bluuebunny/crossref_metadata_2025 huggingface dataset:
Alfvén eigenmodes measured in the TJ-II stellarator
Authors: Jiménez-Gómez R. , Könies A. , Ascasíbar E. , Castejón F. , Estrada T. , Eliseev L. G. , Melnikov A. V. , Jiménez J.A. , Pretty D. G. , Jiménez-Rey D. , Pedrosa M.A. , de Bustos A. , Yamamoto S.
Published: February 2011

High frequency modes (150–300 kHz) are found in several magnetic configurations of TJ-II plasmas heated by neutral beam injection (NBI). The clear dependence of mode frequency on plasma density and mass species suggests them to be Alfvén eigenmodes. The appearance of these modes is linked to the presence of low order rational surfaces close to the rotational transform profile. They can exhibit steady or chirping behaviour depending on the plasma profiles. Frequency chirping is observed in NBI plasmas with broad temperature profiles, but rarely observed with relatively peaked profiles. The Alfvénic activity has been characterized in detail with magnetic coils for the standard configuration. Cross analyses with heavy ion beam probe and reflectometer signals have yielded spatial resolution and radial profiles of the perturbation. Correlation between magnetic coil signals and signals from diagnostics sensitive to edge ion losses, namely Langmuir probes and a fast ion loss detector, has been observed in some cases and characterized taking advantage of the chirping nature of the observed Alfvénic activity.
Metal impurity transport control in JET H-mode plasmas with central ion cyclotron radiofrequency power injection
Authors: Valisa M. , Carraro L. , Predebon I. , Puiatti M.E. , Angioni C. , Coffey I. , Giroud C. , Lauro Taroni L. , Alper B. , Baruzzo M. , Belo daSilva P. , Buratti P. , Garzotti L. , Van Eester D. , Lerche E. , Mantica P. , Naulin V. , Tala T. , Tsalas M.
Published: February 2011

The scan of ion cyclotron resonant heating (ICRH) power has been used to systematically study the pump out effect of central electron heating on impurities such as Ni and Mo in H-mode low collisionality discharges in JET. The transport parameters of Ni and Mo have been measured by introducing a transient perturbation on their densities via the laser blow off technique. Without ICRH Ni and Mo density profiles are typically peaked. The application of ICRH induces on Ni and Mo in the plasma centre (at normalized poloidal flux ρ = 0.2) an outward drift approximately proportional to the amount of injected power. Above a threshold of ICRH power of about 3 MW in the specific case the radial flow of Ni and Mo changes from inwards to outwards and the impurity profiles, extrapolated to stationary conditions, become hollow. At mid-radius the impurity profiles become flat or only slightly hollow. In the plasma centre the variation of the convection-to-diffusivity ratio v/D of Ni is particularly well correlated with the change in the ion temperature gradient in qualitative agreement with the neoclassical theory. However, the experimental radial velocity is larger than the neoclassical one by up to one order of magnitude. Gyrokinetic simulations of the radial impurity fluxes induced by electrostatic turbulence do not foresee a flow reversal in the analysed discharges.
ProtTest 3: fast selection of best-fit models of protein evolution
Authors: Darriba Diego , Taboada Guillermo L. , Doallo Ramón , Posada David
Published: February 2011

Summary: We have implemented a high-performance computing (HPC) version of ProtTest that can be executed in parallel in multicore desktops and clusters. This version, called ProtTest 3, includes new features and extended capabilities.

Availability: ProtTest 3 source code and binaries are freely available under GNU license for download from http://darwin.uvigo.es/software/prottest3, linked to a Mercurial repository at Bitbucket (https://bitbucket.org/).

Contact:  dposada@uvigo.es

Supplementary information:  Supplementary data are available at Bioinformatics online.
Soil Application of SAR Inducers Imidacloprid, Thiamethoxam, and Acibenzolar-S-Methyl for Citrus Canker Control in Young Grapefruit Trees
Authors: Graham James H. , Myers Monty E.
Published: February 2011

Soil applications of inducers of systemic acquired resistance (SAR) imidacloprid, thiamethoxam, or acibenzolar-S-methyl, at various rates and application frequencies, were evaluated for control of citrus canker caused by Xanthomonas citri subsp. citri in a field trial of 3- and 4-year-old ‘Ray Ruby’ grapefruit trees in southeastern Florida. Reduction of foliar incidence of canker produced by one, two, or four soil applications of imidacloprid, thiamethoxam, and acibenzolar-S-methyl was compared with 11 foliar sprays of copper hydroxide and streptomycin applied at 21-day intervals. In the 2008 and 2009 crop seasons, canker incidence on each set of vegetative flushes was assessed as the percentage of the total leaves with lesions. By the end of the 2008 season, despite above-average rainfall and a tropical storm event, all treatments significantly reduced foliar incidence of citrus canker on the combined spring-summer-fall flushes. Sprays of copper hydroxide and streptomycin were effective for reducing canker incidence on shoot flushes produced throughout the season compared with the untreated control, whereas soil-applied SAR inducers reduced foliar disease depending on rate, frequency, and timing of application. Except for the treatment of four applications of acibenzolar-S-methyl at 0.2 g a.i. per tree or two applications of imidacloprid, SAR inducers were ineffective for reducing foliar disease on the flushes that were present during the tropical storm. In 2009, all treatments significantly reduced the incidence of foliar canker on the combined spring-summer-fall flushes but not all treatments of spring-summer flushes with SAR inducers were effective compared with the untreated control. Hence, depending on rate, frequency, and timing of application, soil-applied SAR inducers reduced incidence of canker on foliar flushes of young grapefruit trees under epidemic conditions.
Deinococcus reticulitermitis sp. nov., isolated from a termite gut
Authors: Chen Wen , Wang Baojun , Hong Huazhu , Yang Hong , Liu Shuang-Jiang
Published: February 2011

Bacterial strain TM-1Twas isolated from the gut of a wood-feeding termite,Reticulitermes chinensisSnyder. Cells of strain TM-1Twere Gram-negative, spherical (1.0–2.0 µm in diameter), non-motile, non-sporulating and red-pigmented. Strain TM-1Twas resistant to UV radiation, showing 34 % survival after exposure to UV light at a dose of 100 J m−2. Growth occurred at 20–40 °C (optimum, 30 °C), at pH 6.0–10.0 (optimum, pH 6.0–7.0), and in the presence of 0–1 % (w/v) NaCl (optimum, 0–0.4 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain TM-1Twas related to members of the genusDeinococcus, with sequence similarities ranging from 87.0 to 94.0 %. The peptidoglycan of strain TM-1Tcontained ornithine, alanine, glycine and glutamic acid. The most abundant cellular fatty acids of strain TM-1Twere summed feature 3 (C16 : 1ω7cand/or C16 : 1ω6c; 22.3 %) and C16 : 0(37.5 %). MK-8 was the predominant quinone. The polar lipid profile contained three glycophospholipids, six glycolipids, one aminolipid and three unknown lipids. DNA of the type strain had a G+C content of 65.6 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic data presented, strain TM-1Trepresents a novel species of the genusDeinococcus, for which the nameDeinococcus reticulitermitissp. nov. is proposed, with TM-1T( = CGMCC 1.10218T = NBRC 106334T) as the type strain.
Herbiconiux moechotypicola sp. nov., a xylanolytic bacterium isolated from the gut of hairy long-horned toad beetles, Moechotypa diphysis (Pascoe)
Authors: Kim Byung-Chun , Park Doo-Sang , Kim Hyangmi , Oh Hyun-Woo , Lee Kang Hyun , Shin Kee-Sun , Bae Kyung Sook
Published: February 2011

A novel Gram-positive, non-motile, rod-shaped bacterium, designated strain RB-62T, was isolated during a study of culturable bacteria from the gut of Moechotypa diphysis (Pascoe) and its taxonomic position was investigated. Strain RB-62T grew at 15–30 °C and pH 5.0–8.5. The isoprenoid quinones were menaquinones MK-11 (77.1 %), MK-10 (11.7 %) and MK-12 (11.2 %). The major cellular fatty acids were anteiso-C15 : 0 (34.6 %), anteiso-C17 : 0 (29.8 %), iso-C16 : 0 (17.0 %) and cyclohexyl-C17 : 0 (11.4 %). The diagnostic diamino acid of the cell-wall peptidoglycan was 2,4-diaminobutyric acid. The G+C content of the genomic DNA of strain RB-62T was 70.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain RB-62T was affiliated with the genus Herbiconiux cluster within the family Microbacteriaceae, and was related most closely to Herbiconiux ginsengi wged11T (98.08 % similarity). The level of DNA–DNA relatedness between strain RB-62T and H. ginsengi wged11T was 43.2 % (reciprocal 66.7 %). Phenotypic and phylogenetic characteristics clearly distinguished strain RB-62T from recognized species of the genus Herbiconiux. Based on data from the present polyphasic study, strain RB-62T is considered to represent a novel species of the genus Herbiconiux, for which the name Herbiconiux moechotypicola sp. nov. is proposed. The type strain is RB-62T ( = KCTC 19653T = JCM 16117T).
Staphylococcus agnetis sp. nov., a coagulase-variable species from bovine subclinical and mild clinical mastitis
Authors: Taponen Suvi , Supré Karlien , Piessens Veerle , Van Coillie Els , De Vliegher Sarne , Koort Joanna M. K.
Published: February 2011

Thirteen Gram-positive-staining coagulase-variable staphylococci were isolated from subclinical and mild clinical mastitic bovine milk (n = 12) and a teat apex (n = 1). The results of sequence analysis of the 16S rRNA gene and two housekeeping genes, rpoB and tuf, and DNA fingerprinting with amplified fragment length polymorphism (AFLP) analysis showed that the isolates formed a separate branch within the genus Staphylococcus. The phylogenetically most closely related species were Staphylococcus hyicus and Staphylococcus chromogenes. DNA–DNA hybridization with S. hyicus DSM 20459T and S. chromogenes DSM 20674T confirmed that the isolates belonged to a separate species. The predominant fatty acids were i-C15 : 0, ai-C15 : 0, i-C17 : 0 and C20 : 0 and the peptidoglycan type was A3α l-Lys–Gly5. Based on the results of genotypic and phenotypic analyses, it is proposed that the thirteen isolates represent a novel species, for which the name Staphylococcus agnetis sp. nov. is proposed. Strain 6-4T ( = DSM 23656T = CCUG 59809T) is the type strain.
Cesiribacter roseus sp. nov., a pink-pigmented bacterium isolated from desert sand
Authors: Liu Ming , Qi Huan , Luo Xuesong , Dai Jun , Peng Fang , Fang Chengxiang
Published: February 2011

A pink-pigmented, Gram-negative, rod-shaped, motile, strictly aerobic bacterium, designated strain 311T, was isolated from desert sand in Xinjiang, China. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain 311T was related closely to Cesiribacter
andamanensis AMV16T (94.6 % similarity). The DNA G+C content of strain 311T was 47.1 mol% and the major respiratory quinone was menaquinone 7 (MK-7). The main cellular fatty acids were C16 : 1ω5c (29.9 %), iso-C15 : 0 (21.9 %), iso-C17 : 0 3-OH (13.3 %) and summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B; 13.0 %). Based on phenotypic and chemotaxonomic data and phylogenetic analysis, strain 311T is considered to represent a novel species of the genus Cesiribacter, for which the name Cesiribacter
roseus sp. nov. is proposed. The type strain is 311T ( = CCTCC AB 207142T  = KACC 15456T).
Novel methylotrophic isolates from lake sediment, description of Methylotenera versatilis sp. nov. and emended description of the genus Methylotenera
Authors: Kalyuzhnaya Marina G. , Beck David A. C. , Vorobev Alexey , Smalley Nicole , Kunkel Dennis D. , Lidstrom Mary E. , Chistoserdova Ludmila
Published: February 2011

Phylogenetic positions, and genotypic and phenotypic characteristics of three novel methylotrophic isolates, strains 301T, 30S and SIP3-4, from sediment of Lake Washington, Seattle, USA, are described. The strains were restricted facultative methylotrophs capable of growth on single carbon compounds (methylamine and methanol) in addition to a limited range of multicarbon compounds. All strains used the N-methylglutamate pathway for methylamine oxidation. Strain SIP3-4 possessed the canonical (MxaFI) methanol dehydrogenase, but strains 301T and 30S did not. All three strains used the ribulose monophosphate pathway for C1 assimilation. The major fatty acids in the three strains were C16 : 0 and C16 : 1ω7c. The DNA G+C contents of strains 301T and SIP3-4 were 42.6 and 54.6 mol%, respectively. Based on 16S rRNA gene sequence phylogeny and the relevant phenotypic characteristics, strain SIP3-4 was assigned to the previously defined species Methylovorus glucosotrophus. Strains 301T and 30S were closely related to each other (100 % 16S rRNA gene sequence similarity) and shared 96.6 % 16S rRNA gene sequence similarity with a previously described isolate, Methylotenera mobilis JLW8T. Based on significant genomic and phenotypic divergence with the latter, strains 301T and 30S represent a novel species within the genus Methylotenera, for which the name Methylotenera versatilis sp. nov. is proposed; the type strain is 301T ( = VKM B-2679T = JCM 17579T). An emended description of the genus Methylotenera is provided.
Pseudorhodobacter aquimaris sp. nov., isolated from seawater, and emended description of the genus Pseudorhodobacter Uchino et al. 2002
Authors: Jung Yong-Taek , Oh Ki-Hoon , Oh Tae-Kwang , Yoon Jung-Hoon
Published: February 2011

A Gram-stain-negative, aerobic, motile, ovoid bacterial strain, designated HDW-19T, was isolated from seawater of the west coast of Korea and subjected to a polyphasic taxonomic study. Strain HDW-19T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2–3 % (w/v) NaCl. Bacteriochlorophyll a was not produced by strain HDW-19T. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain HDW-19T clustered with Pseudorhodobacter ferrugineus IAM 12616T, with which it shared 96.4 % similarity. A neighbour-joining phylogenetic tree based on gyrB gene sequences showed that strain HDW-19T also clustered with the type strain of P. ferrugineus, sharing 83.0 % similarity. Strain HDW-19T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, three unidentified aminophospholipids and two unidentified aminolipids. The DNA G+C content of strain HDW-19T was 60.9 mol%. Differential phenotypic properties, together with phylogenetic distinctiveness, showed that strain HDW-19T can be differentiated from P. ferrugineus. On this basis, strain HDW-19T is considered to represent a novel species of the genus Pseudorhodobacter, for which the name Pseudorhodobacter aquimaris sp. nov. is proposed. The type strain is HDW-19T ( = KCTC 23043T  = CCUG 58879T).
Aspergillus saccharolyticus sp. nov., a black Aspergillus species isolated in Denmark
Authors: Sørensen Annette , Lübeck Peter S. , Lübeck Mette , Nielsen Kristian F. , Ahring Birgitte K. , Teller Philip J. , Frisvad Jens C.
Published: February 2011

A novel species, Aspergillus saccharolyticus sp. nov., belonging to the Aspergillus section Nigri group is described. This species was isolated in Denmark from treated hardwood. Its taxonomic status was determined using a polyphasic taxonomic approach including phenotypic (morphology and extrolite profiles) and molecular (β-tubulin, internal transcribed spacer and calmodulin gene sequences, and universally primed PCR fingerprinting) analysis. Phenotypic and molecular data enabled this novel species to be clearly distinguished from other black aspergilli. A. saccharolyticus is a uniseriate Aspergillus species that is morphologically similar to Aspergillus japonicus and Aspergillus aculeatus, but has a totally different extrolite profile compared to any known Aspergillus species. The type strain of A. saccharolyticus sp. nov. is CBS 127449T ( = IBT 28509T).
Saturnispora quitensis sp. nov., a yeast species isolated from the Maquipucuna cloud forest reserve in Ecuador
Authors: James Stephen A. , Cadet Geneviève M. , Carvajal Barriga Enrique Javier , Barahona Patricia Portero , Cross Kathryn , Bond Christopher J. , Roberts Ian N.
Published: February 2011

A single strain, CLQCA-10-114T, representing a novel yeast species belonging to the genus Saturnispora was isolated from the fruit of an unidentified species of bramble (Rubus sp.), collected from the Maquipucuna cloud forest reserve, near Quito, in Ecuador. Sequence analyses of the D1/D2 domains of the large-subunit rRNA gene and ribosomal internal transcribed spacer region indicated that the novel species is most closely related to the recently described species Saturnispora gosingensis, isolated from the fruiting body of a mushroom collected in Taiwan, and Saturnispora hagleri, a Drosophila-associated yeast found in Brazil. The name Saturnispora quitensis sp. nov. is proposed to accommodate this strain; the type strain is CLQCA-10-114T ( = CBS 12184T = NCYC 3744T).
Promicromonospora xylanilytica sp. nov., an endophytic actinomycete isolated from surface-sterilized leaves of the medicinal plant Maytenus austroyunnanensis
Authors: Qin Sheng , Jiang Ji-Hong , Klenk Hans-Peter , Zhu Wen-Yong , Zhao Guo-Zhen , Zhao Li-Xing , Tang Shu-Kun , Xu Li-Hua , Li Wen-Jun
Published: February 2011

A novel xylan-degrading actinomycete, strain YIM 61515T, was isolated from surface-sterilized leaves of the medicinal plant Maytenus austroyunnanensis. Cells were Gram-positive and non-spore-forming, produced primary branches and formed white to yellowish white colonies on the media tested. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 61515T was most similar to Promicromonospora aerolata V54AT and Promicromonospora vindobonensis V45T (99.4 and 99.1 % sequence similarity, respectively). The isolate formed a separate lineage in a cluster containing P. aerolata V54AT. 16S rRNA gene sequence similarity between the isolate and other members of the genus Promicromonospora ranged from 96.3 to 98.4 %. Chemotaxonomic data, including major menaquinones, fatty acid compositions and polar lipid profiles, supported the placement of strain YIM 61515T in the genus Promicromonospora. DNA–DNA relatedness, physiological and biochemical data showed that strain YIM 61515T could be distinguished from members of all known species of the genus Promicromonospora and therefore represented a novel species. The name Promicromonospora xylanilytica sp. nov. is proposed, with YIM 61515T ( = DSM 21603T = CCTCC AA 208046T) as type strain.
The Soybean Rhg1 Locus for Resistance to the Soybean Cyst Nematode Heterodera glycines Regulates the Expression of a Large Number of Stress- and Defense-Related Genes in Degenerating Feeding Cells
Authors: Kandoth Pramod Kaitheri , Ithal Nagabhushana , Recknor Justin , Maier Tom , Nettleton Dan , Baum Thomas J. , Mitchum Melissa G.
Published: February 2011

To gain new insights into the mechanism of soybean (Glycine max) resistance to the soybean cyst nematode (Heterodera glycines), we compared gene expression profiles of developing syncytia in soybean near-isogenic lines differing at Rhg1 (for resistance to Heterodera glycines), a major quantitative trait locus for resistance, by coupling laser capture microdissection with microarray analysis. Gene expression profiling revealed that 1,447 genes were differentially expressed between the two lines. Of these, 241 (16.8%) were stress- and defense-related genes. Several stress-related genes were up-regulated in the resistant line, including those encoding homologs of enzymes that lead to increased levels of reactive oxygen species and proteins associated with the unfolded protein response. These results indicate that syncytia induced in the resistant line are undergoing severe oxidative stress and imbalanced endoplasmic reticulum homeostasis, both of which likely contribute to the resistance reaction. Defense-related genes up-regulated within syncytia of the resistant line included those predominantly involved in apoptotic cell death, the plant hypersensitive response, and salicylic acid-mediated defense signaling; many of these genes were either partially suppressed or not induced to the same level by a virulent soybean cyst nematode population for successful nematode reproduction and development on the resistant line. Our study demonstrates that a network of molecular events take place during Rhg1-mediated resistance, leading to a highly complex defense response against a root pathogen.
A Comparative Analysis of the NADPH Thioredoxin Reductase C-2-Cys Peroxiredoxin System from Plants and Cyanobacteria
Authors: Pascual María Belén , Mata-Cabana Alejandro , Florencio Francisco Javier , Lindahl Marika , Cejudo Francisco Javier
Published: February 2011

Redox regulation based on disulfide-dithiol conversion catalyzed by thioredoxins is an important component of chloroplast function. The reducing power is provided by ferredoxin reduced by the photosynthetic electron transport chain. In addition, chloroplasts are equipped with a peculiar NADPH-dependent thioredoxin reductase, termed NTRC, with a joint thioredoxin domain at the carboxyl terminus. Because NADPH can be produced by the oxidative pentose phosphate pathway during the night, NTRC is important to maintain the chloroplast redox homeostasis under light limitation. NTRC is exclusive for photosynthetic organisms such as plants, algae, and some, but not all, cyanobacteria. Phylogenetic analysis suggests that chloroplast NTRC originated from an ancestral cyanobacterial enzyme. While the biochemical properties of plant NTRC are well documented, little is known about the cyanobacterial enzyme. With the aim of comparing cyanobacterial and plant NTRCs, we have expressed the full-length enzyme from the cyanobacterium Anabaena species PCC 7120 as well as site-directed mutant variants and truncated polypeptides containing the NTR or the thioredoxin domains of the protein. Immunological and kinetic analysis showed a high similarity between NTRCs from plants and cyanobacteria. Both enzymes efficiently reduced 2-Cys peroxiredoxins from plants and from Anabaena but not from the cyanobacterium Synechocystis. Arabidopsis (Arabidopsis thaliana) NTRC knockout plants were transformed with the Anabaena NTRC gene. Despite a lower content of NTRC than in wild-type plants, the transgenic plants showed significant recovery of growth and pigmentation. Therefore, the Anabaena enzyme fulfills functions of the plant enzyme in vivo, further emphasizing the similarity between cyanobacterial and plant NTRCs.
TheArabidopsisbHLH Transcription Factors MYC3 and MYC4 Are Targets of JAZ Repressors and Act Additively with MYC2 in the Activation of Jasmonate Responses
Authors: Fernández-Calvo Patricia , Chini Andrea , Fernández-Barbero Gemma , Chico José-Manuel , Gimenez-Ibanez Selena , Geerinck Jan , Eeckhout Dominique , Schweizer Fabian , Godoy Marta , Franco-Zorrilla José Manuel , Pauwels Laurens , Witters Erwin , Puga María Isabel , Paz-Ares Javier , Goossens Alain , Reymond Philippe , De Jaeger Geert , Solano Roberto
Published: February 2011

Jasmonates (JAs) trigger an important transcriptional reprogramming of plant cells to modulate both basal development and stress responses. In spite of the importance of transcriptional regulation, only one transcription factor (TF), the Arabidopsis thaliana basic helix-loop-helix MYC2, has been described so far as a direct target of JAZ repressors. By means of yeast two-hybrid screening and tandem affinity purification strategies, we identified two previously unknown targets of JAZ repressors, the TFs MYC3 and MYC4, phylogenetically closely related to MYC2. We show that MYC3 and MYC4 interact in vitro and in vivo with JAZ repressors and also form homo- and heterodimers with MYC2 and among themselves. They both are nuclear proteins that bind DNA with sequence specificity similar to that of MYC2. Loss-of-function mutations in any of these two TFs impair full responsiveness to JA and enhance the JA insensitivity of myc2 mutants. Moreover, the triple mutant myc2 myc3 myc4 is as impaired as coi1-1 in the activation of several, but not all, JA-mediated responses such as the defense against bacterial pathogens and insect herbivory. Our results show that MYC3 and MYC4 are activators of JA-regulated programs that act additively with MYC2 to regulate specifically different subsets of the JA-dependent transcriptional response.
12-Oxo-Phytodienoic Acid Accumulation during Seed Development Represses Seed Germination inArabidopsis
Authors: Dave Anuja , Hernández M. Luisa , He Zhesi , Andriotis Vasilios M.E. , Vaistij Fabián E. , Larson Tony R. , Graham Ian A.
Published: February 2011

Arabidopsis thaliana COMATOSE (CTS) encodes an ABC transporter involved in peroxisomal import of substrates for β-oxidation. Various cts alleles and mutants disrupted in steps of peroxisomal β-oxidation have previously been reported to exhibit a severe block on seed germination. Oxylipin analysis on cts, acyl CoA oxidase1 acyl CoA oxidase2 (acx1 acx2), and keto acyl thiolase2 dry seeds revealed that they contain elevated levels of 12-oxo-phytodienoic acid (OPDA), jasmonic acid (JA), and JA-Ile. Oxylipin and transcriptomic analysis showed that accumulation of these oxylipins occurs during late seed maturation in cts. Analysis of double mutants generated by crossing cts with mutants in the JA biosynthesis pathway indicate that OPDA, rather than JA or JA-Ile, contributes to the block on germination in cts seeds. We found that OPDA was more effective at inhibiting wild-type germination than was JA and that this effect was independent of CORONATINE INSENSITIVE1 but was synergistic with abscisic acid (ABA). Consistent with this, OPDA treatment increased ABA INSENSITIVE5 protein abundance in a manner that parallels the inhibitory effect of OPDA and OPDA+ABA on seed germination. These results demonstrate that OPDA acts along with ABA to regulate seed germination in Arabidopsis.
Proteomics and Functional Analyses of Pepper Abscisic Acid–Responsive 1 (ABR1), Which Is Involved in Cell Death and Defense Signaling
Authors: Choi Du Seok , Hwang Byung Kook
Published: February 2011

Abscisic acid (ABA) is a key regulator of plant growth and development, as well as plant defense responses. A high-throughput in planta proteome screen identified the pepper (Capsicum annuum) GRAM (for glucosyltransferases, Rab-like GTPase activators, and myotubularins) domain-containing ABA-RESPONSIVE1 (ABR1), which is highly induced by infection with avirulent Xanthomonas campestris pv vesicatoria and also by treatment with ABA. The GRAM domain is essential for the cell death response and for the nuclear localization of ABR1. ABR1 is required for priming cell death and reactive oxygen species production, as well as ABA-salicylic acid (SA) antagonism. Silencing of ABR1 significantly compromised the hypersensitive response but enhanced bacterial pathogen growth and ABA levels in pepper. High levels of ABA in ABR1-silenced plants antagonized the SA levels induced by pathogen infection. Heterologous transgenic expression of ABR1 in Arabidopsis thaliana conferred enhanced resistance to Pseudomonas syringae pv tomato and Hyaloperonospora arabidopsidis infection. The susceptibility of the Arabidopsis ABR1 putative ortholog mutant, abr1, to these pathogens also supports the involvement of ABR1 in disease resistance. Together, these results reveal ABR1 as a novel negative regulator of ABA signaling and suggest that the nuclear ABR1 pool is essential for the cell death induction associated with ABA-SA antagonism.
Analysis of causes of decohesion of a gas turbine blade made of EI 867‐WD alloy
Authors: Błachnio Józef
Published: February 2011

Purpose

The purpose of this paper is to present results of laboratory testing work on causes of a service failure/damage to an aircraft turbojet's gas‐turbine blade made of the EI 867‐WD alloy.

Design/methodology/approach

The tests comprised comparing the microstructure of a service‐damaged blade with microstructures of specimens drawn from a similar all‐new blade, both subjected to temperatures of different values for different annealing times.

Findings

Findings based on the comparison of experimentally gained results of microstructure examination of both the gas‐turbine blades were: the change in the microstructure of a damaged blade results from the growth and cuboidal‐to‐lamellar change of shape of the reinforcing phase γ′ (Ni3Al); and the size and shape of this phase are comparable to those of the phase γ′ of a new blade subjected to annealing at temperature exceeding 1,223 K for 1 h. The results gained allowed for drawing the conclusion that the damaged turbine blade was operated in the exhaust‐gas temperature exceeding the maximum permissible value of 1,013 K for approximately 1 h in the course of an air mission.

Research limitations/implications

The comparison‐oriented experimental testing work was carried out on a new blade manufactured in the way and from material identical to those of the damaged blade. The applied methodology enables us to gain qualitative results of investigating into the causes of a failure/damage to a gas‐turbine blade.

Practical implications

The presented methodology of identifying (origin‐finding of) a service‐induced damage to a gas‐turbine blade proves helpful in the case of an engine failure, when information on the operating conditions thereof is insufficient.

Originality/value

The paper is an original work by the authors. To the best of their knowledge, the issue has not been found in the literature, approached in this particular way. It has been based on research work on air accidents due to the service‐induced failures/damages to gas‐turbine blades in aircraft turbojet engines.
A new approach to air traffic controller workload measurement and modelling
Authors: Oktal Hakan , Yaman Kadriye
Published: February 2011

Purpose

The purpose of this paper is to develop an analytical approach for workload measurement based on the task times and the changing task priorities of en route air traffic controllers (EATC).

Design/methodology/approach

A model called Total Airspace Workload Measurement Model was developed to measure EATC workload. Turkish airspace was chosen for practical application of the model. A survey was conducted of EATC to calculate the weighting coefficients and times of different tasks defined in the model. The survey results were analyzed with SPSS 15.0. The real traffic data of Turkish airspace for two peak hours period in heavy traffic covering August 2007 was provided by the General Directorate of Turkish airports. Geomedia 6.0 was employed for the visualization of the real traffic data.

Findings

The total airspace workload during two peak hours of traffic, estimated reference sector capacity and the number of operational sector were defined and calculated to analyze the distribution of workload among sectors.

Practical implications

This study can be used for en route sector design such as decision of the number of operational sectors and planning of sectors capacity in the strategic level. Air traffic control service providers can also refer to this study for human resources and equipment planning.

Originality/value

A number of parameters and variables were defined and included in the model by taking into consideration the different service types provided by EATC. All parameters and variables were identified with the task times of the controller. This analytical approach can be applied to those particular airspaces which have different characteristics.
Evaluating MI512: an information literacy course for PhD students
Authors: Secker Jane , Macrae‐Gibson Rowena
Published: February 2011

Purpose

The purpose of this paper is to provide an overview of a six‐week information literacy course for research students that was redesigned following the librarians undertaking the Postgraduate Certificate in Teaching in Higher Education.

Design/methodology/approach

The paper presents a case study and evaluation of the impact of a teaching programme. Findings – Research students appreciate and value the expertise of library staff and are prepared to devote considerable time to an information literacy programme. The programme received excellent feedback.

Research limitations/implications

There is no summative assessment associated with the course and so no quantitative measure of improvement in learning.

Originality/value

The paper provides a model programme other librarians can adapt for use at their own institution. Extended doctoral level information literacy courses are relatively uncommon and demonstrates the benefit of this type of course, to research.
Library education in Greece: history, current status and future prospects
Authors: Gerolimos Michalis
Published: February 2011

Purpose

The purpose of this paper is to report the history of the Greek Library Science (LS) education, to document proposed and current programmes of study and to evaluate the current under‐graduate and post‐graduate status of library studies in Greece.

Design/methodology/approach

The research methodology is based on bibliographic research of papers and articles and the documentation of programmes of study of Greek schools of LS.

Findings

The paper traces the history of library education in Greece with an emphasis on the suggested or implemented curricula over a period of five decades, documents the social conditions that affected the establishment of tertiary library education and proposes some changes to be implemented in schools of LS.

Originality/value

The paper records and evaluates the official library programmes of study over a period of time that covers all the course of formal library education in Greece. These programmes are not always documented in official records. Furthermore, statistical data regarding the library students of all Greek schools of LS are presented.
New trends and future applications/directions of institutional repositories in academic institutions
Authors: Jain Priti
Published: February 2011

Purpose

The purpose of this paper is to review the recent literature about institutional repositories (IRs) including the benefits and possible obstacles of setting up an IR. It will also discuss librarians' and authors' participative roles and open access. In conclusion, the paper aims to consider the future of IRs and finally makes recommendations for their successful implementation in academic institutions.

Design/methodology/approach

This paper is based on the recently published literature discussing current trends in IRs; although, some historical reference is also necessary to provide background to the open access movement and the early development of IRs. Given that the paper is an account of the history and current status of IRs, a formal documented methodology is not applicable.

Findings

The discussion suggests that in spite of all the obstacles to successful implementation, including associated negative perceptions, IRs have been increasingly recognised as a vital tool for scholarly communication and an important source of institutional visibility and a viable source of institutional knowledge management.

Research limitations/implications

This paper is an expression of opinion about current trends and future applications of IRs. It is not based on any formal methodology. This paper will be useful for librarians, academic staff and academic institutions generally, especially in developing countries where IRs are still in a developmental stage. Therefore, some of the general recommendations may not be as relevant for those institutions with well‐established and flourishing IRs.

Practical implications

The paper is aimed at institutions with low‐use repositories. It can be used to persuade management to establish institutional policies and it can also be helpful in clarifying the role of the library. It is also aimed at institutions considering initial development of an IR. The paper outlines the implications for IR practice for different groups, namely authors, librarians and academic administrative staff. It could, therefore, be used to persuade and influence different sets of stakeholders at institutions with under‐populated or embryonic IRs, about the value of open access, the importance of depositing material and the potential functionality afforded by IR packages.

Originality/value

The paper provides a review of the status of IRs and brings together topics previously reported on in isolation.
The future of open access in Croatia: a survey of academic and research libraries
Authors: Hebrang Grgic Ivana , Barbaric Ana
Published: February 2011

Purpose

The purpose of this research paper is to present Croatian librarians' awareness about the importance of institutional open access (OA) repositories.

Design/methodology/approach

The research is based on an online questionnaire sent to all the Croatian research and academic libraries. Online questionnaire was chosen as the most appropriate tool, as the authors wanted it to be anonymous and as quick as possible.

Findings

The findings indicate that all the academic librarians in Croatia are aware of the importance of institutional OA repositories. The number of OA repositories in Croatia is rather small, but the librarians are making lots of efforts towards the development of new repositories. Croatian librarians think that the most appropriate software is open‐source software; that OA repositories have to be open access initiative protocol for metadata harvesting compliant; that copyright owner's consent for archiving is necessary. The biggest problems are the lack of administration support and the researchers' unawareness of the benefits of OA, especially OA repositories.

Practical implications

Based on this research, some steps regarding OA could be done on a national level, e. g. guidelines for establishing OA repositories could be created and the obligation of self‐archiving should be regulated. This research could be a valuable tool for developing new OA repositories.

Originality/value

The paper contributes to the understanding the OA movement in transitional countries and peripheral scientific communities. The knowledge created in such countries can be beneficial for the global scientific community, and OA repositories are valuable way for promoting that knowledge.
Academic library non/low use and undergraduate student achievement
Authors: Goodall Deborah , Pattern David
Published: February 2011

Purpose

This paper aims to report an ongoing investigation of library use at Huddersfield University that has identified a historical correlation between library usage and degree classification.

Design/methodology/approach

Three sets of data – use of electronic resources, book loans, and visits to the library – when represented graphically show consistent amounts of no and low use at campus, academic school, degree‐type and course level. Combining these findings with data showing academic achievement raises the question: is there a positive correlation between library use and attainment?

Findings

Understandably, library usage varies between academic schools and there are often pedagogic reasons for low usage, but it would appear that, in some subjects, students who “read” more, measured in terms of borrowing books and accessing electronic resources, achieve better grades.

Research limitations/implications

Further work will focus on undergraduate, fulltime students at the main university campus.

Practical implications

It is intended to discover the reasons behind non/low use so as to develop then trial effective interventions for improving the grades of all students, from the bottom up, rather than just supporting those that are already high flyers. The results will inform both library service delivery and university goals concerning the quality of the student learning experience, improving retention and improving the level of final degree award.

Originality/value

The paper shows that there are implications for all subjects and all levels of achievement at the university.
Changing scenario of librarianship in Pakistan: managing with the challenges and opportunities
Authors: Ameen Kanwal
Published: February 2011

Purpose

This paper intends to throw light on major challenges and opportunities the twenty‐first century has brought to librarianship due to the emerging academic culture, and growing use of information and communication technologies (ICTs) in Pakistan.

Design/methodology/approach

The content is based on the literature, personal communication with national and foreign peers, the writer's 25 years' experience, observation and research in the field of librarianship.

Findings

Libraries in developing countries are being significantly affected by the ongoing ICT developments from basic infrastructure to collections to services to needed human resources. All quarters of the community need vision and preparedness to turn challenges into opportunities, and instead of being chaotic make change that is productive for society and themselves. It appeared that the overall growth in librarianship is much better since the dawn of the twenty‐first century.

Originality/value

The new aspects discussed in the context of Pakistan may provide guidelines for future planning, and growth of professional and libraries. It is assumed that the situation is similar to other developing countries. So, the work will be useful in creating awareness among professionals of other countries.
Real‐time solving of dynamic problem in industrial robots
Authors: Rosillo Nuria , Valera Angel , Benimeli Francesc , Mata Vicente , Valero Francisco
Published: February 2011

Purpose

The purpose of this paper is to present the development and validation of a methodology which allows modeling and solving the inverse and direct dynamic problem in real time in robot manipulators.

Design/methodology/approach

The robot dynamic equation is based on the Gibbs‐Appell equation of motion, yielding a well‐structured set of equations that can be computed in real time. This paper deals with the implementation and calculation of the inverse and direct dynamic problem in robots, with an application to the real‐time control of a PUMA 560 industrial robot provided with an open control architecture based on an industrial personal computer.

Findings

The experimental results show the validity of the dynamic model and that the proposed resolution method for the dynamic problem in real time is suitable for control purposes.

Research limitations/implications

The accuracy of the applied friction model determines the accuracy of the identified overall model and consequently of the control. This is especially obvious in the case of the PUMA 560 robot, in which the presence of friction is remarkable in some of their joints. Hence, future work should focus on identifying a more precise friction model. The robot model could also be extended by incorporating rotor dynamics and could be applied for different robot configurations as parallel robots.

Originality/value

Gibbs‐Appell equations are used in order to develop the robotic manipulator dynamic model, instead of more usual dynamics formulations, due to several advantages that these exhibit. The obtained non‐physical identified parameters are adapted in order to enable their use in a control algorithm.
Uncalibrated eye‐in‐hand visual servoing: an LMI approach
Authors: Khan Umer , Jan Ibrar , Iqbal Naeem , Dai Jian
Published: February 2011

Purpose

The purpose of this paper is to present the control of six degrees of freedom (PUMA560) robotic arm using visual servoing, based upon linear matrix inequality (LMI). The aim lies in developing such a method that neither involves camera calibration parameters nor inverse kinematics. The approach adopted in this paper includes transpose Jacobian control; thus, inverse of the Jacobian matrix is no longer required. By invoking the Lyapunov's direct method, closed‐loop stability of the system is ensured. Simulation results are shown for three different cases, which exhibit the system stability and convergence even in the presence of large errors.

Design/methodology/approach

The paper presents LMI‐based visual servo control of PUMA560 robotic arm.

Findings

The proposed method is implementable in the dynamic environment due to its independence to camera and object model.

Research limitations/implications

Visibility constraint is not included during servoing – this may cause features to leave the camera field of view (fov).

Originality/value

LMI optimization is employed for visual servo control in an uncalibrated environment. Lyapunov's direct method is utilized which ensures system stability and convergence.
Dynamic role engine and formation control for cooperating agents with robust decision‐making algorithm
Authors: Hamidreza Kasaei S. , Mohammadreza Kasaei S. , Alireza Kasaei S. , Amirhassan Monadjemi S.
Published: February 2011

Purpose

In a soccer robot game, the environment is highly competitive and dynamic. In order to work in the dynamically changing environment, the decision‐making system of a soccer robot system should have the features of flexibility and real‐time adaptation. The purpose of this paper is to focus on the middle‐size soccer robot league (MSL) and present new hierarchical hybrid fuzzy methods for decision making and action selection of an MSL robot.

Design/methodology/approach

In this paper, new hierarchical hybrid fuzzy methods for decision making and action selection of a robot in MSL are presented. First, the behaviors of an agent are introduced, implemented and classified in two layers, the low‐level behaviors and the high‐level behaviors. In the second layer, a two‐phase mechanism for decision making is introduced. In phase one, some useful methods are implemented which check the robot's situation for performing required behaviors. In the next phase, the team strategy, team formation, robot's role and the robot's positioning system are introduced. A fuzzy logical approach is employed to recognize the team strategy and furthermore to tell the player the best position to move.

Findings

This methodology was implemented on the ADRO RoboCup Team and ADRO team performance 2008 was compared with its previous version 2007. The results showed the success of this methodology; the team performance in coordination and collaboration highly improved; in fact, the players switched their strategic area smoothly as the team strategy changed in a reasonable manner, the robots carried out the high‐level behaviors much more efficiently and the final results were enhanced significantly.

Originality/value

This paper is a result of the authors' original research work in the field of autonomous robot‐middle size soccer robot, supported by Islamic Azad University – Khorasgan Branch, Isfahan, Iran.