bluuebunny/crossref_metadata_2025 huggingface dataset:
Harmonic generation by reflecting internal waves
Authors: Rodenborn Bruce , Kiefer D. , Zhang H. P. , Swinney Harry L.
Published: February 2011

The generation of internal gravity waves by tidal flow over topography is an important oceanic process that redistributes tidal energy in the ocean. Internal waves reflect from boundaries, creating harmonics and mixing. We use laboratory experiments and two-dimensional numerical simulations of the Navier–Stokes equations to determine the value of the topographic slope that gives the most intense generation of second harmonic waves in the reflection process. The results from our experiments and simulations agree well but differ markedly from theoretical predictions by S. A. Thorpe [“On the reflection of a train of finite amplitude waves from a uniform slope,” J. Fluid Mech. 178, 279 (1987)] and A. Tabaei et al. [“Nonlinear effects in reflecting and colliding internal wave beams,” J. Fluid Mech. 526, 217 (2005)], except for nearly inviscid, weakly nonlinear flow. However, even for weakly nonlinear flow (where the Dauxois–Young amplitude parameter value is only 0.01), we find that the ratio of the reflected wave number to the incoming wave number is very different from the prediction of weakly nonlinear theory. Further, we observe that for incident beams with a wide range of angles, frequencies, and intensities, the second harmonic beam produced in reflection has a maximum intensity when its width is the same as the width of the incident beam. This observation yields a prediction for the angle corresponding to the maximum in second harmonic intensity that is in excellent accord with our results from experiments and numerical simulations.
Photodissociation of N2O: Potential energy surfaces and absorption spectrum
Authors: Schinke R.
Published: February 2011

The ultraviolet photodissociation of \documentclass[12pt]{minimal}\begin{document}$\rm N_2O$\end{document}N2O is studied by wave packet calculations using global three-dimensional potential energy surfaces for the two lowest 1A′ states. The incorporation of all internal degrees of freedom in the dynamics calculations is essential for a realistic treatment. The room-temperature absorption cross section is well reproduced, including the weak vibrational structures. Classical periodic orbits show that the latter can be attributed to large-amplitude NN stretch motion combined with strong excitation of the bend. Weakening of the NN bond toward the N + NO channel is the necessary prerequisite. The temperature dependence of the calculated cross section is significant, as expected for a dipole-forbidden transition of a linear molecule; but it is not as strong as observed experimentally [G. S. Selwyn and H. S. Johnston, J. Chem. Phys. 74, 3791 (1981)]. This shortcoming is due to an apparent underestimation of the (0,1,0) hot band absorption. On the other hand, the calculations yield reasonable predictions of the ratios of bending-state resolved absorption cross sections, σ(0, 1, 0)/σ(0, 0, 0) and σ(0, 2, 0)/σ(0, 0, 0), measured at 204 nm [H. Kawamata et al. J. Chem. Phys. 125, 133312 (2006)].
Photoluminescence enhancement and quenching in metal-semiconductor quantum dot hybrid arrays
Authors: Haridas M. , Tripathi L. N. , Basu J. K.
Published: February 2011

Hybrid monolayer arrays of metal and semiconductor quantum dots have been prepared to study the exciton-plasmon interaction. We observed crossover from strong quenching to enhancement in photoluminescence of the quantum dots as a function of the emission wavelength for fixed interparticle spacings. Remarkably, the enhancement is observed even for extremely short separation at which strong quenching has been observed and predicted earlier. A significant redshift in emission maxima is also observed for quantum dots with quenched emission. The possible role of collective phenomena as well as strong interactions in such ordered hybrid arrays in controlling the emission is discussed.
The mechanical resonances of electrostatically coupled nanocantilevers
Authors: Perisanu S. , Barois T. , Poncharal P. , Gaillard T. , Ayari A. , Purcell S. T. , Vincent P.
Published: February 2011

We present here an experimental study of the electrostatic coupling between the mechanical resonances of two nanowires or two nanotubes. This coupling occurs when the eigenfrequencies of the two resonators are matched by electrostatic tuning and it changes from a weak coupling to a strong coupling regime as the distance between the cantilevers is decreased. Linear coupling theory is shown to be in excellent agreement with the experimental data.
Attainment of low interfacial trap density absent of a large midgap peak in In0.2Ga0.8As by Ga2O3(Gd2O3) passivation
Authors: Lin C. A. , Chiu H. C. , Chiang T. H. , Lin T. D. , Chang Y. H. , Chang W. H. , Chang Y. C. , Wang W.-E. , Dekoster J. , Hoffmann T. Y. , Hong M. , Kwo J.
Published: February 2011

The pronounced high interfacial densities of states (Dit) commonly observed around the midgap energy of dielectric/GaAs interfaces are generally considered the culprit responsible for the poor electrical performance of the corresponding inversion-channel metal-oxide-semiconductor field-effect-transistors. In this work, comprehensive Dit spectra as the function of energy [Dit(E)] inside the In0.2Ga0.8As band gap were constructed by using the quasistatic capacitance-voltage and the temperature-dependent conductance method on n- and p-type ultrahigh vacuum (UHV)-Ga2O3(Gd2O3)/In0.2Ga0.8As and atomic-layer-deposited (ALD)-Al2O3/In0.2Ga0.8As metal-oxide-semiconductor capacitors. Unlike the ALD-Al2O3/In0.2Ga0.8As interface giving a Dit spectrum with a high midgap Dit peak, the UHV-Ga2O3(Gd2O3)/In0.2Ga0.8As interface shows a Dit spectrum that monotonically decreases from the valence band to the conduction band with no discernible midgap peak.
Study on the carbon fragment anions produced by femtosecond laser ablation of solid C60
Authors: Kobayashi Tohru , Matsuo Yukari
Published: February 2011

Production of the anions (negative ions) has been observed by femtosecond laser ablation (fsLA) of solid C60 with a time-of-flight (TOF) mass spectrometer. In contrast to \documentclass[12pt]{minimal}\begin{document}${\rm C}^{+}_{60}$\end{document}C60+, production of C60− due to an electron capture is found very limited because of the small electron affinity of the C60 molecule. Narrow TOF peaks of small carbon fragment anions Cn− (n ≤ 23) suggest instantaneous production of the fragment anions through dissociative ionization of C60. Production of the mono-hydrogenated carbon fragment anions CnH− has been observed and also the abrupt change in the yield of CnH− has been observed at n = 10, which is attributed to the structural change of the carbon fragments from a linear chain to a monocyclic ring. The results are found similar to those obtained for the carbon fragments produced by nanosecond laser ablation (nsLA) of solid C60, which demonstrates that the thermalization in an ablation plasma washes away any difference in the nature of carbon fragments produced by fsLA and nsLA.
InGaN/GaN quantum wells on self-organized faceted GaN islands: Growth and luminescence studies
Authors: Fang Z. L. , Lin Y. X. , Kang J. Y.
Published: February 2011

The growth behavior and luminescence properties of InGaN/GaN quantum wells (QW) on in situ self-organized GaN islands of various distinct smooth sidewall faceting are simultaneously investigated and directly compared. The QW thickness is found to be specific polar angle dependent, leading to variations in QW thickness on multifaceting islands. As a result, by color tuning through island shaping and modifications of the InGaN/GaN QWs on the faceted islands, polychromatic emissions are achieved.
Sub-100-nm negative bend resistance ballistic sensors for high spatial resolution magnetic field detection
Authors: Gilbertson A. M. , Benstock D. , Fearn M. , Kormányos A. , Ladak S. , Emeny M. T. , Lambert C. J. , Ashley T. , Solin S. A. , Cohen L. F.
Published: February 2011

We report the magnetic field detection properties of ballistic sensors utilizing the negative bend resistance of InSb/In1−xAlxSb quantum well cross junctions as a function of temperature and geometric size. We demonstrate that the maximum responsivity to magnetic field and its linearity increase as the critical device dimension is reduced. This observation deviates from the predictions of the classical billiard ball model unless significant diffuse boundary scattering is included. The smallest device studied has an active sensor area of 35×35 nm2, with a maximum responsivity of 20 kΩ/T, and a noise-equivalent field of 0.87 μT/Hz at 100 K.
Atomic-scale origins of bias-temperature instabilities in SiC–SiO2 structures
Authors: Shen Xiao , Zhang En Xia , Zhang Cher Xuan , Fleetwood Daniel M. , Schrimpf Ronald D. , Dhar Sarit , Ryu Sei-Hyung , Pantelides Sokrates T.
Published: February 2011

We find that atomic-scale mechanisms for bias-temperature instabilities (BTIs) in SiC/SiO2 structures can differ significantly from those in Si/SiO2 structures. The measured effective-activation energies for BTI in 4H-SiC metal-oxide-semiconductor capacitors, 0.23±0.02 eV for p-type and 0.12±0.02 eV for n-type, are essentially identical to the respective dopant ionization energies, which are much larger than in Si. This suggests a key role for carrier release from deep dopants for BTI in SiC. In addition, asymmetric degradation is observed under switched-bias stress in p-type and n-type SiC, as a result of the reconfiguration of O vacancies in SiO2 layer after hole capture.
Group-theoretical framework for potential symmetries of evolution equations
Authors: Huang Qing , Qu Changzheng , Zhdanov Renat
Published: February 2011

We develop algebraic approach to the problem of classification of potential symmetries of nonlinear evolution equations. It is essentially based on the recently discovered fact [R. Zhdanov, J. Math. Phys. 50, 053522 (2009)], that any such symmetry is mapped into a contact symmetry. The approach enables using the classical results on classification of contact symmetries of nonlinear evolution equations by Sokolov and Magadeev to classify evolution equations admitting potential symmetries. We construct several examples of new nonlinear fourth-order evolution equations admitting potential symmetries. Since the symmetries obtained depend on nonlocal variables, they cannot be derived by the infinitesimal Lie approach.
Shielding effects in polymer–polymer reactions. IV. Intermolecular contact formation between star-branched molecules
Authors: Fröhlich Markus G. , Zifferer Gerhard
Published: February 2011

Pairs of star-branched molecules—taken from ensembles of athermal five-way cubic lattice chains prepared by Monte Carlo simulation—are analyzed for the relative probability of mutual contact formation between particularly specified segments i and j belonging to different chains within these pairs. These contact probabilities—termed shielding factors Kij—are calculated by means of exact enumeration as a function of chain length ranging from n = 8 to 256 bonds per arm, as a function of functionality (i.e., the number of arms) ranging from F = 2 to 6 arms, and as a function of segment position within the arms ranging from central to terminal segments. In addition, changes of properties that characterize the size and shape of the involved molecules while approaching and penetration are evaluated as a function of chain separation.
Direct gap electroluminescence from Si/Ge1−ySny p-i-n heterostructure diodes
Authors: Roucka R. , Mathews J. , Beeler R. T. , Tolle J. , Kouvetakis J. , Menéndez J.
Published: February 2011

Electroluminescence spectra from Si/Ge1−ySny heterostructure diodes are reported. The observed emission is dominated by direct gap optical transitions and displays the expected compositional dependence of the peak energy. Weaker indirect gap emission is also observed, and their energies are consistent with a closing of the indirect-direct separation as the Sn concentration is increased. The intensity of the EL spectra shows a superlinear dependence on the injection current, which is modeled using a Van Roosbroeck–Shockley expression for the emission intensity. The model assumes quasiequilibrium conditions for the electrons populating the different valleys in the conduction band of Ge.
Motional modes in bulk powder and few-molecule clusters of tris(8-hydroxyquinoline aluminum) and their relation to spin dephasing
Authors: Das Lopamudra , Mateo Jennette , Bandyopadhyay Saumil , Bandyopadhyay Supriyo , Edwards Jarrod D. , Anderson John
Published: February 2011

The ensemble averaged spin dephasing rate of localized electrons in the organic molecule tris(8-hydroxyquinoline aluminum) or Alq3 has been found to be significantly larger in bulk powder than in single- or few-molecule clusters confined within 1–2 nm sized nanocavities [B. Kanchibotla et al., Phys. Rev. B 78, 193306 (2008)]. To understand this observation, we have compared the midinfrared absorption spectra of bulk powder and single- or few-molecule clusters. It appears that molecules have additional vibrational modes in bulk powder possibly due to multimerization. Their coupling with spin may be responsible for the increased spin dephasing rate in bulk powder.
Single-mode quantum cascade lasers based on a folded Fabry-Perot cavity
Authors: Liu Peter Q. , Wang Xiaojun , Fan Jen-Yu , Gmachl Claire F.
Published: February 2011

We demonstrate single-mode quantum cascade lasers employing a folded Fabry-Perot cavity consisting of two straight sections connected by a semicircular section in a “hairpin” shape. These folded cavity lasers emitting at ∼4.5 μm are fabricated with identical processes as those for plain Fabry-Perot ridge lasers, and show a strong suppression of the comb of Fabry-Perot cavity modes, leading to tunable single-mode emission with up to 27 dB side mode suppression ratio and a single-mode operating current range of up to 60% above the threshold current when operated in pulsed mode; single-mode emission is achieved from 80 to ∼240 K.
In vivo lipidomics using single-cell Raman spectroscopy
Authors: Wu Huawen , Volponi Joanne V. , Oliver Ann E. , Parikh Atul N. , Simmons Blake A. , Singh Seema
Published: February 2011

We describe a method for direct, quantitative, in vivo lipid profiling of oil-producing microalgae using single-cell laser-trapping Raman spectroscopy. This approach is demonstrated in the quantitative determination of the degree of unsaturation and transition temperatures of constituent lipids within microalgae. These properties are important markers for determining engine compatibility and performance metrics of algal biodiesel. We show that these factors can be directly measured from a single living microalgal cell held in place with an optical trap while simultaneously collecting Raman data. Cellular response to different growth conditions is monitored in real time. Our approach circumvents the need for lipid extraction and analysis that is both slow and invasive. Furthermore, this technique yields real-time chemical information in a label-free manner, thus eliminating the limitations of impermeability, toxicity, and specificity of the fluorescent probes common in currently used protocols. Although the single-cell Raman spectroscopy demonstrated here is focused on the study of the microalgal lipids with biofuel applications, the analytical capability and quantitation algorithms demonstrated are applicable to many different organisms and should prove useful for a diverse range of applications in lipidomics.
Free-energy cost for translocon-assisted insertion of membrane proteins
Authors: Gumbart James , Chipot Christophe , Schulten Klaus
Published: February 2011

Nascent membrane proteins typically insert in a sequential fashion into the membrane via a protein-conducting channel, the Sec translocon. How this process occurs is still unclear, although a thermodynamic partitioning between the channel and the membrane environment has been proposed. Experiment- and simulation-based scales for the insertion free energy of various amino acids are, however, at variance, the former appearing to lie in a narrower range than the latter. Membrane insertion of arginine, for instance, requires 14–17 kcal/mol according to molecular dynamics simulations, but only 2–3 kcal/mol according to experiment. We suggest that this disagreement is resolved by assuming a two-stage insertion process wherein the first step, the insertion into the translocon, is energized by protein synthesis and, therefore, has an effectively zero free-energy cost; the second step, the insertion into the membrane, invokes the translocon as an intermediary between the fully hydrated and the fully inserted locations. Using free-energy perturbation calculations, the effective transfer free energies from the translocon to the membrane have been determined for both arginine and leucine amino acids carried by a background polyleucine helix. Indeed, the insertion penalty for arginine as well as the insertion gain for leucine from the translocon to the membrane is found to be significantly reduced compared to direct insertion from water, resulting in the same compression as observed in the experiment-based scale.
Clustering to identify RNA conformations constrained by secondary structure
Authors: Sim Adelene Y. L. , Levitt Michael
Published: February 2011

RNA often folds hierarchically, so that its sequence defines its secondary structure (helical base-paired regions connected by single-stranded junctions), which subsequently defines its tertiary fold. To preserve base-pairing and chain connectivity, the three-dimensional conformations that RNA can explore are strongly confined compared to when secondary structure constraints are not enforced. Using three examples, we studied how secondary structure confines and dictates an RNA’s preferred conformations. We made use of Macromolecular Conformations by SYMbolic programming (MC-Sym) fragment assembly to generate RNA conformations constrained by secondary structure. Then, to understand the correlations between different helix placements and orientations, we robustly clustered all RNA conformations by employing unique methods to remove outliers and estimate the best number of conformational clusters. We observed that the preferred conformation (as judged by largest cluster size) for each type of RNA junction molecule tested is consistent with its biological function. Further, the improved quality of models in our pruned datasets facilitates subsequent discrimination using scoring functions based either on statistical analysis (knowledge based) or experimental data.
Electron emission from diamond films seeded using kitchen-wrap polyethylene
Authors: Varshney D , Makarov V I , Saxena P , Guinel M J F , Kumar A , Scott J F , Weiner B R , Morell G
Published: February 2011

Diamond has many potential electronic applications, but the diamond seeding methods are generally harsh on the substrates rendering them unsuitable for integration in electronics. We report a non-abrasive, scalable and economic process of diamond film seeding using kitchen-wrap polyethylene employing hot filament chemical vapour reaction of H2S/CH4/H2 gas mixtures on Cu substrates. The fabricated diamond films were characterized with scanning electron microscopy, transmission electron microscopy and Raman spectroscopy, which confirm that the deposited film consists of a microcrystalline diamond of size in the range 0.5–1.0 µm. The synthesized diamond films exhibit a turn-on field of about 8.5 V µm−1 and long-term stability. Diamond film synthesis using polyethylene will enable the integration of diamond heat sinks into high-power and high-temperature electronic devices.
GeneReporter—sequence-based document retrieval and annotation
Authors: Bartsch Annekathrin , Bunk Boyke , Haddad Isam , Klein Johannes , Münch Richard , Johl Thorsten , Kärst Uwe , Jänsch Lothar , Jahn Dieter , Retter Ida
Published: February 2011

Summary: GeneReporter is a web tool that reports functional information and relevant literature on a protein-coding sequence of interest. Its purpose is to support both manual genome annotation and document retrieval. PubMed references corresponding to a sequence are detected by the extraction of query words from UniProt entries of homologous sequences. Data on protein families, domains, potential cofactors, structure, function, cellular localization, metabolic contribution and corresponding DNA binding sites complement the information on a given gene product of interest.

Availability and implementation: GeneReporter is available at http://www.genereporter.tu-bs.de. The web site integrates databases and analysis tools as SOAP-based web services from the EBI (European Bioinformatics Institute) and NCBI (National Center for Biotechnology Information).

Contact:  i.retter@tu-bs.de; ida.retter@helmholtz-hzi.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
FISH Finder: a high-throughput tool for analyzing FISH images
Authors: Shirley James W. , Ty Sereyvathana , Takebayashi Shin-ichiro , Liu Xiuwen , Gilbert David M.
Published: February 2011

Motivation: Fluorescence in situ hybridization (FISH) is used to study the organization and the positioning of specific DNA sequences within the cell nucleus. Analyzing the data from FISH images is a tedious process that invokes an element of subjectivity. Automated FISH image analysis offers savings in time as well as gaining the benefit of objective data analysis. While several FISH image analysis software tools have been developed, they often use a threshold-based segmentation algorithm for nucleus segmentation. As fluorescence signal intensities can vary significantly from experiment to experiment, from cell to cell, and within a cell, threshold-based segmentation is inflexible and often insufficient for automatic image analysis, leading to additional manual segmentation and potential subjective bias. To overcome these problems, we developed a graphical software tool called FISH Finder to automatically analyze FISH images that vary significantly. By posing the nucleus segmentation as a classification problem, compound Bayesian classifier is employed so that contextual information is utilized, resulting in reliable classification and boundary extraction. This makes it possible to analyze FISH images efficiently and objectively without adjustment of input parameters. Additionally, FISH Finder was designed to analyze the distances between differentially stained FISH probes.

Availability: FISH Finder is a standalone MATLAB application and platform independent software. The program is freely available from: http://code.google.com/p/fishfinder/downloads/list

Contact:  gilbert@bio.fsu.edu
Entropy-accelerated exact clustering of protein decoys
Authors: Berenger Francois , Zhou Yong , Shrestha Rojan , Zhang Kam Y. J.
Published: February 2011

Motivation: Clustering is commonly used to identify the best decoy among many generated in protein structure prediction when using energy alone is insufficient. Calculation of the pairwise distance matrix for a large decoy set is computationally expensive. Typically, only a reduced set of decoys using energy filtering is subjected to clustering analysis. A fast clustering method for a large decoy set would be beneficial to protein structure prediction and this still poses a challenge.

Results: We propose a method using propagation of geometric constraints to accelerate exact clustering, without compromising the distance measure. Our method can be used with any metric distance. Metrics that are expensive to compute and have known cheap lower and upper bounds will benefit most from the method. We compared our method's accuracy against published results from the SPICKER clustering software on 40 large decoy sets from the I-TASSER protein folding engine. We also performed some additional speed comparisons on six targets from the ‘semfold’ decoy set. In our tests, our method chose a better decoy than the energy criterion in 25 out of 40 cases versus 20 for SPICKER. Our method also was shown to be consistently faster than another fast software performing exact clustering named Calibur. In some cases, our approach can even outperform the speed of an approximate method.

Availability: Our C++ software is released under the GNU General Public License. It can be downloaded from http://www.riken.jp/zhangiru/software/durandal_released.tgz.

Contact:  kamzhang@riken.jp
SiGN-SSM: open source parallel software for estimating gene networks with state space models
Authors: Tamada Yoshinori , Yamaguchi Rui , Imoto Seiya , Hirose Osamu , Yoshida Ryo , Nagasaki Masao , Miyano Satoru
Published: February 2011

Summary: SiGN-SSM is an open-source gene network estimation software able to run in parallel on PCs and massively parallel supercomputers. The software estimates a state space model (SSM), that is a statistical dynamic model suitable for analyzing short time and/or replicated time series gene expression profiles. SiGN-SSM implements a novel parameter constraint effective to stabilize the estimated models. Also, by using a supercomputer, it is able to determine the gene network structure by a statistical permutation test in a practical time. SiGN-SSM is applicable not only to analyzing temporal regulatory dependencies between genes, but also to extracting the differentially regulated genes from time series expression profiles.

Availability: SiGN-SSM is distributed under GNU Affero General Public Licence (GNU AGPL) version 3 and can be downloaded at http://sign.hgc.jp/signssm/. The pre-compiled binaries for some architectures are available in addition to the source code. The pre-installed binaries are also available on the Human Genome Center supercomputer system. The online manual and the supplementary information of SiGN-SSM is available on our web site.

Contact:  tamada@ims.u-tokyo.ac.jp
Hereditary Spastic Paraplegia Associated With Axonal Neuropathy: A Novel Mutation of SPG3A in a Large Family
Authors: Al-Maawali Almundher , Rolfs Arndt , Klingenhaeger Michael , Yoon Grace
Published: February 2011

Spastic paraplegia Type 3A is an autosomal-dominant pure or uncomplicated hereditary spastic paraplegia. It is caused by mutations in SPG3A, the only gene associated with this condition. We identified a novel mutation, c.1040T>C (p. M347T), in a family with axonal neuropathy in addition to spastic paraplegia. This expands the spectrum of neurologic complications associated with SPG3A and highlights the importance of long-term follow-up and neurological surveillance in this patient population.
Motor Root Conduction Block in the Lewis-Sumner Syndrome
Authors: Lo Yew Long , Dan Yang-Fang , Tan Yam-Eng , Leoh Teng-Hee
Published: February 2011

Background:

The Lewis-Sumner syndrome (LSS) is a rare immune-mediated peripheral nerve disorder presenting with asymmetric upper limb sensory complaints and motor weakness. Asian patients with LSS have not been reported in the English literature.

Methods:

Three Asian patients with features of LSS were prospectively studied.

Results:

Our patients tended to older, female, and have involvement of the upper limbs exclusively than those in the West. They have a markedly longer disease duration before a diagnosis was made, which could also be the result of difficulty in eliciting motor root conduction block as a sign of proximal demyelination as observed in every patient. Pain is a universal feature as is sensory nerve conduction abnormality. None responded to immunotherapy, but disease stabilization was observed over the chronic course.

Conclusions:

Although rare, these unique observations in Asian patients with LSS differ from those reported in Western literature. The presence of motor root conduction block demonstrated for the first time is instrumental in establishing a diagnosis.
Altererythrobacter xinjiangensis sp. nov., isolated from desert sand, and emended description of the genus Altererythrobacter
Authors: Xue Xiuqing , Zhang Kundi , Cai Feng , Dai Jun , Wang Yang , Rahman Erkin , Peng Fang , Fang Chengxiang
Published: February 2011

A Gram-negative, rod-shaped, non-motile, strictly aerobic bacterium, strain S3-63T, was isolated from desert sand of Xinjiang, China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S3-63T had highest similarity to type strains of the genus Altererythrobacter, i.e. Altererythrobacter marinus H32T (97.2 % similarity), Altererythrobacter marensis MSW-14T (95.9 %), Altererythrobacter aestuarii KCTC 22735T (95.5 %), Altererythrobacter epoxidivorans JCS350T (95.1 %), Altererythrobacter namhicola KCTC 22736T (95.1 %), Altererythrobacter luteolus SW-109T (95.0 %) and Altererythrobacter indicus LMG 23789T (93.5 %). Growth occurred at 20–37 °C (optimum 30 °C), at pH 7.0–9.0 (optimum pH 8.0) and in 0–3 % (w/v) NaCl (optimum 1 %). The major respiratory quinone was ubiquinone-10 and the predominant cellular fatty acids were C18 : 1ω7c (50.8 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 12.6 %), C16 : 0 (12.3 %), C14 : 0 2-OH (7.3 %) and C17 : 1ω6c (4.5 %). The DNA G+C content was 64.6 mol%. Therefore, the phylogenetic, physiological and chemotaxonomic data demonstrated that strain S3-63T represents a novel species of the genus Altererythrobacter, for which the name Altererythrobacter xinjiangensis sp. nov. is proposed; the type strain is S3-63T ( = CCTCC AB 207166T = CIP 110125T). An emended description of the genus Altererythrobacter is provided.
GapA+
Mycoplasma gallisepticum ts-11 has improved vaccine characteristics
Authors: Shil Pollob K. , Kanci Anna , Browning Glenn F. , Marenda Marc S. , Noormohammadi Amir H. , Markham Philip F.
Published: February 2011

Mycoplasma gallisepticum (MG) is an important poultry pathogen that causes respiratory disease and loss of production worldwide, and is currently controlled with live attenuated vaccines. These vaccines have limitations as they vary in their pathogenicity, the protection afforded and their transmissibility, but have been shown to effectively reduce losses associated with challenge in the field. A live attenuated vaccine, ts-11, has been used for the control of M. gallisepticum in several countries. This vaccine is highly dose-dependent and the flock antibody response is weak. GapA is the primary cytadherence molecule in M. gallisepticum, and the absence of GapA expression has been observed in the vast majority of cells in the ts-11 vaccine strain. In this study the immunogenicity of a GapA+
M. gallisepticum ts-11 vaccine was investigated in specific-pathogen-free chickens. Birds vaccinated with GapA+
M. gallisepticum ts-11 were protected against clinical signs of disease following challenge with virulent M. gallisepticum, and GapA+
M. gallisepticum ts-11 was shown to be non-pathogenic and more immunogenic at a lower dose than the currently available M. gallisepticum ts-11 vaccine. Thus, GapA+
M. gallisepticum ts-11 appears to have improved potential as a vaccine candidate.
Proline Dehydrogenase Contributes to Pathogen Defense in Arabidopsis
Authors: Cecchini Nicolás Miguel , Monteoliva Mariela Inés , Alvarez María Elena
Published: February 2011

l-Proline (Pro) catabolism is activated in plants recovering from abiotic stresses associated with water deprivation. In this catabolic pathway, Pro is converted to glutamate by two reactions catalyzed by proline dehydrogenase (ProDH) and Ɗ1-pyrroline-5-carboxylate dehydrogenase (P5CDH), with Ɗ1-pyrroline-5-carboxylate (P5C) as the intermediate. Alternatively, under certain conditions, the P5C derived from Pro is converted back to Pro by P5C reductase, thus stimulating the Pro-P5C cycle, which may generate reactive oxygen species (ROS) as a consequence of the ProDH activity. We previously observed that Pro biosynthesis is altered in Arabidopsis (Arabidopsis thaliana) tissues that induce the hypersensitive response (HR) in response to Pseudomonas syringae. In this work, we characterized the Pro catabolic pathway and ProDH activity in this model. Induction of ProDH expression was found to be dependent on salicylic acid, and an increase in ProDH activity was detected in cells destined to die. To evaluate the role of ProDH in the HR, ProDH-silenced plants were generated. These plants displayed reduced ROS and cell death levels as well as enhanced susceptibility in response to avirulent pathogens. Interestingly, the early activation of ProDH was accompanied by an increase in P5C reductase but not in P5CDH transcripts, with few changes occurring in the Pro and P5C levels. Therefore, our results suggest that in wild-type plants, ProDH is a defense component contributing to HR and disease resistance, which apparently potentiates the accumulation of ROS. The participation of the Pro-P5C cycle in the latter response is discussed.
LEAF TIP NECROSIS1 Plays a Pivotal Role in the Regulation of Multiple Phosphate Starvation Responses in Rice
Authors: Hu Bin , Zhu Chenguang , Li Feng , Tang Jiuyou , Wang Yiqin , Lin Aihong , Liu Linchuan , Che Ronghui , Chu Chengcai
Published: February 2011

Although phosphate (Pi) starvation signaling is well studied in Arabidopsis (Arabidopsis thaliana), it is still largely unknown in rice (Oryza sativa). In this work, a rice leaf tip necrosis1 (ltn1) mutant was identified and characterized. Map-based cloning identified LTN1 as LOC_Os05g48390, the putative ortholog of Arabidopsis PHO2, which plays important roles in Pi starvation signaling. Analysis of transgenic plants harboring a LTN1 promoter::β-glucuronidase construct revealed that LTN1 was preferentially expressed in vascular tissues. The ltn1 mutant exhibited increased Pi uptake and translocation, which led to Pi overaccumulation in shoots. In association with enhanced Pi uptake and transport, some Pi transporters were up-regulated in the ltn1 mutant in the presence of sufficient Pi. Furthermore, the elongation of primary and adventitious roots was enhanced in the ltn1 mutant under Pi starvation, suggesting that LTN1 is involved in Pi-dependent root architecture alteration. Under Pi-sufficient conditions, typical Pi starvation responses such as stimulation of phosphatase and RNase activities, lipid composition alteration, nitrogen assimilation repression, and increased metal uptake were also activated in ltn1. Moreover, analysis of OsmiR399-overexpressing plants showed that LTN1 was down-regulated by OsmiR399. Our results strongly indicate that LTN1 is a crucial Pi starvation signaling component downstream of miR399 involved in the regulation of multiple Pi starvation responses in rice.
Proteins of Diverse Function and Subcellular Location Are Lysine Acetylated in Arabidopsis
Authors: Finkemeier Iris , Laxa Miriam , Miguet Laurent , Howden Andrew J. M. , Sweetlove Lee J.
Published: February 2011

Acetylation of the ε-amino group of lysine (Lys) is a reversible posttranslational modification recently discovered to be widespread, occurring on proteins outside the nucleus, in most subcellular locations in mammalian cells. Almost nothing is known about this modification in plants beyond the well-studied acetylation of histone proteins in the nucleus. Here, we report that Lys acetylation in plants also occurs on organellar and cytosolic proteins. We identified 91 Lys-acetylated sites on 74 proteins of diverse functional classes. Furthermore, our study suggests that Lys acetylation may be an important posttranslational modification in the chloroplast, since four Calvin cycle enzymes were acetylated. The plastid-encoded large subunit of Rubisco stands out because of the large number of acetylated sites occurring at important Lys residues that are involved in Rubisco tertiary structure formation and catalytic function. Using the human recombinant deacetylase sirtuin 3, it was demonstrated that Lys deacetylation significantly affects Rubisco activity as well as the activities of other central metabolic enzymes, such as the Calvin cycle enzyme phosphoglycerate kinase, the glycolytic enzyme glyceraldehyde 3-phosphate dehydrogenase, and the tricarboxylic acid cycle enzyme malate dehydrogenase. Our results demonstrate that Lys acetylation also occurs on proteins outside the nucleus in Arabidopsis (Arabidopsis thaliana) and that Lys acetylation could be important in the regulation of key metabolic enzymes.
Rapid and Reversible Light-Mediated Chromatin Modifications of Arabidopsis Phytochrome A Locus
Authors: Jang In-Cheol , Chung Pil Joong , Hemmes Hans , Jung Choonkyun , Chua Nam-Hai
Published: February 2011

Recent genome-wide surveys showed that acetylation of H3K9 and H3K27 is correlated with gene activation during deetiolation of Arabidopsis thaliana seedlings, but less is known regarding changes in the histone status of repressed genes. Phytochrome A (phyA) is the major photoreceptor of deetiolation, and phyA expression is reversibly repressed by light. We found that in adult Arabidopsis plants, phyA activation in darkness was accompanied by a significant enrichment in the phyA transcription and translation start sites of not only H3K9/14ac and H3K27ac but also H3K4me3, and there was also moderate enrichment of H4K5ac, H4K8ac, H4K12ac, and H4K16ac. Conversely, when phyA expression was repressed by light, H3K27me3 was enriched with a corresponding decline in H3K27ac; moreover, demethylation of H3K4me3 and deacetylation of H3K9/14 were also seen. These histone modifications, which were focused around the phyA transcription/translation start sites, were detected within 1 h of deetiolation. Mutant analysis showed that HDA19/HD1 mediated deacetylation of H3K9/14 and uncovered possible histone crosstalk between H3K9/14ac and H3K4me3. Neither small RNA pathways nor the circadian clock affected H3 modification status of the phyA locus, and DNA methylation was unchanged by light. The presence of activating and repressive histone marks suggests a mechanism for the rapid and reversible regulation of phyA by dark and light.
Farmers' involvement in value‐added produce: the case of Alabama growers
Authors: Duarte Alonso Abel
Published: February 2011

Purpose

For many farmers across the USA the opportunity to sell their produce directly to the public in different ways allows them to avoid middle‐men and often reap higher benefits that are vital for their survival. However, to what extent do they fully maximise their produce? For instance, do farmers consider developing value‐added products when they have fruit or vegetable leftovers, or those with blemishes? The present paper aims to explore involvement in value‐added food production from the growers' standpoint.

Design/methodology/approach

Data were collected via telephone and face‐to‐face interviews among 30 farm owners located in the state of Alabama.

Findings

While the large majority of participating farmers (93.3 per cent) are involved in selling produce directly to the public, only 33.3 per cent are currently maximising their produce left‐overs, or unsellable produce by developing and marketing value‐added products such as jellies, jams and ice‐creams. Almost one fourth of farmers (23.3 per cent) would consider developing value‐added products. However, the lack of a commercial kitchen, a potentially considerable investment, is one significant barrier preventing the development of value‐added products.

Research limitations/implications

Choosing only farmers that are already involved in retailing their own produce, and their low number (30) are limitations that may not allow for making generalisations of the study's findings.

Practical implications

In times where the threat of food crises is latent, the ability for food growers to maximise their harvests becomes critical. Because farm operators play a significant role in providing food for society at large, they should be accordingly supported to maximise their produce, including through the development of value‐added products.

Originality/value

The study provides a different view of value‐added produce, investigating this dimension from the farmers' viewpoint.
Climate change from the perspective of Spanish wine growers: a three‐region study
Authors: Duarte Alonso Abel , O'Neill Martin A.
Published: February 2011

Purpose

Winery operators and viticulturalists alike face many challenges in their daily and annual work cycle; not least the challenge of producing annually a consistent quality product and getting that product to the market in an ever competitive marketplace. While climate has always been a factor when it comes to meeting this challenge, it has become all the more pronounced recently due to the effects of global climatic change. Against this background, this paper aims to explore the effects of climate change from the perspective of winery operators in three prominent Spanish wine producing regions.

Design/methodology/approach

Wineries in La Mancha, La Rioja and Penedès, totalling 570, were contacted electronically and invited to participate in an online survey. Of these businesses, 94 participated, a 16.5 per cent response rate.

Findings

While it was found that generally climate change is not among growers' main challenges, three distinct groups emerged from this study: the “unbelievers,” the cautiously sceptical and the “believers”. This last and largest group of respondents (41.5 per cent) not only acknowledges changes due to climate change, but also strategies already in place to minimise the effects of climate change, suggesting the severity of the problem.

Research limitations/implications

Comparisons among the three participating wine regions were not possible due to the low number of respondents from one of the regions. Also, the total number of respondents does not allow for making the study's findings generalisable.

Practical implications

The wine industry, its stakeholders and government agencies need to work together to monitor any changes and find ways to address negative effects of climate change that may result in increased water usage, pesticides or changes in labour demand.

Originality/value

The study provides new insights into climate change according to winery operators' perspectives, an area that to date has received very limited attention from researchers.
Health claims regulations
Authors: Lalor Fiona , Wall Patrick G.
Published: February 2011

Purpose

The purpose of this paper is to review and compare the scientific and regulatory environments for nutrition and health claims on foodstuffs in the USA, Japan and the European Union.

Design/methodology/approach

A review of the literature and the relevant legislation in the three different countries is conducted. Regulations are reviewed and scientific evidence requirements are outlined in each country.

Findings

Full regulatory approval for claims across all three countries requires the support of robust scientific evidence. To obtain this, companies must submit comprehensive dossiers and detailed applications to the regulators with full descriptions of the tests and studies completed during product development. However in the USA and Japan, an alternative process exists. A health claim that is suggested but not supported by scientific evidence is known as a qualified health claim and is permitted in the USA and Japan, but not in the EU.

Practical implications

The paper demonstrates the difference in regulatory requirements in different countries which leads to different claims being permitted in different countries. It also leads to different levels of scientific support for similar claims which causes consumer confusion and develops an uneven playing pitch for the industry. Given that the industry operates in a global market place, it is imperative that a consensus is reached as to the level of scientific evidence required to approve a health claim. In that way, consumers can be safeguarded from being misled, consumer confusion will not be a concern and products can be globally distributed in line with the increasing liberalisation of trade.

Originality/value

This paper is of value to regulators and the food industry.
Social search
Authors: McDonnell Michael , Shiri Ali
Published: February 2011

Purpose

The purpose of this paper is to introduce the notion of social search as a new concept, drawing upon the patterns of web search behaviour. It aims to: define social search; present a taxonomy of social search; and propose a user‐centred social search method.

Design/methodology/approach

A mixed method approach was adopted to investigate and conceptualise the notion of social search. A review of literature on social search was carried out to identify the key trends and topics. A model of online collaboration was adopted to delineate the types and categories of social search. Four use case scenarios were developed to provide a more pragmatic approach to the understanding of social search.

Findings

The developed taxonomy of social search reveals important similarities and differences between many social search systems. This analysis reveals a gap in social search approaches. A practical method was identified that allows users to directly leverage social search without special features built into search engines.

Research limitations/implications

For feasibility reasons, Google was used as an example of a search system that can be used for carrying out social searches.

Practical implications

The paper provides several practical implications for web searchers as well as web designers. In particular, some recommendations are provided for the design of search engines, digital libraries and browser add‐ons.

Social implications

The study demonstrates the value and power of “collective intelligence” in web search. It shows how general web searches can be enhanced through using socially enhanced web‐based tools such as social bookmarking systems, social tagging services and social media sites.

Originality/value

This is the first study that provides a granular analysis of the notion of social search and puts forward a taxonomy of social search. The use cases developed and reported are created based on real search topics, and show the value and validity of the approach taken.
Pivoted‐pad journal bearings lubrication design
Authors: Saruhan Hamit
Published: February 2011

Purpose

This paper aims to utilize an evolutionary algorithm as an optimization technique to solve design optimization of a pivoted‐pad journal bearing performance characteristics considering objective functions which are contradictory to each other. These functions include fluid film thickness, film temperature, and power loss along with design variables vector, which consists of pad axial length to journal diameter ratio, pad arc length, bearing radial clearance, pad offset factor, and pad preload factor.

Design/methodology/approach

In order to improve performance characteristics of the pivoted‐pad journal bearing, the genetic algorithm (GA) was employed and the modeling of the bearing was represented with the finite element method. Also, a numerical method, global criterion, was conducted to validate the efficiency and applicability of the proposed method.

Findings

This paper utilizes the GA to solve multi‐objective optimization of the pivoted‐pad journal bearing performance governed by design variables such as pad axial length to journal diameter ratio, pad arc length, bearing radial clearance, pad offset factor, and pad preload factor for a range of rotational speed. The global criterion method (GCM) proves that the proposed method is very efficient and useful for the optimal design of the pivoted‐pad journal bearings. An acceptable results agreement between the GA and the GCM has been obtained. The GA is well suited to find the optimum solutions with a high probability since it starts with an initial set of solutions rather than a single solution. The GA explores different areas of search space in parallel and, it is good at exploitation.

Originality/value

With the help of the proposed method, it will be possible to have an idea about bearing geometric parameters on a more rational basis, and to better predict the dynamic performance of rotor systems supported on the pivoted‐pad journal bearings.