bluuebunny/crossref_metadata_2025 huggingface dataset:
Germanium‐silicon as a flow path tracer: Application to the Rio Icacos watershed
Authors: Kurtz Andrew C. , Lugolobi Festo , Salvucci Guido
Published: June 2011

We use dissolved silicon together with its “geochemical twin” germanium for the first time as a hydrologic tracer to study water delivery to the stream during storm events in the Rio Icacos watershed, Puerto Rico. Ge and Si were measured on base flow, stormflow, springwater, and soil water samples. Compositions of all of these waters appear to reflect varying contributions from three components, which we attribute to solutes released from bedrock weathering (groundwater), from short‐term soil‐water interaction (quick soil water), and longer‐term soil‐water interaction (matrix soil water). Base flow stream waters have high Si and moderate Ge (Ge/Si ratio ∼0.29μmol/mol), consistent with a predominantly bedrock weathering source as indicated by their similarity with water sampled from springs emerging from the saprolite‐bedrock boundary on a hillslope landslide scar. During storm events there is a shift toward more dilute compositions (but higher Ge/Si ratios) similar to those measured on water samples from temporary depression storage and overland flow (quick soil water). Geochemical mass balance shows that 80%–90% of the stream chemistry can be explained by mixing groundwater with this quick soil water composition, which we infer to reflect new water traveling as shallow throughflow. Stream waterδ18O values decrease to more negative values typical of precipitation supporting rapid delivery of rainwater to the stream channel during stormflow. The third component, with a Ge‐rich composition characteristic of soil matrix water sampled by tension lysimeters, is required to explain higher stream water Ge/Si ratios measured during hydrograph recession. We infer from this an additional, slower, and less dominant pathway for delivery of soil water to the stream channel.
Environmental epigenomics and disease susceptibility
Authors: Skinner Michael K
Published: June 2011

The Keystone symposium on ‘Environmental Epigenomics and Disease Susceptibility’ was held in late March 2011 at the Grove Park Inn Resort in Asheville, North Carolina, USA. The meeting helped to define the developing field of ‘environmental epigenetics’ and the research presented established its role in disease aetiology and susceptibility.
Study on plasma parameters and dust charging in an electrostatically plugged multicusp plasma device
Authors: Kakati B. , Kausik S. S. , Saikia B. K. , Bandyopadhyay M.
Published: June 2011

The effect of the electrostatic confinement potential on the charging of dust grains and its relationship with the plasma parameters has been studied in an electrostatically plugged multicusp dusty plasma device. Electrostatic plugging is implemented by biasing the electrically isolated magnetic multicusp channel walls. The experimental results show that voltage applied to the channel walls can be a controlling parameter for dust charging.
Plasmon hybridization in parallel nano-wire systems
Authors: Moradi Afshin
Published: June 2011

We apply the plasmon hybridization method to a double-nano-wire system, providing a simple and intuitive description of the plasmon excitations in the system. We apply the two-center cylindrical coordinate system for mathematical convenience and find an explicit form of the surface plasmon oscillations, in terms of the interaction between the bare plasmon modes of the individual surfaces of the nano-wires. We present numerical results to display how the plasmon excitations of the system depend on nano-wire separation when there is no angular momentum transfer, i.e., when m = 0.
Effect of doping and polarization on carrier collection in InGaN quantum well solar cells
Authors: Neufeld Carl J. , Cruz Samantha C. , Farrell Robert M. , Iza Michael , Lang Jordan R. , Keller Stacia , Nakamura Shuji , DenBaars Steven P. , Speck James S. , Mishra Umesh K.
Published: June 2011

The effect of doping and polarization on carrier collection is investigated for InGaN quantum well solar cells. Energy band diagram simulations of actual devices indicate that spontaneous and piezoelectric polarization sheet charges can inhibit carrier collection unless these charges are screened by sufficient doping. By increasing the doping on both sides of the active region, the polarization-induced barriers to carrier collection were eliminated and the short circuit current density was increased from 0.1 to 1.32 mA/cm2 under 1.5 sun AM1.5G equivalent illumination, leading to devices with an open circuit voltage of 1.9 V and a fill factor of 71%.
High resolution short focal distance Bent Crystal Laue Analyzer for copper K edge x-ray absorption spectroscopy
Authors: Kujala N. G. , Karanfil C. , Barrea R. A.
Published: June 2011

We have developed a compact short focal distance Bent Crystal Laue Analyzer (BCLA) for Cu speciation studies of biological systems with specific applications to cancer biology. The system provides high energy resolution and high background rejection. The system is composed of an aluminum block serving as a log spiral bender for a 15 micron thick Silicon 111 crystal and a set of soller slits. The energy resolution of the BCLA—about 14 eV at the Cu Kα line— allows resolution of the Cu Kα1 and CuKα2 lines. The system is easily aligned by using a set of motorized XYZ linear stages. Two operation modes are available: incident energy scans (IES) and emission energy scans (EES). IES allows scanning of the incident energy while the BCLA system is maintained at a preselected fixed position—typically CuKα1 line. EES is used when the incident energy is fixed and the analyzer is scanned to provide the peak profile of the emission lines of Cu.
Magnetic patterning perpendicular anisotropy FePd alloy films by masked ion irradiation
Authors: Merkel D. G. , Bottyán L. , Tanczikó F. , Zolnai Z. , Nagy N. , Vértesy G. , Waizinger J. , Bommer L.
Published: June 2011

The nanopatterning of magnetic films by ion implantation is reported. Highly L10-ordered Fe47Pd53 epitaxial alloy films on a MgO(001) substrate were covered by a monolayer of silica spheres in a Langmuir film balance. Using this sphere layer as an implantation mask, the samples were irradiated by Ne+ or Fe+ ions with energies of 35 keV and 100 keV, respectively. After the silica mask was removed, the samples were characterized via conversion electron Mössbauer spectroscopy, longitudinal and polar magneto-optical Kerr effect, and atomic force and magnetic force microscopy. We find that the magnetic stripe domains observed in the nonirradiated sample were converted into a regular 2D magnetic pattern of hcp character upon 1 × 1015/cm2 35 keV neon or 1 × 1014/cm2 100 keV iron irradiation, with the direction of magnetization remaining out of plane in the nodes of the hcp lattice and relaxed into the film plane in the inter-node region, resulting in an overall in-plane magnetic softening of the film.
Charge trapping process of nonvolatile memory devices based on CdTe and CdTe–CdSe core-shell nanoparticles/poly(methylmethacrylate) nanocomposites
Authors: Yun Dong Yeol , Son Jung Min , Kim Tae Whan , Kim Sung Woo , Kim Sang Wook
Published: June 2011

Nonvolatile memory devices based on CdTe and CdTe–CdSe core-shell nanoparticles embedded in a poly(methylmethacrylate) (PMMA) layer were fabricated to investigate the variation in the carrier transport mechanisms due to a CdSe shell. Capacitance-voltage (C-V) curves for Al/CdTe nanoparticles embedded in PMMA/p-Si and Al/CdTe–CdSe nanoparticles embedded in PMMA/p-Si devices at 300 K showed that the flatband voltage shift of the C-V curve for the device with the CdTe–CdSe nanoparticles was relatively smaller than that for the device with the CdTe nanoparticle. Carrier transport mechanisms of the memory devices are described by using the C-V results, energy band diagrams, and capacitance-time retentions.
Three-dimensional magneto-resistive random access memory devices based on resonant spin-polarized alternating currents
Authors: Vogler Christoph , Bruckner Florian , Fuger Markus , Bergmair Bernhard , Huber Thomas , Fidler Josef , Suess Dieter
Published: June 2011

Selective switching of a magneto-resistive random access memory (MRAM) multilayer stack is demonstrated using resonant spin-polarized alternating currents (AC) superimposed on spin-polarized direct currents. Finite element micromagnetic simulations show that the use of frequency triggered AC allows one to maximize the transferred spin transfer torque selectively in order to merely reverse the magnetization of a single storage layer in a stack. Using layers with different resonance frequencies, which are realized by altering the anisotropy constants, allows one to address them by tuning the AC frequency. A rapid increase of the storage density of MRAM devices is shown by using three-dimensional sandwich structures.
Symmetry-adapted non-equilibrium molecular dynamics of chiral carbon nanotubes under tensile loading
Authors: Aghaei Amin , Dayal Kaushik
Published: June 2011

We report on non-equilibrium molecular dynamics calculations of chiral single-wall carbon nanotubes using the framework of Objective Structures. This enables us to adapt molecular dynamics to the symmetry of chiral nanotubes and efficiently simulate these systems with small unit cells. We outline the method and the adaptation of a conventional thermostat and barostat to this setting. We then apply the method in order to examine the behavior of nanotubes with various chiralities subject to a constant extensional strain rate. We examine the effects of temperature, strain rate, and pre-compression/pre-tension. We find a range of failure mechanisms, including the formation of Stone-Wales defects, the opening of voids, and the motion of atoms out of the cross-section.
Photothermovoltaic effect in carbon nanotubes: En route toward junctionless infrared photocells and light sensors
Authors: Omari M. , Kouklin N. A.
Published: June 2011

Optically induced voltage was studied in carbon nanotube films configured as two-terminal resistive elements and operating as junctionless photocells in the infrared. The photovoltage is found to appear only for asymmetric/off-contact illuminations and the effect is explained based on photogenerated heat flow model. The engineered cell prototypes were found to yield electrical powers of ∼30 pW while demonstrating improved conversion efficiency under high-flux illumination. The cell is also shown to act as uncooled infrared sensor with its dark-to-photocurrent ratio improving as temperature increases. The concept might enable nanotube’s use in applications ranging from heat recycling to self-powered infrared sensors.
Further evidences of the quality of double-hybrid energy functionals for π-conjugated systems
Authors: Sancho-García J. C.
Published: June 2011

Despite numerous interesting efforts along decades to improve the accuracy of density functionals with broad applicability, such as B3LYP, there are still large sets of molecular systems where improvements are badly needed. We select π-conjugated systems as an example of the latter due to the subtle interplay between some physical effects affecting possibly most of the calculations: self-interaction or delocalization error, medium-range correlation signatures, dispersive-like weak interactions, and static correlation effects. We further assess a recently proposed modification of the B2-PLYP double-hybrid functional, called B2π-PLYP, that is expected to yield substantial progress for this kind of systems. Generally speaking, when compared with other more popular and older density functionals, double hybrids behave particularly accurate for π-conjugated systems without suffering the large errors that are common in former yet conventional methods.
Recombination models for spatio-temporal Monte Carlo transport of interacting carriers in semiconductors
Authors: Sharma Diksha , Fang Yuan , Zafar Fahad , Karim Karim S. , Badano Aldo
Published: June 2011

When the secondary electron generated from an x-ray interaction within a photoconductor deposits energy, clouds of charge carriers (electron–hole pairs) with random spatial and energy distributions are created. Even under high electric field bias, a fraction of the carriers recombine affecting the detection statistics. We propose and compare modeling approaches for recombination including a nearest-neighbor model (NN) and a first-hit model (FH) that recombines the first pair from the vector of candidate carriers. We find that the mean of the NN model correlates with the mean of the FH model but differs for individual clouds.
Manipulation of magnetization states of ferromagnetic nanorings by an applied azimuthal Oersted field
Authors: Yang T , Pradhan Nihar R. , Goldman Abby , Licht Abigail S. , Li Yihan , Kemei M. , Tuominen Mark T. , Aidala Katherine E.
Published: June 2011

We manipulate the magnetic states of ferromagnetic nanorings with an azimuthal Oersted field directed along the ring circumference. The circular field is generated by passing current through an atomic force microscope tip positioned at the center of the ring, and can directly control the chirality of the vortex state. We demonstrate switching from an onion state to a vortex state and between two vortex states, using magnetic force microscopy to image the resulting magnetic states. The understanding of the magnetization switching behavior in an azimuthal Oersted field could improve practical magnetic data storage devices.
Surface and interface phonon polariton characteristics of wurtzite ZnO/GaN heterostructure
Authors: Lee S. C. , Ng S. S. , Ooi P. K. , Abu Hassan H. , Hassan Z. , Al-Hardan N. H. , Abdullah M. J. , Yakovlev V. A. , Novikova N. N.
Published: June 2011

Surface and interface phonon polariton modes in wurtzite ZnO/GaN heterostructure on wurtzite 6H–SiC substrate were investigated by a variable angle p-polarized infrared attenuated total reflection spectroscopy. Three dips corresponding to the surface and interface phonon polariton modes were observed; two of the dips that having a lower intensity level of reflectivity were the leaky modes whereas, another one was a real mode. The observations were verified with the surface polariton dispersion curve simulated based on an anisotropy model for a four-layer system. It was shown that the frequencies of leaky modes are predictable by considering the damping of the substrate.
Curvature-induced dielectrophoresis for continuous separation of particles by charge in spiral microchannels
Authors: Zhu Junjie , Xuan Xiangchun
Published: June 2011

The separation of particles from a heterogeneous mixture is critical in chemical and biological analyses. Many methods have been developed to separate particles in microfluidic devices. However, the majority of these separations have been limited to be size based and binary. We demonstrate herein a continuous dc electric field driven separation of carboxyl-coated and noncoated 10 μm polystyrene beads by charge in a double-spiral microchannel. This method exploits the inherent electric field gradients formed within the channel turns to manipulate particles by dielectrophoresis and is thus termed curvature-induced dielectrophoresis. The spiral microchannel is also demonstrated to continuously sort noncoated 5 μm beads, noncoated 10 μm beads, and carboxyl-coated 10 μm beads into different collecting wells by charge and size simultaneously. The observed particle separation processes in different situations are all predicted with reasonable agreements by a numerical model. This curvature-induced dielectrophoresis technique eliminates the in-channel microelectrodes and obstacles that are required in traditional electrode- and insulator-based dielectrophoresis devices. It may potentially be used to separate multiple particle targets by intrinsic properties for lab-on-a-chip applications.
Comparison of hole traps in n-GaN grown by hydride vapor phase epitaxy, metal organic chemical vapor deposition, and epitaxial lateral overgrowth
Authors: Polyakov A. Y. , Lee I.-H. , Smirnov N. B. , Govorkov A. V. , Kozhukhova E. A. , Pearton S. J.
Published: June 2011

Optical deep level spectroscopy (ODLTS) and microcathodoluminescence (MCL) spectra were measured for a large group of n-GaN samples grown via metalorganic chemical vapor deposition (MOCVD), epitaxial lateral overgrowth (ELOG), or hydride vapor phase epitaxy (HVPE). In the MOCVD and ELOG samples, the ionization energy of dominant hole traps H1 was dependent on the excitation conditions and was ∼0.9 eV for high injection levels providing saturation of the ODLTS peak magnitude. The trap concentration increased with increasing Si donor concentration and correlated with the yellow band intensity in the MCL spectra. For the HVPE samples, the hole trap spectra were radically different from the MOCVD case: four hole traps—H2, H3, H4, and H5—with activation energies of 0.55, 0.65, 0.85, and 1.2 eV, respectively, were detected. In the MCL spectra, a broad green band that peaked near 2.5 eV was observed in addition to the usual yellow luminescence near 2.3 eV. This green band was attributed to the transitions involving the H4 hole traps. Possible identities of the hole traps detected in the MOCVD/ELOG and HVPE samples are discussed.
Enhanced performance of Pb0.8La0.1Ca0.1Ti0.975O3/Pb(Nb0.01Zr0.2Ti0.8)O3 multilayer thin films for pyroelectric applications
Authors: Chi Q. G. , Wang X. , Li W. L. , Fei W. D. , Lei Q. Q.
Published: June 2011

Taking advantage of the relatively low temperature crystallization and high orientation of thin films of Pb0.8La0.1Ca0.1Ti0.975O3 (PLCT), growth of a highly (100)-oriented PLCT/Pb(Nb0.01Zr0.2Ti0.8)O3 (PNZT) multilayer film on a Pt/Ti/SiO2/Si substrate is achieved at a temperature as low as 450 °C. The interfacial diffusion in the multilayer film is decreased by the low temperature of crystallization. A relatively low dielectric constant and high pyrocoefficient are simultaneously achieved in the highly (100)-oriented PLCT/PNZT multilayer film. The high figure-of-merit obtained for this multilayer film make it a good candidate for application in pyroelectric thin-film devices.
Bending a periodically layered structure for transformation acoustics
Authors: Liang Zixian , Li Jensen
Published: June 2011

Anisotropic acoustic metamaterials have been proved very useful for their high potential in guiding and manipulating sound energy. In this letter, we further develop the idea by using periodically layered structures for transformational acoustics. Such a simple scheme periodically inserts identically bent solid plates in a background fluid. It forms a metamaterial with high refractive index normal to the curved plates and an index near to one along the plates. We show that the periodically layered structure, combined with transformation approach, can be cut into particular device shapes for acoustic cloaking and illusion.
Communication: Observation of homonuclear propensity in collisional relaxation of the 13C12CD2 (v2 = 1) isotopologue of acetylene by stimulated Raman spectroscopy
Authors: Martínez R. Z. , Doménech J. L. , Bermejo D. , Lonardo G. Di , Fusina L.
Published: June 2011

We report the first experimental observation of homonuclear propensity in collisional relaxation of a polyatomic molecule. A pump-probe stimulated Raman setup is used to pump population to a single rotational level of the v2 = 1 vibrationally excited state in 13C12CD2 and then monitor the redistribution of the rotational population that has taken place after a fixed delay. The Q-branch of the 2ν2–ν2 band shows a pattern of intensity alternation between the even and the odd rotational components, with the greater intensities always corresponding to the rotational levels with the same parity as the one where all the population was initially deposited. The effect can be explained by the existence of a propensity rule that favors collisional relaxation between rovibrational levels of the same parity.
Communication: Non-adiabatic coupling and resonances in the F + H2 reaction at low energies
Authors: Lique François , Li Guoliang , Werner Hans-Joachim , Alexander Millard H.
Published: June 2011

Quantum reactive scattering calculations on accurate potential energy surfaces predict that at energies below ∼5 meV, the reaction of F atoms with H2 is dominated by the Born-Oppenheimer (BO) forbidden reaction of the spin-orbit excited F(2P1/2) atom. This non-BO dominance is amplified by low-energy resonances corresponding to quasi-bound states of the HF(v = 3, j = 3) + H product channel. Neglect of non-adiabatic coupling between the electronic states of the F atom leads to a qualitatively incorrect picture of the reaction dynamics at low energy.
Textured growth of the high moment material Gd(0 0 0 1)/Cr(0 0 1)/Fe(0 0 1)
Authors: Stromberg F , Antoniak C , von Hörsten U , Keune W , Sanyal B , Eriksson O , Wende H
Published: June 2011

By magnetic coupling of Fe and Gd via Cr interlayers, the large local moment of Gd can be combined with the high Curie temperature of Fe. The textured growth of a Gd film is studied here by preparing trilayer systems of Fe/Cr/Gd on MgO(1 0 0) substrates by molecular-beam epitaxy (MBE). The thickness of the Cr interlayer was varied between 3 and 5 monolayers. The structural quality of the samples was confirmed by in situ RHEED and ex situ XRD measurements. Epitaxial Cr(0 0 1)/Fe(0 0 1) growth was observed, as expected. By use of 57Fe-CEMS (conversion electron Mössbauer spectroscopy) in combination with the 57Fe tracer layer method the Fe/Cr interface could be examined on an atomic scale and well separated Fe/Gd layers for all Cr thicknesses were confirmed. The unusual Gd/Cr crystallographic relationship of Gd(0 0 0 1)∥Cr(0 0 1), with domains of the hexagonal Gd basal planes randomly oriented in the sample plane and not in registry with the underlying Cr(0 0 1) lattice, was found from combined RHEED and x-ray measurements. Annealing of the samples resulted in a remarkable improvement of the crystalline structure of the Gd layers. On the other hand, the appearance of a single line in the CEM spectrum leads to the conclusion that during annealing a small amount of Fe diffuses into the Cr layer. The electronic structure and magnetism of this system are investigated by first-principles theory.
Magnetostatic interaction effects in switching field distribution of conventional and staggered bit-patterned media
Authors: Ranjbar M , Tavakkoli K G A , Piramanayagam S N , Tan K P , Sbiaa R , Wong S K , Chong T C
Published: June 2011

Effect of magnetostatic interaction on the switching field distribution (SFD) of nanodots with a diameter of 30 nm was investigated in square (conventional) and hexagonal (staggered) lattice configurations. The objective of the study is to achieve different kinds of magnetostatic interaction in experimental samples and to understand their influence on SFD. It was observed that the SFD was wider in the staggered lattice. Micromagnetic simulation was carried out and a fit of experimental results to the simulation was made to understand the observed trends. In addition, magnetic layers with an antiferromagnetic coupling configuration were also studied in the two geometries. The SFD of antiferromagnetically coupled dots was further reduced, highlighting the effect of magnetostatic interaction.
Probe measurements of electron-energy distributions in plasmas: what can we measure and how can we achieve reliable results?
Authors: Godyak V A , Demidov V I
Published: June 2011

On page 4 in equations (4) and (5) as well as in the first line in the right column, 'f0' should be replaced by 'f'.

On page 4, equation (9) should be replaced by

On page 5, equation (11) should be replaced by
Template-free detection of macromolecular complexes in cryo electron tomograms
Authors: Xu Min , Beck Martin , Alber Frank
Published: June 2011

Motivation: Cryo electron tomography (CryoET) produces 3D density maps of biological specimen in its near native states. Applied to small cells, cryoET produces 3D snapshots of the cellular distributions of large complexes. However, retrieving this information is non-trivial due to the low resolution and low signal-to-noise ratio in tomograms. Current pattern recognition methods identify complexes by matching known structures to the cryo electron tomogram. However, so far only a small fraction of all protein complexes have been structurally resolved. It is, therefore, of great importance to develop template-free methods for the discovery of previously unknown protein complexes in cryo electron tomograms.

Results: Here, we have developed an inference method for the template-free discovery of frequently occurring protein complexes in cryo electron tomograms. We provide a first proof-of-principle of the approach and assess its applicability using realistically simulated tomograms, allowing for the inclusion of noise and distortions due to missing wedge and electron optical factors. Our method is a step toward the template-free discovery of the shapes, abundance and spatial distributions of previously unknown macromolecular complexes in whole cell tomograms.

Contact:  alber@usc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Uncover disease genes by maximizing information flow in the phenome–interactome network
Authors: Chen Yong , Jiang Tao , Jiang Rui
Published: June 2011

Motivation: Pinpointing genes that underlie human inherited diseases among candidate genes in susceptibility genetic regions is the primary step towards the understanding of pathogenesis of diseases. Although several probabilistic models have been proposed to prioritize candidate genes using phenotype similarities and protein–protein interactions, no combinatorial approaches have been proposed in the literature.

Results: We propose the first combinatorial approach for prioritizing candidate genes. We first construct a phenome–interactome network by integrating the given phenotype similarity profile, protein–protein interaction network and associations between diseases and genes. Then, we introduce a computational method called MAXIF to maximize the information flow in this network for uncovering genes that underlie diseases. We demonstrate the effectiveness of this method in prioritizing candidate genes through a series of cross-validation experiments, and we show the possibility of using this method to identify diseases with which a query gene may be associated. We demonstrate the competitive performance of our method through a comparison with two existing state-of-the-art methods, and we analyze the robustness of our method with respect to the parameters involved. As an example application, we apply our method to predict driver genes in 50 copy number aberration regions of melanoma. Our method is not only able to identify several driver genes that have been reported in the literature, it also shed some new biological insights on the understanding of the modular property and transcriptional regulation scheme of these driver genes.

Contact:  ruijiang@tsinghua.edu.cn
MeSH: a window into full text for document summarization
Authors: Bhattacharya Sanmitra , Ha−Thuc Viet , Srinivasan Padmini
Published: June 2011

Motivation: Previous research in the biomedical text-mining domain has historically been limited to titles, abstracts and metadata available in MEDLINE records. Recent research initiatives such as TREC Genomics and BioCreAtIvE strongly point to the merits of moving beyond abstracts and into the realm of full texts. Full texts are, however, more expensive to process not only in terms of resources needed but also in terms of accuracy. Since full texts contain embellishments that elaborate, contextualize, contrast, supplement, etc., there is greater risk for false positives. Motivated by this, we explore an approach that offers a compromise between the extremes of abstracts and full texts. Specifically, we create reduced versions of full text documents that contain only important portions. In the long-term, our goal is to explore the use of such summaries for functions such as document retrieval and information extraction. Here, we focus on designing summarization strategies. In particular, we explore the use of MeSH terms, manually assigned to documents by trained annotators, as clues to select important text segments from the full text documents.

Results: Our experiments confirm the ability of our approach to pick the important text portions. Using the ROUGE measures for evaluation, we were able to achieve maximum ROUGE-1, ROUGE-2 and ROUGE-SU4 F-scores of 0.4150, 0.1435 and 0.1782, respectively, for our MeSH term-based method versus the maximum baseline scores of 0.3815, 0.1353 and 0.1428, respectively. Using a MeSH profile-based strategy, we were able to achieve maximum ROUGE F-scores of 0.4320, 0.1497 and 0.1887, respectively. Human evaluation of the baselines and our proposed strategies further corroborates the ability of our method to select important sentences from the full texts.

Contact:  sanmitra-bhattacharya@uiowa.edu; padmini-srinivasan@uiowa.edu
A conditional random fields method for RNA sequence–structure relationship modeling and conformation sampling
Authors: Wang Zhiyong , Xu Jinbo
Published: June 2011

Accurate tertiary structures are very important for the functional study of non-coding RNA molecules. However, predicting RNA tertiary structures is extremely challenging, because of a large conformation space to be explored and lack of an accurate scoring function differentiating the native structure from decoys. The fragment-based conformation sampling method (e.g. FARNA) bears shortcomings that the limited size of a fragment library makes it infeasible to represent all possible conformations well. A recent dynamic Bayesian network method, BARNACLE, overcomes the issue of fragment assembly. In addition, neither of these methods makes use of sequence information in sampling conformations. Here, we present a new probabilistic graphical model, conditional random fields (CRFs), to model RNA sequence–structure relationship, which enables us to accurately estimate the probability of an RNA conformation from sequence. Coupled with a novel tree-guided sampling scheme, our CRF model is then applied to RNA conformation sampling. Experimental results show that our CRF method can model RNA sequence–structure relationship well and sequence information is important for conformation sampling. Our method, named as TreeFolder, generates a much higher percentage of native-like decoys than FARNA and BARNACLE, although we use the same simple energy function as BARNACLE.

Contact:  zywang@ttic.edu; j3xu@ttic.edu

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Predicting site-specific human selective pressure using evolutionary signatures
Authors: Sadri Javad , Diallo Abdoulaye Banire , Blanchette Mathieu
Published: June 2011

Motivation: The identification of non-coding functional regions of the human genome remains one of the main challenges of genomics. By observing how a given region evolved over time, one can detect signs of negative or positive selection hinting that the region may be functional. With the quickly increasing number of vertebrate genomes to compare with our own, this type of approach is set to become extremely powerful, provided the right analytical tools are available.

Results: A large number of approaches have been proposed to measure signs of past selective pressure, usually in the form of reduced mutation rate. Here, we propose a radically different approach to the detection of non-coding functional region: instead of measuring past evolutionary rates, we build a machine learning classifier to predict current substitution rates in human based on the inferred evolutionary events that affected the region during vertebrate evolution. We show that different types of evolutionary events, occurring along different branches of the phylogenetic tree, bring very different amounts of information. We propose a number of simple machine learning classifiers and show that a Support-Vector Machine (SVM) predictor clearly outperforms existing tools at predicting human non-coding functional sites. Comparison to external evidences of selection and regulatory function confirms that these SVM predictions are more accurate than those of other approaches.

Availability: The predictor and predictions made are available at http://www.mcb.mcgill.ca/~blanchem/sadri.

Contact:  blanchem@mcb.mcgill.ca
Multi-view methods for protein structure comparison using latent dirichlet allocation
Authors: Shivashankar S. , Srivathsan S. , Ravindran B. , Tendulkar Ashish V.
Published: June 2011

Motivation: With rapidly expanding protein structure databases, efficiently retrieving structures similar to a given protein is an important problem. It involves two major issues: (i) effective protein structure representation that captures inherent relationship between fragments and facilitates efficient comparison between the structures and (ii) effective framework to address different retrieval requirements. Recently, researchers proposed vector space model of proteins using bag of fragments representation (FragBag), which corresponds to the basic information retrieval model.

Results: In this article, we propose an improved representation of protein structures using latent dirichlet allocation topic model. Another important requirement is to retrieve proteins, whether they are either close or remote homologs. In order to meet diverse objectives, we propose multi-viewpoint based framework that combines multiple representations and retrieval techniques. We compare the proposed representation and retrieval framework on the benchmark dataset developed by Kolodny and co-workers. The results indicate that the proposed techniques outperform state-of-the-art methods.

Availability:  http://www.cse.iitm.ac.in/~ashishvt/research/protein-lda/.

Contact:  ashishvt@cse.iitm.ac.in
Quantification of the Components of Resistance to Rice Sheath Blight Using a Detached Tiller Test Under Controlled Conditions
Authors: Willocquet Laetitia , Lore Jagjeet S. , Srinivasachary S. , Savary Serge
Published: June 2011

Resistance of rice (Oryza sativa) to sheath blight, caused by Rhizoctonia solani, is quantitative and involves two mechanisms: physiological resistance and disease escape. The epidemiological concept of components of resistance was applied using a detached tiller method under controlled conditions, to specifically address physiological resistance to sheath blight in rice. A sclerotium was inserted below the leaf collar of individual rice tillers maintained in tubes filled with water. Different variables were measured after incubation: number of lesions, lesion length, vertical sheath colonization, presence or absence of dark margin at the edge of lesions, and survival duration of the leaf blade. Several rice varieties reported to have different levels of susceptibility to sheath blight were assessed, together with varieties that are cultivated over large areas. Although numerical differences between rice varieties were observed for all disease variables, only the number of lesions significantly differed among varieties tested in this study. The varieties Pecos and IR64 had the consistently lowest and highest disease intensities, respectively. This methodology may allow the detection of sources of resistance that specifically involve defense mechanisms. When combined with field assessment, this methodology should also enable to quantitatively assess the relative role of both mechanisms of resistance to sheath blight.
Distribution and Survival of Ascochyta Blight Pathogens in Field-Pea-Cropping Soils of Australia
Authors: Davidson J. A. , Krysinska-Kaczmarek M. , Wilmshurst C. J. , McKay A. , Herdina  , Scott E. S.
Published: June 2011

Phoma koolunga, Didymella pinodes, and P. medicaginis var. pinodella were detected in DNA extracted from soil following field pea crops across four states in the southeastern and western regions of Australia. P. koolunga was commonly detected in soil from South Australia but rarely in other states whereas D. pinodes plus P. medicaginis var. pinodella were widespread in all regions tested. The quantity of DNA of these pathogens detected in soils prior to growing field pea was positively correlated with ascochyta blight lesions on field pea subsequently grown in infested soil in a pot bioassay and also on field pea in naturally infected field trials. The quantity of DNA of the soilborne pathogens was greatest following a field pea crop and gradually decreased in the following 3 years. The DNA tests were used to quantify the DNA of the pathogens in field pea plants sampled from naturally infected field trials in South Australia over two seasons. The combined results of DNA tests and pathogen isolation from the plants indicated that P. koolunga and D. pinodes were equally responsible for the ascochyta blight symptoms in the diseased trials, while P. medicaginis var. pinodella had a minor role in the disease complex.
Two Promoter Rearrangements in a Drug Efflux Transporter Gene Are Responsible for the Appearance and Spread of Multidrug Resistance Phenotype MDR2 inBotrytis cinereaIsolates in French and German Vineyards
Authors: Mernke D. , Dahm S. , Walker A.-S. , Lalève A. , Fillinger S. , Leroch M. , Hahn M.
Published: June 2011

In French and German vineyards, Botrytis cinerea isolates with multiple fungicide resistance phenotypes have been observed with increasing frequencies. Multidrug resistance (MDR) results from mutations that lead to constitutive overexpression of genes encoding drug efflux transporters. In MDR2 and MDR3 strains, overexpression of the major facilitator superfamiliy transporter gene mfsM2 has been found to result from a rearrangement in the mfsM2 promoter (type A), caused by insertion of a retroelement (RE)-derived sequence. Here, we report the discovery of another, similar RE-induced rearrangement of the mfsM2 promoter (type B) in a subpopulation of French MDR2 isolates. MDR2 isolates harboring either type A or type B mutations in mfsM2 show the same resistance phenotypes and similar levels of mfsM2 overexpression. RE sequences similar to those in mfsM2 were found in low copy numbers in other but not all B. cinerea strains analyzed, including non-MDR2 strains. Population genetic analyses support the hypothesis that the two rearrangement mutations have only occurred once, and are responsible for the appearance and subsequent spread of all known MDR2 and MDR3 strains in French and German wine-growing regions.
Integration host factor alleviates H-NS silencing of the Salmonella enterica serovar Typhimurium master regulator of SPI1, hilA
Authors: Queiroz Mário H. , Madrid Cristina , Paytubi Sònia , Balsalobre Carlos , Juárez Antonio
Published: June 2011

Coordination of the expression ofSalmonella entericainvasion genes onSalmonellapathogenicity island 1 (SPI1) depends on a complex circuit involving several regulators that converge on expression of thehilAgene, which encodes a transcriptional activator (HilA) that modulates expression of the SPI1 virulence genes. Two of the global regulators that influencehilAexpression are the nucleoid-associated proteins Hha and H-NS. They interact and form a complex that modulates gene expression. A chromosomal transcriptional fusion was constructed to assess the effects of these modulators onhilAtranscription under several environmental conditions as well as at different stages of growth. The results obtained showed that these proteins play a role in silencinghilAexpression at both low temperature and low osmolarity, irrespective of the growth phase. H-NS accounts for the main repressor activity. At high temperature and osmolarity, H-NS-mediated silencing completely ceases when cells enter the stationary phase, andhilAexpression is induced. Mutants lacking IHF did not inducehilAin cells entering the stationary phase, and this lack of induction was dependent on the presence of H-NS. Band-shift assays andin vitrotranscription data showed that forhilAinduction under certain growth conditions, IHF is required to alleviate H-NS-mediated silencing.
Growth-dependent secretome of Candida utilis
Authors: Buerth Christoph , Heilmann Clemens J. , Klis Frans M. , de Koster Chris G. , Ernst Joachim F. , Tielker Denis
Published: June 2011

Recently, the food yeastCandida utilishas emerged as an excellent host for production of heterologous proteins. Since secretion of the recombinant product is advantageous for its purification, we characterized the secreted proteome ofC. utilis.Cells were cultivated to the exponential or stationary growth phase, and the proteins in the medium were identified by MS. In parallel, a draft genome sequence ofC. utilisstrain DSM 2361 was determined by massively parallel sequencing. Comparisons of protein and coding sequences established thatC. utilisis not a member of the CUG clade ofCandidaspecies. In total, we identified 37 proteins in the culture solution, 17 of which were exclusively present in the stationary phase, whereas three proteins were specific to the exponential growth phase. Identified proteins represented mostly carbohydrate-active enzymes associated with cell wall organization, while no proteolytic enzymes and only a few cytoplasmic proteins were detected. Remarkably, cultivation in xylose-based medium generated a protein pattern that diverged significantly from glucose-grown cells, containing the invertase Inv1 as the major extracellular protein, particularly in its highly glycosylated S-form (slow-migrating). Furthermore, cultivation without ammonium sulfate induced the secretion of the asparaginase Asp3. Comparisons of the secretome ofC. utiliswith those ofKluyveromyces lactisandPichia pastoris, as well as with those of the human fungal pathogensCandida albicansandCandida glabrata, revealed a conserved set of 10 and six secretory proteins, respectively.
Association between deficient mismatch repair system and efficacy to irinotecan‐containing chemotherapy in metastatic colon cancer
Authors: Kim Jeong Eun , Hong Yong Sang , Ryu Min‐Hee , Lee Jae‐Lyun , Chang Heung Moon , Lim Seok‐Byung , Kim Jong Hoon , Jang Se‐Jin , Kim Mi‐Jung , Yu Chang Sik , Kang Yoon‐Koo , Kim Jin Cheon , Kim Tae Won
Published: June 2011

The present study investigated the association between deficient mismatch repair (dMMR) and efficacy outcomes of irinotecan‐based first‐line chemotherapy in patients with metastatic colorectal cancer (mCRC). Among 297 patients with sporadic mCRC receiving an irinotecan‐containing regimen as first‐line chemotherapy, 197 with available paraffin‐embedded tissues were included in the current analysis. Tumors displaying loss of MMR protein (MLH1 or MSH2) and/or a microsatellite instability‐high (MSI‐H) genotype by PCR were classified as dMMR. Deficient mismatch repair was found in 23 evaluable tumors, among which eight displayed negativity for MLH1 expression, 11 for MSH2 expression, and four for both. The overall response rate was 47.2% (46.0% in proficient MMR (pMMR) and 56.5% in dMMR), with no significant difference between the two groups (P = 0.569). Median progression‐free survival was 8.85 months in patients with dMMR tumors and 6.82 months in patients with pMMR tumors, but this difference did not reach statistical significance (P = 0.089). Median overall survival was not different between the two groups (P = 0.413). Efficacy outcomes of first‐line irinotecan‐based chemotherapy did not differ significantly between mCRC patients with pMMR and those with dMMR. Our data collectively indicate that MMR status is not effective as a single predictive marker for response to irinotecan‐based chemotherapy in mCRC patients. (Cancer Sci 2011; 102: 1706–1711)
Airway dysfunction in nasal polyposis: a spectrum of asthmatic disease?
Authors: Williamson P. A. , Vaidyanathan S. , Clearie K. , Barnes M. , Lipworth B. J.
Published: June 2011

Background Chronic rhinosinusitis with nasal polyposis (CRSwNP) represents an interesting model to investigate the existence of a non‐allergic unified airway. The factors associated with airway dysfunction in CRSwNP are not fully understood.

Objective To assess the impact of nasal disease on lower airway dysfunction in CRSwNP.

Methods Fifty‐seven patients with CRSwNP underwent spirometry, nasal endoscopy, exhaled nitric oxide, methacholine bronchial challenge, blood sampling for total IgE, eosinophil count and radioallergosorbent testing (NCT00788749). Three phenotypic groups were identified: ‘asthma group’ (asthma diagnosis); ‘inflammatory group’ [no asthma diagnosis, but elevated fractionated exhaled nitric oxide (FENO) and/or bronchial‐hyperreactivity (BHR)]; and ‘non‐inflammatory group’ (no asthma diagnosis, no BHR and normal FENO). Group comparisons, univariate and multivariate analyses were performed to examine associations with airway dysfunction.

Results FEV1 and FEF25−75% were reduced in asthma, but there was no difference between the non‐asthmatic groups. Total IgE and eosinophils were elevated in asthma vs. the non‐inflammatory group, but there was no difference for asthma vs. inflammatory groups. BHR was the only significant predictor of FEV1 (P<0.001). For FEF25−75, BHR and eosinophil count were independent predictors (P<0.001 and P=0.04). Nasal outcomes were not predictors of spirometry.

Conclusion and Clinical Relevance In CRSwNP there is asymptomatic airway dysfunction suggestive of an asthmatic phenotype. Impairment of lung function is significantly associated with BHR and eosinophilia but not parameters of nasal disease suggesting that severity of airway dysfunction relates to the spectrum of asthma rather than rhinosinusitis. Lower airway dysfunction is common in CRSwNP but does not correlate to the severity of nasal disease. Signs and symptoms of asthma should be sought and treated in CRSwNP.

Cite this as: P. A. Williamson, S. Vaidyanathan, K. Clearie, M. Barnes and B. J. Lipworth, Clinical & Experimental Allergy, 2011 (41) 1379–1385.
Survey on physicians' knowledge and attitudes towards clinical practice guidelines at the Mexican Institute of Social Security
Authors: Constantino‐Casas Patricia , Medécigo‐Micete Consuelo , Millán‐Gámez Yuribia K. , Torres‐Arreola Laura d. P. , Valenzuela‐Flores Adriana A. , Viniegra‐Osorio Arturo , Echevarría‐Zuno Santiago , Sandoval‐Castellanos Fernando J.
Published: June 2011

Objective  A survey was organized to determine the general level of knowledge and attitudes of medical personnel towards clinical practice guidelines (CPG).

Methods  A questionnaire modified from two validated instruments was used. Multi‐stratified sampling was applied, and 1782 questionnaires were completed.

Results  A total of 80.4% of physicians had regular employment contract, 8.6% managerial post and 9.3% temporary work contract. Average age and working time were 43.7 and 15 years respectively; 64.3% were male. It was reported that 47.9% participated in academic activities, 70.8% belonged to a medical association, 40.3% identified CPG as steps towards arriving at a diagnosis and/or treatment and 14.9% thought that CPG were norms. A total of 10.7% of the physicians believed that guidelines are based on scientific evidence, 10% perceived them as supporting tools, 10.8% had no knowledge of them, 65% said that they used them, 76.7% thought that personal experience was as important as CPG recommendations and 57.4% thought that CPG were necessary for good medical practice. Physicians preferred that CPG be produced by personnel from outside the Mexican Institute of Social Security, or who had followed validity criteria.

Conclusions  The majority of physicians considered CPG to be useful tools. It was evident that few knew where to acquire CPG, and this would lead to their limited use. Findings from this study enabled procuring a broader idea of the level of knowledge and attitudes of Mexican Institute of Social Security physicians towards CPG. This information is relevant when planning strategies for the purpose of sharing and implementing CPG.