bluuebunny/crossref_metadata_2025 huggingface dataset:
Communications: Infrared spectroscopy of gas phase C3H3+ ions: The cyclopropenyl and propargyl cations
Authors: Ricks Allen M. , Douberly Gary E. , Schleyer Paul v. R. , Duncan Michael A.
Published: February 2010

C 3 H 3 + ions produced with a pulsed discharge source and cooled in a supersonic beam are studied with infrared laser photodissociation spectroscopy in the 800–4000 cm−1 region using the rare gas tagging method. Vibrational bands in the C–H stretching and fingerprint regions confirm the presence of both the cyclopropenyl and propargyl cations. Because there is a high barrier separating these two structures, they are presumed to be produced by different routes in the plasma chemistry; their relative abundance can be adjusted by varying the ion source conditions. Prominent features for the cyclopropenyl species include the asymmetric carbon stretch (ν5) at 1293 cm−1 and the asymmetric C–H stretch (ν4) at 3182 cm−1, whereas propargyl has the CH2 scissors (ν4) at 1445, the C–C triple bond stretch (ν3) at 2077 and three C–H stretches (ν2, ν9, and ν1) at 3004, 3093, and 3238 cm−1. Density functional theory computations of vibrational spectra for the two isomeric ions with and without the argon tag reproduce the experimental features qualitatively; according to theory the tag atom only perturbs the spectra slightly. Although these data confirm the accepted structural pictures of the cyclopropenyl and propargyl cations, close agreement between theoretical predictions and the measured vibrational band positions and intensities cannot be obtained. Band intensities are influenced by the energy dependence and dynamics of photodissociation, but there appear to be fundamental problems in computed band positions independent of the level of theory employed. These new data provide infrared signatures in the fingerprint region for these prototypical carbocations that may aid in their astrophysical detection.
Simulation of pseudopolyrotaxane formation and orientational order between pseudopolyrotaxanes
Authors: Urakami Naohito , Imada Junko , Yamamoto Takashi
Published: February 2010

We have performed Brownian dynamics simulations in order to investigate the formation of a pseudopolyrotaxane (PPRX) with cyclodextrins (CDs) and a polymer chain and the development of orientational order between PPRXs. The coarse-grained model is used to model the CDs and the polymer chain. In our simulations, we observe the formation of a rodlike PPRX with up to six rings for 40 monomer chains. After the formation of the PPRX, the processes of inclusion and dissociation repeat for the rings at the end of the chain. However, the PPRX has more than three rings and maintains the rodlike shape. With regard to the motion of rings in the PPRX, we observe two kinds of motions—oscillating motion and shifting motion. In the oscillating motion, the rings move around a particular position on the chain and display thermal fluctuation and collisions with neighboring rings. In the shifting motion, all rings shift to another location along the chain during the processes of inclusion and dissociation. In our simulations, we also observed that the orientational order between PPRXs develops at low temperatures.
Maximum Li storage in Si nanowires for the high capacity three-dimensional Li-ion battery
Authors: Kang Kibum , Lee Hyun-Seung , Han Dong-Wook , Kim Gil-Sung , Lee Donghun , Lee Geunhee , Kang Yong-Mook , Jo Moon-Ho
Published: February 2010

Nanowires can serve as three-dimensional platforms at the nanometer scale for highly efficient chemical energy storage and conversion vehicles, such as fuel cells and secondary batteries. Here we report a coin-type Si nanowire (NW) half-cell Li-ion battery showing the Li capacity of approximately 4000 mAh/g, which nearly approaches the theoretical limit of 4200 mAh/g, with very high Coulombic efficiency of up to 98%. Concomitantly, we provide direct evidence of reversible phase transitions in the Si NW anodes at the full electrochemical cycles, varying from pure Si to Li22Si5 phase, which has been known empirically inaccessible in the bulk limit.
Reactions of ruthenium and rhodium atoms with carbon monoxide and dinitrogen mixtures: A combined experimental and theoretical study
Authors: Jiang Ling , Lu Zhang-Hui , Xu Qiang
Published: February 2010

Laser-ablated Ru and Rh atoms react with CO and N2 mixture in excess neon to produce the carbonylmetal dinitrogen complexes, (NN)nMCO (M=Ru,Rh; n=1,2) and NNRu(CO)2, as well as metal carbonyls and dinitrogen complexes. These carbonylmetal dinitrogen complexes are characterized using infrared spectroscopy on the basis of the results of the isotopic substitution and mixed isotopic splitting patterns. Density functional theory calculations have been performed on these complexes. Overall agreement between the experimental and calculated vibrational frequencies, relative absorption intensities, and isotopic shifts supports the identification of these species from the matrix infrared spectra. Furthermore, a plausible reaction pathway for the formation of the products has been proposed. This work reveals that the reactivity of Ru and Rh atoms toward CO is prior to N2.
Short-time Fourier transform analysis of real-time time-dependent Hartree–Fock and time-dependent density functional theory calculations with Gaussian basis functions
Authors: Akama Tomoko , Nakai Hiromi
Published: February 2010

We propose a novel analysis of real-time (RT) time-dependent Hartree–Fock and time-dependent density functional theory (TDHF/TDDFT) calculations using a short-time Fourier transform (STFT) technique. RT-TDHF/TDDFT calculations of model dimers were carried out and analyzed using the STFT technique, in addition to the usual Fourier transform (FT). STFT analysis revealed that the induced polarization propagated between the molecules through the intermolecular interaction; that is, it directly showed the electron dynamics of the excited system. The dependence of the propagation period on the intermolecular distance of the dimer was investigated. We also proved the possibility of describing, not just the valence, but also the core excitations by FT analysis of the RT-TDHF/TDDFT calculations of a formaldehyde monomer with Gaussian basis functions compared with conventional TDHF/TDDFT results.
Charge pumping technique to analyze the effect of intrinsically retained charges and extrinsically trapped charges in biomolecules by use of a nanogap embedded biotransistor
Authors: Kim Sungho , Ahn Jae-Hyuk , Park Tae Jung , Lee Sang Yup , Choi Yang-Kyu
Published: February 2010

Charge pumping technique is investigated for label-free electrical biosensing using a nanogap-embedded biotransistor. Biomolecules immobilized in a nanogap provide additional trap states and charges in the gate dielectric. These two effects give rise to a change of the charge pumping current, which are analyzed by the aid of numerical simulations. To utilize the trap density of gate dielectric as a sensing parameter, proper amplitude of pulse should be applied for charge pumping to exclude the effect of intrinsically retained charges in biomolecules, thereby this proposed technique is available for detection of biomolecules regardless of retained charges.
Observation of sub-100 femtosecond electron cooling time in InN
Authors: Su Yi-En , Wen Yu-Chieh , Lee Hong-Mao , Gwo Shangjr , Sun Chi-Kuang
Published: February 2010

We report that the electron cooling time in indium nitride can be as fast as sub-100 femtosecond at low electron concentration (<5×1017/cm3), which is much faster than previous reports. Through investigating the dependence of the measured carrier cooling time on electron density, our study proved the dominant role of the screened Fröhlich interaction in the reduction in carrier cooling rate at an electron density higher than 1.8×1018/cm3.
Role of carrier and spin in tuning ferromagnetism in Mn and Cr-doped In2O3 thin films
Authors: Jiang Feng-Xian , Xu Xiao-Hong , Zhang Jun , Fan Xiao-Chen , Wu Hai-Shun , Gehring G. A.
Published: February 2010

Mn and Cr-doped In2O3 films with Sn codoping were deposited on sapphire substrate by pulsed laser deposition. The ferromagnetism of Mn-doped In2O3 films shows reversible behavior, which can be switched between “on” and “off” states by controlling the carrier density via varying Sn concentration. The enhanced ferromagnetism in Cr-doped In2O3 films is observed due to the significant increase in the carrier density with Sn doping, and the saturation magnetization can reach 2.10 μB/Cr. Most importantly, both of the experiment results reveal that the carrier density and the net spin are two crucial factors for producing and tuning ferromagnetism.
Hydrogen generation by solar water splitting using p-InGaN photoelectrochemical cells
Authors: Aryal K. , Pantha B. N. , Li J. , Lin J. Y. , Jiang H. X.
Published: February 2010

Photoelectrochemical effects in p-InxGa1−xN (0≤x≤0.22) alloys have been investigated. Hydrogen generation was observed in p-InGaN semiconducting electrodes under white light illumination with additional bias. It was found that p-InGaN alloys possess much higher conversion efficiencies than p-GaN. Time dependent photocurrent density characteristics showed that the stability of p-InGaN in aqueous HBr is excellent. The photocurrent density was found to increase almost linearly with hole mobility and excitation light intensity.
Effect of vacuum ultraviolet and ultraviolet Irradiation on capacitance-voltage characteristics of low-k-porous organosilicate dielectrics
Authors: Sinha H. , Lauer J. L. , Nichols M. T. , Antonelli G. A. , Nishi Y. , Shohet J. L.
Published: February 2010

High frequency capacitance-voltage (C-V) measurements are used to determine the effects of vacuum ultraviolet (VUV) and ultraviolet (UV) irradiation on defect states in porous low-k organosilicate (SiCOH) dielectrics. The characteristics show that VUV photons depopulate trapped electrons from defect states within the dielectric creating trapped positive charge. This is evidenced by a negative shift in the flat-band voltage of the C-V characteristic. UV irradiation reverses this effect by repopulating the defect states with electrons photoinjected from the silicon substrate. Thus, UV reduces the number of trapped positive charges in the dielectric and can effectively repair processing-induced damage.
Evidence of Al induced conducting filament formation in Al/amorphous silicon/Al resistive switching memory device
Authors: Won Seo Jung , Baik Seung Jae , Kang Sang Jung , Hong Yun Ho , Yang Ji-Hwan , Fang Liang , Lim Koeng Su
Published: February 2010

We demonstrated that an Al/p-type amorphous silicon (p-a-Si)/Al switching device exhibits stable, nonvolatile resistive switching characteristics as well as reliable data retention at 85 °C. It is directly observed that the conducting filament is created after electroforming and incorporates the top metal migrated or diffused into a-Si layer. In addition, by analyzing the constitution of the conducting filament, we investigated the microscopic nature of the conducting filament. These results suggest that the Al/p-a-Si/Al device has potential for future nonvolatile memory applications.
Partitioning of assimilates to deeper roots is associated with cooler canopies and increased yield under drought in wheat
Authors: Lopes Marta S. , Reynolds Matthew P.
Published: February 2010

Dehydration avoidance through cooler canopy temperature (CT) has been shown to explain over 60% yield variation in a random progeny derived from a Seri/Babax cross. A near ‘isomorphic’ subset of Seri/Babax progeny and parents encompassing a restricted range of height and phenology were used for detailed characterisation of drought-adaptive trait expression under contrasting water regimes. Under drought, five of the six progeny out yielded the best parent Babax by up to 35%. The main physiological attributes associated with drought adaptation were increased root dry weight at depth, transpiration rate – evidenced by grain carbon isotope discrimination (Δ13C) – grain filling duration and decreased CT during grain filling. Furthermore, increased root mass at depth was associated with reduced levels of stem water soluble carbohydrates (WSC) when comparing genotypes. It is concluded that differences in rooting depth expressed among iso-morphic wheat sister lines explains superior adaptation to drought. These effects can be detected in season using remote sensing. In addition, the data suggest that accumulation of stem carbohydrates and deep rooting may be two alternative strategies for adapting to drought stress, the latter being beneficial where water is available at depth.
Stem solidness and its relationship to water-soluble carbohydrates: association with wheat yield under water deficit
Authors: Saint Pierre Carolina , Trethowan Richard , Reynolds Matthew
Published: February 2010

A study of 36 wheat (Triticum aestivum L.) genotypes with different levels of stem solidness was conducted to assess the heritability and relationship among stem morphological properties, stem water-soluble carbohydrates (WSC) storage capacity and grain yield. The total amount of pith-fill in the upper stem internode (VOL) was highly correlated with the total content of WSC per stem under both water deficit (DEF) (r = 0.56) and well irrigated conditions (IRR) (r = 0.49). A positive correlation was also found between VOL and grain yield under DEF (r = 0.49), which was explained by the positive contribution of WSC to grain yield. A closer association of grain yield and morphological traits was identified under DEF than under IRR. The closer associations found among estimations of %WSC and WSC-area and grain yield under DEF indicate that these variables may be adaptive rather than constitutive traits. High heritability values (0.77–0.84) observed for stem morphological traits reinforce their potential use in breeding for high WSC and ultimately, higher grain yield under water-limited environments. Stem length, diameter and solidness could be combined in an ideal plant ideotype to maximise WSC reserves as a strategy to improve yield under water-limited conditions.
Improvement of drought tolerance in white clover (Trifolium repens) by transgenic expression of a transcription factor gene WXP1
Authors: Jiang Qingzhen , Zhang Ji-Yi , Guo Xiulin , Bedair Mohamed , Sumner Lloyd , Bouton Joseph , Wang Zeng-Yu
Published: February 2010

White clover (Trifolium repens L.) is an important pasture legume in many regions of the world. A commercial cultivar of white clover (cv. Patriot) was transformed with a Medicago truncatula L. transcription factor gene, WXP1, and a reporter gene, β-glucuronidase (GUS). The WXP1 gene and the GUS gene were placed under control of the Arabidopsis CER6 promoter. GUS staining and cross-section analysis revealed the CER6 promoter directed constitutive expression in leaves and epidermis preferential expression in petioles of white clover. Independent transgenic WXP1 lines, empty vector and wild-type controls were subjected to drought stress treatment. The plants were characterised by measuring several physiological parameters including gas exchange, chlorophyll fluorescence, relative water content and leaf water potential. The WXP1 transgenic lines had higher net photosynthetic rates, higher efficiency of PSII, higher relative water content and leaf water potential under drought-stressed conditions. Consistent with the results from physiological analyses, the transgenic white clover plants carrying WXP1 showed improved tolerance to drought stress.
Improved plant nitrogen nutrition contributes to higher water use efficiency in tomatoes under alternate partial root-zone irrigation
Authors: Wang Yaosheng , Liu Fulai , Andersen Mathias N. , Jensen Christian R.
Published: February 2010

Comparative effects of partial root-zone irrigation (PRI) and deficit irrigation (DI) on stomatal conductance (gs), nitrogen accumulation and distribution in tomato (Lycopersicon esculentum L.) plants were investigated in a split-root pot experiment. Results showed that both PRI and DI saved 25% water and led to 10.0% and 17.5% decreases in dry biomass, respectively, compared with the fully irrigated (FI) controls. Consequently, water use efficiency (WUE) was increased by 18.6% and 10.8% in the PRI and DI plants, respectively. The highest WUE in the PRI plants was associated with the highest carbon isotope composition (δ13C), indicating that the improvement of WUE might have been a result of long-term optimisation of stomatal control over gas exchange. The constantly higher xylem sap ABA concentration in PRI compared with DI plants was seemingly responsible for the greater control over stomatal conductance during the treatment. At the end of the experiment, N accumulation and 15N recovery was highest in FI, intermediate in PRI and lowest in DI. In addition, PRI plants consistently allocated more N into the upper and middle leaf layers than in the FI and DI treatments. The improved N nutrition and distribution in the canopy may indicate that PRI plants have a greater photosynthetic capacity than DI plants; this is confirmed by the observed positive linear relationship between specific leaf N content and δ13C. It is concluded that PRI improves N nutrition and optimises N distribution in the canopy, which might have been partly contributed to the high WUE in PRI tomato plants.
Brain estrogens rapidly strengthen auditory encoding and guide song preference in a songbird
Authors: Remage-Healey Luke , Coleman Melissa J. , Oyama Randi K. , Schlinger Barney A.
Published: February 2010

Higher cognitive function depends on accurate detection and processing of subtle features of sensory stimuli. Such precise computations require neural circuits to be modulated over rapid timescales, yet this modulation is poorly understood. Brain-derived steroids (neurosteroids) can act as fast signaling molecules in the vertebrate central nervous system and could therefore modulate sensory processing and guide behavior, but there is no empirical evidence for this possibility. Here we report that acute inhibition of estrogen production within a cortical-like region involved in complex auditory processing disrupts a songbird’s ability to behaviorally respond to song stimuli. Identical manipulation of local estrogen levels rapidly changes burst firing of single auditory neurons. This acute estrogen-mediated modulation targets song and not other auditory stimuli, possibly enabling discrimination among species-specific signals. Our results demonstrate a crucial role for neuroestrogen synthesis among vertebrates for enhanced sensory encoding. Cognitive impairments associated with estrogen depletion, including verbal memory loss in humans, may therefore stem from compromised moment-by-moment estrogen actions in higher-order cortical circuits.
Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities
Authors: Denef Vincent J. , Kalnejais Linda H. , Mueller Ryan S. , Wilmes Paul , Baker Brett J. , Thomas Brian C. , VerBerkmoes Nathan C. , Hettich Robert L. , Banfield Jillian F.
Published: February 2010

Bacterial species concepts are controversial. More widely accepted is the need to understand how differences in gene content and sequence lead to ecological divergence. To address this relationship in ecosystem context, we investigated links between genotype and ecology of two genotypic groups ofLeptospirillumgroup II bacteria in comprehensively characterized, natural acidophilic biofilm communities. These groups share 99.7% 16S rRNA gene sequence identity and 95% average amino acid identity between their orthologs. One genotypic group predominates during early colonization, and the other group typically proliferates in later successional stages, forming distinct patches tens to hundreds of micrometers in diameter. Among early colonizing populations, we observed dominance of five genotypes that differed from each other by the extent of recombination with the late colonizing type. Our analyses suggest that the specific recombinant variant within the early colonizing group is selected for by environmental parameters such as temperature, consistent with recombination as a mechanism for ecological fine tuning. Evolutionary signatures, and strain-resolved expression patterns measured via mass spectrometry–based proteomics, indicate increased cobalamin biosynthesis, (de)methylation, and glycine cleavage in the late colonizer. This may suggest environmental changes within the biofilm during development, accompanied by redirection of compatible solutes from osmoprotectants toward metabolism. Across 27 communities, comparative proteogenomic analyses show that differential regulation of shared genes and expression of a small subset of the ∼15% of genes unique to each genotype are involved in niche partitioning. In summary, the results show how subtle genetic variations can lead to distinct ecological strategies.
Cell density and mobility protect swarming bacteria against antibiotics
Authors: Butler Mitchell T. , Wang Qingfeng , Harshey Rasika M.
Published: February 2010

Swarming bacteria move in multicellular groups and exhibit adaptive resistance to multiple antibiotics. Analysis of this phenomenon has revealed the protective power of high cell densities to withstand exposure to otherwise lethal antibiotic concentrations. We find that high densities promote bacterial survival, even in a nonswarming state, but that the ability to move, as well as the speed of movement, confers an added advantage, making swarming an effective strategy for prevailing against antimicrobials. We find no evidence of induced resistance pathways or quorum-sensing mechanisms controlling this group resistance, which occurs at a cost to cells directly exposed to the antibiotic. This work has relevance to the adaptive antibiotic resistance of bacterial biofilms.
Reactive collisions of sulfur dioxide with molten carbonates
Authors: Krebs Thomas , Nathanson Gilbert M.
Published: February 2010

Molecular beam scattering experiments are used to investigate reactions of SO2at the surface of a molten alkali carbonate eutectic at 683 K. We find that two-thirds of the SO2molecules that thermalize at the surface of the melt are converted to gaseous CO2via the reaction. The CO2product is formed from SO2in less than 10-6 s, implying that the reaction takes place in a shallow liquid region less than 100 Å deep. The reaction probability does not vary between 683 and 883 K, further implying a compensation between decreasing SO2residence time in the near-interfacial region and increasing reactivity at higher temperatures. These results demonstrate the remarkable efficiency of SO2 → CO2conversion by molten carbonates, which appear to be much more reactive than dry calcium carbonate or wet slurries commonly used for flue gas desulfurization in coal-burning power plants.
X chromosome-wide analyses of genomic DNA methylation states and gene expression in male and female neutrophils
Authors: Yasukochi Yukio , Maruyama Osamu , Mahajan Milind C. , Padden Carolyn , Euskirchen Ghia M. , Schulz Vincent , Hirakawa Hideki , Kuhara Satoru , Pan Xing-Hua , Newburger Peter E. , Snyder Michael , Weissman Sherman M.
Published: February 2010

The DNA methylation status of human X chromosomes from male and female neutrophils was identified by high-throughput sequencing of HpaII and MspI digested fragments. In the intergenic and intragenic regions on the X chromosome, the sites outside CpG islands were heavily hypermethylated to the same degree in both genders. Nearly half of X chromosome promoters were either hypomethylated or hypermethylated in both females and males. Nearly one third of X chromosome promoters were a mixture of hypomethylated and heterogeneously methylated sites in females and were hypomethylated in males. Thus, a large fraction of genes that are silenced on the inactive X chromosome are hypomethylated in their promoter regions. These genes frequently belong to the evolutionarily younger strata of the X chromosome. The promoters that were hypomethylated at more than two sites contained most of the genes that escaped silencing on the inactive X chromosome. The overall levels of expression of X-linked genes were indistinguishable in females and males, regardless of the methylation state of the inactive X chromosome. Thus, in addition to DNA methylation, other factors are involved in the fine tuning of gene dosage compensation in neutrophils.
Dynamics of intracellular bacterial replication at the single cell level
Authors: Helaine Sophie , Thompson Jessica A. , Watson Kathryn G. , Liu Mei , Boyle Cliona , Holden David W.
Published: February 2010

Several important pathogens cause disease by surviving and replicating within host cells. Bacterial proliferation is the product of both replication and killing undergone by the population. However, these processes are difficult to distinguish, and are usually assessed together by determination of net bacterial load. In addition, measurement of net load does not reveal heterogeneity within pathogen populations. This is particularly important in persistent infections in which slow or nongrowing bacteria are thought to have a major impact. Here we report the development of a reporter system based on fluorescence dilution that enables direct quantification of the replication dynamics ofSalmonella entericaserovar Typhimurium (S.Typhimurium) in murine macrophages at both the population and single-cell level. We used this technique to demonstrate that a majorS.Typhimurium virulence determinant, theSalmonellapathogenicity island 2 type III secretion system, is required for bacterial replication but does not have a major influence on resistance to killing. Furthermore, we found that, upon entry into macrophages, many bacteria do not replicate, but appear to enter a dormant-like state. These could represent an important reservoir of persistent bacteria. The approach could be extended to other pathogens to study the contribution of virulence and host resistance factors to replication and killing, and to identify and characterize nonreplicating bacteria associated with chronic or latent infections.
Induction of IFN-αβ enables Listeria monocytogenes to suppress macrophage activation by IFN-γ
Authors: Rayamajhi Manira , Humann Jessica , Penheiter Kristi , Andreasen Karl , Lenz Laurel L.
Published: February 2010

Production of type I interferon (IFN; IFN-αβ) increases host susceptibility to Listeria monocytogenes, whereas type II IFN (IFN-γ) activates macrophages to resist infection. We show that these opposing immunological effects of IFN-αβ and IFN-γ occur because of cross talk between the respective signaling pathways. We found that cultured macrophages infected with L. monocytogenes were refractory to IFN-γ treatment as a result of down-regulation of the IFN-γ receptor (IFNGR). The soluble factor responsible for these effects was identified as host IFN-αβ. Accordingly, macrophages and dendritic cells (DCs) showed reduced IFNGR1 expression and reduced responsiveness to IFN-γ during systemic infection of IFN-αβ–responsive mice. Furthermore, the increased resistance of mice lacking the IFN-αβ receptor (IFNAR−/−) to L. monocytogenes correlated with increased expression of IFN-γ–dependent activation markers by macrophages and DCs and was reversed by depletion of IFN-γ. Thus, IFN-αβ produced in response to bacterial infection and other stimuli antagonizes the host response to IFN-γ by down-regulating the IFNGR. Such cross talk permits prioritization of IFN-αβ–type immune responses and may contribute to the beneficial effects of IFN-β in treatment of inflammatory diseases such as multiple sclerosis.
Non-equilibrium constricted dc glow discharge in N2 flow at atmospheric pressure: stable and unstable regimes
Authors: Akishev Yu , Grushin M , Karalnik V , Petryakov A , Trushkin N
Published: February 2010

The experimental results from the study of a constricted glow discharge in turbulent flow of nitrogen at atmospheric pressure are presented. The discharge was induced by a dc high voltage superimposed between pin-to-plane electrodes inserted inside a glass tube of 1 cm diameter. At a low current I < 20 mA it is established that the properties of the constricted glow discharge in gas flow are strongly different from those in gas at rest: the discharge in gas flow exhibits four different current regimes instead of only a single one in gas at rest. One of these regimes corresponds to a spiral twisting of gas flow by the constricted glow discharge. This effect can be used properly in plasma actuators designed for atmospheric pressure flow control. Gas blowing also enables the constricted N2 plasma to be in a strong non-equilibrium state with vibration and gas temperatures of about 6000 K and 600 K, respectively. So, a constricted discharge in N2 flow can serve as a compact and effective non-thermal plasma source useful in the remote treatment of different surfaces.
Performance of harvest control rules in a variable environment
Authors: Brunel Thomas , Piet Gerjan J. , van Hal Ralf , Röckmann Christine
Published: February 2010

Brunel, T., Piet, G. J., van Hal, R., and Röckmann, C. 2010. Performance of harvest control rules in a variable environment. – ICES Journal of Marine Science, 67: 1051–1062. Population dynamic models used for fisheries management assume that stocks are isolated entities, ignoring the influence of environmental factors on stock productivity. An operating model parameterized for North Sea cod, plaice, and herring is developed, in which the link between recruitment and environment is assumed to be known and described by generalized additive models. This tool is used to compare the performance of harvest control rules (HCRs) when recruitment is independent of the environment or when recruitment is affected by an environment varying according to different scenarios. The first HCR exploited the stock with a fixed fishing mortality (F) corresponding to maximum sustainable yield, and in the second HCR, F was set equal to the precautionary approach F (i.e. Fpa), but reduced from Fpa when stock biomass fell below Bpa. The performance of the HCRs altered only slightly in a randomly varying environment compared with a constant one. For a detrimental change in the environment, however, no HCR could prevent a massive decrease in stock size. The performance of the HCRs was also influenced by the stock characteristics, such as recruitment variability or the shape of the stock–recruitment relationship. The performance of “environmental” HCRs (eHCRs), in which F varies depending on environmental conditions, was compared with that of conventional HCRs. The gain in using the eHCR was small, except for a detrimental change in the environment, where the eHCR performed markedly better than a conventional HCR. The benefits of using the eHCR were the greatest for the stock with the strongest environment–recruitment relationship.
Occurrence and Diversity of Xanthomonas campestris pv. campestris in Vegetable Brassica Fields in Nepal
Authors: Jensen Brita Dahl , Vicente Joana G. , Manandhar Hira K. , Roberts Steven J.
Published: February 2010

Black rot caused by Xanthomonas campestris pv. campestris was found in 28 sampled cabbage fields in five major cabbage-growing districts in Nepal in 2001 and in four cauliflower fields in two districts and a leaf mustard seed bed in 2003. Pathogenic X. campestris pv. campestris strains were obtained from 39 cabbage plants, 4 cauliflower plants, and 1 leaf mustard plant with typical lesions. Repetitive DNA polymerase chain reaction-based fingerprinting (rep-PCR) using repetitive extragenic palindromic, enterobacterial repetitive intergenic consensus, and BOX primers was used to assess the genetic diversity. Strains were also race typed using a differential series of Brassica spp. Cabbage strains belonged to five races (races 1, 4, 5, 6, and 7), with races 4, 1, and 6 the most common. All cauliflower strains were race 4 and the leaf mustard strain was race 6. A dendrogram derived from the combined rep-PCR profiles showed that the Nepalese X. campestris pv. campestris strains clustered separately from other Xanthomonas spp. and pathovars. Race 1 strains clustered together and strains of races 4, 5, and 6 were each split into at least two clusters. The presence of different races and the genetic variability of the pathogen should be considered when resistant cultivars are bred and introduced into regions in Nepal to control black rot of brassicas.
Genomics-Based Diagnostic Marker Development for Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola
Authors: Lang Jillian M. , Hamilton John P. , Diaz Maria Genaleen Q. , Van Sluys Marie Anne , Burgos Ma. Ruby G. , Vera Cruz Casiana M. , Buell C. Robin , Tisserat Ned A. , Leach Jan E.
Published: February 2010

A computational genomics pipeline was used to compare sequenced genomes of Xanthomonas spp. and to rapidly identify unique regions for development of highly specific diagnostic markers. A suite of diagnostic primers was selected to monitor diverse loci and to distinguish the rice bacterial blight and bacterial leaf streak pathogens, Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola, respectively. A subset of these primers was combined into a multiplex polymerase chain reaction set that accurately distinguished the two rice pathogens in a survey of a geographically diverse collection of X. oryzae pv. oryzae, X. oryzae pv. oryzicola, other xanthomonads, and several genera of plant-pathogenic and plant- or seed-associated bacteria. This computational approach for identification of unique loci through whole-genome comparisons is a powerful tool that can be applied to other plant pathogens to expedite development of diagnostic primers.
Identification and Distribution of Soybean mosaic virus Strains in Southern China
Authors: Li K. , Yang Q. H. , Zhi H. J. , Gai J. Y.
Published: February 2010

From 1,417 leaf samples with Soybean mosaic virus (SMV)-like symptoms collected from about 1,500 fields of 117 counties of 13 provinces in Southern China during 2004 to 2006, 201 SMV isolates were obtained after biological purification with single-lesion isolation and serological determination. Based on disease reactions on 10 differentials used in China as a representative from various reported differential cultivar systems, the isolates were grouped into 12 strains. Among them, eight were the same as those previously reported from Northeast China and the Huang-Huai Valleys while the other four were new and were designated as SC18, SC19, SC20, and SC21. Strains SC15 and SC18, which were predominant and widespread in Southern China, accounted for 32.3 and 26.4% of the total isolates and were distributed in 9 and 10 provinces, respectively. Thus far, 21 strains have been identified in the three soybean-producing regions in China under the uniform differentials system. According to their responses on the 10 differentials, the strains were clustered into five groups at similarity coefficient 0.6. Among them, SC15 in cluster V is the most virulent strain because it infects all differentials. Therefore, specific attention should be placed on control of its prevalence in soybean production.
Tomato Plants Transformed with the Inhibitor-of-Virus-Replication Gene Are Partially Resistant to Botrytis cinerea
Authors: Loebenstein Gad , David Dalia Rav , Leibman Diana , Gal-On Amit , Vunsh Ron , Czosnek Henryk , Elad Yigal
Published: February 2010

Tomato plants transformed with a cDNA clone encoding the inhibitor-of-virus-replication (IVR) gene were partially resistant to Botrytis cinerea. This resistance was observed as a significant reduction in the size of lesions induced by the fungus in transgenic plants compared with the lesions on the nontransgenic control plants. This resistance was weakened when plants were kept at an elevated temperature, 32°C, before inoculation with B. cinerea compared with plants kept at 17 to 22°C prior to inoculation. Resistance correlated with the presence of IVR transcripts, as detected by reverse transcription-polymerase chain reaction. This is one of the few cases in which a gene associated with resistance to a virus also seems to be involved in resistance to a fungal disease.
Screening Molecules for Control of Citrus Huanglongbing Using an Optimized Regeneration System for ‘Candidatus Liberibacter asiaticus’-Infected Periwinkle (Catharanthus roseus) Cuttings
Authors: Zhang Muqing , Duan Yongping , Zhou Lijuan , Turechek William W. , Stover Ed , Powell Charles A.
Published: February 2010

Citrus huanglongbing is one of the most destructive diseases of citrus worldwide. The disease is associated with three different species of ‘Candidatus Liberibacter’, of which ‘Ca. L. asiaticus’ is the most widely distributed. An optimized system using ‘Ca. L. asiaticus’-infected periwinkle cuttings was developed to screen chemical compounds effective for controlling the bacterial population while simultaneously assessing their phytotoxicity. The optimal regeneration conditions were determined to be the use of vermiculite as a growth medium for the cuttings, and a fertilization routine using half-strength Murashige and Tucker medium supplemented with both naphthalene acetic acid (4 μg/ml) and indole-3-butyric acid (4 μg/ml). This system allowed a plant regeneration rate of 60.6% for ‘Ca. L. asiaticus’-infected cuttings in contrast to the <1% regeneration rate with water alone. Two chemical agents, penicillin G sodium and 2,2-dibromo-3-nitrilopropionamide (DBNPA), were found to be effective at eliminating or suppressing the ‘Ca. L. asiaticus’ bacterium in this periwinkle regeneration system. When treated with penicillin G sodium at 50 μg/ml, all plants regenerated from ‘Ca. L. asiaticus’-infected cuttings were ‘Ca. L. asiaticus’ negative as determined by both nested polymerase chain reaction (PCR) and quantitative real-time PCR. In addition, DBNPA was also able to significantly reduce the percentage of ‘Ca. L. asiaticus’-positive plants and the titer of the ‘Ca. L. asiaticus’ bacterium at 200 μl/liter.
The evolution of organellar metabolism in unicellular eukaryotes
Authors: Ginger Michael L. , McFadden Geoffrey I. , Michels Paul A. M.
Published: February 2010

Metabolic innovation has facilitated the radiation of microbes into almost every niche environment on the Earth, and over geological time scales transformed the planet on which we live. A notable example of innovation is the evolution of oxygenic photosynthesis which was a prelude to the gradual transformation of an anoxic Earth into a world with oxygenated oceans and an oxygen-rich atmosphere capable of supporting complex multicellular organisms. The influence of microbial innovation on the Earth's history and the timing of pivotal events have been addressed in other recent themed editions of
Philosophical Transactions of Royal Society B
(

Cavalier-Smith
et al
. 2006

;

Bendall
et al
. 2008

). In this issue, our contributors provide a timely history of metabolic innovation and adaptation within unicellular eukaryotes. In eukaryotes, diverse metabolic portfolios are compartmentalized across multiple membrane-bounded compartments (or organelles). However, as a consequence of pathway retargeting, organelle degeneration or novel endosymbiotic associations, the metabolic repertoires of protists often differ extensively from classic textbook descriptions of intermediary metabolism. These differences are often important in the context of niche adaptation or the structure of microbial communities. Fundamentally interesting in its own right, the biochemical, cell biological and phylogenomic investigation of organellar metabolism also has wider relevance. For instance, in some pathogens, notably those causing some of the most significant tropical diseases, including malaria, unusual organellar metabolism provides important new drug targets. Moreover, the study of organellar metabolism in protists continues to provide critical insight into our understanding of eukaryotic evolution.
Relationship between the distribution of pseudoxanthoma elasticum skin and mucous membrane lesions and cardiovascular involvement
Authors: UTANI Atsushi , TANIOKA Miki , YAMAMOTO Yosuke , TAKI Reiko , ARAKI Eri , TAMURA Hiroshi , MIYACHI Yoshiki
Published: February 2010

Pseudoxanthoma elasticum (PXE) primarily affects organs that are abundant in elastic fibers, such as the skin, eye and blood vessels, and may eventually cause loss of vision or cardiovascular disease (CVD). Because CVD is a potentially life‐threatening complication, its early detection is important for improving the quality of life of PXE patients. To determine the relationship between the distribution of skin and mucous membrane lesions and the prevalence of CVD in patients with PXE, we examined 14 PXE cases who presented between 2004 and 2007. All patients had angioid streaks (AS) and positive pathological findings. The skin lesions in PXE patients are distributed discontinuously and thus the degrees of skin involvement were assessed by determining the presence or absence of PXE skin and mucous membrane lesions in six sites (oral mucosa, neck, periumbilical region, cubital fossa, axillae and inguinal regions). Each site was given a binary score (i.e. present = 1, absent = 0) irrespective of severity and the scores were summed to yield a total distribution score (potential range of 0–6). Four cases had PXE‐associated CVD. Their mean distribution score was 5.7, which was significantly higher than the score of the cases without CVD (1.8) (P = 0.0049). There was also significant correlation between the high distribution score (P = 0.0053) as well as CVD (P = 0.029) with the maximum width of AS. A higher distribution score and the presence of oral mucosal lesions were associated with CVD. This scoring method may be useful for predicting the presence of CVD in PXE patients.
Efficacy of a far erythemogenic dose of narrow‐band ultraviolet B phototherapy in chronic plaque‐type psoriasis
Authors: AKARAPHANTH Rutsanee , KITTIPAVARA Yotsinee , VORAVUTINON Nataya , WACHIRATARAPADORN Usa , GRITIYARANGSAN Pimonpun
Published: February 2010

The aim of the present study was to examine the effect of far erythemogenic dose of narrow‐band ultraviolet B (NB‐UVB; starting dose at 35% minimal erythematous dose [MED]) on clinical response by measuring the severity, extent of disease and the changes in quality of life. Fifty patients with chronic plaque‐type psoriasis were enrolled. Therapy was held for 3 days a week. The severity of the disease was assessed based on the Psoriasis Area and Severity Index (PASI) score and Dermatology Life Quality Index (DLQI) scores. The percentage improvement of PASI at 30 sessions was 68.99%. The improvement in DLQI scores at 30 sessions was 79.67%. Pearson correlation coefficients showed that PASI scores were not correlated with DLQI scores at the beginning of treatment (P = 0.330, r = 0.14), but after the 30th session of NB‐UVB therapy improvements in quality of life were correlated (P < 0.05, r = 0.399). Therefore, far erythemogenic dose of NB‐UVB is considered to be effective treatment for plaque‐type psoriasis in our patients. However, we cannot confirm that it is safer than higher MED starting dose in term of cumulative UV irradiation.
Comorbidities associated with psoriasis: An experience from the Middle East
Authors: AL‐MUTAIRI Nawaf , AL‐FARAG Shahat , AL‐MUTAIRI Ahmed , AL‐SHILTAWY Mazen
Published: February 2010

Recent studies suggest that psoriasis patients have higher rates of comorbidities. We sought to determine the prevalence of comorbidities and co‐medications in our psoriasis patients. We conducted case‐control study in 1835 patients with psoriasis vulgaris and age‐ and gender‐matched cohort without psoriasis. Patients were examined for clinical characteristics of psoriasis, PASI scores, and data of age, sex, body mass index (BMI), smoking status, comorbidities, and co‐medications were analysed for both patients and controls. We identified 1661 (92.8%) patients with mild to moderate psoriasis (PASI < 10) and 129 patient’s (7.03%) with severe psoriasis (PASI > 10). Patients with psoriasis were more likely to be current smokers (51.34% vs 32.51% controls). Respective prevalence rates of risk factors in those with mild–moderate psoriasis, severe psoriasis, and controls were as follows: inflammatory arthritis (20%, 31% and 10.68%); coronary heart disease (4.1%, 8.35% and 1.42%); obesity (BM1) (32.5%, 41% and 17%); diabetes mellitus type II (37.4%, 41% and 16%); hypertension (32%, 40.3% and 11.55%); dyslipidemia (14.1%, 22.48% and 4.96%); metabolic syndrome (16%, 26.35% and 6.76%); chronic obstructive pulmonary disease (COPD) (5.36%, 6.98% and 4.03%); cancer (0.3%, 1.55% and 0.16%). They had a higher odds of inflammatory arthritis, coronary heart disease, obesity, diabetes mellitus II, hypertension, dyslipidemia, and metabolic syndrome. They were receiving significantly wider varieties of drugs. Which most commonly included antidiabetic drugs, antihypertensives, and hypolipidemic drugs.
Favorable response of reticular erythematous mucinosis to ultraviolet B irradiation using a 308‐nm excimer lamp
Authors: MIYOSHI Ken , MIYAJIMA Osamu , YOKOGAWA Maki , SANO Shigetoshi
Published: February 2010

Reticular erythematous mucinosis (REM) is a rare chronic mucinosis. Histologically, the presence of mucin in the upper dermis is the most specific feature. A 73‐year‐old woman presented to our outpatient clinic with a 4‐year history of netlike macular erythema with slight edema on her left arm. She was diagnosed as having REM on the basis of the clinical picture and histological findings. She was treated with ultraviolet B irradiation using the VTRAC Excimer Lamp system with favorable response. This is the first reported case that was treated with a 308‐nm excimer lamp.
Good’s syndrome (hypogammaglobulinemia with thymoma) presenting intractable opportunistic infections and hyperkeratotic lichen planus
Authors: HANAFUSA Takaaki , UMEGAKI Noriko , YAMAGUCHI Yuji , KATAYAMA Ichiro
Published: February 2010

Good’s syndrome (GS) is a rare acquired combined T‐ and B‐cell immunodeficiency accompanying thymoma. This report concerns a case of a 57‐year‐old man with GS manifesting intractable opportunistic infections and hyperkeratotic lichen planus. He had a past history of extended thymectomy for removal of thymoma. He consulted us about scaly and exudative intractable erythematous plaque on his right forearm. The histology was compatible with phlegmon coexisting with lichen planus. Laboratory examination results indicated hypogammaglobulinemia accompanied by complete absence of B cells, which is consistent with GS. Combined treatment with immunoglobulin replacement and administration of antibiotics and antifungal drugs was effective for the phlegmon and overlying fungal infection. The patient also presented with hyperkeratotic lichen planus on both knees and the right elbow, suggesting that intractable opportunistic infection and lichen planus may be associated with GS.