bluuebunny/crossref_metadata_2025 huggingface dataset:
Anisotropic electrical transport properties of a two-dimensional electron gas at SrTiO3–LaAlO3 interfaces
Authors: Brinks P. , Siemons W. , Kleibeuker J. E. , Koster G. , Rijnders G. , Huijben M.
Published: June 2011

Experimental evidence of strong in-plane anisotropy in electrical properties of the confined electron gas at the SrTiO3–LaAlO3 interface on top of (LaAlO3)0.3(Sr2AlTaO3)0.7 substrates is provided by detailed transport measurements. Structured measurement geometries in multiple directions are used to show dependence of the sheet resistance with the in-plane angle θ, which is fitted with a sine function with a period of 180°. The carrier density remains constant and a directional dependence of the carrier mobility of more than one order of magnitude is determined with respect to the orientation of the unit cell height steps present at the SrTiO3–LaAlO3 interface.
Five-element Johann-type x-ray emission spectrometer with a single-photon-counting pixel detector
Authors: Kleymenov Evgeny , van Bokhoven Jeroen A. , David Christian , Glatzel Pieter , Janousch Markus , Alonso-Mori Roberto , Studer Marco , Willimann Markus , Bergamaschi Anna , Henrich Beat , Nachtegaal Maarten
Published: June 2011

A Johann-type spectrometer with five spherically bent crystals and a pixel detector was constructed for a range of hard x-ray photon-in photon-out synchrotron techniques, covering a Bragg-angle range of 60°–88°. The spectrometer provides a sub emission line width energy resolution from sub-eV to a few eV and precise energy calibration, better than 1.5 eV for the full range of Bragg angles. The use of a pixel detector allows fast and easy optimization of the signal-to-background ratio. A concentration detection limit below 0.4 wt% was reached at the Cu Kα1 line. The spectrometer is designed as a modular mobile device for easy integration in a multi-purpose hard x-ray synchrotron beamline, such as the SuperXAS beamline at the Swiss Light Source.
The impact of temperature and strain-induced band gap variations on current competition and emitter power in laser bars
Authors: Amuzuvi C. K. , Bull S. , Tomm J. W. , Nagle J. , Sumpf B. , Erbert G. , Michel N. , Krakowski M. , Larkins E. C.
Published: June 2011

We report on current competition and emitter power distributions of unaged 650 nm red-emitting and 980 nm infrared tapered high-power laser bars. We observe a correlation between temperature and packaging-induced strain with respect to the emitter output power. A frown-shaped profile of the output power distribution is seen when the temperatures of the emitters near the center of the bar increase compared to those at the edges of the bar. The effect of temperature is found to dominate that of strain and therefore determine the output power distribution across the bar.
Performance improvement of polymer solar cells by using a solvent-treated poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) buffer layer
Authors: Peng Bo , Guo Xia , Cui Chaohua , Zou Yingping , Pan Chunyue , Li Yongfang
Published: June 2011

Photovoltaic performance of the polymer solar cell (PSC) based on poly(3-hexylthiophene) (P3HT) as donor and [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) as acceptor was improved by using the poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) modification layer treated by ethanol or 2-propanol. Power conversion efficiency (PCE) of the PSC based on P3HT:PCBM (1:1, w/w) with the 2-propanol-treated PEDOT:PSS modification layer reached 4.74%, in comparison with a PCE of 3.39% for the PSC with the PEDOT:PSS layer without the organic solvent treatment. The enhanced performance of the PSCs is attributed to higher conductivity and optimized surface morphology of the PEDOT:PSS layers treated by the organic solvent.
Wave-optical studies of light trapping in submicrometre-textured ultra-thin crystalline silicon solar cells
Authors: Chutinan Alongkarn , Li Catherine Wei Wei , Kherani Nazir P , Zukotynski Stefan
Published: June 2011

Wave optics calculations are performed to determine the energy conversion efficiency of pyramidal textured thin c-Si solar cells. For an optimized 20 µm thick c-Si device backed by a silver mirror an efficiency of 21.3% is obtained. An alternative approach to back reflection, submicrometre phase-shifted pyramid texturization on the back surface instead of the lossy metal mirror is demonstrated to yield a higher efficiency of 21.5%. More significantly the phase-shifted texturization approach permits light to enter the solar cell from both the front and back surfaces. For 10 µm and 5 µm thicknesses, efficiencies of 20.4% and 19.0% are obtained, respectively. Thus, the architecture is amenable to fabrication of high-efficiency ultra-thin bifacial solar cells.
Evidence of a new form of self-organization in DBD Plasmas: the quincunx structure
Authors: Bernecker B , Callegari T , Boeuf J P
Published: June 2011

Self-organized, stable or dynamic, filamentary structures are known to form in dielectric barrier discharges (DBDs) operating in a glow regime. The common ‘classical’ understanding of stable filamentary structures in DBDs is that a glow-discharge filament forms at each half cycle of the sinusoidal applied voltage at the same spatial location along the dielectric surface. The ‘memory’ charges deposited by the previous filament on the dielectric surfaces are responsible for the ignition of a new discharge at the same location. On the other hand, the formation of a filamentary discharge at a given location inhibits discharge development in its vicinity because of charge spreading along the dielectric surface leading to a decrease in the gap voltage in this region. In this paper we show using experiments and models that another self-organized filamentary regime is possible and coexists with the ‘classical’ regime. In this regime, never reported before, discharge filaments at successive half cycles do not occur at the same location but are shifted by half a spatial period. We call this regime the ‘quincunx’ regime. We also show that the mechanisms of this regime may be responsible for some dynamical aspects of self-organization in DBDs.
Four-state nanomagnetic logic using multiferroics
Authors: D'Souza Noel , Atulasimha Jayasimha , Bandyopadhyay Supriyo
Published: June 2011

The authors theoretically demonstrate the implementation of a low-power 4-state universal logic gate (NOR) using a linear array of three dipole-coupled magnetostrictive-piezoelectric multiferroic nanomagnets (e.g. Ni/PZT) with biaxial magnetocrystalline anisotropy. The two peripheral nanomagnets in the array encode the 4-state input bits in their magnetization orientations and the central nanomagnet's magnetization orientation represents the output bit. Numerical simulations are performed to confirm that the 4-state output bit is the Boolean NOR function of the two 4-state inputs bits when the array reaches its ground state. A voltage pulse alternating between −0.2 and +0.2 V, applied to the piezoelectric layer of the central nanomagnet, generates alternating tensile and compressive stress in its magnetostrictive layer. This drives the array to the correct ground state where dipole interaction between the magnets ensures that the output is the NOR function of the input. For the system considered, the gate operation is executed while dissipating only ∼33 000 kT (0.138 fJ) of energy.
Role of cobalt in ZnO : Co thin films
Authors: Su Xueqiong , Wang Li , Chen Jiangbo , Wan Xiaojing , Zhang XinPing , Wang R P
Published: June 2011

We prepared a series of Co-doped thin films using the pulsed laser deposition method at deposition temperatures from 400 to 800 °C under oxygen pressures from 10−4 to 15 Pa. We found that the ferromagnetic signals in ZnO : Co thin films only appear simultaneously with the detectable Co 2p spectra from incompletely oxidized Co metal. Therefore, we concluded that the ferromagnetism in ZnO : Co thin films is not an inherent magnetism in the material. On the other hand, we proposed that the inhomogeneous distribution of Co in the films could improve the link of the grains and increase the carrier concentration of the films, leading to positive Hall signals although the film is n-type. Therefore, the coexistence of ferromagnetism and p-type conductivity in ZnO : Co thin films need to be re-examined carefully.
Numerical simulation of inverse spin Hall spectra in Pt/GaAs hybrid structure
Authors: Khamari Shailesh K , Dixit V K , Oak S M
Published: June 2011

The inverse spin Hall spectra in Pt/GaAs hybrid structure in the range 1–3 eV photon energy are estimated using numerical calculations. The numerical model used here takes account of both energy and spin relaxation phenomena for optically induced hot electrons, tunnelling and thermionic transport effects at Pt/GaAs interface and circular dichroism for the light transmitted through the Pt layer. The optically excited electrons in GaAs induces a spin current in the Pt layer after crossing the Schottky barrier that leads to transverse electrical voltage due to large spin–orbit coupling in Pt. The magnitude and polarity of this voltage depend on photon energy, angle of incidence of light, and barrier height. It is found that the magnitude of this voltage is maximum for 60° angle of incidence irrespective of photon energy and barrier height.
Formation, cationic site exchange and surface structure of mechanosynthesized EuCrO3 nanocrystalline particles
Authors: Widatallah H M , Al-Harthi S H , Johnson C , Klencsár Z , Gismelseed A M , Moore E A , Al-Rawas A D , Wynter C I , Brown D E
Published: June 2011

Nanocrystalline EuCrO3 particles (∼25 nm) have been prepared by pre-milling a 1 : 1 molar mixture of Eu2O3 and Cr2O3 for 60 h followed by sintering at 700 °C (12 h). This temperature is ∼500–600 °C lower than those at which the material, in bulk form, is conventionally prepared. Rietveld analysis of the x-ray powder diffraction pattern of the EuCrO3 nanoparticles favours a structural model involving a slight degree of cationic exchange where ∼11% of the Eu3+ and Cr3+ ions exchange their normal dodecahedral A- and octahedral B-sites, respectively, in the perovskite-related structure. This cationic site exchange, which is unusual in a perovskite structure, has been well supported by the corresponding room-temperature 151Eu Mössbauer spectrum of the nanoparticles that in addition to displaying a distribution in the principal component of the EFG tensor (V

zz
) at the usual A-sites of the 151Eu nuclei, also revealed the presence of a subcomponent with ∼11% area fraction and a considerably increased |V

zz
| value that was associated with Eu3+ ions at octahedral B-sites. X-ray photoelectron and Auger electron spectroscopic techniques reveal a complex surface structure where extremely thin layers of un-reacted Eu2O3 and Cr2O3 cover most of the EuCrO3 nanoparticles' surfaces together with some traces of elemental Cr. The binding energies associated with Eu3+ 3d5/2, Eu3+ 4d3/2, Cr3+ 2p3/2 and O2− 1s core-level electrons in EuCrO3 are estimated from the x-ray photoelectron data for the first time.
Suitability of post-Newtonian/numerical-relativity hybrid waveforms for gravitational wave detectors
Authors: MacDonald Ilana , Nissanke Samaya , Pfeiffer Harald P
Published: June 2011

This paper presents a study of the sufficient accuracy of post-Newtonian and numerical relativity waveforms for the most demanding usage case: parameter estimation of strong sources in advanced gravitational wave detectors. For black hole binaries, these detectors require accurate waveform models which can be constructed by fusing an analytical post-Newtonian inspiral waveform with a numerical relativity merger-ringdown waveform. We perform a comprehensive analysis of errors that enter such ‘hybrid waveforms’. We find that the post-Newtonian waveform must be aligned with the numerical relativity waveform to exquisite accuracy, about 1/100 of a gravitational wave cycle. Phase errors in the inspiral phase of the numerical relativity simulation must be controlled to ≲  0.1 rad. (These numbers apply to moderately optimistic estimates about the number of GW sources; exceptionally strong signals require even smaller errors.) The dominant source of error arises from the inaccuracy of the investigated post-Newtonian Taylor approximants. Using our error criterion, even at 3.5th post-Newtonian order, hybridization has to be performed significantly before the start of the longest currently available numerical waveforms which cover 30 gravitational wave cycles. The current investigation is limited to the equal-mass, zero-spin case and does not take into account calibration errors of the gravitational wave detectors.
Nab2 functions in the metabolism of RNA driven by polymerases II and III
Authors: González-Aguilera Cristina , Tous Cristina , Babiano Reyes , de la Cruz Jesús , Luna Rosa , Aguilera Andrés
Published: June 2011

Gene expression in eukaryotes is an essential process that includes transcription, RNA processing, and export. One important player in this interface is the poly(A)+-RNA–binding protein Nab2, which regulates the mRNA poly(A)+-tail length and export. Here we show that Nab2 has additional roles during mRNA transcription, tRNA metabolism, and ribosomal subunit export. Nab2 is associated with the entire open reading frame of actively transcribed RNA polymerase (RNAP) II and III genes. As a consequence, nab2 mutations confer translation defects that are detected by polysome profiling. Genome-wide analysis of expression of a conditional degron nab2 mutant shows that the role of Nab2 in RNAPII transcription and RNAPIII metabolism is direct. Taken together, our results identify novel functions for Nab2 in transcription and metabolism of most types of RNAs, indicating that Nab2 function is more ubiquitous than previously anticipated, and that it is a central player in the general and coordinated control of gene expression from transcription to translation.
Market Evidence of Packer Willingness to Pay for Traceability
Authors: Pouliot Sébastien
Published: June 2011

This article measures the willingness to pay for the traceability of steers. I use data on the price of steers in Quebec and Ontario to identify a demand shifter in a hedonic framework. I estimate error correction models to provide the first market‐based econometric estimates of the willingness to pay for traceability. My best assessment is that a premium between C.02 and C.05 per pound of carcass (between 1.2% and 3.1%) is paid for traceable steers.
ccSVM: correcting Support Vector Machines for confounding factors in biological data classification
Authors: Li Limin , Rakitsch Barbara , Borgwardt Karsten
Published: June 2011

Motivation: Classifying biological data into different groups is a central task of bioinformatics: for instance, to predict the function of a gene or protein, the disease state of a patient or the phenotype of an individual based on its genotype. Support Vector Machines are a wide spread approach for classifying biological data, due to their high accuracy, their ability to deal with structured data such as strings, and the ease to integrate various types of data. However, it is unclear how to correct for confounding factors such as population structure, age or gender or experimental conditions in Support Vector Machine classification.

Results: In this article, we present a Support Vector Machine classifier that can correct the prediction for observed confounding factors. This is achieved by minimizing the statistical dependence between the classifier and the confounding factors. We prove that this formulation can be transformed into a standard Support Vector Machine with rescaled input data. In our experiments, our confounder correcting SVM (ccSVM) improves tumor diagnosis based on samples from different labs, tuberculosis diagnosis in patients of varying age, ethnicity and gender, and phenotype prediction in the presence of population structure and outperforms state-of-the-art methods in terms of prediction accuracy.

Availability: A ccSVM-implementation in MATLAB is available from http://webdav.tuebingen.mpg.de/u/karsten/Forschung/ISMB11_ccSVM/.

Contact:  limin.li@tuebingen.mpg.de; karsten.borgwardt@tuebingen.mpg.de
Error correction of high-throughput sequencing datasets with non-uniform coverage
Authors: Medvedev Paul , Scott Eric , Kakaradov Boyko , Pevzner Pavel
Published: June 2011

Motivation: The continuing improvements to high-throughput sequencing (HTS) platforms have begun to unfold a myriad of new applications. As a result, error correction of sequencing reads remains an important problem. Though several tools do an excellent job of correcting datasets where the reads are sampled close to uniformly, the problem of correcting reads coming from drastically non-uniform datasets, such as those from single-cell sequencing, remains open.

Results: In this article, we develop the method Hammer for error correction without any uniformity assumptions. Hammer is based on a combination of a Hamming graph and a simple probabilistic model for sequencing errors. It is a simple and adaptable algorithm that improves on other tools on non-uniform single-cell data, while achieving comparable results on normal multi-cell data.

Availability:  http://www.cs.toronto.edu/~pashadag.

Contact:  pmedvedev@cs.ucsd.edu
Construction of co-complex score matrix for protein complex prediction from AP-MS data
Authors: Xie Zhipeng , Kwoh Chee Keong , Li Xiao-Li , Wu Min
Published: June 2011

Motivation: Protein complexes are of great importance for unraveling the secrets of cellular organization and function. The AP-MS technique has provided an effective high-throughput screening to directly measure the co-complex relationship among multiple proteins, but its performance suffers from both false positives and false negatives. To computationally predict complexes from AP-MS data, most existing approaches either required the additional knowledge from known complexes (supervised learning), or had numerous parameters to tune.

Method: In this article, we propose a novel unsupervised approach, without relying on the knowledge of existing complexes. Our method probabilistically calculates the affinity between two proteins, where the affinity score is evaluated by a co-complexed score or C2S in brief. In particular, our method measures the log-likelihood ratio of two proteins being co-complexed to being drawn randomly, and we then predict protein complexes by applying hierarchical clustering algorithm on the C2S score matrix.

Results: Compared with existing approaches, our approach is computationally efficient and easy to implement. It has just one parameter to set and its value has little effect on the results. It can be applied to different species as long as the AP-MS data are available. Despite its simplicity, it is competitive or superior in performance over many aspects when compared with the state-of-the-art predictions performed by supervised or unsupervised approaches.

Availability: The predicted complex sets in this article are available in the Supplementary information or by sending email to asckkwoh@ntu.edu.sg

Contact:  xlli@i2r.a-star.edu.sg

Supplementary information:  Supplementary data are available at Bioinformatics online.
Physical Module Networks: an integrative approach for reconstructing transcription regulation
Authors: Novershtern Noa , Regev Aviv , Friedman Nir
Published: June 2011

Motivation: Deciphering the complex mechanisms by which regulatory networks control gene expression remains a major challenge. While some studies infer regulation from dependencies between the expression levels of putative regulators and their targets, others focus on measured physical interactions.

Results: Here, we present Physical Module Networks, a unified framework that combines a Bayesian model describing modules of co-expressed genes and their shared regulation programs, and a physical interaction graph, describing the protein–protein interactions and protein-DNA binding events that coherently underlie this regulation. Using synthetic data, we demonstrate that a Physical Module Network model has similar recall and improved precision compared to a simple Module Network, as it omits many false positive regulators. Finally, we show the power of Physical Module Networks to reconstruct meaningful regulatory pathways in the genetically perturbed yeast and during the yeast cell cycle, as well as during the response of primary epithelial human cells to infection with H1N1 influenza.

Availability: The PMN software is available, free for academic use at http://www.compbio.cs.huji.ac.il/PMN/.

Contact:  aregev@broad.mit.edu; nirf@cs.huji.ac.il
Mapping ancestral genomes with massive gene loss: A matrix sandwich problem
Authors: Gavranović Haris , Chauve Cedric , Salse Jérôme , Tannier Eric
Published: June 2011

Motivation: Ancestral genomes provide a better way to understand the structural evolution of genomes than the simple comparison of extant genomes. Most ancestral genome reconstruction methods rely on universal markers, that is, homologous families of DNA segments present in exactly one exemplar in every considered species. Complex histories of genes or other markers, undergoing duplications and losses, are rarely taken into account. It follows that some ancestors are inaccessible by these methods, such as the proto–monocotyledon whose evolution involved massive gene loss following a whole genome duplication.

Results: We propose a mapping approach based on the combinatorial notion of ‘sandwich consecutive ones matrix’, which explicitly takes gene losses into account. We introduce combinatorial optimization problems related to this concept, and propose a heuristic solver and a lower bound on the optimal solution. We use these results to propose a configuration for the proto-chromosomes of the monocot ancestor, and study the accuracy of this configuration. We also use our method to reconstruct the ancestral boreoeutherian genomes, which illustrates that the framework we propose is not specific to plant paleogenomics but is adapted to reconstruct any ancestral genome from extant genomes with heterogeneous marker content.

Availability: Upon request to the authors.

Contact:  haris.gavranovic@gmail.com; eric.tannier@inria.fr
TREEGL: reverse engineering tree-evolving gene networks underlying developing biological lineages
Authors: Parikh Ankur P. , Wu Wei , Curtis Ross E. , Xing Eric P.
Published: June 2011

Motivation: Estimating gene regulatory networks over biological lineages is central to a deeper understanding of how cells evolve during development and differentiation. However, one challenge in estimating such evolving networks is that their host cells not only contiguously evolve, but also branch over time. For example, a stem cell evolves into two more specialized daughter cells at each division, forming a tree of networks. Another example is in a laboratory setting: a biologist may apply several different drugs individually to malignant cancer cells to analyze the effects of each drug on the cells; the cells treated by one drug may not be intrinsically similar to those treated by another, but rather to the malignant cancer cells they were derived from.

Results: We propose a novel algorithm, Treegl, an ℓ1 plus total variation penalized linear regression method, to effectively estimate multiple gene networks corresponding to cell types related by a tree-genealogy, based on only a few samples from each cell type. Treegl takes advantage of the similarity between related networks along the biological lineage, while at the same time exposing sharp differences between the networks. We demonstrate that our algorithm performs significantly better than existing methods via simulation. Furthermore we explore an application to a breast cancer dataset, and show that our algorithm is able to produce biologically valid results that provide insight into the progression and reversion of breast cancer cells.

Availability: Software will be available at http://www.sailing.cs.cmu.edu/.

Contact:  epxing@cs.cmu.edu
Piecewise linear approximation of protein structures using the principle of minimum message length
Authors: Konagurthu Arun S. , Allison Lloyd , Stuckey Peter J. , Lesk Arthur M.
Published: June 2011

Simple and concise representations of protein-folding patterns provide powerful abstractions for visualizations, comparisons, classifications, searching and aligning structural data. Structures are often abstracted by replacing standard secondary structural features—that is, helices and strands of sheet—by vectors or linear segments. Relying solely on standard secondary structure may result in a significant loss of structural information. Further, traditional methods of simplification crucially depend on the consistency and accuracy of external methods to assign secondary structures to protein coordinate data. Although many methods exist automatically to identify secondary structure, the impreciseness of definitions, along with errors and inconsistencies in experimental structure data, drastically limit their applicability to generate reliable simplified representations, especially for structural comparison.

This article introduces a mathematically rigorous algorithm to delineate protein structure using the elegant statistical and inductive inference framework of minimum message length (MML). Our method generates consistent and statistically robust piecewise linear explanations of protein coordinate data, resulting in a powerful and concise representation of the structure. The delineation is completely independent of the approaches of using hydrogen-bonding patterns or inspecting local substructural geometry that the current methods use. Indeed, as is common with applications of the MML criterion, this method is free of parameters and thresholds, in striking contrast to the existing programs which are often beset by them.

The analysis of results over a large number of proteins suggests that the method produces consistent delineation of structures that encompasses, among others, the segments corresponding to standard secondary structure.

Availability:  http://www.csse.monash.edu.au/~karun/pmml.

Contact:  arun.konagurthu@monash.edu; lloyd.allison@monesh.edu
Efficient spatial segmentation of large imaging mass spectrometry datasets with spatially aware clustering
Authors: Alexandrov Theodore , Kobarg Jan Hendrik
Published: June 2011

Motivation: Imaging mass spectrometry (IMS) is one of the few measurement technology s of biochemistry which, given a thin sample, is able to reveal its spatial chemical composition in the full molecular range. IMS produces a hyperspectral image, where for each pixel a high-dimensional mass spectrum is measured. Currently, the technology is mature enough and one of the major problems preventing its spreading is the under-development of computational methods for mining huge IMS datasets. This article proposes a novel approach for spatial segmentation of an IMS dataset, which is constructed considering the important issue of pixel-to-pixel variability.

Methods: We segment pixels by clustering their mass spectra. Importantly, we incorporate spatial relations between pixels into clustering, so that pixels are clustered together with their neighbors. We propose two methods. One is non-adaptive, where pixel neighborhoods are selected in the same manner for all pixels. The second one respects the structure observable in the data. For a pixel, its neighborhood is defined taking into account similarity of its spectrum to the spectra of adjacent pixels. Both methods have the linear complexity and require linear memory space (in the number of spectra).

Results: The proposed segmentation methods are evaluated on two IMS datasets: a rat brain section and a section of a neuroendocrine tumor. They discover anatomical structure, discriminate the tumor region and highlight functionally similar regions. Moreover, our methods provide segmentation maps of similar or better quality if compared to the other state-of-the-art methods, but outperform them in runtime and/or required memory.

Contact:  theodore@math.uni-bremen.de
Antibiosis Activity of Pantoea agglomerans Biocontrol Strain E325 Against Erwinia amylovora on Apple Flower Stigmas
Authors: Pusey P. L. , Stockwell V. O. , Reardon C. L. , Smits T. H. M. , Duffy B.
Published: June 2011

Pantoea agglomerans E325, the active ingredient in a commercial product for fire blight control, was previously shown in vitro to produce a unique alkaline- and phosphate-sensitive antibiotic specific to Erwinia amylovora. Antibiosis was evaluated as a mode of antagonism on flower stigmas using two antibiosis-deficient mutants. On King's medium B, mutants E325ad1 and E325ad2 have stable smooth-butyrous or hypermucoid colony morphologies, respectively, and the parental strain E325 exhibits phenotypic plasticity with predominantly hypermucoid colonies accompanied by slower-growing, smooth-butyrous colonies. Mutants were tested against E. amylovora on stigmas of detached flowers of crab apple (Malus mandshurica) in growth chambers and apple (Malus domestica) in the orchard. Epiphytic fitness of the antibiosis-negative mutants was similar or greater than the parental strain as determined by relative area under the population curve (RAUPC). In laboratory and orchard trials, both mutants had significantly lower inhibitory activity against the pathogen (i.e., less reduction of E. amylovora RAUPC) compared with the parental strain. E325 and the mutants caused similar decreases in pH in a broth medium, indicating that acidification, which was previously reported as a possible mechanism of pathogen inhibition on stigmas, is not directly related to antibiosis. In this study we provide the first evidence for E325 antibiosis involved in E. amylovora growth suppression on apple flower stigmas.
Vortex wake, downwash distribution, aerodynamic performance and wingbeat kinematics in slow-flying pied flycatchers
Authors: Muijres Florian T. , Bowlin Melissa S. , Johansson L. Christoffer , Hedenström Anders
Published: June 2011

Many small passerines regularly fly slowly when catching prey, flying in cluttered environments or landing on a perch or nest. While flying slowly, passerines generate most of the flight forces during the downstroke, and have a ‘feathered upstroke’ during which they make their wing inactive by retracting it close to the body and by spreading the primary wing feathers. How this flight mode relates aerodynamically to the cruising flight and so-called ‘normal hovering’ as used in hummingbirds is not yet known. Here, we present time-resolved fluid dynamics data in combination with wingbeat kinematics data for three pied flycatchers flying across a range of speeds from near hovering to their calculated minimum power speed. Flycatchers are adapted to low speed flight, which they habitually use when catching insects on the wing. From the wake dynamics data, we constructed average wingbeat wakes and determined the time-resolved flight forces, the time-resolved downwash distributions and the resulting lift-to-drag ratios, span efficiencies and flap efficiencies. During the downstroke, slow-flying flycatchers generate a single-vortex loop wake, which is much more similar to that generated by birds at cruising flight speeds than it is to the double loop vortex wake in hovering hummingbirds. This wake structure results in a relatively high downwash behind the body, which can be explained by the relatively active tail in flycatchers. As a result of this, slow-flying flycatchers have a span efficiency which is similar to that of the birds in cruising flight and which can be assumed to be higher than in hovering hummingbirds. During the upstroke, the wings of slowly flying flycatchers generated no significant forces, but the body–tail configuration added 23 per cent to weight support. This is strikingly similar to the 25 per cent weight support generated by the wing upstroke in hovering hummingbirds. Thus, for slow-flying passerines, the upstroke cannot be regarded as inactive, and the tail may be of importance for flight efficiency and possibly manoeuvrability.
The Örebro prevention programme revisited: a cluster‐randomized effectiveness trial of programme effects on youth drinking
Authors: Bodin Maria C. , Strandberg Anna K.
Published: June 2011

Aims  This study aimed to assess the effectiveness of the Örebro prevention programme (ÖPP), an alcohol misuse prevention programme that aims to reduce youth drinking by changing parental behaviour.

Design  Cluster‐randomized trial, with schools assigned randomly to the ÖPP or no intervention.

Setting  Forty municipal schools in 13 counties in Sweden.

Participants  A total of 1752 students in the 7th grade and 1314 parents were assessed at baseline. Students' follow‐up rates in the 8th and 9th grades were 92.1% and 88.4%, respectively.

Measurements  Classroom questionnaires to students and postal questionnaires to parents were administered before randomization and 12 and 30 months post‐baseline.

Findings  Two‐level logistic regression models, under four different methods of addressing the problem of loss to follow‐up, revealed a statistically significant programme effect for only one of three drinking outcomes under one loss‐to‐follow‐up method, and that effect was observed only at the 12‐month follow‐up.

Conclusions  The Örebro prevention programme as currently delivered in Sweden does not appear to reduce or delay youth drunkenness.
Family members’ perceived meaning of visiting nursing home residents in Taiwan
Authors: Tsai Hsiu‐Hsin , Tsai Yun‐Fang
Published: June 2011

tsai h.‐h. & tsai y.‐f. (2012) Family members’ perceived meaning of visiting nursing home residents in Taiwan. Journal of Advanced Nursing 68(2), 302–311.

Aim.  The purpose of this article is to report the findings of a study to explore perceived family meaning of visiting older nursing home residents in Taiwan.

Background.  Family involvement in the care of institutionalized elders benefits residents, family and staff. Families have traditionally been involved through in‐person visits. One factor influencing family visits is motivation, which is a vague concept, creating a need to better understand the meaning families ascribe to visiting nursing home residents. Understanding this meaning is necessary to develop intervention programmes that facilitate the quality of families’ nursing‐home visits. However, little is known about the meaning of family visits to nursing home residents in Asian countries.

Methods.  Data were collected April 2009–2010 in audiotaped, individual, in‐depth interviews with 15 family members of residents at four nursing homes in Taiwan. These family members included five women and 10 men, predominantly residents’ children and spouses.

Results.  The meaning of family visits to nursing home residents was captured by five major themes: hoping for recovery, honouring filial/karmic responsibility, insuring care quality, maintaining family relationships and making up for guilt.

Conclusions.  The findings of this study can be considered by nurses and policy makers when designing interventions and allocating resources to improve the quality of family visits with nursing home residents. These interventions can be tailored to family members’ perceived meanings for visiting, e.g. those hoping for residents’ recovery may benefit from health‐promotion programmes, and those honouring filial/karmic responsibility might be helped by education on different ways to show filial respect.
Identification of isolate‐specific resistance QTLs to phytophthora root rot using an intraspecific recombinant inbred line population of pepper (Capsicum annuum)
Authors: Truong H. T. H. , Kim K. T. , Kim D. W. , Kim S. , Chae Y. , Park J. H. , Oh D. G. , Cho M. C.
Published: June 2011

Quantitative trait loci (QTL) for resistance to phytophthora root rot caused by Phytophthora capsici were investigated using two Korean P. capsici isolates and 126 F8 recombinant inbred lines derived from a cross of Capsicum annuum line YCM334 (resistant parent) and local cv. Tean (susceptible parent). The experimental design was a split plot with two replications. Highly significant effects of pathogen isolate, plant genotype, and genotype × isolate were detected. QTL mapping was performed using a genetic linkage map covering 1486·6 cM of the pepper genome, and consisted of 249 markers including 136 AFLPs (Amplified Fragment Length Polymorphisms), 112 SSRs (Simple Sequence Repeats) and one CAPS (Cleaved Amplified Polymorphic Sequence). Fifteen QTLs were detected on chromosomes 5 (P5), 10 (P10), 11 (P11), Pb and Pc using two data processing methods: percentage of wilted plants (PWP) and relative area under the disease progress curves (RAUDPC). The phenotypic variation explained by each QTL (R2) ranged from 6·0% to 48·2%. Seven QTLs were common to resistance for the two isolates on chromosome 5 (P5); six were isolate‐specific for isolate 09‐051 on chromosomes 10 (P10) and Pc, and two for isolate 07‐127 on chromosomes 11 (P11) and Pb. The QTLs in common with the major effect on the resistance for two isolates explained 20·0–48·2% of phenotypic variation. The isolate‐specific QTLs explained 6·0–17·4% of phenotypic variation. The result confirms a gene‐for‐gene relationship between C. annuum and P. capsici for root rot resistance.
Evidence against sink limitation by the sucrose‐to‐starch route in potato plants expressing fructosyltransferases
Authors: Zuther Ellen , Hoermiller Imke I. , Heyer Arnd G.
Published: June 2011

To investigate whether the route from sucrose to starch limits sink strength of potato tubers, we established an additional storage carbohydrate pool and analyzed allocation of imported assimilates to the different pools. Tuber specific expression of the fructan biosynthetic enzymes of globe artichoke resulted in accumulation of fructans to about 5% of the starch level, but did not increase tuber dry weight per plant. While partial repression of starch synthesis caused yield reduction in wild‐type plants, it stimulated fructan accumulation, and yield losses were ameliorated in tubers expressing fructosyltransferases. However, a nearly complete block of the starch pathway by inhibition of sucrose synthase could not be compensated by the fructan pathway. Although fructan concentrations rose, yield reduction was even enhanced, probably because of a futile cycle of fructan synthesis and degradation by invertase, which is induced when sucrose synthase is knocked out. The data do not support a limitation of sink strength by enzyme activities of the starch pathway but point to an energy limitation of storage carbohydrate formation in potato tubers.
N‐Methyl‐d‐aspartate receptor modulators block hyperalgesia induced by acute low‐dose morphine
Authors: Gupta LK , Gupta R , Tripathi CD
Published: June 2011

1. Following opioid‐induced antinociception in mice, hyperalgesic responses may be observed. The present study was designed to evaluate the effect of different N‐methyl‐d‐aspartate (NMDA) receptor modulators (magnesium, dextromethorphan, d‐serine) on the development of morphine‐induced hyperalgesia in mice. The tail‐flick test was used to assess the effects of morphine alone and in combination with the NMDA receptor modulators.

2. Administration of a single low dose (2 mg/kg) of morphine to mice produced antinociception that was followed by hyperalgesia.

3. Administration of magnesium sulphate (5 mg/kg) and d‐serine (10 mg/kg) alone produced a transient antinociceptive response, whereas dextromethorphan (10 mg/kg) alone produced a prolonged antinociceptive response that had a relatively delayed onset after 4 h.

4. When coadministered with morphine, the NMDA receptor blockers magnesium (2 mg/kg) and dextromethorphan (2 and 5 mg/kg) and the NMDA receptor agonist d‐serine (2, 5 and 10 mg/kg), maintained the duration of the antinociceptive response to morphine and inhibited the development of the hyperalgesic response. Coadministration of dextromethorphan (10 mg/kg) with morphine produced antinociception at 30–120 min and at 4–24 h.

5. The results of the present study suggest that coadministration of low‐dose NMDA receptor antagonists, as well as the NMDA receptor agonist d‐serine, with morphine can inhibit morphine‐induced hyperalgesia.
Resistance of Helicobacter pylori to quinolones and clarithromycin assessed by genetic testing in Japan
Authors: Yamade Mihoko , Sugimoto Mitsushige , Uotani Takahiro , Nishino Masafumi , Kodaira Chise , Furuta Takahisa
Published: June 2011

Background and Aim:  As bacterial resistance to clarithromycin limits the efficacy of clarithromycin‐based regimens for Helicobacter pylori infection, attention has turned to quinolone‐based rescue therapies. Resistance of H. pylori to both clarithromycin and quinolone can be predicted by genetic testing. Here, we used this approach to evaluate the prevalence of clarithromycin‐ and quinolone‐resistant strains of H. pylori in Japan.

Methods:  DNA was extracted from gastric tissue samples obtained from 153 patients infected with H. pylori (103 naive for eradication therapy and 50 with previous eradication failure following triple proton pump inhibitor/amoxicillin/clarithromycin therapy). Mutations in H. pylori 23S rRNA and gyrA genes associated with resistance to clarithromycin and quinolones, respectively, were determined.

Results:  Of 153 patients, 85 (55.6%) were infected with clarithromycin‐resistant strains. The prevalence of clarithromycin‐resistant strains in patients with previous eradication failure (90.0%, 45/50) was significantly higher than that (38.8%, 40/103) of those naive for eradication therapy (P < 0.001). Fifty‐nine patients (38.6%) were infected with strains resistant to quinolones. The incidence of quinolone‐resistant strains also appeared higher in patients with eradication failure (48.0%, 24/50) than in those who had not undergone therapy (34.0%, 35/103); however, the difference was not statistically significant (P = 0.112). The incidence of quinolone‐resistance in clarithromycin‐resistant strains (44/85, 51.8%) was significantly higher than that in clarithromycin‐sensitive strains (15/68, 22.1%) (P < 0.001).

Conclusions:  A high incidence of quinolone‐resistance was found in clarithromycin‐resistant strains of H. pylori, particularly in patients with previous eradication failure. Our results suggest that testing for susceptibility of H. pylori to quinolones is useful for determining the optimal rescue eradication regimen.
The influence of atmospheric deposition of pollutants on cross–domain causal relationships for three tropical freshwater lakes in India
Authors: Pandey Jitendra
Published: June 2011

This long‐term study on three freshwater lakes in India was designed to investigate the following: (i) atmospheric deposition of major nutrient elements; (ii) microbial biomass (Cmic) and activity at the land–water interface and their relation to lake ecosystem functioning, as influenced by catchment inputs; and (iii) the modifying influence of atmospheric deposition on trans‐surface causal relationships. These study results illustrated significant differences (P < 0.001) in the atmospheric deposition of nitrate (), ammonia (), phosphate (), sulfate (), calcium (Ca2+), and magnesium (Mg2+), with consistently rising inputs over time. The interface of Lake Baghdara, characterized by woodland catchment, was found to be rich in phenolics and supported low Cmic and activity. Alkaline phosphatase in humus declined by 13.60–25.30% over time, although the Cmic, SIR, and FDAase at the land–water interface increased significantly in response to atmospheric nutrient deposition. Although it increased primary productivity, nutrient deposition exhibited a significant (P < 0.001) modifying influence on the Cmic and lake productivity relationships, with a time lag of 3 years. A substantial increase in dissolved organic carbon (DOC), especially in Lake Baghdara, indicated that the modifying influence of atmospheric deposition on microbial biomass and activity at the land–water interface could significantly alter the carbon capture and storage in surface waters and consequently future carbon balance and climate change processes. This study demonstrated that, if present trends of atmospheric deposition of pollutant elements continue, they can modify the microbial processes at the land–water interface and productivity of lakes and will alter the cross–domain causal relationships of freshwater tropical lakes over the long term.
Soil chemical properties, rather than landscape context, influence woodland fungal communities along an urban‐rural gradient
Authors: NEWBOUND MARK , BENNETT LAUREN T. , TIBBITS JOSQUIN , KASEL SABINE
Published: June 2011

With the expansion of cities around the world there is a growing interest in the factors that influence biodiversity and ecosystem processes in urban areas. Fungi are exceptionally diverse and play key roles in ecosystem function, yet despite predictions of negative impacts due to urbanization, fungi have been generally overlooked in urban ecological studies. We surveyed fungi in 16 remnant river red gum (Eucalyptus camaldulensis: Myrtaceae) woodlands along a gradient of 4–35 km from the city of Melbourne (south‐east Australia). Using both sporocarp surveys and terminal restriction fragment length polymorphism (T‐RFLP; primer pair ITS1‐F‐ITS4), we examined relationships between fungal community composition, landscape context (i.e. urbanization) and soil physicochemical properties. Community compositions from sporocarp data were significantly correlated with those from T‐RFLP data, largely because of correlations with ectomycorrhizal sporocarps (Spearman rank correlation coefficients ρ 0.31–0.42) rather than saprotrophic fungi (ρ 0.18–0.21). Principal components analysis of soil properties and non‐metric multidimensional scaling ordinations of fungal community composition showed no clear separation of sites according to urbanization, and there were no significant correlations between fungal community composition and urbanization. However, fungal community composition was significantly correlated with soil chemical properties (ρ 0.41–0.55). These data suggest that site‐scale soil properties, and associated effects of past and current land management activities, were more important in determining fungal community composition than the landscape‐level influences of urbanization.
Interference and economic threshold of horse purslane (Trianthema portulacastrum) in soybean cultivation in northern India
Authors: HAZRA DIPAK , DAS TAPAS K. , YADURAJU NANJAPUR T.
Published: June 2011

Soybean is the most important oilseed crop that is grown in India. Horse purslane (Trianthema portulacastrumL.) infests soybean heavily, causing enormous yield losses and threatening the sustainability of the soybean production system. Information on the interference and economic threshold of horse purslane will be useful for the effective management of horse purslane in soybean. This will lead to the rationalization of herbicide use and the reduction of herbicide input into the environment. It was observed in this study that “a composite stand of weeds including horse purslane”, and 200 horse purslane plants per m2were equally competitive to soybean. These two treatments resulted in a higher dry weight, growth rate, and uptake of N, P, and K by the weeds and/or horse purslane, compared to the other treatments. They caused more reductions in soybean growth (dry weight, height, crop growth rate, net assimilation rate, and leaf area index) and resulted in a more significant yield reduction than did the other treatments. The weed density–crop yield and the relative leaf area–crop yield models were found to be equally effective in simulating soybean yield losses in relation to a wide range of horse purslane densities and the regression equations were a good fit. The quadratic equations revealed that a density of approximately six, five, and four horse purslane plants per m2would be the economic threshold levels of horse purslane in soybean cultivation, when considering the 70, 80, and 90% horse purslane control efficiencies, respectively, of the herbicide, lactofen.