bluuebunny/crossref_metadata_2025 huggingface dataset:
Optimal configuration of microstructure in ferroelectric materials by stochastic optimization
Authors: Jayachandran K. P. , Guedes J. M. , Rodrigues H. C.
Published: July 2010

An optimization procedure determining the ideal configuration at the microstructural level of ferroelectric (FE) materials is applied to maximize piezoelectricity. Piezoelectricity in ceramic FEs differs significantly from that of single crystals because of the presence of crystallites (grains) possessing crystallographic axes aligned imperfectly. The piezoelectric properties of a polycrystalline (ceramic) FE is inextricably related to the grain orientation distribution (texture). The set of combination of variables, known as solution space, which dictates the texture of a ceramic is unlimited and hence the choice of the optimal solution which maximizes the piezoelectricity is complicated. Thus, a stochastic global optimization combined with homogenization is employed for the identification of the optimal granular configuration of the FE ceramic microstructure with optimum piezoelectric properties. The macroscopic equilibrium piezoelectric properties of polycrystalline FE is calculated using mathematical homogenization at each iteration step. The configuration of grains characterized by its orientations at each iteration is generated using a randomly selected set of orientation distribution parameters. The optimization procedure applied to the single crystalline phase compares well with the experimental data. Apparent enhancement of piezoelectric coefficient d33 is observed in an optimally oriented BaTiO3 single crystal. Based on the good agreement of results with the published data in single crystals, we proceed to apply the methodology in polycrystals. A configuration of crystallites, simultaneously constraining the orientation distribution of the c-axis (polar axis) while incorporating ab-plane randomness, which would multiply the overall piezoelectricity in ceramic BaTiO3 is also identified. The orientation distribution of the c-axes is found to be a narrow Gaussian distribution centered around 45°. The piezoelectric coefficient in such a ceramic is found to be nearly three times as that of the single crystal. Our optimization model provide designs for materials with enhanced piezoelectric performance, which would stimulate further studies involving materials possessing higher spontaneous polarization.
Effect of Ti incorporation on the interfacial and optical properties of HfTiO thin films
Authors: Liu M. , Zhang L. D. , He G. , Wang X. J. , Fang M.
Published: July 2010

Interfacial and optical properties of HfTiO films with different Ti concentration grown by radio frequency reactive magnetron sputtering have been investigated by x-ray photoelectron spectroscopy (XPS) and spectroscopy ellipsometry (SE). XPS spectra indicate that interfacial layer is formed unavoidably for Ti doped and undoped HfO2 thin films and the interfacial structure is stable for Ti doped films. The composition of interfacial layer is most likely silicate and SiOx. Meanwhile, SE results indicate that the band gap of HfTiO thin films decreases with the increase in Ti concentration. Further results show that the valence band offset (ΔEv) decreases from 2.32 to 1.91 eV while the conduction band offset (ΔEc) decreases from 2.05 eV to 0.99 with the increase in Ti content. The optical constants consist of refractive index and extinction coefficient have also been investigated to provide the valuable references to prepare and select the HfTiO thin films for future high-k gate dielectrics.
Conservative solutions for higher-order Camassa–Holm equations
Authors: Ding Danping , Lv Peng
Published: July 2010

This paper studies the existence of global solutions to higher-order Camassa–Holm equations. Global solution is constructed by the small viscosity method for the frequency localized equation, especially global solution is energy conservative for given finite band initial data.
Nanostructure band engineering of gadolinium oxide nanocrystal memory by CF4 plasma treatment
Authors: Wang Jer-Chyi , Lin Chih-Ting , Lai Chao-Sung , Hsu Jui-Lin
Published: July 2010

Nanostructure band engineering accomplished by CF4 plasma treatment on Gd2O3 nanocrystal memory was investigated. Under the CF4 plasma treatment, the fluorine was incorporated into the Gd2O3 film and resulted in the modification of energy-band. A physical model was proposed to explain the relationship between the built-in electric field in Gd2O3 nanostructure and the improved program/erase (P/E) efficiency and data retention characteristics. The memory window of the Gd2O3–NC memory with CF4 plasma treatment and postplasma annealing was increased to 3.4 V after 104 P/E cycling. It is demonstrated that the Gd2O3–NC memory with nanostructure band engineering is promising for future nonvolatile memory application.
Substrate-mediated crosstalk between elastic pillars
Authors: Schoen Ingmar
Published: July 2010

Cellular traction forces are routinely measured on arrays of flexible microscopic pillars whose deflections are regarded as independent. Here it is shown that vertical deformations of the underlying elastic substrate constitute a coupling between individual pillars. The crosstalk is dominated by a force dipole term that diminishes with the third power of the pillar-to-pillar distance and shows a characteristic angular dependence. The analytical results were verified by finite element simulations and are valid for pillar arrays of any dimensions. For commonly used pillar arrays, the crosstalk between pillars can be neglected.
Charge transport in ultrathin silicon rich oxide/SiO2 multilayers under solar light illumination and in dark conditions
Authors: Puglisi R. A. , Vecchio C. , Lombardo S. , Lorenti S. , Camalleri M. C.
Published: July 2010

An extensive study on the electrical properties of Si nanocrystals under dark and solar light exposure in AM1.5G conditions is presented. The nanostructures have been obtained through chemical vapor deposition of multilayers of ultrathin silicon rich oxide/SiO2 films and subsequent thermal annealing. The electrical data demonstrate that the current transport in such systems is mediated by tunnel effect, and the lowest effective energy barrier limiting the carrier transport has been found to be 1.7 eV, well below the values of 3.1 eV and 4.7 eV of free electrons and holes, respectively, at the standard Si/silicon dioxide interface. Under AM1.5G solar light illumination the contribution of the photocarriers increases with the voltage and above 60 V shows a trend toward saturation. A quantitative explanation of this saturation is discussed. Moreover, the photocarrier generation rate in the nanocrystals averaged over the solar spectrum region is evaluated.
Enhancement of the conversion efficiency of GaN-based photovoltaic devices with AlGaN/InGaN absorption layers
Authors: Yang C. C. , Sheu J. K. , Liang Xin-Wei , Huang Min-Shun , Lee M. L. , Chang K. H. , Tu S. J. , Huang Feng-Wen , Lai W. C.
Published: July 2010

InGaN/sapphire-based p-i-n type photovoltaic (PV) devices were shown to have Al0.14Ga0.86N/In0.21Ga0.79N heterostructures that enhance the extraction of photogenerated carriers from active layers. With an appropriately increased barrier height in AlGaN/InGaN absorption layers, PV devices exhibit lower RS despite the increase in conduction-band discontinuity compared with GaN/InGaN superlattice absorption layers. This improvement can be attributed to polarization-induced electric fields enhanced by the incorporated aluminum in barrier layers. The enhancement is beneficial to increase built-in electric fields. Subsequently, the photogenerated carriers can escape more easily from recombination or scattering centers. Under 1 sun air-mass 1.5 standard testing conditions, the Al0.14Ga0.86N/In0.21Ga0.79N PV device exhibits high VOC (2.10 V) as well as an enhanced fill factor (0.66) and JSC (0.84 mA/cm2) corresponding to a power conversion efficiency of 1.16%.
Probing magnetization reversal process in ferromagnetic disk by superconductor-ferromagnet junction
Authors: Bakaul S. R. , Wu B. L. , Han G. C. , Wu Y. H.
Published: July 2010

We use lateral superconductor (SC)-ferromagnet (FM)-SC device to probe the magnetization reversal process of micron sized FM disk. Upon decreasing external magnetic field from saturated state, a buckling pattern forms first. The onset of buckling pattern and its switching to vortex state are studied with the help of Andreev conductance of the SC-FM interface below the critical temperature (Tc) of SC and the magnetoresistances both below and above the Tc. In the latter case, micromagnetic modeling has been carried out to interpret the experimental results by taking into account the current distributions when the electrodes are at different states.
Charge interactions can dominate the dimensions of intrinsically disordered proteins
Authors: Müller-Späth Sonja , Soranno Andrea , Hirschfeld Verena , Hofmann Hagen , Rüegger Stefan , Reymond Luc , Nettels Daniel , Schuler Benjamin
Published: July 2010

Many eukaryotic proteins are disordered under physiological conditions, and fold into ordered structures only on binding to their cellular targets. Such intrinsically disordered proteins (IDPs) often contain a large fraction of charged amino acids. Here, we use single-molecule Förster resonance energy transfer to investigate the influence of charged residues on the dimensions of unfolded and intrinsically disordered proteins. We find that, in contrast to the compact unfolded conformations that have been observed for many proteins at low denaturant concentration, IDPs can exhibit a prominent expansion at low ionic strength that correlates with their net charge. Charge-balanced polypeptides, however, can exhibit an additional collapse at low ionic strength, as predicted by polyampholyte theory from the attraction between opposite charges in the chain. The pronounced effect of charges on the dimensions of unfolded proteins has important implications for the cellular functions of IDPs.
Anomalies in the vibrational dynamics of proteins are a consequence of fractal-like structure
Authors: Reuveni Shlomi , Granek Rony , Klafter Joseph
Published: July 2010

Proteins have been shown to exhibit strange/anomalous dynamics displaying non-Debye density of vibrational states, anomalous spread of vibrational energy, large conformational changes, nonexponential decay of correlations, and nonexponential unfolding times. The anomalous behavior may, in principle, stem from various factors affecting the energy landscape under which a protein vibrates. Investigating the origins of such unconventional dynamics, we focus on the structure-dynamics interplay and introduce a stochastic approach to the vibrational dynamics of proteins. We use diffusion, a method sensitive to the structural features of the protein fold and them alone, in order to probe protein structure. Conducting a large-scale study of diffusion on over 500 Protein Data Bank structures we find it to be anomalous, an indication of a fractal-like structure. Taking advantage of known and newly derived relations between vibrational dynamics and diffusion, we demonstrate the equivalence of our findings to the existence of structurally originated anomalies in the vibrational dynamics of proteins. We conclude that these anomalies are a direct result of the fractal-like structure of proteins. The duality between diffusion and vibrational dynamics allows us to make, on a single-molecule level, experimentally testable predictions. The time dependent vibrational mean square displacement of an amino acid is predicted to be subdiffusive. The thermal variance in the instantaneous distance between amino acids is shown to grow as a power law of the equilibrium distance. Mean first passage time analysis is offered as a practical tool that may aid in the identification of amino acid pairs involved in large conformational changes.
Organocatalytic asymmetric assembly reactions for the syntheses of carbohydrate derivatives by intermolecular Michael-Henry reactions
Authors: Uehara Hisatoshi , Imashiro Ritsuo , Hernández-Torres Gloria , Barbas Carlos F.
Published: July 2010

Given the significance of carbohydrates in life, medicine, and industry, the development of simple and efficient de novo methods to synthesize carbohydrates are highly desirable. Organocatalytic asymmetric assembly reactions are powerful tools to rapidly construct molecules with stereochemical complexity from simple precursors. Here, we present a simple and robust methodology for the asymmetric synthesis of pyranose derivatives with
talo
- and
manno
- configurations from simple achiral precursors through organocatalytic asymmetric intermolecular Michael–Henry reaction sequences. In this process, (
tert
-butyldimethylsilyloxy)acetaldehyde
1
was successfully utilized in two ways: as a donor in a highly selective
anti
-Michael reaction and as an acceptor in a consecutive Henry reaction. Varied nitroolefins served as Michael acceptors and varied aldehydes substituted for
1
as Henry acceptors providing for the construction of a wide range of carbohydrates with up to 5 stereocenters. In these reactions, a catalyst-controlled Michael reaction followed by a substrate-controlled Henry reaction provided 3,4-dideoxytalose derivatives
6
in a highly stereoselective manner. The Henry reaction was affected by addition of a simple base such as triethylamine: A complex chiral base was not necessary. 3,4-Dideoxymannose derivatives
7
were produced by simply changing the base from triethylamine to 1,8-diazabicyclo[5.4.0]undec-7-ene. Extension of this methodology to a
syn
-Michael initiated sequence was also successful. A mechanistic discussion is provided to explain the unusual substrate-induced stereoselectivity of the Henry reaction.
President Obama's Offshore Drilling Policy and Energy Security: A Game-Theoretic Policy Analysis
Authors: Levy Jason K. , Gopalakrishnan Chennat
Published: July 2010

In the post-9/11 era, security has become a primary collective concern for governments, communities, industry, policy analysts, NGOs, and decision-makers. A powerful confluence of ideas from the fields of sustainable development, environmental justice, ecological engineering, political ecology, and energy security is transforming US national security policy. It is shown that the decision whether or not to expand offshore drilling in the US involves complex multi-criteria negotiation processes, many decision-makers (with conflicting priorities and dynamic preferences), high decision stakes, limited technical information (both in terms of quality and quantity), and difficult tradeoffs. Specifically, this paper applies advances in game-theoretic decision-making to President Obama's March 2010 decision to open new coastal areas of the US to drilling for offshore oil and gas. Our findings can be applied to environmental, political, energy, and socio-economic decision-making at strategic, operational, and tactical levels.
Promoting Ecological Sustainability and Community Resilience in the US Gulf Coast after the 2010 Deepwater Horizon Oil Spill
Authors: Levy Jason K. , Gopalakrishnan Chennat
Published: July 2010

On 20 April 2010, the 5000-foot-deep Macondo Mississippi Canyon Block 252 (MC252) well erupted after a blowout caused a catastrophic explosion and fire aboard the BP PLC-leased Deepwater Horizon offshore oil drilling platform (owned by Transocean Ltd.) about 40 miles (64 km) southeast of the Louisiana coast. The 2010 Deepwater Horizon Gulf Coast oil spill now imperils ecologically sensitive lands, affects the livelihoods of thousands of workers, and threatens a way of life that has been passed down for generations. An oil spill management Decision Support System (DSS) architecture is put forth that integrates the latest advances in MCDA and geomatics engineering in order to cope with the worst environmental disaster in US history. It is shown that policy-makers should improve the sustainability and resilience of Gulf Coast ecosystems and communities so that they are healthier and more robust than before the oil spill. Policy recommendations with respect to the 2010 Deepwater Horizon spill are put forth. We discuss how to best assist disrupted businesses, rehabilitate polluted ecosystems, and improve regulatory oversight of the oil and gas industry in order to prevent future oil spill disasters.
Answer-set programming encodings for argumentation frameworks
Authors: Egly Uwe , Gaggl Sarah Alice , Woltran Stefan
Published: July 2010

Answer-set programming (ASP) has emerged as a declarative programming paradigm where problems are encoded as logic programs, such that the so-called answer sets of theses programs represent the solutions of the encoded problem. The efficiency of the latest ASP solvers reached a state that makes them applicable for problems of practical importance. Consequently, problems from many different areas, including diagnosis, data integration, and graph theory, have been successfully tackled via ASP. In this work, we present such ASP-encodings for problems associated to abstract argumentation frameworks (AFs) and generalisations thereof. Our encodings are formulated as fixed queries, such that the input is the only part depending on the actual AF to process. We illustrate the functioning of this approach, which is underlying a new argumentation system called ASPARTIX in detail and show its adequacy in terms of computational complexity.
Kinetic model for low-density non-stationary gas discharge in water vapour
Authors: Avtaeva S V , General A A , Kel'man V A
Published: July 2010

A capacitive discharge in water vapour in the pressure range 133–150 Pa was studied. The discharge is an effective ecologically pure source of OH* hydroxyl emission in the VUV and UV spectral range (A 
2Σ+ → X 
2Π transition). The time profiles of densities of plasma species at different values of reduced electric field (E/N) were calculated using a kinetic model of the discharge. It is shown that E/N ∼ 190–200 Td is a breaking field for water vapour plasma, and with an increase in E/N a transition from electronegative to electropositive plasma takes place. The primary positive ions in the water vapour plasma are H3O+ ions, and the primary negative ions are OH− ions.
Demonstration of NO production in air plasma–metallic surface interaction by broadband laser-induced fluorescence
Authors: Studer D , Boubert P , Vervisch P
Published: July 2010

This paper deals with high temperature chemistry of air in interaction with a metallic surface. A subsonic air plasma is created with an inductive torch and is investigated using broadband KrF laser-induced fluorescence. Nitrogen monoxide fluorescence spectra are recorded in the free subsonic plasma jet as well as within the boundary layer above a stainless steel flat plate water-cooled to 300 K. The comparison between calculated and experimental calibrated fluorescence spectra allows the determination of rotational and vibrational temperatures as well as densities of NO ground state. The results demonstrate a strong non-equilibrium between rotational and vibrational temperatures in both the free jet and the boundary layer including very close to the wall. Density determinations show that nitrogen monoxide is in chemical equilibrium on the axis of the free jet but not on its boundaries. The NO results are analysed together with previous O2 and N2 results obtained by Raman spectroscopy in order to explain the increasing NO densities observed within the boundary layer. The discussion highlights a double production of NO due to catalytic reactions at the wall and to the exothermic reaction N + O2 → NO + O within the boundary layer following O2 recombination at the wall.
Investigating the plasma chemistry for the synthesis of carbon nanotubes/nanofibres in an inductively coupled plasma-enhanced CVD system: the effect of processing parameters
Authors: Mao M , Bogaerts A
Published: July 2010

A parameter study is carried out for an inductively coupled plasma used for the synthesis of carbon nanotubes or carbon nanofibres (CNTs/CNFs), by means of the Hybrid Plasma Equipment Model. The influence of processing parameters including gas ratio for four different gas mixtures typically used for CNT/CNF growth (i.e. CH4/H2, CH4/NH3, C2H2/H2 and C2H2/NH3), inductively coupled plasma (ICP) power (50–1000 W), operating pressure (10 mTorr–1 Torr), bias power (0–1000 W) and temperature of the substrate (0–1000 °C) on the plasma chemistry is investigated and the optimized conditions for CNT/CNF growth are analysed. Summarized, our calculations suggest that a lower fraction of hydrocarbon gases (CH4 or C2H2, i.e. below 20%) and hence a higher fraction of etchant gases (H2 or NH3) in the gas mixture result in more ‘clean’ conditions for controlled CNT/CNF growth. The same applies to a higher ICP power, a moderate ICP gas pressure above 100 mTorr (at least for single-walled carbon nanotubes), a high bias power (for aligned CNTs) and an intermediate substrate temperature.
Nonlinear behaviour of electrostatically actuated carbon nanotube-based devices
Authors: Rasekh M , Khadem S E , Tatari M
Published: July 2010

In this paper nonlinear behaviour of electrostatically actuated carbon nanotubes (CNTs) is investigated. The model comprises a clamped–clamped CNT suspended over a graphite ground electrode plate from which a potential difference is imposed. The actuation is based on ac and dc applied voltages and it is assumed that the neutral axis of bending is stretched when the beam is deflected, and also, the interatomic interaction forces between CNT and ground plate are considered. The versatile Galerkin's method is employed to reduce the nonlinear integral-partial-differential equation of motion to a nonlinear ordinary differential equation in time, and then, the reduced equation is solved by direct numerical integration. In the dc voltage actuation case, the pull-in/pull-out phenomena, hysteresis characteristic, pull-in time duration and the response of the system are studied. The obtained results are compared with the molecular dynamics method. Eventually, a nano-switch immune to input noise is proposed, which relies on the hysteresis characteristic of the system. In combined ac and dc voltage actuations, the vibrational behaviour and nonlinear frequency response of nano-resonator are studied.
SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data
Authors: Zeitouni Bruno , Boeva Valentina , Janoueix-Lerosey Isabelle , Loeillet Sophie , Legoix-né Patricia , Nicolas Alain , Delattre Olivier , Barillot Emmanuel
Published: July 2010

Summary: We present SVDetect, a program designed to identify genomic structural variations from paired-end and mate-pair next-generation sequencing data produced by the Illumina GA and ABI SOLiD platforms. Applying both sliding-window and clustering strategies, we use anomalously mapped read pairs provided by current short read aligners to localize genomic rearrangements and classify them according to their type, e.g. large insertions–deletions, inversions, duplications and balanced or unbalanced inter-chromosomal translocations. SVDetect outputs predicted structural variants in various file formats for appropriate graphical visualization.

Availability: Source code and sample data are available at http://svdetect.sourceforge.net/

Contact:  svdetect@curie.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Fashion as a System: Changes in Demand as the Basis for the Establishment of the Italian Fashion System (1960–1970)
Authors: Paris Ivan
Published: July 2010

The 1960s proved to be a crucial decade for the emergent Italian fashion industry. In these pages, we seek to demonstrate that in Italy, an evolution of demand took place, structurally different from the Fifties, causing fundamental changes which impacted upon supply. This was a decisive change in the path which led Italy to complete the establishment of an authentic fashion system.

Interest in the question is two-fold. The formalization of relations between players in the Italian fashion industry using systematic logic facilitated the positioning of the made in Italy brand at the pinnacle of the world market: understanding the underlying mechanism of this process is useful for the identification of the characteristics of an Italian model, distinct from those of other countries which make up the history of the fashion industry. Analyses of the reference settings and development methods of the Italian fashion system can represent a further key to understanding the characteristics and the context in which the social transformation of post-war Italy took place.
Litorimicrobium taeanense gen. nov., sp. nov., isolated from a sandy beach
Authors: Jin Hyun Mi , Lee Hyo Jung , Kim Jeong Myeong , Park Moon Su , Lee Kangseok , Jeon Che Ok
Published: July 2010

A Gram-reaction-negative, strictly aerobic, non-motile bacterium, designated strain G4T, was isolated from a sandy beach of Taean in South Korea. Cells were ovoid rods and were catalase- and oxidase-positive. Growth of strain G4T was determined at 15–35 °C (optimum 25–30 °C) and pH 6–8 (optimum pH 6.5–7.5). Strain G4T contained Q-10 as the predominant isoprenoid quinone and C18 : 1ω7c (59.0 %), C18 : 1
ω7c 11-methyl (11.3 %) and C12 : 1 3-OH (9.8 %) as the major fatty acids. The major cellular polar lipids were identified as phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, an unidentified amino lipid, an unidentified phospholipid and an unidentified lipid. The DNA G+C content was 62.4 mol%. Phylogenetic and comparative analysis based on 16S rRNA gene sequences indicated that strain G4T fell within the family Rhodobacteraceae of Alphaproteobacteria and was most closely related to members of the genera Marinovum, Leisingera and Phaeobacter with 95.5–96.4 % sequence similarities. On the basis of phenotypic, chemotaxonomic and molecular properties, strain G4T represents a novel species of a novel genus within the family Rhodobacteraceae, for which the name Litorimicrobium taeanense gen. nov., sp. nov. is proposed. The type strain is G4T ( = KACC 13706T  = DSM 22007T).
Serinicoccus chungangensis sp. nov., isolated from tidal flat sediment, and emended description of the genus Serinicoccus
Authors: Traiwan Jitsopin , Park Mi-Hak , Kim Wonyong
Published: July 2010

A Gram-positive, halophilic bacterium, strain CAU 9536T, was isolated from a tidal flat sediment in the Yellow Sea, Republic of Korea. Strain CAU 9536T grew optimally at 30 °C, at pH 9.0 and in the presence of 13.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CAU 9536T belonged to the genus Serinicoccus, and showed sequence similarity levels of 99.0 % to Serinicoccus profundi MCCC 1A05965T and 98.0 % to Serinicoccus marinus JC1078T. DNA–DNA relatedness values between strain CAU 9536T and the above two type strains were below 45.0 %. The cell-wall peptidoglycan of strain CAU 9536T was based on meso-diaminopimelic acid, in contrast to those of S. profundi and S. marinus. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and phosphatidylinositol. Whole-cell hydrolysates contained mainly glucose and ribose. The major isoprenoid quinone was menaquinone MK-8 (H4), and the predominant cellular fatty acid was iso-C15 : 0. The DNA G+C content of strain CAU 9536T was 73.5 mol%. Based on phenotypic, chemotaxonomic and genotypic data, strain CAU 9536T is considered to represent a novel species of the genus Serinicoccus, for which the name Serinicoccus chungangensis sp. nov. is proposed. The type strain is CAU 9536T ( = KCTC 19774T = CCUG 59777T).
Tyloses and Phenolic Deposits in Xylem Vessels Impede Water Transport in Low-Lignin Transgenic Poplars: A Study by Cryo-Fluorescence Microscopy
Authors: Kitin Peter , Voelker Steven L. , Meinzer Frederick C. , Beeckman Hans , Strauss Steven H. , Lachenbruch Barbara
Published: July 2010

Of 14 transgenic poplar genotypes (Populus tremula × Populus alba) with antisense 4-coumarate:coenzyme A ligase that were grown in the field for 2 years, five that had substantial lignin reductions also had greatly reduced xylem-specific conductivity compared with that of control trees and those transgenic events with small reductions in lignin. For the two events with the lowest xylem lignin contents (greater than 40% reduction), we used light microscopy methods and acid fuchsin dye ascent studies to clarify what caused their reduced transport efficiency. A novel protocol involving dye stabilization and cryo-fluorescence microscopy enabled us to visualize the dye at the cellular level and to identify water-conducting pathways in the xylem. Cryo-fixed branch segments were planed in the frozen state on a sliding cryo-microtome and observed with an epifluorescence microscope equipped with a cryo-stage. We could then distinguish clearly between phenolic-occluded vessels, conductive (stain-filled) vessels, and nonconductive (water- or gas-filled) vessels. Low-lignin trees contained areas of nonconductive, brown xylem with patches of collapsed cells and patches of noncollapsed cells filled with phenolics. In contrast, phenolics and nonconductive vessels were rarely observed in normal colored wood of the low-lignin events. The results of cryo-fluorescence light microscopy were supported by observations with a confocal microscope after freeze drying of cryo-planed samples. Moreover, after extraction of the phenolics, confocal microscopy revealed that many of the vessels in the nonconductive xylem were blocked with tyloses. We conclude that reduced transport efficiency of the transgenic low-lignin xylem was largely caused by blockages from tyloses and phenolic deposits within vessels rather than by xylem collapse.
TaCHP: A Wheat Zinc Finger Protein Gene Down-Regulated by Abscisic Acid and Salinity Stress Plays a Positive Role in Stress Tolerance
Authors: Li Cuiling , Lv Jian , Zhao Xin , Ai Xinghui , Zhu Xinlei , Wang Mengcheng , Zhao Shuangyi , Xia Guangmin
Published: July 2010

The plant response to abiotic stresses involves both abscisic acid (ABA)-dependent and ABA-independent signaling pathways. Here we describe TaCHP, a CHP-rich (for cysteine, histidine, and proline rich) zinc finger protein family gene extracted from bread wheat (Triticum aestivum), is differentially expressed during abiotic stress between the salinity-sensitive cultivar Jinan 177 and its tolerant somatic hybrid introgression cultivar Shanrong No.3. TaCHP expressed in the roots of seedlings at the three-leaf stage, and the transcript localized within the cells of the root tip cortex and meristem. TaCHP transcript abundance was higher in Shanrong No.3 than in Jinan 177, but was reduced by the imposition of salinity or drought stress, as well as by the exogenous supply of ABA. When JN17, a salinity hypersensitive wheat cultivar, was engineered to overexpress TaCHP, its performance in the face of salinity stress was improved, and the ectopic expression of TaCHP in Arabidopsis (Arabidopsis thaliana) also improved the ability of salt tolerance. The expression level of a number of stress reporter genes (AtCBF3, AtDREB2A, AtABI2, and AtABI1) was raised in the transgenic lines in the presence of salinity stress, while that of AtMYB15, AtABA2, and AtAAO3 was reduced in its absence. The presence in the upstream region of the TaCHP open reading frame of the cis-elements ABRE, MYBRS, and MYCRS suggests that it is a component of the ABA-dependent and -independent signaling pathways involved in the plant response to abiotic stress. We suggest that TaCHP enhances stress tolerance via the promotion of CBF3 and DREB2A expression.
Repeated Polyploidy Drove Different Levels of Crossover Suppression between Homoeologous Chromosomes inBrassica napusAllohaploids
Authors: Cifuentes Marta , Eber Frédérique , Lucas Marie-Odile , Lode Maryse , Chèvre Anne-Marie , Jenczewski Eric
Published: July 2010

Allopolyploid species contain more than two sets of related chromosomes (homoeologs) that must be sorted during meiosis to ensure fertility. As polyploid species usually have multiple origins, one intriguing, yet largely underexplored, question is whether different mechanisms suppressing crossovers between homoeologs may coexist within the same polyphyletic species. We addressed this question using Brassica napus, a young polyphyletic allopolyploid species. We first analyzed the meiotic behavior of 363 allohaploids produced from 29 accessions, which represent a large part of B. napus genetic diversity. Two main clear-cut meiotic phenotypes were observed, encompassing a twofold difference in the number of univalents at metaphase I. We then sequenced two chloroplast intergenic regions to gain insight into the maternal origins of the same 29 accessions; only two plastid haplotypes were found, and these correlated with the dichotomy of meiotic phenotypes. Finally, we analyzed genetic diversity at the PrBn locus, which was shown to determine meiotic behavior in a segregating population of B. napus allohaploids. We observed that segregation of two alleles at PrBn could adequately explain a large part of the variation in meiotic behavior found among B. napus allohaploids. Overall, our results suggest that repeated polyploidy resulted in different levels of crossover suppression between homoeologs in B. napus allohaploids.
Spatial Uncoupling of Mitosis and Cytokinesis during Appressorium-Mediated Plant Infection by the Rice Blast FungusMagnaporthe oryzae
Authors: Saunders Diane G.O. , Dagdas Yasin F. , Talbot Nicholas J.
Published: July 2010

To infect plants, many pathogenic fungi develop specialized infection structures called appressoria. Here, we report that appressorium development in the rice blast fungus Magnaporthe oryzae involves an unusual cell division, in which nuclear division is spatially uncoupled from the site of cytokinesis and septum formation. The position of the appressorium septum is defined prior to mitosis by formation of a heteromeric septin ring complex, which was visualized by spatial localization of Septin4:green fluorescent protein (GFP) and Septin5:GFP fusion proteins. Mitosis in the fungal germ tube is followed by long-distance nuclear migration and rapid formation of an actomyosin contractile ring in the neck of the developing appressorium, at a position previously marked by the septin complex. By contrast, mutants impaired in appressorium development, such as Δpmk1 and ΔcpkA regulatory mutants, undergo coupled mitosis and cytokinesis within the germ tube. Perturbation of the spatial control of septation, by conditional mutation of the SEPTATION-ASSOCIATED1 gene of M. oryzae, prevented the fungus from causing rice blast disease. Overexpression of SEP1 did not affect septation during appressorium formation, but instead led to decoupling of nuclear division and cytokinesis in nongerminated conidial cells. When considered together, these results indicate that SEP1 is essential for determining the position and frequency of cell division sites in M. oryzae and demonstrate that differentiation of appressoria requires a cytokinetic event that is distinct from cell divisions within hyphae.
A Nitrogen Response Pathway Regulates Virulence Functions in Fusarium oxysporum via the Protein Kinase TOR and the bZIP Protein MeaB
Authors: López-Berges Manuel S. , Rispail Nicolas , Prados-Rosales Rafael C. , Di Pietro Antonio
Published: July 2010

During infection, fungal pathogens activate virulence mechanisms, such as host adhesion, penetration and invasive growth. In the vascular wilt fungus Fusarium oxysporum, the mitogen-activated protein kinase Fmk1 is required for plant infection and controls processes such as cellophane penetration, vegetative hyphal fusion, or root adhesion. Here, we show that these virulence-related functions are repressed by the preferred nitrogen source ammonium and restored by treatment with l-methionine sulfoximine or rapamycin, two specific inhibitors of Gln synthetase and the protein kinase TOR, respectively. Deletion of the bZIP protein MeaB also resulted in nitrogen source–independent activation of virulence mechanisms. Activation of these functions did not require the global nitrogen regulator AreA, suggesting that MeaB-mediated repression of virulence functions does not act through inhibition of AreA. Tomato plants (Solanum lycopersicum) supplied with ammonium rather than nitrate showed a significant reduction in vascular wilt symptoms when infected with the wild type but not with the ΔmeaB strain. Nitrogen source also affected invasive growth in the rice blast fungus Magnaporthe oryzae and the wheat head blight pathogen Fusarium graminearum. We propose that a conserved nitrogen-responsive pathway might operate via TOR and MeaB to control virulence in plant pathogenic fungi.
DNA Replication Factor C1 Mediates Genomic Stability and Transcriptional Gene Silencing inArabidopsis
Authors: Liu Qian , Wang Junguo , Miki Daisuke , Xia Ran , Yu Wenxiang , He Junna , Zheng Zhimin , Zhu Jian-Kang , Gong Zhizhong
Published: July 2010

Genetic screening identified a suppressor of ros1-1, a mutant of REPRESSOR OF SILENCING1 (ROS1; encoding a DNA demethylation protein). The suppressor is a mutation in the gene encoding the largest subunit of replication factor C (RFC1). This mutation of RFC1 reactivates the unlinked 35S-NPTII transgene, which is silenced in ros1 and also increases expression of the pericentromeric Athila retrotransposons named transcriptional silent information in a DNA methylation-independent manner. rfc1 is more sensitive than the wild type to the DNA-damaging agent methylmethane sulphonate and to the DNA inter- and intra- cross-linking agent cisplatin. The rfc1 mutant constitutively expresses the G2/M-specific cyclin CycB1;1 and other DNA repair-related genes. Treatment with DNA-damaging agents mimics the rfc1 mutation in releasing the silenced 35S-NPTII, suggesting that spontaneously induced genomic instability caused by the rfc1 mutation might partially contribute to the released transcriptional gene silencing (TGS). The frequency of somatic homologous recombination is significantly increased in the rfc1 mutant. Interestingly, ros1 mutants show increased telomere length, but rfc1 mutants show decreased telomere length and reduced expression of telomerase. Our results suggest that RFC1 helps mediate genomic stability and TGS in Arabidopsis thaliana.
Perceived environmental uncertainty in the agrifood supply chain
Authors: Yanes‐Estévez Vanessa , Ramón Oreja‐Rodríguez Juan , García‐Pérez Ana Maria
Published: July 2010

Purpose

The paper's aim is to develop a diagnosis of the environment of the agrifood supply chain based on members' perceptions of environmental uncertainty.

Design/methodology/approach

Environmental uncertainty is defined as the lack of information about the external environment and is obtained by integrating the perceived dynamism and complexity of the environmental variables. The measurements that are used are the result of applying the Rasch methodology to the information obtained by means of a questionnaire completed by the deciders of firms in the Canary Islands (Spain). Those measures permit the complexity and dynamism perceived by the groups of firms in the supply chain together with the levels of perceived dynamism and complexity of the environmental variables to be jointly positioned on a map.

Findings

According to the perceptions of the members of the agrifood supply chain (agriculture, agrifood industry and distribution), the main sources of environmental uncertainty are demand and competitors. The agricultural sector perceives somewhat more uncertainty than agrifood industry sector, while the distribution sector perceives a stable environment.

Research limitations/implications

The paper presents a useful tool for the business population and public institutions to identify which variables are perceived as the most dynamic and complex and how those variables are perceived by each member of the agrifood supply chain.

Originality/value

The paper operationalises the proposal of Duncan by means of a new application of the Rasch methodology. The results reflect the thinking of the members of all sectors of a supply chain. It is one of the first to study the environmental uncertainty perceived in the agrifood supply chain from a strategic perspective as a fundamental antecedent of the promotion of vertical collaboration in the agrifood supply chain.
Effect of calcium salts on fortified apple juice
Authors: Russell L.F. , Sanford K.A. , Gaul S.O. , Haskett J. , Johnston E.M. , McRae K.B. , Stark R.
Published: July 2010

Purpose

This paper aims to examine the effect of selected calcium salts on the colour, clarity and calcium content of fortified apple juice in extended storage.

Design/methodology/approach

Apple juice was fortified with calcium lactate, calcium lactate gluconate, or anhydrous calcium gluconate and was processed along with an unfortified control juice. The bottled product was stored at 3 and 18°C for 30 weeks, and was assessed for calcium ion concentration, colour and haze. Consumer acceptance of the juices was confirmed using sensory evaluation.

Findings

Anhydrous calcium gluconate and calcium lactate gluconate are easily dissolved in apple juice and are as acceptable to consumers as the unfortified control juice. All three calcium salts remain in solution in apple juice after 30 weeks of storage.

Originality/value

The paper shows that, unlike a number of commercially marketed, calcium‐fortified beverages, these calcium salts stayed in solution in apple juice during extended storage. The ease of dissolution of anhydrous calcium gluconate and calcium lactate gluconate make them excellent candidates for commercial processing; their incorporation should cause minimal disruption to existing apple juice production practices.
Imagining the internet: learning and access to information in Singapore's public libraries
Authors: Kay Heng Heok Adrian , Luyt Brendan
Published: July 2010

Purpose

This study aims to investigate the discourses surrounding the provision of internet access in Singapore through the public library system and to consider what the government, librarians and members of the public consider are the legitimate uses of the internet in Singapore's public libraries, how these compare with what the librarians see as their role in facilitating access and to what extent the internet as an educational tool features in public libraries according to users.

Design/methodology/approach

A discourse analysis of public documents and semi‐structured interviews with ten senior librarians, managers, and 40 members of the public were conducted. Observation was also conducted of library users and of their usage at the computer terminals in the library.

Findings

Findings from the study throw up very different definitions of what constitutes learning through the internet within the context of a public library. This reinforces conclusions from previous studies that what is termed learning through the internet is variously constructed, and understood in multiple ways. This defies what is often presented of the internet as a technical quick fix of policy makers to help its population leap frog into the future.

Research limitations/implications

While the study provided a glimpse into the discourse surrounding the internet in one country, similar work should be carried in more Asian countries to provide a more comprehensive survey of the region and compare this with findings conducted in an Occidental setting.

Originality/value

The study provides an Asian perspective that complements findings on the various discourses that had surrounded internet technology in the USA and Europe. It also calls for a new spirit of awareness on the part of librarians to the views of library users with regard to internet access.
PERCIRS: a system to combine personalized and collaborative information retrieval
Authors: Naderi Hassan , Rumpler Beatrice
Published: July 2010

Purpose

This paper aims to discuss and test the claim that utilization of the personalization techniques can be valuable to improve the efficiency of collaborative information retrieval (CIR) systems.

Design/methodology/approach

A new personalized CIR system, called PERCIRS, is presented based on the user profile similarity calculation (UPSC) formulas. To this aim, the paper proposes several UPSC formulas as well as two techniques to evaluate them. As the proposed CIR system is personalized, it could not be evaluated by Cranfield, like evaluation techniques (e.g. TREC). Hence, this paper proposes a new user‐centric mechanism, which enables PERCIRS to be evaluated. This mechanism is generic and can be used to evaluate any other personalized IR system.

Findings

The results show that among the proposed UPSC formulas in this paper, the (query‐document)‐graph based formula is the most effective. After integrating this formula into PERCIRS and comparing it with nine other IR systems, it is concluded that the results of the system are better than the other IR systems. In addition, the paper shows that the complexity of the system is less that the complexity of the other CIR systems.

Research limitations/implications

This system asks the users to explicitly rank the returned documents, while explicit ranking is still not widespread enough. However it believes that the users should actively participate in the IR process in order to aptly satisfy their needs to information.

Originality/value

The value of this paper lies in combining collaborative and personalized IR, as well as introducing a mechanism which enables the personalized IR system to be evaluated. The proposed evaluation mechanism is very valuable for developers of personalized IR systems. The paper also introduces some significant user profile similarity calculation formulas, and two techniques to evaluate them. These formulas can also be used to find the user's community in the social networks.
The rhizome and the tree: changing metaphors for information organisation
Authors: Robinson Lyn , Maguire Mike
Published: July 2010

Purpose

The paper aims to review Deleuze and Guttari's concept of the rhizome as a model for information organisation.

Design/methodology/approach

This is a critical review of selected literature.

Findings

The rhizome concept is a promising model for understanding hyperlinked information services. It may be of practical value, particularly if it can be integrated with more traditional forms of information organisation. More research, conceptual and practical, is needed before this can be achieved.

Research limitations/implications

The literature review is not comprehensive, and the conclusions are open‐ended.

Originality/value

This is the only paper to review the rhizome concept in this way.