinger Jan Amaru , Lochmann Anatol , Toropov Aleksandr I. , Moshchenko Sergej A. , Dmitriev Dimitry V. , Haisler Vladimir A. , Bimberg Dieter
Published: March 2010

In this letter, we demonstrate that self-organized InGaAs quantum dots (QDs) grown on GaAs (111) substrate using droplet epitaxy have great potential for the generation of entangled photon pairs. The QDs show spectrally sharp luminescence lines and low spatial density. A second order correlation value of g(2)(0)<0.3 proves single-photon emission. By comparing the power dependence of the luminescence from a number of QDs we identify a typical luminescence fingerprint. In polarization dependent microphotoluminescence studies a fine-structure splitting ranging ≤40 μeV down to the determination limit of our setup (10 μeV) was observed.
Vertical gradient of magnetic anisotropy in the ferromagnetic semiconductor (Ga,Mn)As film
Authors: Son Hyunji , Chung Sunjae , Yea Sun-young , Kim Shinhee , Yoo Taehee , Lee Sanghoon , Liu X. , Furdyna J. K.
Published: March 2010

The properties of magnetic anisotropy of GaMnAs films along the growth direction were studied by Hall effect measurements. The magnetic anisotropy fields were obtained by analyzing the angular dependence of the planar Hall resistance and the anomalous Hall resistance for in-plane and out-of plane components of the Hall signal, respectively. The magnetic anisotropy fields obtained by this process were used to construct a three-dimensional magnetic free energy diagram, which clearly shows that the out-of-plane characteristics of magnetic anisotropy become more pronounced as we approach the bottom part of the film.
Multiferroic GaN nanofilms grown within Na-4 mica channels
Authors: Bhattacharya Santanu , Datta A. , Chakravorty D.
Published: March 2010

Gallium nitride nanofilms grown within nanochannels of Na-4 mica structure, exhibit ferromagnetism even at room temperature due to the presence of gallium vacancies at the surfaces of the nanofilms. These nanofilms also show a ferroelectric behavior at room temperature ascribed to a small distortion in the crystal structure of GaN due to its growth within the Na-4 mica nanochannels. A colossal increase in 338% in dielectric constant was observed for an applied magnetic field of 26 kOe. The magnetoelectric effect is ascribed to magnetostriction of magnetic GaN phase.
Electronic properties of ultrananocrystalline diamond surfaces
Authors: Lud Simon Q. , Niedermeier Martin , Koch Philipp S. , Bruno Paola , Gruen Dieter M. , Stutzmann Martin , Garrido Jose A.
Published: March 2010

We have characterized ultrananocrystalline diamond films with different surface terminations by x-ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM), scanning tunneling microscopy (STM) and scanning tunneling spectroscopy (STS). The surface terminations were performed by plasma functionalization in atmospheres of hydrogen, fluorine, and oxygen. XPS proves the dense monolayer coverage of the surface functionalization. AFM and STM show low impact of the plasma treatment on the surface morphology. STS has been used to investigate the surface electronic properties, for H-terminated surfaces the electronic structure is dominated by the sp3 carbon phase of the grain surfaces; for O- and F-terminated surfaces, however, sp2 carbon from the grain boundaries seems to determine the surface band gap.
Roles of carbon in light emission of ZnO
Authors: Lu Y. H. , Hong Z. X. , Feng Y. P. , Russo S. P.
Published: March 2010

The origin of green light emission of ZnO has been a controversial topic. First-principles electronic structure calculations so far failed to provide useful evidence due to severe underestimation of band gap and ambiguous defect energy levels. In this work, we carried out first-principles electronic structure calculations on defected ZnO with a hybrid density functional. It was found that carbon, which cannot be completely avoided in fabricating processes, plays an important role in the commonly observed green emission, and could be the origin of green emission of ZnO. We also propose a method for the selection of emission by controlling defect types and ratio in ZnO.
Stable temperature characteristics of InGaN blue light emitting diodes using AlGaN/GaN/InGaN superlattices as electron blocking layer
Authors: Kim Kyu Sang , Kim Jin Ha , Jung Su Jin , Park Yong Jo , Cho S. N.
Published: March 2010

P-type AlGaN/GaN/InGaN superlattices were incorporated in a InGaN based blue light emitting diode as electron blocking layer to minimize the temperature dependence on optical output power. For the characteristic temperatures in range of 10 to 100 °C and at operation current of 350 mA, the external quantum efficiency varied by less than 0.5%. For the presented device, the negative characteristic temperature was shown to occur below temperature of 50 °C. The improved temperature stability in optical output power is thought to be attributed to (1) the efficiency of hole carrier transport in AlGaN/GaN/InGaN superlattices and (2) the enhanced blocking of electron overflow between multiple quantum wells and AlGaN/GaN/InGaN superlattices.
Compensation between magnetoresistance and switching current in Co/Cu/Co spin valve pillar structure
Authors: Cheng K. W. , Yu C. , Lin L. K. , Yao Y. D. , Liou Y. , Huang J. H. , Lee S. F.
Published: March 2010

We examine the effects of modifying the Co hard layer thickness of Co/Cu/Co spin valve submicron pillars with current flowing perpendicular to the plane. The magnetoresistance (MR) ratios and switching currents show complementary behaviors. As the Co hard layer thickness is increased, the MR ratio shows an initial increase with a peak around 21 nm. The critical switching current shows a dip around the same thickness, which is close to the spin diffusion length. The product of the MR ratio and critical current density is about a constant independent of the Co hard layer thickness. Thus, we provide an approach to achieving maximum efficiency (MR ratio) and minimum consumption (critical current) for a practical device.
Suppression of flux avalanches in superconducting films by electromagnetic braking
Authors: Colauto F. , Choi E. , Lee J. Y. , Lee S. I. , Patiño E. J. , Blamire M. G. , Johansen T. H. , Ortiz W. A.
Published: March 2010

Magnetic fields perpendicular to superconducting films often trigger vortex avalanches, which always are very harmful for electronic devices and other applications. Such avalanches can be suppressed by a metal layer placed in contact with the superconductor surface, an effect that up to now has been thought to be a consequence of improved heat conduction. Here we show experimentally that the role of the metal layer is not that of a heat-sink, but rather that of an electromagnetic drag due to eddy currents induced in the metal layer during the abrupt onset of the flux avalanches. The effect is demonstrated for films of MgB2 and Nb.
Anharmonic decay of g-process longitudinal optical phonons in silicon
Authors: Aksamija Z. , Ravaioli U.
Published: March 2010

We study phonons produced by transitions between the equivalent X valleys in silicon. We use the Monte Carlo method first to select stochastically the time between phonon collisions, and then to select a final-state pair of phonons from the probability distribution for anharmonic decay. Our results show that g-process phonons decay into one near-equilibrium transverse acoustic phonon and another intermediate longitudinal phonon either on the acoustic or optical branch. This second phonon has energies between 40 and 50 meV and undergoes further decay before turning into a pair of near-equilibrium transverse acoustic phonons, presenting a potential additional bottleneck.
Towards second-harmonic generation micropatterning of glass surface
Authors: Delestre Aurelien , Lahaye Michel , Fargin Evelyne , Bellec Matthieu , Royon Arnaud , Canioni Lionel , Dussauze Marc , Adamietz Frederic , Rodriguez Vincent
Published: March 2010

Thermal poling of sodium borophosphate niobium glasses, previously coated with a thin silver layer micropatterned by femtosecond laser irradiation, is demonstrated. The field-assisted ion-exchange process for fabricating planar surface in this glass substrate is analyzed. Inside the silver ablated lines obtained by femtosecond laser irradiation, we clearly observe a change in the distribution of the frozen electrostatic field that is modulated by the Ag+/Na+ ion-exchange process during the thermal poling.
Current-induced phase transition in ballistic Ni nanocontacts
Authors: Gatiyatov R. G. , Lisin V. N. , Bukharaev A. A.
Published: March 2010

Local phase transition from ferromagnetic to paramagnetic state in the region of the ballistic Ni nanocontacts (NCs) has been experimentally observed. We found that contact size reduction leads to an increase in the bias voltage at which the local phase transition occurs. Presented theoretical interpretation of this phenomenon takes into account the specificity of the local heating of the ballistic NC and describes the electron’s energy relaxation dependences on the applied voltage. The experimental data are in good qualitative and quantitative agreement with the theory proposed.
Competitiveness between direct and indirect radiative transitions of Ge
Authors: Cheng T.-H. , Ko C.-Y. , Chen C.-Y. , Peng K.-L. , Luo G.-L. , Liu C. W. , Tseng H.-H.
Published: March 2010

Both direct and indirect transitions of photoluminescence and electroluminescence are observed in a Ge n+p diode. The relative intensity of direct radiative recombination with respect to indirect radiative recombination increases with the increase in the optical pumping power, injection current density, and temperature. The increase in electron population in the direct valley is responsible for the enhancement. The spectra can be fitted by the combination of direct and indirect transition models. The direct radiative transition rate is ∼1600 times of the indirect transition, estimated by electroluminescence and photoluminescence spectra near room temperature.
Effect of Active Exploration of 3-D Object Views on the View-Matching Process in Object Recognition
Authors: Sasaoka Takafumi , Asakura Nobuhiko , Kawahara Tetsuo
Published: March 2010

Harman et al (1999, Current Biology9 1315–1318) showed that active exploration of novel objects allows faster recognition of these objects than passive viewing. Here, we examined whether active exploration of particular objects can facilitate subsequent view matching of different objects within the same category. In the generalisation phase, participants performed a matching task between two serially presented views of novel paper-clip objects. When the two views were of the same object, these were related by rotation about the vertical or horizontal axis. Subsequently, in the observation phase, participants were presented with another 5 paper-clip objects. One group of participants (active group) actively explored each of the objects for 20 s using a trackball over a limited range (−45° to +45°) of the horizontal axis. The other participants observed a replay of the active exploration of each of these objects by a participant in the active group (passive group) or observed a static view of the objects (still group). Following this observation phase, the generalisation phase was repeated twice for all groups of participants. The active group showed a clear expansion of the generalisation range about the horizontal axis. However, this expansion disappeared when we replicated the experiment using a smaller range of active exploration (−30° to +30°) and the experiment in which the participants observed a rotating object within the range of −45° to +45°. Furthermore, we found a significant improvement in view generalisation about the vertical axis when participants actively explored objects using a turntable over a range in −45° to +45° of the vertical axis. Most importantly, since participants explored different objects from the ones that were used in the generalisation phase, these results cannot be explained by improvement of the encoding process. The present findings therefore suggest that: (i) active exploration facilitates the process of view matching, (ii) this effect depends on the exploration range and rotational axis, and (iii) interaction between motor and visual information is necessary to facilitate the process of view matching.
Stream use by the large-footed myotis Myotis macropus in relation to environmental variables in northern New South Wales.
Authors: Anderson J. , Law B. , Tidemann C.
Published: March 2010

The large-footed myotis (Myotis macropus) feeds by trawling aquatic invertebrates and small fish from water surfaces, but little is known about what types of streams are used. We investigated habitat use by M. macropus in northern New South Wales (NSW) by analysing data-base records, conducting field surveys and assessing environmental variables on or near waterways. A GIS comparison of 222 data-base records of M. macropus with broad environmental patterns indicated that most records were near large and permanent waterways at low elevations, in flat or undulating terrain, usually surrounded by vegetation. Three different field surveys were carried-out. First, 25 waterways on the NSW mid-north coast were stratified into five size classes and sampled (December 1996-January 1997) using harp traps and ultrasonic detectors. Just two captures and 20 passes were recorded. No M. macropus were detected on either the smallest or largest waterways, although the latter may have been under-sampled due to their broad expanse. Records of M. macropus were significantly associated with larger, more permanent waterways (when the largest size class was omitted). Non-metric multi-dimensional scaling of sites, described by their environmental attributes, failed to separate sites on the basis of presence/absence of M. macropus. The second survey (February 1998) targeted 25 sites on waterways within 10 km of a known roost in Kerewong State Forest. Twenty-eight passes were recorded, all confined to just three sites on Upsalls Creek, a large 4th order stream. The third survey (February 2000) investigated the use of adjacent riparian vegetation in the vicinity of the Kerewong roost. At each of 12 sites, one detector was placed on the stream, one 10 m from it and a third 20 m into adjacent vegetation. An average of 11 M. macropus passes per night was recorded over streams (total passes = 273), whereas no passes were recorded in adjacent vegetation. We conclude that M. macropus is sparsely dispersed across streams in forests of north-east NSW and that they are most likely to be recorded on large streams in the lower end of catchments. Management implications for timber production forests include redirecting effort from pre-logging surveys to monitoring the changing status of M. macropus over time, especially at day roosts where local populations are concentrated.
The mammals of Croker Island, Northern Territory, Australia.
Authors: Firth R. S. C. , Panton W. J.
Published: March 2010

This is a report on the mammals found in April 2001 during a brief terrestial vertebrate fauna survey on previously unsurveyed Croker Island which is 3 km offshore from the Cobourg Peninusula. Seven mammals were recorded but only 3 were native. These were black flying -fox (Pteropus alecto), grassland melomys (Melomys burtoni) and the dingo (Canis lupus dingo). The remaining 4 species were domestic and feral animals (horse, cat, cattle and pig).
Low-frequency depolarized light scattering from aqueous solutions of oxo acids and their sodium salts
Authors: James DW , Irmer R
Published: March 2010

The depolarized scattering
profile between 3 and 300 cm-1 has been studied for aqueous
solutions of perchloric acid and nitric acid, and
their sodium salts. The profile has been analysed in terms off our component
bands, two of which are at zero energy shift, one is at c. 60 cm-1
and one at c.180 cm-1. In addition, solutions containing the nitrate
ion show evidence for two extra bands which have been assigned to a tunnelling mode of the NO3- ion (c.
10 cm-1) and a cooperative librational
mode (c. 120 cm-1). Changes in half width have been interpreted in
terms of a decrease in motional damping due to the presence of foreign species.
The intensity of all components shows a considerable change with concentration;
this is dependent on ion polarizability. Interpretation of the results in terms
of cooperative phenomena in the condensed phase is also discussed.
Metal template reactions. XVII. The attempted dimerization of amino carbonyl compounds containing a supporting donor atom
Authors: Black DSC , Rothnie NE
Published: March 2010

Attempts to effect metal
template condensative dimerizations
of the amino aldehydes (4), (11) and(12) and the amino ketone (24) have been
unsuccessful. Oxidation of the alcohol(9) did not allow isolation of the aldehyde (4). The alcohol (17) underwent oxidation to give
crude aldehyde (11),but the latter gave an
unidentified mixture of products on attempted reaction with metal ions. The alcohol
(20) was stable to oxidation, probably because of hydrogen bonding. The amino aldehyde(12) could not be isolated from the reduction of
the nitro aldehyde (22), the product being the
alcohol(20). The amino ketone (24) was fully characterized, but proved unreactive in attempted reactions with metal ions, again
possibly as a result of strong hydrogen bonding.
Synthesis of analogues of GABA. X. The bicyclic β-diketone Octahydro-1H-2-pyrindine-5,7-dione
Authors: Allan RD , Fong J
Published: March 2010

The synthesis is described
of octahydro-1H-2-pyrindine-5,7-dione (4) and its 6-diazo and 6-bromo derivatives.
These are analogues of GABA in which the carboxyl group is replaced by an enolic β-diketone. The compounds showed negligible or
very weak activity as GABA agonists with respect to inhibition of [3H] GABA
binding, uptake and transamination in rat brain
membranes.
The reaction of N-dichloromethylene-N,N-dialkylammonium chlorides with free sugars: an efficient synthesis of glycosyl chlorides
Authors: Copeland C , Mcadam DP , Stick RV
Published: March 2010

The treatment of aldose derivatives that are protected at all but the anomeric hydroxy groups with N-dichloromethylene-N,N-dialkylammonium
chlorides (alkyl = Me, Et) provides an improved method of preparing the
corresponding glycosyl chlorides. Analogous derivatives
containing anunprotected C1-C2 diol give 2-O-(N,N-dialkylcarbamoyl)glycosyl chlorides.
A convenient synthesis of two dibenzofurans
Authors: Sierakowski AF
Published: March 2010

1-Nitrodibenzofuran (4) and
dibenzofuran (5) have been prepared in high yield
from 2',6'-dinitro-biphenyl-2-ol (2) and 2'-nitrobiphenyl-2-ol (3),
respectively, by a cyclization involving intramolecular displacement of a nitro
group.
Protein Kinase Cζ Regulates Cdk5/p25 Signaling during Myogenesis
Authors: Thonel Aurélie de , Ferraris Saima E. , Pallari Hanna-Mari , Imanishi Susumu Y. , Kochin Vitaly , Hosokawa Tomohisa , Hisanaga Shin-ichi , Sahlgren Cecilia , Eriksson John E.
Published: March 2010

Atypical protein kinase Cζ (PKCζ) is emerging as a mediator of differentiation. Here, we describe a novel role for PKCζ in myogenic differentiation, demonstrating that PKCζ activity is indispensable for differentiation of both C2C12 and mouse primary myoblasts. PKCζ was found to be associated with and to regulate the Cdk5/p35 signaling complex, an essential factor for both neuronal and myogenic differentiation. Inhibition of PKCζ activity prevented both myotube formation and simultaneous reorganization of the nestin intermediate filament cytoskeleton, which is known to be regulated by Cdk5 during myogenesis. p35, the Cdk5 activator, was shown to be a specific phosphorylation target of PKCζ. PKCζ-mediated phosphorylation of Ser-33 on p35 promoted calpain-mediated cleavage of p35 to its more active and stable fragment, p25. Strikingly, both calpain activation and the calpain-mediated cleavage of p35 were shown to be PKCζ-dependent in differentiating myoblasts. Overall, our results identify PKCζ as a controller of myogenic differentiation by its regulation of the phosphorylation-dependent and calpain-mediated p35 cleavage, which is crucial for the amplification of the Cdk5 activity that is required during differentiation.
Cross-species common regulatory network inference without requirement for prior gene affiliation
Authors: Gholami Amin Moghaddas , Fellenberg Kurt
Published: March 2010

Motivation: Cross-species meta-analyses of microarray data usually require prior affiliation of genes based on orthology information that often relies on sequence similarity.

Results: We present an algorithm merging microarray datasets on the basis of co-expression alone, without any requirement for orthology information to affiliate genes. Combining existing methods such as co-inertia analysis, back-transformation, Hungarian matching and majority voting in an iterative non-greedy hill-climbing approach, it affiliates arrays and genes at the same time, maximizing the co-structure between the datasets. To introduce the method, we demonstrate its performance on two closely and two distantly related datasets of different experimental context and produced on different platforms. Each pair stems from two different species. The resulting cross-species dynamic Bayesian gene networks improve on the networks inferred from each dataset alone by yielding more significant network motifs, as well as more of the interactions already recorded in KEGG and other databases. Also, it is shown that our algorithm converges on the optimal number of nodes for network inference. Being readily extendable to more than two datasets, it provides the opportunity to infer extensive gene regulatory networks.

Availability and Implementation: Source code (MATLAB and R) freely available for download at http://www.mchips.org/supplements/moghaddasi_source.tgz

Contact:  kurt@tum.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Modeling sample variables with an Experimental Factor Ontology
Authors: Malone James , Holloway Ele , Adamusiak Tomasz , Kapushesky Misha , Zheng Jie , Kolesnikov Nikolay , Zhukova Anna , Brazma Alvis , Parkinson Helen
Published: March 2010

Motivation: Describing biological sample variables with ontologies is complex due to the cross-domain nature of experiments. Ontologies provide annotation solutions; however, for cross-domain investigations, multiple ontologies are needed to represent the data. These are subject to rapid change, are often not interoperable and present complexities that are a barrier to biological resource users.

Results: We present the Experimental Factor Ontology, designed to meet cross-domain, application focused use cases for gene expression data. We describe our methodology and open source tools used to create the ontology. These include tools for creating ontology mappings, ontology views, detecting ontology changes and using ontologies in interfaces to enhance querying. The application of reference ontologies to data is a key problem, and this work presents guidelines on how community ontologies can be presented in an application ontology in a data-driven way.

Availability:  http://www.ebi.ac.uk/efo

Contact:  malone@ebi.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Biphasic Effect of Curcumin on Morphine Tolerance: A Preliminary Evidence from Cytokine/Chemokine Protein Array Analysis
Authors: Lin Jui-An , Chen Jenn-Han , Lee Yuan-Wen , Lin Chao-Shun , Hsieh Ming-Hui , Chang Chuen-Chau , Wong Chih-Shung , Chen Judy Ju-Yi , Yeh Geng-Chang , Lin Feng-Yen , Chen Ta-Liang
Published: March 2010

The aim of this study was to evaluate the effect of curcumin on morphine tolerance and the corresponding cytokine/chemokine changes. Male ICR mice were made tolerant to morphine by daily subcutaneous injection for 7 days. Intraperitoneal injections of vehicle, low‐dose or high‐dose curcumin were administered 15 min after morphine injection, either acutely or chronically for 7 days to test the effect of curcumin on morphine‐induced antinociception and development of morphine tolerance. On day 8, cumulative dose‐response curves were generated and the 50% of maximal analgesic dose values were calculated and compared among groups. Corresponding set of mice were used for analyzing the cytokine responses by antibody‐based cytokine protein array. Acute, high‐dose curcumin enhanced morphine‐induced antinociception. While morphine tolerance was attenuated by administration of low‐dose curcumin following morphine injections for 7 days, it was aggravated by chronic high‐dose curcumin following morphine injection, suggesting a biphasic effect of curcumin on morphine‐induced tolerance. Of the 96 cytokine/chemokines analyzed by mouse cytokine protein array, 14 cytokines exhibited significant changes after the different 7‐day treatments. Mechanisms for the modulatory effects of low‐dose and high‐dose curcumin on morphine tolerance were discussed. Even though curcumin itself is a neuroprotectant and low doses of the compound serve to attenuate morphine tolerance, high‐doses of curcumin might cause neurotoxicity and aggravate morphine tolerance by inhibiting the expression of antiapoptotic cytokines and neuroprotective factors. Our results indicate that the effect of curcumin on morphine tolerance may be biphasic, and therefore curcumin should be used cautiously.
Virulence Phenotypes and Molecular Genotypes in Collections of Puccinia triticina from Italy
Authors: Mantovani Paola , Maccaferri Marco , Tuberosa Roberto , Kolmer James
Published: March 2010

Twenty-four isolates of Puccinia triticina from Italy were characterized for virulence to seedlings of 22 common wheat Thatcher isolines, each with a different leaf rust resistance gene, and for molecular genotypes at 15 simple sequence repeat (SSR) loci. The isolates were compared to a set of 13 previously characterized P. triticina isolates from either durum or common wheat. Clustering based on virulence phenotypes and SSR genotypes grouped the Italian P. triticina isolates into three groups. In the first group, the isolates had virulence phenotypes and SSR genotypes that were similar to the isolates collected from durum wheat. Isolates in the second group were unique because they had virulence similar to the isolates from common wheat but were distinct for SSR genotypes compared to the isolates from durum wheat and from common wheat. Isolates in the third group had virulence phenotypes and SSR genotypes closely related to the isolates from common wheat. The isolates were grouped based on the known or assumed host of origin, virulence phenotype, and SSR genotypes. Measures of FST and RST for SSR genotypes, and ΦST for virulence phenotype were significant, which indicated differentiation among the three groups of isolates. Virulence phenotypes and molecular genotypes were highly correlated with r = 0.74.
First Report of Brown Rot on Plum Caused by Monilia polystroma in China
Authors: Zhu X. Q. , Guo L. Y.
Published: March 2010

In August 2008, mummies of dwarf sweet plum (Prunus aitianli) fruit covered with grayish, conidial tufts were found in an orchard in Mudanjiang City of Heilongjiang in China. Conidial masses were touched with a sterilized wire loop and streaked onto the surface of water agar (WA) plates. After incubating at 22 ± 2°C for 16 to 24 h, individual germinated spores were picked out with a sterilized scalpel blade under a microscope in a laminar flow cabinet, and transferred to potato dextrose agar (PDA) in petri dishes. Mycelium grew an average of 10.7 mm per day on PDA and formed a white-to-grayish colony with irregular, black stroma 12 days after incubation at 22 ± 2°C under 12-h light/12-h dark. The average size of stroma was 8.19 cm2 per petri dish 37 days after incubation in the dark. The conidia were one-celled, hyaline, lemon-shaped, 15.2 (10.8 to 18.9) × 10.9 (8.3 to 16.3) μm, and arranged in branched monilioid chains on inoculated apples. The PCR products of internal transcribed spacer (ITS) region 1 and 2 and 5.8S gene of the ribosomal RNA amplified with primers ITS1 and ITS4 was directly sequenced in both directions using the PCR primers. The sequence of the Monilia polystroma isolate (GenBank Accession No. GU067539) was identical to the reference isolate of M. polystroma (CBS102686), containing five nucleotides that distinguish it from Monilinia fructigena (1,3). The pathogen was identified as M. polystroma on the basis of morphological characteristics (3) and the sequence of internal transcribed spacer (ITS) region 1 and 2 and 5.8S gene of the ribosomal RNA. Pathogenicity was confirmed by inoculating surface-sterilized, mature plum and apple fruit wounded with a nail, with a mycelial plug (5 mm in diameter) of the fungus at each wound. Fruit treated with plain PDA plugs were used as a control. Inoculated fruits were placed in a sterilized moist chamber at room temperature (23 to 28°C). Fifteen plums and nine apples were used in each of two replicated tests. All inoculated fruit developed typical brown rot symptoms 4 days after inoculation, while the control fruit remained healthy. M. polystroma was reisolated from the inoculated fruit and identified by the above methods. M. polystroma was first reported on apple in Japan (3) and it was recently discovered in an apple orchard in Hungary (2). Although the occurrence of Monilinia fructicola, Monilinia laxa, and Monilinia fructigena (teleomorphs of the three Monilia spp.) in China have been documented, to our knowledge, this is the first report of the occurrence of M. polystroma in China.

References: (1) C. E. Fulton et al. Eur. J. Plant Pathol. 105:495, 1999. (2) M. Petróczy and L. Palkovics. Eur. J. Plant Pathol. 125:343, 2009. (3) G. C. M. van Leeuwen et al. Mycol. Res. 106:444, 2002.
First Report of ‘Candidatus Liberibacter asiaticus’ Associated with Huanglongbing in Sweet Orange in Ethiopia
Authors: Saponari M. , De Bac G. , Breithaupt J. , Loconsole G. , Yokomi R. K. , Catalano L.
Published: March 2010

Huanglongbing (HLB) is a serious disease of citrus worldwide. Three different ‘Candidatus Liberibacter’ species are associated with HLB: ‘Ca. Liberibacter asiaticus’, ‘Ca. L. africanus’, and ‘Ca. L. americanus’ (1). ‘Ca. L. africanus’ and its vector, Trioza erytreae, are both heat sensitive, and when present, occur in citrus when temperatures remain below 30 to 32°C. In Africa, ‘Ca. L. africanus’ and T. erytreae have been reported in South Africa, Zimbabwe, Malawi, Burundi, Kenya, Somalia, Ethiopia, Cameroon, and Madagascar (1). Inspection of citrus trees in orchards and budwood sources in nurseries located in the warmer citrus-growing areas of Tigray and North Wollo in northern Ethiopia revealed nearly 100 trees with symptoms of leaf yellowing with a blotchy mottle pattern, dead branches, and decreased fruit quality and yield. Two symptomatic sweet orange budwood trees and three symptomatic orchard plants were sampled in April 2009, along with three healthy-looking sweet orange plants. DNA was extracted from 200 mg of desiccated leaf midribs using the CTAB method (4) and subjected to conventional PCR using the primer pairs A2/J5 (2) and OI2/23S1 (3) that amplify the ribosomal protein gene in the rplKAJL-rpoBC operon and the 16S/23S ribosomal intergenic regions, respectively, of ‘Ca. L. africanus’ and ‘Ca. L. asiaticus’. Positive PCR reactions were obtained for all five symptomatic samples with both primer pairs. PCR amplicons of 703 bp (A2/J5) and 892 bp (OI2/23S) recovered from two of these samples were purified, cloned, and sequenced. BLAST analysis revealed that the nucleotide sequences we obtained for the ribosomal protein (GenBank Accessions Nos. GQ890155 and GQ890156) shared 100% identity with each other and 99% identity with sequences of ‘Ca. L. asiaticus’ from Brazil (DQ471904), Indonesia (AB480161), China (DQ157277), and Florida (CP001677). Similarly, the 16S/23S ribosomal intergenic sequences (GU296538 and GU296539) shared 100% identity with each other and 99% identity with homologous ‘Ca. L. asiaticus’ sequences from Brazil (DQ471903), Indonesia (AB480102), China (DQ778016), and Florida (CP001677) and contained two tRNA genes as occurs in ‘Ca. L. asiaticus’ but not in ‘Ca. L. africanus’ (3). To our knowledge, this is the first report of ‘Ca. L. asiaticus’ in Africa. The presence of ‘Ca. L. asiaticus’ is a threat for warmer citrus-growing areas of Africa that are less favorable for ‘Ca. L. africanus’ and T. erytreae. In areas where ‘Ca. L. asiaticus’ was confirmed, symptomatic trees must be promptly eradicated and surveys to determine spread of the disease and its vectors are necessary.

References: (1) J. M. Bove. J. Plant Pathol. 88:7, 2006. (2) A. Hocquellet et al. Mol. Cell. Probes 13:373, 1999. (3) S. Jagoueix et al. Int. J. Syst. Bacteriol. 47:224, 1997. (4) M. G. Murray and W. F Thompson. Nucleic Acids Res. 8:4321, 1980.
First Report of Rhizoctonia solani Causing a Disease of Sunflower in India
Authors: Srinivasan K. , Visalakchi S.
Published: March 2010

During the spring of 2009, symptoms including leaf yellowing and wilting, root rot, and death of plants were noted in sunflower (Helianthus annuus L.) crops in Dharmapuri District, Tamilnadu, India. In some fields, approximately 30% of the plants were affected. The disease began when plants were approximately 10 weeks old and occurred on scattered or adjacent plants. The presence of white mycelium was observed on necrotic crowns. Symptomatic tissue was surface disinfested in 70% alcohol for 30 s and 0.5% sodium hypochlorite for 1 min and plated onto potato dextrose agar (PDA) (1). One isolate (coded SV001) had near right-angle branching with basal constriction and adjacent septa and sclerotia typical of Rhizoctonia spp. (2). Cream-colored colonies produced irregular, light brown sclerotia that were 3.0 to 7.3 mm (average 3.8 mm) in diameter. Hyphae were 6.8 to 7.0 μm (average 6.9 μm) wide and multinucleate (8 to 15 nuclei per cell). On the basis of hyphal anastomosis with several known AG testers, the fungus was characterized as Rhizoctonia solani Kühn AG-IV (3). One culture was deposited at the Madras University Botany Laboratory, Center for Advanced Studies in Botany, University of Madras, Chennai, India. In a pathogenicity test, R. solani SV001 was grown on PDA for 5 days at 24°C in the dark. Five-millimeter-diameter disks were placed at the base of sunflower plants (cv. Mordan). Four sunflower plants in each of three pots were inoculated; noninoculated plants served as controls. Plants were placed in a glasshouse maintained at 25 to 27°C. Inoculated plants developed yellow foliage and crown rot and root rot symptoms after 7 to 12 days and died in 17 to 20 days. No symptoms were observed on noninoculated plants. The pathogen was reisolated from fragments of necrotic crown tissue of inoculated plants. To our knowledge, this is the first report of R. solani AG-IV causing a disease of sunflower plants in India.

References: (1). R. C. Fenille et al. Plant Pathol. 54:325, 2005. (2). J. R. Parmeter et al. Phytopathology 59:1270, 1969. (3) B. Sneh et al. Identification of Rhizoctonia Species. The American Phytopathological Society, St Paul, MN, 1991.
More individuals but fewer species: testing the ‘more individuals hypothesis’ in a diverse tropical fauna
Authors: McGlynn Terrence P. , Weiser Michael D. , Dunn Robert R.
Published: March 2010

A positive relationship between species richness and productivity is often observed in nature, but the causes remain contentious. One mechanism, the ‘more individuals hypothesis’ (MIH), predicts richness increases monotonically with density, as a function of resource flux. To test the MIH, we manipulated resource abundance in a community of tropical rainforest litter ants and measured richness and density responses. A unimodal relationship between richness and density most closely fitted the control and disturbance (resource removal) treatments in contrast to expectations of the MIH. Resource addition resulted in a monotonic increase in richness relative to density, a shift from the pattern in the control. In the disturbance treatment, richness was greater than in the control, opposite to expectations of the MIH. While large-scale correlations between ant diversity and net primary productivity or temperature are reconcilable with the MIH, key elements of the hypothesis are not supported.
A novel route for processing cobalt–chromium–molybdenum orthopaedic alloys
Authors: Patel Bhairav , Inam Fawad , Reece Mike , Edirisinghe Mohan , Bonfield William , Huang Jie , Angadji Arash
Published: March 2010

Spark plasma sintering has been used for the first time to prepare the ASTM F75 cobalt–chromium–molybdenum (Co–Cr–Mo) orthopaedic alloy composition using nanopowders. In the preliminary work presented in this report, the effect of processing variables on the structural features of the alloy (phases present, grain size and microstructure) has been investigated. Specimens of greater than 99.5 per cent theoretical density were obtained. Carbide phases were not detected in the microstructure but oxides were present. However, harder materials with finer grains were produced, compared with the commonly used cast/wrought processing methods, probably because of the presence of oxides in the microstructure.
The asymmetry of the carpal joint and the evolution of wing folding in maniraptoran theropod dinosaurs
Authors: Sullivan Corwin , Hone David W. E. , Xu Xing , Zhang Fucheng
Published: March 2010

In extant birds, the hand is permanently abducted towards the ulna, and the wrist joint can bend extensively in this direction to fold the wing when not in use. Anatomically, this asymmetric mobility of the wrist results from the wedge-like shape of one carpal bone, the radiale, and from the well-developed convexity of the trochlea at the proximal end of the carpometacarpus. Among the theropod precursors of birds, a strongly convex trochlea is characteristic of Coelurosauria, a clade including the highly derived Maniraptora in addition to tyrannosaurs and compsognathids. The shape of the radiale can be quantified using a ‘radiale angle’ between the proximal and distal articular surfaces. Measurement of the radiale angle and reconstruction of ancestral states using squared-change parsimony shows that the angle was small (15°) in primitive coelurosaurs but considerably larger (25°) in primitive maniraptorans, indicating that the radiale was more wedge-shaped and the carpal joint more asymmetric. The radiale angle progressively increased still further within Maniraptora, with concurrent elongation of the forelimb feathers and the forelimb itself. Carpal asymmetry would have permitted avian-like folding of the forelimb in order to protect the plumage, an early advantage of the flexible, asymmetric wrist inherited by birds.
Reproductive competition promotes the evolution of female weaponry
Authors: Watson Nicola L. , Simmons Leigh W.
Published: March 2010

Secondary sexual traits in females are a relatively rare phenomenon. Empirical studies have focused on the role of male mate choice in their evolution; however, recently it has been suggested that secondary sexual traits in females are more likely to be under selection via reproductive competition. We investigated female competition and the influence of female phenotype on fitness in
Onthophagus sagittarius
, a species of dung beetle that exhibits female-specific horns. We compared reproductive fitness when females were breeding in competition versus breeding alone and found that competition for breeding resources reduced fitness for all females, but that smaller individuals suffered a greater fitness reduction than larger individuals. When females were matched for body size, those with the longest horns gained higher reproductive fitness. The fitness function was positive and linear, favouring increased horn expression. Thus, we present evidence that female body size and horn size in
O. sagittarius
are under directional selection via competition for reproductive resources. Our study is a rare example of female contest competition selecting for female weaponry.
Parasite virulence when the infection reduces the host immune response
Authors: Cornet Stéphane , Sorci Gabriele
Published: March 2010

Parasite infections often induce a reduction in host immune response either because of a direct manipulation of the immune system by the parasite or because of energy depletion. Although infection-induced immunodepression can favour the establishment of the parasite within the host, a too severe immunodepression may increase the risk of infection with opportunistic pathogens, stopping the period over which the parasite can be transmitted to other hosts. Here, we explore how the risk of contracting opportunistic diseases affects the survival of the amphipod
Gammarus pulex
infected by the acanthocephalan
Pomphorhynchus laevis
. Previous work with this system has shown that upon infection,
G. pulex
has a substantially reduced immune response. Non-infected and
P. laevis
-infected hosts were maintained either in control or in micro-organism-enriched water, so as to vary the risk of encountering opportunistic pathogens. As predicted, we found that host mortality was exacerbated when infected gammarids were maintained in micro-organism-enriched water compared with clean, control water; whereas for non-infected gammarids, living in micro-organism-enriched water only moderately increased the risk of mortality. These results show that the virulence of parasites that reduce the host immune response is an environmentally sensitive trait that depends on the concomitant risk for the host of contracting opportunistic diseases. This extra source of host mortality probably represents a cost for
P. laevis
, and we tentatively predict that the optimal level of parasite exploitation should depend on environmental conditions.